Cell Calcium 57 (2015) 151–165

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Review

Calcium binding proteins and calcium signaling in prokaryotes Delfina C. Domínguez a,∗ , Manita Guragain b , Marianna Patrauchan b a b

Clinical Laboratory Sciences Program, The University of Texas at El Paso, El Paso, TX, 79902, USA Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 74075, USA

a r t i c l e

i n f o

Article history: Received 1 October 2014 Received in revised form 8 December 2014 Accepted 9 December 2014 Available online 17 December 2014 Keywords: Ca2+ homeostasis Ca2+ signaling in bacteria Prokaryotic Ca2+ transporters Bacterial Ca2+ -binding motifs

a b s t r a c t With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca2+ ) binding motifs including the canonical and pseudo EF-hand motifs, Ca2+ -binding ␤-roll, Greek key motif and a novel putative Ca2+ -binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca2+ in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca2+ in prokaryotes. Published by Elsevier Ltd.

1. Introduction Calcium ions (Ca2+ ) are perhaps the most versatile intracellular messengers in eukaryotic cells, regulating many cellular processes including cell cycle, transport, motility, gene expression and metabolism [1–6]. Cells respond to various stimuli by transient changes in intracellular free Ca2+ concentration ([Ca2+ ]i ). However, the diverse physiological processes regulated by Ca2+ do not merely occur due to increases and decreases in cytosolic Ca2+ concentration, but also depend on the specific speed, magnitude, frequency and spatio-temporal patterns of the signal [7]. The combination of changes characterizing the Ca2+ signal, including final Ca2+ resting levels and the source of the signal induced by a specific stimulus, is called the “Calcium Signature” [3,8]. Calcium signatures are sensed and decoded by Ca2+ binding proteins (CaBP) that act as Ca2+ sensors, transmitting the information via phosphorylation events, protein–protein-interactions and gene expression [8]. While the role of Ca2+ in eukaryotes has been extensively studied, the role of Ca2+ in prokaryotes still remains elusive. Indirect evidence suggests that Ca2+ affects various bacterial physiological processes such as spore formation, chemotaxis, heterocyst

∗ Correspondence to: Clinical Laboratory Science Program, College of Health Sciences, The University of Texas at El Paso, 500W. University Ave., Rm 420, El Paso, TX 79902, USA. Tel.: +1 915 7477238; fax: +1 915 747 7207. E-mail address: delfi[email protected] (D.C. Domínguez). http://dx.doi.org/10.1016/j.ceca.2014.12.006 0143-4160/Published by Elsevier Ltd.

differentiation, transport and virulence [9–14]. Several reports have shown that bacteria are capable of maintaining intracellular Ca2+ homeostasis [15–18]. Ca2+ transients are produced in response to nitrogen starvation, environmental stress [17,19] and metabolites of carbohydrate metabolism [20,21]. Moreover, proteomic and transcriptomic analyses in Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa revealed that the expression of hundreds of genes are modulated by changes in [Ca2+ ]i in response to elevated external calcium [21–25] (Domínguez et al., unpublished). The processes affected by these changes include swarming, type III secretion [26], polysaccharide production, iron acquisition, quinolone signaling and general stress responses [25]. These and other findings clearly indicate that Ca2+ plays a regulatory role in the physiology of prokaryotes. Sequence analyses of prokaryotic genomes have shown the presence of CaBPs with different Ca2+ -binding motifs [27–31] including helix-loop-helix EF-hand domain [28,31–33], ␤-rolls motif of repeats in toxin (RTX), Greek key motifs of ␤␥-crystallins and the Big Ca2+ domain [34–39]. Several calmodulin-like CaBPs have been documented in several genera of bacteria based on biochemical and/or immunological evidence [33,40–42]. A few other CaBPs have been at least partially characterized [32,33,41,43]. However, the functional roles of most other CaBPs remain to be elucidated. Even though some progress has been made in recent years, the role of Ca2+ in prokaryotes remains intriguing and indeterminate. Unfortunately through the years many studies have not been

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followed up and the appreciation of the role of Ca2+ in bacteria lags well behind. The aim of this review is to present the most recent developments in the field of CaBPs in bacteria and introduce novel advancements regarding the role of Ca2+ in prokaryotes.

2. Calcium homeostasis 2.1. Regulation of intracellular calcium In eukaryotic cells, Ca2+ is involved in nearly every aspect of cellular life. As with most ionic systems, Ca2+ overload can be cytotoxic, making a homeostatic system necessary to regulate ionic balance. The [Ca2+ ]i is 10,000-fold lower (10−7 M) than in the extracellular fluid (10−3 M) [6,44]. Because Ca2+ ions bind water less tightly than Mg2+ ions and precipitate phosphate leading to cellular conditions incompatible with life, they are zealously excluded from the cytosol [44]. High external Ca2+ concentrations create a concentration gradient utilized by cells to transmit signals [6]. Eukaryotic cells possess several mechanisms to keep cytosolic Ca2+ low and maintain a steep Ca2+ gradient. Some of these include organelles that sequester Ca2+ such as the endoplasmic reticulum and mitochondria, efflux and influx transport systems, acidic organelles and peroxisomes, a number of CaBPs that act as reservoirs or buffers, and small organic anions, ATP, and metabolites that bind Ca2+ [7,44,45]. Similar to eukaryotes, prokaryotic cells maintain tight control of their cytosolic Ca2+ [13,15–17,24]. But the molecular mechanisms behind how bacteria maintain Ca2+ homeostasis remain unclear. Gangola and Rosen (1987) have proposed that the level of bound [Ca2+ ]i in E. coli was 100 to 1000-fold higher than that of free Ca2+ , with recent studies showing that free cytosolic Ca2+ levels in various bacteria are quite low (100–300 nM), similar to the levels found in eukaryotic cells [16,17,46]. Gradient systems such as these require tight control of [Ca2+ ]i suggesting that transporters, CaBPs, and other proteins or cellular compartments may be participating in the adaptive response. Bacterial cells possess primary and secondary transporters and ion channels, most of which do not transport Ca2+ specifically. The putative EF-hand protein EfhP from P. aeruginosa, is necessary for maintenance of intracellular Ca2+ homeostasis as evidenced by mutation analysis [47]. Several other CaBPs including those with EF-hand motifs are present in bacteria, but their contributions to Ca2+ homeostasis have not been established [31,48]. A number of cytosolic proteins capable of binding Ca2+ but lacking known Ca2+ binding domains were identified in a B. subtilis proteome analysis using Ca45 Cl2 autoradiography [24]. Some of these proteins were induced following treatment with the extracellular divalent cation chelator ethylene glycol tetraacetic acid (EGTA) and down-regulated following exposure to high extracellular Ca2+ treatment [24]. Notably, the genes encoding some of these proteins including adenylate kinase, fructose-bisphosphate aldolase and the GrpE heat-shock protein were also found to be regulated by Ca2+ levels in E. coli [21]. Significantly, adenylate kinase and fructosebisphosphate-aldolase have also been linked to Ca2+ regulation in eukaryotic organisms [49–51], suggesting that other proteins yet to be characterized in bacteria could be involved in adaptive responses affecting cytosolic Ca2+ concentrations. Some bacteria have the capability to store Ca2+ in membranebound structures. In 2003–04, Seufferheld et al. reported that large membrane-bound vesicles called volutin granules found in Agrobacterium tumefaciens and Rhodospiriullum rubrum were very similar to acidocalcisomes first described in eukaryotic microbes [52–54]. Acidocalcisomes are acidic organelles that serve as the main storage compartment for Ca2+ , other elements such as Na+ , K+ , Mg2+ , Zn2+ and phosphorus (P) in the form of pyrophosphate (PPi)

and polyphosphate (poly P) [55]. In eukaryotic microbes, acidocalcisomes function in P metabolism, Ca2+ homeostasis, maintenance of intracellular pH, and osmoregulation [55,56]. Prokaryotic acidocalcisomes are very similar to their eukaryotic counterparts containing the transporters H+ -ATPase and the vacuolar proton translocating pyrophosphatase responsible for their acidification [53]. The ability of R. rubrum acidocalcisomes to store Ca2+ was demonstrated by X-ray microanalysis when bacterial cells were grown in 100 mM CaCl2 [53] suggesting that acidocalcisomes could be involved in Ca2+ homeostasis in some bacterial species. In Gram negative bacteria, the periplasmic space comprises the region between the outer membrane and the cytoplasmic membrane [57]. The existence of this compartment has also been documented in Gram positive bacteria [58–60]. X-ray mapping and electron loss spectroscopy has shown that high concentrations of Ca2+ are associated with the cellular envelope of E. coli [61]. The periplasm contains oligosaccharides and anionic proteins, which may play a role in storing Ca2+ in this compartment [62]. According to Jones and colleagues (2002), the outer membrane and periplasm may play a crucial role in Ca2+ regulation by first serving as a barrier to Ca2+ entry and second, by buffering or storing Ca2+ [62]. They observed that under certain conditions, the periplasm can store 3–6-fold Ca2+ with respect to the external medium by measuring the [Ca2+ ]i in the periplasm of living E. coli cells through targeting the photoprotein aequorin using the N-terminal OmpT signal sequence. These results support the hypothesis that bacterial cells may have the ability to regulate Ca2+ concentration utilizing different mechanisms including sequestration within cellular compartments. Based on the aforementioned data, two questions remain unanswered: (1) Does the eukaryotic paradigm of CaBPs, transporters and Ca2+ stores translate to prokaryotes? (2) To what extent do microcompartments in bacteria contribute to Ca2+ homeostasis? 3. Calcium transporters Earlier studies of Ca2+ transport in prokaryotes mainly utilized cell-level and membrane vesicles approaches. These studies showed that bacteria possess molecular mechanisms for both uptake and extrusion of Ca2+ [63–68], and earlier works reviewed in [69]). It was proposed that Ca2+ enters bacterial cells by means of either non-proteinaceous polyhydroxybutyrate-polyphosphate (PHB-PP) complexes (not discussed here) or Ca2+ channels and it is extruded by either Ca2+ -translocating ATPases or electrochemical potential driven Ca2+ transporters. More recent studies focused on purification and characterization of individual functional transporters, and these new developments are summarized below. Selected proteins whose role in Ca2+ transport is experimentally supported are listed in Table 1. 3.1. Channels Sequence analyses and the effect of eukaryotic Ca2+ channels inhibitors on the [Ca2+ ]i suggest that Ca2+ channels are present in bacteria. However, only two gene/protein-level studies have been reported so far. A mechanosensitive channel was proposed to be encoded by the mscL gene in Synechocystis sp. PCC 6803 [70]. The function of the protein was studied using the inhibitors known to block Ca2+ mechanosensitve channels in eukaryotes. Gene deletion followed by external Ca2+ measurements suggested that MscL contributes to, but is not the only mechanism for releasing Ca2+ into the medium in response to membrane depolarization in a temperature dependent manner. A second case is an atypical Ca2+ leakage channel BsYetJ shown to pass extracellular Ca2+ into the cytoplasm of B. subtilis [71]. This

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Table 1 Prokaryotic proteins involved in Ca2+ transport. Protein name, accession number organism

Major physiological and biochemical characteristics, Km, Structural analysis

Ref.

Is required for heat resistance and early germination of spores; has no effect on Ca2+ flux; forms Ca2+ dependent phosphoenzyme intermediate at low ATP concentration in sporulating bacteria. Protects cells against Ca2+ toxicity; is required for pathogenesis; chemical inhibition of CaxP is bacteriostatic at elevated Ca2+ ; affects Ca2+ flux. Ca2+ dependent phosphorylation of the enzyme is inhibited by vanadate, LaCl3 , N-ethylmaleimide, DCCD, and SERCA inhibitors; induced by thaspigargin and ionophore A23187. ATP dependent Ca2+ uptake is insensitive to nigericin, valinomycin, and CCCP, but is sensitive to vanadate; requires both ATP and free Ca2+ ; plays no role in cell sensitivity to Ca2+ . Rate of Ca2+ transport at pH 7.5 is 10 nmol/min/mg protein; max ATP hydrolysis at pH 8 is75 ␮mol ATP/min/mg; unlike SERCA, it is phosphorylated by Pi in the presence of Ca2+ ; Km = 1.5 ␮M; is inhibited by vandate and lanthanide; is insensitive to disruption of ion gradients across the membrane and SERCA inhibitors. Structure resembles SERCA and LMCA1

[79]

ATP driven transporters YloB, P-type Ca2+ ATPase, NP 389448.1 Bacillus subtilis 168

CaxP, cation transporting P-ATPase, YP 816843, Streptococcus pneumonia D39 PMA1, E1-E2 ATPase, WP 010872526.1, Synechocystis sp. PCC 6803 PacL, Ca2+ transporting P-ATPase, BAA03906.1, Synechococcus sp. PCC7942 Cda, Ca2+ dependent ATPase, 47910.2, Flavobacterium odoratum

Lm0818, Ca2+ transporting P-ATPases, NP 464345.1, Listeria monocytogenes LMCA1, Ca2+ transport ATPase, CAC98919.1, L.monocytogenes

PA2435, Putative heavy metal translocating P type ATPase, NP 252609.1 Pseudomonas aeruginosa PAO1 PA3920, Putative metal transporting P-type ATPase, NP 251125.1, P. aeruginosa PAO1 AtpD, Beta subunit of F0-F1 ATP synthase, NP 418188.1, Escherichia coli Bacteriorhodopsin, YP 001689404.1 Halobacterium salinarum (halobium) R1

Electrochemical potential driven transporters No name/accession ID, Ca2+ /H+ antiporter, B. subtilis W23

ApCAX, Ca2+ /H+ antiporter, BAD08687.1, Aphanothece halophytica SynCAX, Ca2+ /H+ antiporter, P74072.1, Synechococystis sp. strain PCC6803 YfkE/ChaA, Ca2+ /H+ antiport, NC 388673.1, B. subtilis 168

ChaA, Ca2+ /Na+ : H+ antiporter, YP 489486.1, E. coli

PitB, symporter of H+ /Pi, AAC76023.1, E. coli Pit, Low affinity inorganic phosphate transporter, O34436.2, B. subtilis 168 PA2092 putative MFS transporter, NP 250782.1, P. aeruginosa PAO1 LmrP, MFS transporter, NP 268322.1, Lactococcus lactis Channels BsYetJ, pH sensitive Ca2+ leak channel, O31539.1; B. subtilis 168 4614, Putative mechanosensitive channel, NP 253304.1, P. aeruginosa PAO1

+

2+

2+

[14] [73,74]

[80]

[75,76,181]

[81]

Exchanges H for Ca by ATP dependent transport; is stimulated by Sr , is inhibited by Cd2+ , Ag2+ , Zn2+ and vanadate; max Ca2+ uptake is at pH 9 with K0.5 of 160 ␮M. Structure resembles SERCA with only one Ca2+ binding site. Transposon mutant accumulates intracellular Ca2+ ; plays no role in cell tolerance to Ca2+ . Plays role in Ca2+ -induced swarming motility; transposon mutant accumulates intracellular Ca2+ ; plays no role in cell tolerance to Ca2+ . atpD mutant is defective in Ca2+ efflux and has lower growth rate and ATP content at high Ca2+ ; rate of Ca2+ efflux is ATP-dependent. Performs light-dependent Ca2+ uptake in membrane vesicles fused with bacteriorhodopsin proteoliposomes; is induced by valinomycin and inhibited by CCCP and nigericin.Structure analysis showed that Ca2+ binding site is adjacent to chromophore.

[77,182]

Extrudes Ca2+ using NADH as energy source, Km = 40 ␮M; is inhibited by nigericin and LaCl3 ; a proposed H+ /Ca2+ stoichiometry in transport is above 2. Rescues Ca2+ sensitive phenotype of E. coli mutant; enhances salt tolerance in PCC7942 at alkaline pH; catalyzes Ca2+ /H+ , but not Na+ /H+ or Li+ /H+ exchange, Ca2+ /H+ exchange is max at pH 8.8 and is increased by K+ . Rescues Ca2+ sensitive phenotype of E. coli mutant; Ca2+ /H+ exchange is max at pH 8 and is increased by K+ ; enhances salt tolerance in PCC7942 at alkaline pH; catalyzes Ca2+ /H+ , but not Na+ /H+ or Li+ /H+ exchange. Performs Ca2+ /H+ antiport; is regulated by intracellular pH; yfkE transcription is regulated by sigma factors SigG and SigB; Km = 12.5 ␮M at pH8.5, 113 ␮M at pH7.5, 51 ␮M at pH 8.5, and 320 ␮M at pH 7.5. YfkE structure showed that four conserved alpha repeat helices in a X-like conformation form a Ca2+ /H+ exchange pathway. K+ /H+ antiport activity; Na+ and Ca2+ efflux at alkaline pH; chaA has 40% less of Ca2+ extrusion; protects cells against high K+ , Na+ at alkaline pH; inhibited by Mg2+ and protonophore. Performs Pi dependent uptake of Ca2+ and Mg2+ ; Ca2+ uptake is inhibited by Mg2+ , membrane potential, and low internal pH. Performs Pi dependent low affinity transport of Ca2+ and Co2+ ; is inhibited by Mg2+ . Transposon mutant accumulates intracellular Ca2 +; plays no role in cell tolerance to Ca2+ Selectively binds Ca2+ and Ba2+ , but not Co2+ , Mn2+ , or Mg2+ . Performs specific Ca2+ /H+ antiport by electrogenic mechanism; Kd = 7.2 uM

[84]

Has Ca2+ leak activity; performs two-phase Ca2+ influx regulated by pH. Structure showed seven trans -membrane helix fold which opens at lower pH and closes at higher pH. Transposon mutant accumulates intracellular Ca2+ ; plays role in Ca2+ – induced swarming motility, but not in cell tolerance to Ca2+ .

[71]

[13] [13] [21] [83,183–185]

[85]

[85]

[88,186]

[89,91]

[87] [95] [13] [93]

[13]

Proteins were selected based on the experimental evidence supporting their role in Ca2+ transport. The accession numbers were obtained from NCBI.

protein is homologous to the human hBI-1 channel mediating Ca2+ release from the ER into the cytoplasm. The crystal structure analysis of BsYetJ indicated its distinct molecular architecture suggesting it passes Ca2+ through without binding in a pH-dependent manner. This finding, although did not address the ion specificity of

the channel, opens new possibilities of discovering proteins interacting with Ca2+ without binding it and thus providing much less of sequence clues for bioinformatic predictions. It also strengthens evolutionary connections between eukaryotic and prokaryotic mechanisms of Ca2+ homeostasis.

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3.2. ATPases Ca2+ ATPases are mostly high-affinity Ca2+ pumps that export the cation from the cytosol to the extracellular environment by using the energy stored in ATP. Two types of ATPases (P- and F-) have been shown to play role in ATP-dependent Ca2+ flux in bacteria and archaea. P-type ATPases form a transient phosphorylated intermediate upon hydrolyzing ATP and thus released energy is used to translocate cations across the membrane [72]. Although most identified P-type ATPases in prokaryotes are putative and their in-vivo functions are poorly characterized, four bacterial P-type ATPases were purified and shown to either translocate Ca2+ or perform Ca2+ dependent phosphorylation (Table 1). PMA1 from Synechocystis showed vanadate-sensitive Ca2+ -dependent phosphorylation, and based on its size, sequence, and sensitivity to inhibitors, appears to be closer related to eukaryotic sarcoplasmic reticulum Ca2+ ATPases (SERCA) [73,74]. Another vanadate-sensitive and constitutively expressed Ca2+ ATPase Cda was purified from Flavobacterium odoratum [75]. This protein is phosphorylated by ATP only in the presence of Ca2+ with a maximum activity at pH 8. Based on the lack of sequence similarity between Cda and other P-type ATPases, the authors proposed it to be a new class of ATP-ases that is closely related to F-type ATPases [76]. More recently, a P-type ATPase LMCA1 purified from Listeria monocytogenes exhibited different biochemistry including low Ca2+ affinity, high pH 9 optimum, and the ability to counter-transport 1 H+ in per 1 Ca2+ out by electrogenic mechanism [77]. In agreement with the pH-dependent activity, LMCA1 expression was shown to be induced in response to alkaline pH [78]. Five other Ca2+ P-type ATPases: CaxP from Streptococcus pneumonia [14], YloB from B. subtilis [79], PacL from Synechococcus sp. [80], and PA2435, PA3920 from P. aeruginosa [13] were identified using bioinformatic prediction and loss-offunction mutations. The mutants lacking caxP, PA2435, and PA3920, but not yloB accumulated intracellular Ca2+ . Preliminary crystallographic studies of a second, putative L. monocytogenesis Ca2+ ATPase LM0818, homologous to PacL, suggested structural and functional similarities with the other Listeria ATPase LMCA1 and the eukaryotic SERCA ATPase [81]. F-type ATPases or ATP synthases are known to reversibly phosphorylate ADP at the expense of the transmembrane electrochemical gradient of, most commonly, protons. So far, only one example of F-type ATPase, ␤-subunit AtpD in E. coli, has been shown to be required for Ca2+ efflux in bacteria [21], which is most likely due to its role in ATP synthesis. The phylogenetic tree including all the experimentally identified prokaryotic Ca2+ P-type ATPases (Fig. 1) confirms that (1) most of them are closer related to the eukaryotic SERCA than PMCA (plasma membrane Ca2+ -ATPase) P-type ATPases, (2) Cda is a unique P-type ATPase closely related to F-type AtpD, and (3) both P. aeruginosa ATPases significantly diverge from the rest and therefore, although shown to be required for Ca2+ efflux [13], may have a different substrate specificity or a mechanism of translocation. Finally, an interesting case of a light-driven proton pump bacteriorhodopsin from Halobacterium halobium fused into Streptococccus cremoris membrane vesicles was shown to translocate Ca2+ in a light-dependent manner [82]. Ca2+ binding to bacteriorhodopsin is known to facilitate chromophore reprotonation and prevent proton back-transfer [83], however Ca2+ translocation by this protein has not been shown yet in its native host. 3.3. Electrochemical potential driven transporters Electrochemical potential driven Ca2+ transporters are mostly low-affinity Ca2+ transport systems that use the energy stored in the electrochemical gradient of ions. Depending on the gradient, exchangers can operate in both directions (uptake and export). The phylogenetic analysis of the experimentally identified prokaryotic

Ca2+ exchangers groups the proteins according to which ions (H+ , Na+ and PO4 3− ) are used to translocate Ca2+ , with the exception of major facilitator superfamily (MFS) transporters forming a separate cluster (Fig. 2). Ca2+ /H+ and Ca2+ /Na+ antiporters have been identified in a number of bacterial genera and were thought to serve as a major mechanism for Ca2+ transport in prokaryotes. Some of the proteins were purified and reconstituted into membrane vesicles or proteoliposomes followed by Ca2+ measurements. For others, physiological or even structural data are available. Glu-Asp-reach Ca2+ /H+ antiporter (with no name or sequence available) was purified from B. subtilis [84]. This protein translocates Ca2+ in everted membrane vesicles using NADH as an energy source and generates membrane potential. The electrogenic mechanism of actions was also shown for several other Ca2+ /H+ exchangers [85,86], probable Ca2+ /Na+ antiporter [63], as well as Ca2+ /PO4 3- /H+ symporter [87]. Several studies have shown that Ca2+ exchangers (CAX) differ in ion specificity. For example, YftkE (designated as ChaA) from B. subtilis as well as ApCAX and SynCAX from cyanobacteria are Ca2+ -specific [85,88], whereas ChaA from E. coli, in addition to Ca2+ /H+ , exhibits Na+ /H+ and K+ /H+ antiport activity [89,90]. The latter protein was proposed to play role in E. coli resistance to alkali and excessive K+ [90]. Ca2+ exchangers also differ in pH requirements. Thus, ApCAX and SynCAX in cyanobacteria and ChaA in E. coli translocate Ca2+ at alkaline but not neutral pH [85,91]. YfkE (ChaA) in B. subtilis is active at pH 7.5, but with almost ten times higher Km than at pH 8.5 [88]. One peculiar case is presented by a major facilitator superfamily (MFS) transporter, LmrP from Lactobacillus lactis. This protein belongs to multidrug transporters known to mediate the extrusion of structurally different molecules, and exports monovalent cationic ethidium [92]. In addition, LmrP was shown to selectively bind Ca2+ and Ba2+ and efflux Ca2+ via electrogenic exchange (antiport) with three or more protons [93]. Another, predicted MFS transporter, PA2092 from P. aeruginosa is likely involved in Ca2+ efflux, as suggested by the accumulation of intracellular Ca2+ in the corresponding disruption mutant [13]. In addition to Ca2+ /H+ and Ca2+ /Na+ exchangers, specific inorganic phosphate (Pi) transporting systems (PitB in E.coli) also translocate Ca2+ (as well as other divalent ions) in the form of neutral metal phosphate complex MeHPO4 . Equimolar symport of Pi and Ca2+ can be directed as efflux (rate increases with pH) or uptake (inhibited at low cytosolic pH and by a proton motive force) [87]. Identification of several other metal phosphate symporters translocating divalent cations in different bacteria [94,95] suggests that they may serve as a general mechanism of co-translocating Pi and divalent cations including Ca2+ . However, this route may be experimentally overlooked in Ca2+ transport studies because of the general use of phosphate buffers [87]. Although several Ca2+ transporters have been demonstrated to transport Ca2+ in-vitro, the deletion of some of them did not show major defects in the in-vivo Ca2+ flux under the conditions tested [21,70,91,96], which raises questions about the role of these proteins in maintaining Ca2+ homeostasis in-vivo and perhaps the (conditionally regulated) functional redundancy of Ca2+ transporters. Supporting the latter point, a functional survey of Ca2+ transporters in P. aeruginosa showed that at least 13 transporters from different families contribute to the maintenance of intracellular Ca2+ homeostasis with two putative P-type ATPases, mechanosensitive channel and MFS transporter playing a major role in Ca2+ efflux [13]. The physiological roles of prokaryotic Ca2+ transporters have not been studied systematically, and only a few reports are available. For example, it was shown that ChaA from E.coli and ApCAX and SynCAX from cyanobacteria provide tolerance to high Ca2+ and enhance salt tolerance [85,89]. Indirect evidence using inhibitors

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Fig. 1. Phylogenetic analysis of nine experimentally characterized Ca2+ P-type ATPases in prokaryotes. The unrooted neighbor-joining tree was calculated using MEGA6 software from a ClustalO alignment of the amino acid sequences of the following proteins: YloB, NP 389448.1; CaxP, YP 816843; PMA1, WP 010872526.1; PacL, BAA03906.1; Cda, Q47910.2; Lm0818, NP 464345.1; LMCA1, CAC98919.1; PA2435, NP 252609.1; PA3920, NP 251125.1; and two eukaryotic proteins SERCA, Q93084; PMCA1, P23634 from the NCBI database. * Represents the proteins, for which crystal structures are available. The branch length indicates the amount of changes estimated to have occurred between nodes.

suggested that Ca2+ channels may be involved in chemotaxis in E. coli [10] and B. subtilis [97]. Ca2+ ATPases have been shown to play role in heat-resistance and germination of spores in B. subtilis, B. anthracis and C. perfringes [79]. Interestingly, transcription of ChaA, Ca2+ /H+ antiporter in B. subtilis is regulated by the sporulationspecific sigma factor, SigG, as well as by the general stress response regulator, SigB [88], implying a potential role of ChaA in these processes. The CaxP, P-type Ca2+ ATPase, was shown to be required for growth at elevated Ca2+ , for pathogenesis and survival in a host of S. pneumonia; and its chemical inhibition showed bacteriostatic effect [14]. The lack of a putative Ca2+ ATPase PA3920 abolished Ca2+ -induced swarming in P. aeruginosa [13]. These data suggest that Ca2+ flux systems are involved in a broad range of prokaryotic physiology and may present new targets for the development of future antimicrobial agents. Overall, the acquired so far knowledge on Ca2+ transport in prokaryotes is still limited and raises several important points. (1) Prokaryotes contain multiple mechanisms for Ca2+ translocation as well as multiple homologs of Ca2+ transporters. Is there a centralized regulatory network and how does it relate to Ca2+ signaling? (2) It is likely that Ca2+ transporters play a dual role by protecting cells from Ca2+ toxicity as well as maintaining steep Ca2+ gradients across cellular membrane required for signaling. What is the mechanistic and regulatory relationship between Ca2+ transporters and Ca2+ signaling? (3) It was suggested that prokaryotic Ca2+ transporters may have lower efficiency of Ca2+ translocation in comparison to eukaryotic transporters [96]. If confirmed for other transporters, how does it relate to the regulation of Ca2+

homeostasis and signaling in prokaryotes? These as well as other questions about the evolutionary relationship between prokaryotic and eukaryotic Ca2+ transport systems warrant further detailed studies. 4. Prokaryotic Ca2+ -binding protein structure A number of previously unknown CaBPs have been recently discovered in prokaryotic organisms using a combination of molecular and bioinformatic strategies. These proteins contain sequences closely resembling eukaryotic Ca2+ -binding motifs including the canonical EF-hand and EF-hand-like motifs, Ca2+ -binding ␤-roll and Ca2+ -binding Greek key motifs. Crystal structures of prokaryotic CaBPs containing these motifs are shown in Fig. 3. 4.1. EF-hand and EF-hand-like protein motifs Sequence analyses of prokaryotic genomes have identified 397 novel proteins containing putative EF-hand domains [29]. Functional studies confirming whether most of the identified proteins can bind calcium are lacking, with the exception of the following proteins: calerythrin from Saccharopolyspora erythraea [32,41], calsymin from Rhizobium etli [98], CabA [99], CabC [100], CabD from Streptomyces coelicolor [99], and CcbP from Anabaena sp. [12]. Zhou and colleagues [29] predict that 358 of the identified proteins contain a single EF-hand domain, whereas 39 contain multiple domains (between 2 and 6). Sixteen of the proteins containing multiple EF-hand domains had been previously described by Michiels et al.

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Fig. 2. Phylogenetic analysis of eight experimentally characterized electrochemical potential driven Ca2+ transporters in prokaryotes. The unrooted neighbor-joining tree was calculated using MEGA6 software from a ClustalO alignment of the amino acid sequences of the following proteins from the NCBI: ApCAX, BAD08687.1; SynCAX, P74072.1; YfkE, NC 388673.1; ChaA, YP 489486.1; PitB, AAC76023.1; Pit, O34436.2; PA2092, NP 250782.1; LmrP, NP 268322.1. * Represents the protein, for which crystal structure is available. The branch length indicates the amount of changes estimated to have occurred between nodes.

in 2002. On average, most EF-hand proteins range from 70 to 184 amino acids in length, have a high Phe/Tyr ratio and are either acidic (pI 4.2–5.0) or basic (pI 9.6–10.3) [31]. The superfamily of EF-hand proteins is the largest (at least 66 families and 3000 EF-hand entries in the NCBI Data Bank) and best characterized group of CaBPs [101–104]. All of the proteins within this superfamily share a common structural motif consisting of a Ca2+ -binding loop flanked by two ␣-helices [102] Acidic amino acids within the loop are responsible for binding Ca2+ [101,105]. Residues of the EF-hand Ca2+ -binding loop typically form the sequence pattern Dx[DN]xDGx[ILV][DSTN]x [106]. Although there is substantial variation in the Ca2+ loop sequence, Asp residues are the most commonly observed coordinating the Ca2+ loop, forming a DxDxDG pattern [106]. Oxygen atoms mediate EF-hand Ca2+ -binding stability through interaction with side chain carbonyls. Residues within the Ca2+ -binding loop (positions 1, 3, 5, 7, 9 and 12) provide the ligands for Ca2+ binding in a pentagonal, bipyramidal fashion. Residues 1, 3 and 5 act as monodentate ligands with residue 12, usually a Glu or Asp, acting as a bidentate Ca2+ ligand [101,107]. Proteins containing variations in the canonical 12-residue EF-hand loop or the helix-loop-helix structure are called pseudoEF-hand proteins or EF-hand-like proteins [106,108]. Significant differences exist between canonical EF-hand and pseudo-EF hand proteins within the Ca2+ -binding loop. While the canonical EF-hand loop binds Ca2+ primarily at side-chain residues 1, 3, 5 and 12, the pseudo EF-hand proteins have a longer loop where Ca2+ binding is coordinated by oxygen atoms in residues 1, 4, 6 and 9. Furthermore, the chelating ligands Glu or Asp are located in the 14th position of the pseudo-EF hand domain rather than the 12th position as observed within the canonical EF-hand domains [106–108]. The structural geometry of prokaryotic CaBP homologs resembles the classical EF-hand motif, and in fact, protein

homologues containing authentic EF-hand motifs have been identified [33,98,109]. However, prokaryotic proteins show great sequence and structural diversity. Some of these proteins differ in the length of the Ca2+ -binding loop, which may be shorter or longer than 12 residues, while other proteins deviate in the secondary structure flanking the Ca2+ -binding loop [28,29]. These orphan motifs have been proposed as EF-hand-like or pseudo-EF-hand (Table 2). Examples of CaBP mentioned above include: the typical helix-loop-helix EF-hand structure seen in calerythrin [33,109] and calsymin [98], the longer 15 residue Ca2+ -binding loop as in the E. coli lytic transglycosylase B Slt35 [110], the lacking of the first helix or lacking of the second helix as described in the C. thermocellum dockerin and the Sphingomonas sp alginate-binding protein, respectively [111,112], the extracellular Ca2+ -binding region found in several bacteria, which has a shorter loop containing 10 residue motif DxDxDGxxCE has been called “Excalibur” by Ridgen et al. [28]. The structural diversity of the Ca2+ -binding loop was analyzed for various CaBPs containing the Dx[DN]xDG linear motif by Rigden and colleagues in 2011. Interestingly, they found that the Ca2+ -binding motif was located in bacterial proteins containing ␤/␣-propeller folds that closely superimposed on the typical EF-hand motif. These proteins have a symmetrical, circular arrangement like blades of a propeller turbine [113] with the number of antiparallel ␤-sheets varying between 4 and 8 [113,114]. Entirely new folds containing the Dx[DN]xDG Ca2+ -binding loops that superimpose very closely on the typical EF-hand motif in different groups of bacteria include: all-␣ (E. coli glycoside hydrolase YgjK [115]); all-␤ (Bifidobacterium longum glycoside hydrolase supersandwich [116], and the Porphyromonas adhesin galactose-binding domain-like fold [117]); and mixed ␣ + ␤ (Thermococcus subtilisin [118] [103]). The Dx[DN]xDG Ca2+ -binding motif was found at the tips of the blades of ␤-propeller domains in the proteins of

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Fig. 3. Crystal structures of various prokaryotic Calcium Binding Motifs. (A) Canonical EF-hand motif, Calerythrin from Saccharopolyspora erythrea (PDB code: 1nya); (B) EFhand like motif, the exiting helix was replaced by a ␤-strand, periplasmic alginate-binding protein from Sphingomonas sp. (PDB code: 1kwh); (C) EF-hand like motif, absence of entering helix at Ca2+ -binding site of dockerin from Clostridium thermocellum (PDB code: 1daq); (D) ␤␥-crystallin motif of M-crystallin from the archaeon Methanosarcina acetivorans (PDB code:3HZ2); (E) Alkaline protease from Pseudomonas aeruginosa showing the Ca2+ -binding ␤-roll circled in black (PDB code: 1alk); (Ea) Front face of the ␤-roll of Alkaline protease, enlarged view from panel E (black circle). Ca2+ ions are shown as red spheres. This material is copyrighted by John Wiley and Sons, ACS Publications and BioMed Central. Figures were reprinted, with some modifications, from Zhou et al. [29] (A–C) Zhuo et al. [29]; Roujeinikova et al. [188]; Aravind et al. [30] (D), and Scotter et al. [196] (E,Ea) with permission.

two bacterial species, rhamnogalacturonan lyase of B. subtilis [119] and PilYl of P. aeruginosa [120]. These findings demonstrate the impressive variety and yet remarkable similarity of the EF-hand structural motif in prokaryotes. 4.2. Ca2+ -binding ß-roll Motif of RTX The ␤-roll motif is found in many proteins with unrelated functions. A number of Gram-negative bacteria secrete proteins with a ␤-roll or parallel ␤-helix structures containing multiple Ca2+ -binding and glycine-rich sequence motifs. These proteins contain a region referred to as a repeats-in-toxin (RTX) domain located upstream of the C-terminal uncleaved secretion signal sequence [31,34,121]. While it has been estimated that more than 1000 RTX family members exist to date, most of the proteins remain uncharacterized [38]. Structurally, the RTX domain consists of tandemly-repeating nonamers of the sequence GGXGXDXUX, where G is glycine, U is an aliphatic amino acid and X can be any amino acid. The first six amino acids of the domain are responsible for binding Ca2+ , whereas the last three residues form a ␤-strand. The number of tandem repeats within the domain can vary significantly amongst proteins, ranging anywhere from 5 to 45. The highly conserved Asp residue is required for Ca2+ binding; without

Ca2+ the beta-roll structure cannot be formed [122]. Importantly, Ca2+ is essential for the folding of RTX proteins, which takes place outside the cell [123]. RTX proteins including cytotoxins, proteases and lipases [38] produced by Gram negative bacteria are secreted via a type I secretion system (TISS) [38,123]. A related family of proteins with the sequence signature PE PGRS (Proline P-Glutamate E Polymorphic GC-rich Repetitive Sequence) was discovered upon sequencing the Mycobacterium tuberculosis genome [124,125]. These proteins appear to have multiple Ca2+ -binding sites and glycine-rich motifs (GGXGXD/NXUX), a characteristic also seen in RTX toxins [125]. The PE protein family accounts for 4% of the M. tuberculosis genome and contains a total of 99 members [126]. It is divided into 2 sub-families PE and PEGRS based on whether the C-terminal has the Gly-Gly-Ala or GlyGly-Asn multiple tandem repeat sequence [126]. PGRS domain of PE PGRS proteins contains the sequence repeat GGXGXD/NXUX, where X represents any amino acid and U indicates C-terminal non-polar/large hydrophobic residues. The sequence forms a Ca2+ -binding structure called a parallel ␤-roll or parallel ␤-helix structure with typical features of CaBPs [126]. The PE domain is comprised of 110 amino acids and is highly conserved, whereas, in the PEGRS domain the C-terminus varies in both size and repeat copy number [127].

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Table 2 Examples of bacterial prokaryotic proteins containing EF-hand and EF-hand-like motifs with known structure. Accession number

Deviation from Protein length a.a. EF-hand/EFhand-like motif EF-hand

Potential role of Ca2+

Ca2+ binding status

Ref.

Saccharopolyspora erythrea Calerythrin

P06495

177

None

Buffer

Confirmed

[32,41,187]

Rhizobium etli

Calsymin

Q9F6V9

293

None

Transducer

Confirmed

[31,98]

Thermotoga4-␣-Maritime

Glucanotransferase P80099

441

Shorter loop

Unknown

Confirmed

[29,188]

Escherichia. coli

B Slt35

P41052

361

Bacillus anthracis

Protective antigen

P13423

764

Clostridium thermocellum

Dockerin

A3DCJ4

350

Salmonella typhimurium

P23905

332

Q9KWT6

Pseudomonas aeruginosa

Periplasmic galactose binding protein Periplasmic alginate binding protein Alkaline protease

Halothermothrix␣-orenii

Amylase A

Organism

Sphingomonassp

Protein name

Helix-loophelix Helix-loophelix Helix-loophelix Helix-loophelix Helix-loophelix Helix-loophelix Helix-loopstrand

Longer loop

Structural

Confirmed

[29,110]

Entering helix missing Entering helix missing Entering helix missing

Structural

Confirmed

[28,189]

Structural

Confirmed

[28,111]

Structural

Confirmed

[28,190]

526

Helix-looploop

Second helix missing

Regulatory

Confirmed

[28,112]

Q03023

479

Helix missing

Unknown

Confirmed

[29,191]

Q8GPL8

515

Strand-loopstrand Strand-loophelix

Shorter loop

Structural

Confirmed

[192]

Protein accession numbers in UniProtKB database.

Although the genes encoding the PE proteins show high genetic variability, some of them contain homologous epitopes [128]. Studies by Meena (2014) and Copin (2014) suggest that these proteins may be involved in cell evasion by employing mechanisms of antigenic variation [128,129]. While investigating the function of PE PGRS proteins, Delogu and his colleagues (2004) determined that the PE domain is not only necessary for protein cellular localization, but that the PGRS domain (not PE) also influences cell structure and colony morphology. Whether Ca2+ is capable of binding to PE-PGRS and the effects it may elicit on protein function has yet to be experimentally determined.

Myxoccoccus xanthus [133], clostrillin from Clostriduym beijerinckii, flavollin from Flavobacterium johnsoniae [30] and M crystallin from Methanosarcina acetivorans [134] (Tables 3). Ca2+ -binding affinities of ␤␥-crystallins operate within the ␮M range, similar to extracellular CaBPs. Conversely, eukaryotic Ca2+ sensors of the EF-hand superfamily exhibit higher Ca2+ -binding affinities, often within the lower ␮M to nM range [6,30,101]. Conformational changes upon binding Ca2+ vary amongst domains of ␤␥-crystallins compared to EF-hand proteins, which undergo large conformational changes [35,36,107,135]. Ca2+ -binding sites of the EF-hand and ␤␥-crystallin motifs are continuous and discontinuous, respectively.

4.3. Ca2+ -binding greek key motif of the ˇ-crystallins 4.4. The BIg domain, Ca2+ -binding motif The ␤␥-crystallin superfamily contains Ca2+ -binding proteins found in organisms from various taxa including eukaryotes, eubacteria and archea [30,130]. Recent studies indicate that the ␤␥crystallin family is widespread amongst several hundred species. ␤␥-crystallins have been identified as major structural proteins of the vertebrate lens [131], components of serine proteases, metalloproteases and glycosyl hydrolases in various organisms, and as part of a large Vibrio-specific protein in Vibrio species [39,130]. The functional capabilities of these proteins have yet to be elucidated. The common topological feature of these proteins is a double Greek key motif consisting of four adjacent antiparallel ␤-strands, with the opposite motif sharing the third ␤-strand forming a domain. ␤␥-crystallins from distinct organisms showed that Ca2+ coordination is conserved in the form of N/D-N/D-#-I-S/T-S, where the residue in the position # provides a carbonyl chain for direct Ca2+ coordination and the non-polar residue I contributes to the hydrophobic core of the domain [132]. The coordination number for Ca2+ in ␤␥-crystallins varies from 5 to 8, with four provided by protein ligands and the remainder by water molecules [39]. A unique characteristic of this motif is the coordination of Ca2+ via the Ser/Thr hydroxyl group, since other Ca2+ -binding sites do not include these residues [39]. The ␤␥-domain arrangement commonly seen in bacterial proteins consists of two Ca2+ -binding sites formed from two loops containing the N/DN/DXXT/SS sequence residing adjacently but running in opposite directions. Some of the bacterial proteins containing this domain include: protein S from

A group of bacterial proteins with immunoglobulin-like (BIglike) domains was recently discovered to have Ca2+ -binding sites [136]. The BIg-like domain can be observed in several organisms within all kingdoms [137]. BIg-domains have been identified within enzymes, chaperones, molecular transporters and cell surface proteins [37,137–139]. The first examples of prokaryotic BIg-like domain proteins were identified in E. coli [140] and B. circulans [141]. Structural similarities between the BIg-like fold and the Greek key motif of the ␤␥-crystallins [142] led to the investigation of the Leptospiral BIg-like proteins LigA and B for Ca2+ binding properties [37,136]. The central region of Lig B (LigBCen2) containing a BIg-like domain was shown to bind four Ca2+ ions with a dissociation constant of 7 ␮M, as determined by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) and Isothermal titration calorimetry (ITC), respectively. Binding Ca2+ ions directly influenced the global conformation of the protein and stabilized the protein structure [136]. Raman and colleagues (2010) confirmed that BIg-like domains of Lig proteins are capable of binding Ca2+ by measuring dissociation constants, which were in the range of 2-4 ␮M, [37]. Even though the nature of Ca2+ binding sites was not determined each tandem repeat was noted to contain the consensus sequence DNSNKDITSAVTDxSNxDxxSxVT [143]. NMR spectroscopy of the putative surface protein SP0498 from Streptococcus pneumoniae has revealed that sequence and

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Table 3 Examples of Prokaryotic ␤␥-crystallin proteins with known structures. Organism

Protein name number

Accession length a.a

Protein for Ca2+

Ca2+ Motif

Role of Ca2+

Ref.

Myxococcusxanthus Clostridium beijerinckii Flavobacteriumjohnsoniae Methanosarcina acetivorans

Protein S Clostrillin Flavollin M crystalline

P02966 A6LX94 A5FC88 Q8TMX3

173 589 957 120

Greek key Greek key Greek Key Greek key

Structural Structural Structural Structural

[193] [30] [30] [134]

Protein accession numbers in UniProtKB database.

structural diversity exists in the BIg-like domain [144]. Wang and colleagues observed that the structure of the SP0498 BIg-like domain differs from the typical Ig-like domain (human Fc fragment HsFc) by adopting a barrel-like conformation comprised of eight ␤-strands that form three separate regions. In addition, the conserved disulfide bond of the Ig-domain was not identified and the ␤-strands are shorter than those within the classical Ig-like fold [30,144]. The Ca2+ -binding properties of SP0498 were confirmed using 1 H–15 N Heteronuclear Single Quantum Coherence (HSQC) and ITC and revealed dissociation constants of 0.24 ␮M [144]. The Ca2+ coordination patterns of the BIg-like domains need to be determined and even though a functional role has not been established these proteins appear to be involved in processes such as host cell adhesion and invasion. Altogether, the unique physicochemical characteristics of BIg-like domain-containing proteins suggest a novel group of CaBP [37,136,144]. In summary, prokaryotic CaBPs comprise a wide variety of proteins with great structural diversity. Binding Ca2+ may lead to different molecular consequences, such as structure stabilization or folding into a functional state. Some proteins when bind Ca2+ with high affinity undergo significant conformational changes while others exhibit only moderate changes in conformation. Structural characteristics of prokaryotic CaBPs suggest these proteins may function as buffers, sensors, signal transducers or play structural and/or regulatory roles. One essential aspect for future structurefunction studies that must be considered is the correlation of the cytosolic Ca2+ concentration of a particular organism and the assessment of the Ca2+ binding affinities of intracellular CaBP to establish a potential regulatory role for a given protein. Furthermore, detailed biochemical and genetic characterization of CaBPs is necessary to further elucidate the physiological roles of CaBP proteins in prokaryotes, which have to this day remained elusive, therefore offering one of the most exciting challenges for the future. 4.5. CaBPs in calcium signaling The idea of Ca2+ signaling in prokaryotes has been puzzling researchers for quite some time. There is a growing body of evidence that elevated Ca2+ not only triggers a variety of physiological responses, but also modulates gene expression in prokaryotes (reviewed in [48,145–147] and references above). The molecular mechanisms of the multiple effects of Ca2+ range from Ca2+ playing a role as a structural component stabilizing lipopolyscharide layer and cell wall [148–150] to Ca2+ playing a role in structural stability of proteins or protein complexes [110,151], [152–156] to Ca2+ effecting transcription of two component systems, regulatory proteins, and protein phosphorylation, which may have eitther positive or negative regulatory outcomes [23,157] [158,159]. Ca2+ also serves as a mean of molecular communication between organisms, for example, increased plant (tobacco seedling) Ca2+ decreases the transcription of pehA endopolygalacturonase required for bacterial (Erwinia carotovora) infection [160]. Another example is Ca2+ negative regulation of type 3 (TTSS) and type 6 secretion systems (T6SS) that are responsible for translocating bacterial effectors directly into the host cell cytoplasm and periplasm of rival bacteria, correspondingly [151,157].

Several lines of evidence suggest that Ca2+ may also play a role of an intracellular messenger in prokaryotes. First, resting cells of several Gram-positive and Gram-negative bacteria maintain their intracellular free Ca2+ ([Ca2+ ]i ) at 100–300 nm level, which increases rapidly in response to elevated extracellular Ca2+ , and then restores back to the basal level [13,16,17,24,96]. Second, the [Ca2+ ]i transiently changes in response to other stimuli, including photosensitization in Propionibacterium acnes [161], quorum sensing molecules in Serratia liquefaciens [162], oxidative stress in Bacillus subtilis [15], heat-cold shock in Anabaena sp. [17], repellents/attractants [163] and carbohydrate metabolites in E. coli [20,164]. These changes can mobilize Ca2+ from both intracellular and extracellular sources. The former implies there is an intracellular Ca2+ storage that can release the ion in response to a stimulus. In the latter case, it was suggested that extracellular stimuli can open Ca2+ channels [20,164]. Third, increased [Ca2+ ]i can trigger changes in gene transcription, in the levels of cytosolic ATP [21], in protein abundance by release from inclusion bodies [165], and in Ca2+ dependent swarming [13]. However, direct experimental evidence illustrating the intracellular Ca2+ transients regulate Ca2+ -mediated processes are to be provided. In Fig. 4, we propose a prokaryotic Ca2+ signaling network, which includes both experimentally proven and hypothetical components. When a cell is exposed to external Ca2+ , in addition to Ca2+ uptake and its possible effect on the production of other intracellular messengers (ex, cAMP), it may be recognized by two component regulatory systems whose primary role is adjusting bacterial physiology to environmental conditions. Several two component systems and regulatory proteins were shown to respond to external Ca2+ . PhoQ kinase from the PhoPQ system in Salmonella typhimurium and P. aeruginosa binds Ca2+ , Mg2+ and Mn2+ , which represses its phosphatase activity required for transcriptional regulation of hundreds of genes encoding the majority of virulence properties in Salmonella (reviewed in [166]). The observation that PhoQ likely has distinct Ca2+ and Mg2+ binding sites [167] suggests an intricate nature of PhoPQ regulation by the ions. The expression of calcium-regulated CarSR two component system negatively regulating polysaccharide production and biofilm formation in Vibrio cholerae is reduced by elevated extracellular Ca2+ [23]. In P. aeruginosa, a two-component system PA2656–PA2657, which shares 18–31% amino acid sequence identity with CarSR, is highly induced by elevated Ca2+ and regulates the expression of putative periplasmic CaBPs (Guragain et. al., in preparation). In addition, 24 transcriptional regulators in this organism were shown to be positively or negatively regulated by external Ca2+ [157]. Another two component system, AtoSC, is induced by Ca2+ and regulates the biosynthesis and the intracellular distribution of cPHB (complexed poly-(R)-3-hydroxybutyrate) composing the non-proteinaceous complexes that act as voltage-gated Ca2+ channels in Escherichia coli [168–170]. Ca2+ represses CIRCE (controlling inverted repeat of chaperone expression)-regulated thermoresistance in Streptococcus pneumonia likely by causing conformational changes in the repressor HrcA, which controls the transcription of dnaK and groE chaperones [171]. A number of CaBPs have been identified and shown to mediate Ca2+ effects in prokaryotes. For example, several identified

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Other external stimuli •Quorum sensing (HSL) •Heat and cold shock •Carbohydrate metabolites •Oxidative Stress (H2O2) •Red light

External Ca2+

Ca2+ influx •Channels

Two-component systems •PA2656/57 •PhoP/Q •CarS/R •AtoSC

Specific sensors or transporters

Intracellular messengers

Internally stored Ca2+

Increased [Ca2+]in 1-5.4 µM

Resting [Ca2+]in 0.09-0.3µM

Ca2+ binding proteins Physiological Responses · Cell cycle/division/differentiation · Gene expression · Protein phosphorylation · Proteolysis · Phospholipid metabolism · Chemotaxis/motility · Virulence factors · Photo-orientation · Cell adhesion/Biofilm formation · Cytoplasmic pH homeostasis · Competence · Sporulation · Stress resistance · Host/pathogen interaction

Ca2+ efflux •P-ATPases •Electrochemical potential driven transporters

Fig. 4. Calcium (Ca2+ ) network in bacteria. The experimentally characterized components and pathways are shown in white boxes and with solid lines, respectively. Dashed lines and gray boxes represent hypothetical pathways and components.

EF-hand proteins [28,29,31] may function as Ca2+ sensors transducing signal to target proteins or Ca2+ buffers changing the spatiotemporal levels of intracellular Ca2+ [172]. A four-EF-hand CabC in Streptomyces coelicolor binds Ca2+ without consequent structural modifications, and was proposed to act as a Ca2+ buffer regulating spore germination and aerial hyphae formation possibly by controlling intracellular Ca2+ concentration [100]. In contrast, CabB, another EF-hand protein in S. coelicolor, undergoes large conformational changes upon binding Ca2+ , contributes to cell resistance to high Ca2+ , but was not yet ascribed a regulatory role in the developmental processes [99]. Another homolog, CabA with four EF hands binds Ca2+ , but its role in S. coelicolor physiology is yet to be discovered [173]. P. aeruginosa possess a putative Ca2+ binding EF-hand protein EfhP, which is required for maintenance of the intracellular Ca2+ homeostasis and several Ca2+ -mediated processes including pyocyanin production, oxidative stress resistance and plant infection. Sequence analysis suggests that EfhP is likely spanning the outer membrane exposing the two EF hands into the periplasm where it likely binds Ca2+ [47]. The ability of bacterial membrane-bound protein systems to transduce Ca2+ signal was confirmed in-vitro by using a hybrid inner membrane transducer, Taz1. The protein was constructed using an N-terminal receptor domain of Tar chemoreceptor and a C-terminal signaling domain of EnvZ, an inner membrane protein believed to transduce stress signals to OmpR [174]. The presence of as low as 60 ␮M of Ca2+ activates phosphorylation of Taz1, which in turn, donates its phosphate to OmpR, known to activate transcription of porin genes in E. coli [175]. This Ca2+ -stimulated Taz1 phosphorylation was not associated with membrane permeability or Ca2+ translocation and is likely to be due to the structural changes upon direct interaction between Taz1 and Ca2+ . However, whether

Ca2+ interacts with EnvZ in-vivo, and the subcellular localization of the interaction remain to be determined [175]. A possible functional link between intracellular Ca2+ and its regulatory outcome was proposed for a cyanobacterial Ca2+ -binding protein, CcbP [12]. This acidic amino acids rich protein with two distinct Ca2+ -binding domains is expressed only in vegetative cells with low [Ca2+ ]i and is absent from mature heterocysts with 10 times higher [Ca2+ ]i . At the early stages of heterocyst formation, CcbP is likely degraded by HetR protease leading to Ca2+ release, which is required for cellular differentiation [42]. Another possible venue of Ca2+ signaling is using Ca2+ -dependent K+ channels [176–178] controlling cell membrane potential, which, however, is somewhat challenged by their fairly high requirements of millimolar level of Ca2+ (Table 4). Overall, different aspects of Ca2+ signaling role in prokaryotic physiology have been demonstrated, however direct experimental evidence of intracellular signaling events connecting [Ca2+ ]i transients, their amplitude and rate to the regulatory outcomes are still to be discovered. Characterization of intracellular Ca2+ signaling has been challenged by technical difficulties of monitoring intracellular Ca2+ . Commonly used Fura and aequorin-based systems although enabled generation of a significant amount of experimental data, are limited by the necessity of multi-step cell preparation (also discussed in [146]), and therefore prohibit sensitive in-vivo screenings in growing cells. Alternative approaches possibly including fluorescent indicators [179,180] may provide a solution. Further detailed studies are necessary to elucidate the molecular mechanisms of cellular Ca2+ homeostasis and intracellular Ca2+ storage, to identify the components and regulation of Ca2+ signal transduction pathways as well as their possible relationships with other signaling systems in bacteria.

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Table 4 Bacterial proteins possibly involved in Ca2+ signaling. Protein name, accession number organism Surface proteins Bap, AAK38834.2, biofilm associated protein, Staphylococcus aureus V329 ClfA, YP 001331790.1, clumping factor A, Staphylococcus aureus Newman ClfB, CAA12115.1, clumping factor B Staphylococcus aureus Newman SdrD, CAA06651.1* , serine–aspartate surface protein, Staphylococcus aureus Newman

Cah, AIF92899.1, Ca2+ binding antigen 43 homolog, E. coli O157:H7

Two-component regulatory systems PhoPQ: PhoQ, P0DM78.1, sensor histidine kinase, PhoP, P0DM80.1, trasncriptional regulator, Salmonella enterica Typhimurium

VpsR, AAK00610.1, transcriptional regulator CarS, AAF94477.1, Ca2+ regulated sensor, CarR, AAF94478.1, Ca2+ regulated regulator, Vibrio cholera O1E1 HrcA, Q8DQW9.2* , heat inducible transcription repressor, Streptococcus pneumonia CP1200

AtoSC: AtoS, AIN32630.1, sensory histidine kinase, AtoC, AIN32631.1, Response regulator, E. coli BW25113 Intracellular Ca2+ binding protein CcbP, AAX13998.1 Ca2+ binding protein Anabaena sp. PCC7120 Ca2+ -binding protein

EF-hand proteins CabC, NP 631687.1 Ca2+ binding protein, Streptomyces coelicolor

CabB, NP 629601.1, Ca2+ binding protein, Streptomyces coelicolor A3 CabA, BAB19055.1, Ca2+ binding protein A, Streptomyces ambofaciens Slt35, 1QDT A, transglycosylase, E. coli EfhP, NP 252796.1, EF hand protein, Pseudomonas aeruginosa PAO1

Tse3, 4M5E A, membrane binding lysozyme, P. aeruginosa PAO1

Physiological role, relationship to Ca2+

Ref.

Mediates Ca2+ dependent cellular adhesion; responsible for Ca2+ inhibition of biofilm formation; its expression is not affected by Ca2+ . Bap contains EF-hand motifs; binding Ca2+ protects BAP protein from proteolysis. Promotes binding of bacterial cells to fibrinogen and fibrin; Ca2+ and Mn2+ inhibit interaction of ClfA and fibrinogen; ClfA contains EF-hand like motif with Ca2+ -dependent inhibitory site at residues 310–321. Is detectable only in the exponential phase cells and promotes cell clumping in a solution of fibrinogen as well as cell adherence to immobilized fibrinogen in vitro; this activity is inhibited by Ca2+ and Mn2+ . Ca2+ binding is required for the structural integrity of SdrD B-repeat regions. 15 Ca2+ -binding sites: five with high and 10 with low binding affinity likely serve for SdrD structural stability and cellular Ca2+ homeostasis, respectively. Mediates changes in cell morphology and cellular aggregation; plays role in biofilm formation; reduces adhesion to HeLa cells; EDTA treatment increases cah transcription, but addition of Ca2+ has no effect. Ca2+ binding is reduced by MgCl2.

[155]

Regulates virulence, cell physiology, entry and survival in the host cells; is negatively regulated by Mg2+ and Ca2+ ; mediates Ca2+ repression of pag (PhoP-activated genes) loci. Altered sensing of Mg2+ /Ca2+ may lead to avirulence. PhoQ has distinct non-interacting binding sites for Mg2+ and Ca2+ . Ca2+ decreases the expression of genes required for biofilm matrix production by the decreased transcription of vpsR, which is a negative regulator of biofilm formation. CarSR is negatively regulated by Ca2+ . Elevated Ca2+ represses thermoresistance and decreases heat shock-induced expression of CIRCE regulon, which can be partially attributed to HrcA, since binding of HcrA to CIRCE is modulated by Ca2+ . Ca2+ enhances HrcA stability and promotes its association with GroEL. Elevated Ca2+ induces transcription of atoC, which positively regulates cPHB synthesis

[167,194,195]

Negatively regulates heterocyst formation under nitrogen limited conditions; prevents up-regulation of HetR protease degrading CcbP and increasing intracellular Ca2+ ; contains two Ca2+ binding sites with distinct binding abilities; rich in acidic amino acid residues; Ca2+ -bound form has more compact structure.

[12,42]

Plays role in spore germination and hyphae formation. Contains EF-hand motifs; binds 3 Ca2+ per molecule; undergoes small conformational change in the presence of Ca2+ . CabC likely acts as a Ca2+ buffer and exerts its regulatory role by controlling the intracellular Ca2+ concentration. Plays role in cellular resistance to Ca2+ . Ca2+ binding ability and Ca2+ -mediated conformational changes are similar to calmodulin. Plays role in Ca2+ -dependent aerial mycelia formation; contains four typical EF hand motifs; Ca2+ binding activity is similar to calmodulin. Contains EF-hand-like Ca2+ binding site; although it can bind both Ca2+ and Na+ , Ca2+ binding affinity is higher; Ca2+ binding increases Slt35 stability. Contains two EF-hand domains which are likely localized in the periplasm; involved in the maintenance of intracellular Ca2+ homeostasis, Ca2+ -induced virulence, and expression of genes involved in iron acquisition, pyocyanin biosynthesis, proteolysis, and stress response. Tse3, muramidase, is delivered by the type 6 secretion system (T6SS) into the periplasm of rival bacteria to degrade petidoglycan (PG). Tsi3, periplasmic immunity protein, prevents potential self-intoxication. Tse3-Tsi3complex binds to membrane in a Ca2+ dependent manner, which is essential for Tse3 activity. Tse3 binds two Ca2+ ions: one using EF hand motif (likely required for substrate binding) and the other using a second Ca2+ binding site (possibly involved in acid base catalysis).

[100]

[153]

[154]

[152]

[156]

[23]

[171]

[170]

[99] [173] [110] [47]

[151]

Proteins were selected based on the experimental evidence supporting their role in Ca2+ signaling. The accession numbers were obtained from NCBI. Strain information was not provided in the cited studies and therefore the accession numbers were obtained from the strains available in the NCBI.

*

5. Concluding remarks and future directions A significant body of evidence indicates that Ca2+ and CaBPs play a very important role in prokaryotes. However, several important questions remain to be answered. First of all, the signaling role of Ca2+ needs to be experimentally confirmed, which will lead to identification and characterization of structural and regulatory components of Ca2 signal transduction pathways. The molecular mechanisms required for maintaining cellular Ca2+ homeostasis

await further studies. Finally, a possible role of Ca2+ and CaBPs in physiological adaptations and cellular communication between prokaryotes and eukaryotes deserves research attention. Acknowledgments This work was supported by the Research Grant from OCAST (Award HR12-167) and funding from the National Institutes of Health SCORE grant #2S066M008012-39.

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References [1] E.A. Permyakov, R.H. Kretsinger, Cell signaling, beyond cytosolic calcium in eukaryotes, J. Inorg. Biochem. 103 (2009) 77–86. [2] M. Ikura, M. Osawa, J.B. Ames, The role of calcium-binding proteins in the control of transcription: structure to function, BioEssays 24 (2002) 625–636. [3] M.J. Berridge, M.D. Bootman, H.L. Roderick, Calcium signalling: dynamics, homeostasis and remodelling, Nat. Rev. Mol. Cell Biol. 4 (2003) 517–529. [4] M.J. Berridge, P. Lipp, M.D. Bootman, The versatility and universality of calcium signalling, Nat. Rev. Mol. Cell Biol. 1 (2000) 11–21. [5] D. Sanders, C. Brownlee, J.F. Harper, Communicating with calcium, Plant Cell 11 (1999) 691–706. [6] A.K. Campbell, Intracellular Calcium, Its Universal Role as Regulator, John Wiley & Sons, Chichester, 1983. [7] E. Zampese, P. Pizzo, Intracellular organelles in the saga of Ca2+ homeostasis: different molecules for different purposes? Cell. Mol. Life Sci. 69 (2012) 1077–1104. [8] K. Hashimoto, J. Kudla, Calcium decoding mechanisms in plants, Biochimie 93 (2011) 2054–2059. [9] S.C. Straley, G.V. Plano, E. Skrzypek, P.L. Haddix, K.A. Fields, Regulation by Ca2+ in the Yersinia low-Ca2+ response, Mol. Microbiol. 8 (1993) 1005–1010. [10] L.S. Tisa, J. Adler, Cytoplasmic free-Ca2+ level rises with repellents and falls with attractants in Escherichia coli chemotaxis, Proc. Natl. Acad. Sci. U S A 92 (1995) 10777–10781. [11] S. Sarkisova, M.A. Patrauchan, D. Berglund, D.E. Nivens, M.J. Franklin, Calciuminduced virulence factors associated with the extracellular matrix of mucoid Pseudomonas aeruginosa biofilms, J. Bacteriol. 187 (2005) 4327–4337. [12] Y. Hu, X. Zhang, Y. Shi, Y. Zhou, W. Zhang, X.D. Su, B. Xia, J. Zhao, C. Jin, Structures of Anabaena calcium-binding protein CcbP: insights into Ca2+ signaling during heterocyst differentiation, J. Biol. Chem. 286 (2011) 12381– 12388. [13] M. Guragain, D.L. Lenaburg, F.S. Moore, I. Reutlinger, M.A. Patrauchan, Calcium homeostasis in Pseudomonas aeruginosa requires multiple transporters and modulates swarming motility, Cell Calcium 54 (2013) 350–361. [14] J.W. Rosch, J. Sublett, G. Gao, Y.D. Wang, E.I. Tuomanen, Calcium efflux is essential for bacterial survival in the eukaryotic host, Mol. Microbiol. 70 (2008) 435–444. [15] M.L. Herbaud, A. Guiseppi, F. Denizot, J. Haiech, M.C. Kilhoffer, Calcium signalling in Bacillus subtilis, Biochim. Biophys. Acta 1448 (1998) 212–226. [16] H.E. Jones, I.B. Holland, H.L. Baker, A.K. Campbell, Slow changes in cytosolic free Ca2+ in Escherichia coli highlight two putative influx mechanisms in response to changes in extracellular calcium, Cell Calcium 25 (1999) 265– 274. [17] I. Torrecilla, F. Leganes, I. Bonilla, F. Fernandez-Pinas, Use of recombinant aequorin to study calcium homeostasis and monitor calcium transients in response to heat and cold shock in cyanobacterial, Plant Physiol. 123 (2000) 161–175. [18] M.R. Knight, A.K. Campbell, S.M. Smith, A.J. Trewavas, Recombinant aequorin as a probe for cytosolic free Ca2+ in Escherichia coli, FEBS Lett. 282 (1991) 405–408. [19] F. Leganes, K. Forchhammer, F. Fernandez-Pinas, Role of calcium in acclimation of the cyanobacterium Synechococcus elongatus PCC 7942 to nitrogen starvation, Microbiology 155 (2009) 25–34. [20] A.K. Campbell, R. Naseem, K. Wann, I.B. Holland, S.B. Matthews, Fermentation product butane 2,3-diol induces Ca2+ transients in E. coli through activation of lanthanum-sensitive Ca2+ channels, Cell Calcium 41 (2007) 97–106. [21] R. Naseem, K.T. Wann, I.B. Holland, A.K. Campbell, ATP regulates calcium efflux and growth in E. coli, J. Mol. Biol. 391 (2009) 42–56. [22] S.J. Oomes, M.J. Jonker, F.R. Wittink, J.O. Hehenkamp, T.M. Breit, S. Brul, The effect of calcium on the transcriptome of sporulating B. subtilis cells, Int. J. Food Microbiol. 133 (2009) 234–242. [23] K. Bilecen, F.H. Yildiz, Identification of a calcium-controlled negative regulatory system affecting Vibrio cholerae biofilm formation, Environ. Microbiol. 11 (2009) 2015–2029. [24] D.C. Dominguez, Proteome analysis of B. subtilis in response to calcium, J. Anal. Bioanal. Tech. (2011) S6. [25] M.A. Patrauchan, S.A. Sarkisova, M.J. Franklin, Strain-specific proteome responses of Pseudomonas aeruginosa to biofilm-associated growth and to calcium, Microbiology 153 (2007) 3838–3851. [26] C.J. Gode-Potratz, D.M. Chodur, L.L. McCarter, Calcium and iron regulate swarming and type III secretion in Vibrio parahaemolyticus, J. Bacteriol. 192 (2010) 6025–6038. [27] K. Yang, Prokaryotic calmodulins: recent developments and evolutionary implications, J. Mol. Microbiol. Biotechnol. 3 (2001) 457–459. [28] D.J. Rigden, M.J. Jedrzejas, O.V. Moroz, M.Y. Galperin, Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands? Trends Microbiol. 11 (2003) 295–297. [29] Y. Zhou, W. Yang, M. Kirberger, H.W. Lee, G. Ayalasomayajula, J.J. Yang, Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins, Proteins 65 (2006) 643–655. [30] P. Aravind, A. Mishra, S.K. Suman, M.K. Jobby, R. Sankaranarayanan, Y. Sharma, The betagamma-crystallin superfamily contains a universal motif for binding calcium, Biochemistry 48 (2009) 12180–12190. [31] J. Michiels, C. Xi, J. Verhaert, J. Vanderleyden, The functions of Ca(2+) in bacteria: a role for EF-hand proteins? Trends Microbiol. 10 (2002) 87–93.

[32] N. Bylsma, T. Drakenberg, I. Andersson, P.F. Leadlay, S. Forsen, Prokaryotic calcium-binding protein of the calmodulin superfamily. Calcium binding to a Saccharopolyspora erythraea 20 kDa protein, FEBS Lett. 299 (1992) 44–47. [33] D.G. Swan, R.S. Hale, N. Dhillon, P.F. Leadlay, A bacterial calcium-binding protein homologous to calmodulin, Nature 329 (1987) 84–85. [34] R.A. Welch, RTX toxin structure and function: a story of numerous anomalies and few analogies in toxin biology, Curr. Top Microbiol. Immunol. 257 (2001) 85–111. [35] M.K. Jobby, Y. Sharma, Calcium-binding crystallins from Yersinia pestis. Characterization of two single betagamma-crystallin domains of a putative exported protein, J. Biol. Chem. 280 (2005) 1209–1216. [36] M.K. Jobby, Y. Sharma, Caulollins from Caulobacter crescentus, a pair of partially unstructured proteins of betagamma-crystallin superfamily, gain structure upon binding calcium, Biochemistry 46 (2007) 12298–12307. [37] R. Raman, V. Rajanikanth, R.U. Palaniappan, Y.P. Lin, H. He, S.P. McDonough, Y. Sharma, Y.F. Chang, Big domains are novel Ca(2)+ -binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig) proteins, PloS One 5 (2010) e14377. [38] I. Linhartova, L. Bumba, J. Masin, M. Basler, R. Osicka, J. Kamanova, K. Prochazkova, I. Adkins, J. Hejnova-Holubova, L. Sadilkova, J. Morova, P. Sebo, RTX proteins: a highly diverse family secreted by a common mechanism, FEMS Microbiol. Rev. 34 (2010) 1076–1112. [39] S.S. Srivastava, A. Mishra, B. Krishnan, Y. Sharma, Ca2+ -binding motif of betagamma-crystallins, J. Biol. Chem. 289 (2014) 10958–10966. [40] D.C. Dominguez, H. Adams, J.H. Hageman, Immunocytochemical localization of a calmodulinlike protein in Bacillus subtilis cells, J. Bacteriol. 181 (1999) 4605–4610. [41] H. Tossavainen, P. Permi, A. Annila, I. Kilpelainen, T. Drakenberg, NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea, Eur. J. Biochem. 270 (2003) 2505–2512. [42] Y. Zhao, Y. Shi, W. Zhao, X. Huang, D. Wang, N. Brown, J. Brand, J. Zhao, CcbP, a calcium-binding protein from Anabaena sp. PCC 7120, provides evidence that calcium ions regulate heterocyst differentiation, Proc. Natl. Acad. Sci. U S A 102 (2005) 5744–5748. [43] X. Zhao, H. Pang, S. Wang, W. Zhou, K. Yang, M. Bartlam, Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein, Protein Cell 1 (2010) 771–779. [44] D.E. Clapham, Calcium signaling, Cell 131 (2007) 1047–1058. [45] J.A. Gilabert, Cytoplasmic calcium buffering, Adv. Exp. Med. Biol. 740 (2012) 483–498. [46] P. Gangola, B.P. Rosen, Maintenance of intracellular calcium in Escherichia coli, J. Biol. Chem. 262 (1987) 12570–12574. [47] S.A. Sarkisova, S.R. Lotlikar, M. Guragain, R. Kubat, J. Cloud, M.J. Franklin, M.A. Patrauchan, A Pseudomonas aeruginosa EF-hand protein, EfhP (PA4107), modulates stress responses and virulence at high calcium concentration, PloS One 9 (2014) e98985. [48] D.C. Dominguez, Calcium signalling in bacteria, Mol. Microbiol. 54 (2004) 291–297. [49] L. Notari, I.M. Pepe, C. Cugnoli, A. Morelli, Adenylate kinase activity in rod outer segments of bovine retina, Biochim. Biophys. Acta 1504 (2001) 438–443. [50] H. Nakamura, W. Satoh, S. Hidaka, Y. Kagaya, S. Ejiri, K. Tsutsumi, Genomic structure of the rice aldolase isozyme C-1 gene and its regulation through a Ca2+ -mediated protein kinase-phosphatase pathway, Plant Mol. Biol. 30 (1996) 381–385. [51] H.K. Kim, W.S. Park, S.H. Kang, M. Warda, N. Kim, J.H. Ko, B. Prince Ael, J. Han, Mitochondrial alterations in human gastric carcinoma cell line, Am. J. Physiol. Cell Physiol. 293 (2007) C761–C771. [52] R. Docampo, P. Ulrich, S.N.J. Moreno, Evolution of acidocalcisomes and their role in polyphosphate storage and osmoregulation in eukaryotic microbes, Philos. Trans. R. Soc. Lond. B Biol. Sci. 365 (2010) 775–784. [53] M. Seufferheld, C.R. Lea, M. Vieira, E. Oldfield, R. Docampo, The H+ pyrophosphatase of Rhodospirillum rubrum is predominantly located in polyphosphate-rich acidocalcisomes, J. Biol. Chem. 279 (2004) 51193–51202. [54] M. Seufferheld, M.C.F. Vieira, F.A. Ruiz, C.O. Rodrigues, S.N.J. Moreno, R. Docampo, Identification of organelles in bacteria similar to acidocalcisomes of unicellular eukaryotes, J. Biol. Chem. 278 (2003) 29971–29978. [55] R. Docampo, S.N.J. Moreno, Acidocalcisomes, Cell Calcium 50 (2011) 113–119. [56] R. Docampo, W. de Souza, K. Miranda, P. Rohloff, S.N.J. Moreno, Acidocalcisomes—conserved from bacteria to man, Nat. Rev. Microbiol. 3 (2005) 251–261. [57] L.L. Graham, T.J. Beveridge, N. Nanninga, Periplasmic space and the concept of the periplasm, Trends Biochem. Sci. 16 (1991) 328–329. [58] V.R.F. Matias, T.J. Beveridge, Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space, Mol. Microbiol. 56 (2005) 240–251. [59] V.R.F. Matias, T.J. Beveridge, Native cell wall organization shown by cryoelectron microscopy confirms the existence of a periplasmic space in Staphylococcus aureus, J. Bacteriol. 188 (2006) 1011–1021. [60] B. Zuber, M. Haenni, T. Ribeiro, K. Minnig, F. Lopes, P. Moreillon, J. Dubochet, Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections, J. Bacteriol. 188 (2006) 6652–6660. [61] C.F. Chang, H. Shuman, A.P. Somlyo, Electron probe analysis, X-ray mapping, and electron energy-loss spectroscopy of calcium, magnesium, and

D.C. Domínguez et al. / Cell Calcium 57 (2015) 151–165

[62]

[63]

[64] [65] [66]

[67]

[68] [69] [70]

[71]

[72] [73]

[74]

[75]

[76]

[77]

[78]

[79]

[80]

[81]

[82]

[83]

[84] [85]

[86] [87]

[88]

[89]

[90]

monovalent ions in log-phase and in dividing Escherichia coli B cells, J. Bacteriol. 167 (1986) 935–939. H.E. Jones, I.B. Holland, A.K. Campbell, Direct measurement of free Ca(2+) shows different regulation of Ca(2+) between the periplasm and the cytosol of Escherichia coli, Cell Calcium 32 (2002) 183–192. M.C. Trombe, Characterization of a calcium porter of Streptococcus pneumoniae involved in calcium regulation of growth and competence, J. Gen. Microbiol. 139 (1993) 433–439. L.S. Tisa, Calcium transport by Frankia sp. strain EAN1pec, Curr. Microbiol. 37 (1998) 12–16. T. Matsushita, H. Hirata, I. Kusaka, Calcium channels in bacteria: purification and characterization, Ann. N. Y. Acad. Sci. 560 (1989) 426–429. K. Kanamaru, S. Kashiwagi, T. Mizuno, The cyanobacterium, Synechococcus sp. PCC7942, possesses two distinct genes encoding cation-transporting P-type ATPases, FEBS Lett. 330 (1993) 99–104. S.V. Ambudkar, A.R. Lynn, P.C. Maloney, B.P. Rosen, Reconstitution of ATPdependent calcium transport from streptococci, Biol. Chem. 261 (1986) 15596–15600. H.S. Houng, A.R. Lynn, B.P. Rosen, ATP-driven calcium transport in membrane vesicles of Streptococcus sanguis, J. Bacteriol. 168 (1986) 1040–1044. B.P. Rosen, Bacterial calcium transport, Biochim. Biophys. Acta 906 (1987) 101–110. L.V. Nazarenko, I.M. Andreev, A.A. Lyukevich, T.V. Pisareva, D.A. Los, Calcium release from Synechocystis cells induced by depolarization of the plasma membrane: MscL as an outward Ca2+ channel, Microbiology 149 (2003) 1147–1153. Y. Chang, R. Bruni, B. Kloss, Z. Assur, E. Kloppmann, B. Rost, W.A. Hendrickson, Q. Liu, Structural basis for a pH-sensitive calcium leak across membranes, Science 344 (2014) 1131–1135. M.G. Palmgren, K.B. Axelsen, Evolution of P-type ATPases, Biochim. Biophys. Acta 1365 (1998) 37–45. M. Geisler, W. Koenen, J. Richter, J. Schumann, Expression and characterization of a Synechocystis PCC 6803 P-type ATPase in E. coli plasma membranes, Biochim. Biophys. Acta 1368 (1998) 267–275. M. Geisler, J. Richter, J. Schumann, Molecular cloning of a P-type ATPase gene from the cyanobacterium Synechocystis sp. PCC 6803. Homology to eukaryotic Ca(2+) -ATPases, J. Mol. Biol. 234 (1993) 1284–1289. M.G. Desrosiers, L.J. Gately, A.M. Gambel, D.R. Menick, Purification and characterization of the Ca2+ -ATPase of Flavobacterium odoratum, J. Biol. Chem. 271 (1996) 3945–3951. W.E. Peiffer, M.G. Desrosiers, D.R. Menick, Cloning and expression of the unique Ca2+ -ATPase from Flavobacterium odoratum, J. Biol. Chem. 271 (1996) 5095–5100. K. Faxen, J.L. Andersen, P. Gourdon, N. Fedosova, J.P. Morth, P. Nissen, J.V. Moller, Characterization of a Listeria monocytogenes Ca(2+) pump: a SERCAtype ATPase with only one Ca(2+) -binding site, J. Biol. Chem. 286 (2011) 1609–1617. E.S. Giotis, A. Muthaiyan, I.S. Blair, B.J. Wilkinson, D.A. McDowell, Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S, BMC Microbiol. 8 (2008) 102. L. Raeymaekers, E. Wuytack, I. Willems, C.W. Michiels, F. Wuytack, Expression of a P-type Ca(2+) -transport ATPase in Bacillus subtilis during sporulation, Cell Calcium 32 (2002) 93. T. Berkelman, P. Garret-Engele, N.E. Hoffman, The pacL gene of Synechococcus sp. strain PCC 7942 encodes a Ca(2+) -transporting ATPase, J. Bacteriol. 176 (1994) 4430–4436. K.L. Hein, P. Nissen, J.P. Morth, Purification, crystallization and preliminary crystallographic studies of a PacL homologue from Listeria monocytogenes, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 424–427. A.J.M. Driessen, W. Devrij, W.N. Konings, Incorporation of beef-heart cytochrome-C Oxidase as a proton-motive force-generating mechanism in bacterial-membrane vesicles, Proc. Natl. Acad. Sci. U S A 82 (1985) 7555–7559. R.R. Birge, D.S.K. Govender, K.C. Izgi, E.H.L. Tan, Role of calcium in the proton pump of bacteriorhodopsin. Microwave evidence for a cation-gated mechanism, J. Phys. Chem. 100 (1996) 9990–10004. T. Matsushita, T. Ueda, I. Kusaka, Purification and characterization of Ca2+ /H+ antiporter from Bacillus subtilis, Eur. J. Biochem. 156 (1986) 95–100. R. Waditee, G.S. Hossain, Y. Tanaka, T. Nakamura, M. Shikata, J. Takano, T. Takabe, Isolation and functional characterization of Ca2+ /H+ antiporters from cyanobacteria, J. Biol. Chem. 279 (2004) 4330–4338. R.N. Brey, B.P. Rosen, Cation/proton antiport systems in Escherichia coli. Properties of the calcium/proton antiporter, J. Biol. Chem. 254 (1979) 1957–1963. H.W. van Veen, T. Abee, G.J. Kortstee, W.N. Konings, A.J. Zehnder, Translocation of metal phosphate via the phosphate inorganic transport system of Escherichia coli, Biochemistry 33 (1994) 1766–1770. M. Fujisawa, Y. Wada, T. Tsuchiya, M. Ito, Characterization of Bacillus subtilis YfkE (ChaA): a calcium-specific Ca2+ /H+ antiporter of the CaCA family, Arch. Microbiol. 191 (2009) 649–657. D.M. Ivey, A.A. Guffanti, J. Zemsky, E. Pinner, R. Karpel, E. Padan, S. Schuldiner, T.A. Krulwich, Cloning and characterization of a putative Ca2+ /H+ antiporter gene from Escherichia coli upon functional complementation of Na+ /H+ antiporter-deficient strains by the overexpressed gene, J. Biol. Chem. 268 (1993) 11296–11303. M.V. Radchenko, K. Tanaka, R. Waditee, S. Oshimi, Y. Matsuzaki, M. Fukuhara, H. Kobayashi, T. Takabe, T. Nakamura, Potassium/proton antiport system of Escherichia coli, J. Biol. Chem. 281 (2006) 19822–19829.

163

[91] T. Ohyama, K. Igarashi, H. Kobayashi, Physiological role of the chaA gene in sodium and calcium circulations at a high pH in Escherichia coli, J. Bacteriol. 176 (1994) 4311–4315. [92] H. Bolhuis, H.W. van Veen, J.R. Brands, M. Putman, B. Poolman, A.J. Driessen, W.N. Konings, Energetics and mechanism of drug transport mediated by the lactococcal multidrug transporter LmrP, J. Biol. Chem. 271 (1996) 24123–24128. [93] T.A. Schaedler, Z. Tong, H.W. van Veen, The multidrug transporter LmrP protein mediates selective calcium efflux, J. Biol. Chem. 287 (2012) 27682–27690. [94] H.W. Van Veen, T. Abee, G.J. Kortstee, W.N. Konings, A.J. Zehnder, Characterization of two phosphate transport systems in Acinetobacter johnsonii 210A, J. Bacteriol. 175 (1993) 200–206. [95] W.W. Kay, O.K. Ghei, Inorganic cation transport and the effects on C4 dicarboxylate transport in Bacillus subtilis, Can. J. Microbiol. 27 (1981) 1194– 1201. [96] R. Naseem, I.B. Holland, A. Jacq, K.T. Wann, A.K. Campbell, pH and monovalent cations regulate cytosolic free Ca(2+) in E. coli, Biochim. Biophys Acta 1778 (2008) 1415–1422. [97] T. Matsushita, H. Hirata, I. Kusaka, Calcium channel blockers inhibit bacterial chemotaxis, FEBS Lett. 236 (1988) 437–440. [98] C. Xi, E. Schoeters, J. Vanderleyden, J. Michiels, Symbiosis-specific expression of Rhizobium etli casA encoding a secreted calmodulin-related protein, Proc. Natl. Acad. Sci. U S A 97 (2000) 11114–11119. [99] T. Yonekawa, Y. Ohnishi, S. Horinouchi, A calmodulin-like protein in the bacterial genus Streptomyces, FEMS Microbiol. Lett. 244 (2005) 315–321. [100] S.L. Wang, K.Q. Fan, X. Yang, Z.X. Lin, X.P. Xu, K.Q. Yang, CabC, an EF-hand calcium-binding protein, is involved in Ca2+ -mediated regulation of spore germination and aerial hypha formation in Streptomyces coelicolor, J. Bacteriol. 190 (2008) 4061–4068. [101] R.H. Kretsinger, Calcium-binding proteins, Annu. Rev. Biochem. 45 (1976) 239–266. [102] H. Kawasaki, S. Nakayama, R.H. Kretsinger, Classification and evolution of EF-hand proteins, Biometals 11 (1998) 277–295. [103] D.J. Rigden, D.D. Woodhead, P.W.H. Wong, M.Y. Galperin, New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins, PloS One 6 (2011). [104] M. Mazumder, N. Padhan, A. Bhattacharya, S. Gourinath, Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca2+ binding affinity, Plos One (2014) 9. [105] S. Nakayama, H. Kawasaki, R.H. Kretsinger, Evolution of EF-Hand Proteins, Springer Berlin Heidelberg, Berlin, 2000. [106] D.J. Rigden, M.Y. Galperin, The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution, J. Mol. Biol. 343 (2004) 971–984. [107] J.L. Gifford, M.P. Walsh, H.J. Vogel, Structures and metal-ion-binding properties of the Ca2+ -binding helix-loop-helix EF-hand motifs, Biochem. J. 405 (2007) 199–221. [108] Y.Y. Chen, S.H. Xue, Y.B. Zhou, J.J. Yang, Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering, Sci. China Chem. 53 (2010) 52–60. [109] P.F. Leadlay, G. Roberts, J.E. Walker, Isolation of a novel calcium-binding protein from Streptomyces erythreus, FEBS Lett. 178 (1984) 157–160. [110] E.J. van Asselt, B.W. Dijkstra, Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability, FEBS Lett. 458 (1999) 429–435. [111] B.L. Lytle, B.F. Volkman, W.M. Westler, M.P. Heckman, J.H. Wu, Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain, J. Mol. Biol. 307 (2001) 745–753. [112] K. Momma, B. Mikami, Y. Mishima, W. Hashimoto, K. Murata, Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution, J. Mol. Biol. 316 (2002) 1051–1059. [113] A.G. Murzin, Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry, Proteins 14 (1992) 191–201. [114] I. Chaudhuri, J. Soding, A.N. Lupas, Evolution of the beta-propeller fold, Proteins 71 (2008) 795–803. [115] Y. Kurakata, A. Uechi, H. Yoshida, S. Kamitori, Y. Sakano, A. Nishikawa, T. Tonozuka, Structural Insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63, J. Mol. Biol. 381 (2008) 116 (383, 745-745). [116] R. Suzuki, T. Katayama, M. Kitaoka, H. Kumagai, T. Wakagi, H. Shoun, H. Ashida, K. Yamamoto, S. Fushinobu, Crystallographic and mutational analyses of substrate recognition of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum, J. Biochem. 146 (2009) 389–398. [117] N. Li, P. Yun, M.A. Nadkarni, N.B. Ghadikolaee, K.A. Nguyen, M. Lee, N. Hunter, C.A. Collyer, Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis, Mol. Microbiol. 76 (2010) 861–873. [118] Y. Takeuchi, S. Tanaka, H. Matsumura, Y. Koga, K. Takano, S. Kanaya, Requirement of a unique Ca2+ -binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon, Biochemistry 48 (2009) 10637–10643. [119] A. Ochiai, T. Itoh, Y. Maruyama, A. Kawamata, B. Mikami, W. Hashimoto, K. Murata, A novel structural fold in polysaccharide lyases—Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller, J. Biol. Chem. 282 (2007) 37134–37145. [120] J. Orans, M.D.L. Johnson, K.A. Coggan, J.R. Sperlazza, R.W. Heiniger, M.C. Wolfgang, M.R. Redinbo, Crystal structure analysis reveals Pseudomonas PilY1 as

164

[121]

[122]

[123]

[124] [125]

[126]

[127]

[128]

[129]

[130]

[131]

[132]

[133]

[134]

[135]

[136]

[137] [138] [139]

[140] [141]

[142] [143]

[144]

[145] [146]

[147] [148] [149]

[150]

[151]

D.C. Domínguez et al. / Cell Calcium 57 (2015) 151–165 an essential calcium-dependent regulator of bacterial surface motility, Proc. Natl. Acad. Sci. U S A 107 (2010) 1065. A. Chenal, J.I. Guijarro, B. Raynal, M. Delepierre, D. Ladant, RTX calcium binding motifs are intrinsically disordered in the absence of calcium: implication for protein secretion, J. Biol. Chem. 284 (2009) 1781–1789. M.A. Blenner, O. Shur, G.R. Szilvay, D.M. Cropek, S. Banta, Calcium-induced folding of a beta roll motif requires C-terminal entropic stabilization, J. Mol. Biol. 400 (2010) 244–256. S. Thomas, P.J. Bakkes, S.H.J. Smits, L. Schmitt, Equilibrium folding of proHlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate, BBA-Proteins Proteomics 1844 (2014) 1500–1510. M.J. Brennan, G. Delogu, The PE multigene family: a ‘molecular mantra’ for mycobacteria, Trends Microbiol. 10 (2002) 246–249. N. Bachhawat, B. Singh, Mycobacterial PE PGRS proteins contain calciumbinding motifs with parallel beta-roll folds, Genomics Proteomics Bioinform. 5 (2007) 236–241. C. Tian, X. Jian-Ping, Roles of PE PGRS family in Mycobacterium tuberculosis pathogenesis and novel measures against tuberculosis, Microb. Pathog. 49 (2010) 311–314. D. Bottai, R. Brosch, Mycobacterial PE, PPE and ESX clusters: novel insights into the secretion of these most unusual protein families, Mol. Microbiol. 73 (2009) 325–328. L.S. Meena, An overview to understand the role of PE PGRS family proteins in Mycobacterium tuberculosis H Rv and their potential as new drug targets, Biotechnol. Appl. Biochem. (2014). R. Copin, M. Coscolla, S.N. Seiffert, G. Bothamley, J. Sutherland, G. Mbayo, S. Gagneux, J.D. Ernst, Sequence diversity in the pe pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition, MBio 5 (2014). S.K. Suman, D. Ravindra, Y. Sharma, A. Mishra, Association properties and unfolding of a betagamma-crystallin domain of a Vibrio-specific protein, PloS One 8 (2013) e53610. A. Mishra, S.K. Suman, P. Aravind, Y. Sharma, From microbial to lens ␤␥crystallins: presence of a universal calcium-binding motif in ␤␥-crystallin superfamily, Curr. Trends Sci. (2009) 6. G. Wistow, Evolution of a protein superfamily: relationships between vertebrate lens crystallins and microorganism dormancy proteins, J. Mol. Biol. 30 (1990) 140–145. M. Wenk, R. Baumgartner, T.A. Holak, R. Huber, R. Jaenicke, E.M. Mayr, The domains of protein S from Myxococcus xanthus: structure, stability and interactions, J. Mol. Biol. 286 (1999) 1533–1545. R.P. Barnwal, M.K. Jobby, K.M. Devi, Y. Sharma, K.V. Chary, Solution structure and calcium-binding properties of M-crystallin, a primordial betagammacrystallin from archaea, J. Mol. Biol. 386 (2009) 675–689. A.K. Srivastava, Y. Sharma, K.V. Chary, A natively unfolded betagammacrystallin domain from Hahella chejuensis, Biochemistry 49 (2010) 9746–9755. Y.P. Lin, R. Raman, Y. Sharma, Y.F. Chang, Calcium binds to leptospiral immunoglobulin-like protein, LigB, and modulates fibronectin binding, J. Biol. Chem. 283 (2008) 25140–25149. D.M. Halaby, J.P. Mornon, The immunoglobulin superfamily: an insight on its tissular, species, and functional diversity, J. Mol. Biol. 46 (1998) 389–400. D.M. Halaby, A. Poupon, J. Mornon, The immunoglobulin fold family: sequence analysis and 3D structure comparisons, Protein Eng. 12 (1999) 563–571. J. Matsunaga, M.A. Barocchi, J. Croda, T.A. Young, Y. Sanchez, I. Siqueira, C.A. Bolin, M.G. Reis, L.W. Riley, D.A. Haake, A.I. Ko, Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily, Mol. Microbiol. 49 (2003) 929–945. A. Holmgren, C.I. Branden, Crystal structure of chaperone protein PapD reveals an immunoglobulin fold, Nature 342 (1989) 248–251. B.E. Hofmann, H. Bender, G.E. Schulz, Three-dimensional structure of cyclodextrin glycosyltransferase from Bacillus circulans at 3.4 A resolution, J. Mol. Biol. 209 (1989) 793–800. M.J. Crabbe, D. Goode, Protein folds and functional similarity; the Greek key/immunoglobulin fold, Comput. Chem. 19 (1995) 343–349. R. Raman, Y. Sharma, Y.F. Chang, Ca-binding and spectral properties of the common region of surface-exposed Lig proteins of leptospira, Commun. Integr. Biol. 4 (2011) 331–333. T. Wang, J.H. Zhang, X.C. Zhang, C. Xu, X.M. Tu, Solution structure of the Big domain from Streptococcus pneumoniae reveals a novel Ca2+ -binding module, Sci. Rep. 3 (2013). L.A. Onek, R.J. Smith, Calmodulin and calcium mediated regulation in prokaryotes, J. Gen. Microbiol. 138 (1992) 1039–1049. V. Norris, S. Grant, P. Freestone, J. Canvin, F.N. Sheikh, I. Toth, M. Trinei, K. Modha, R.I. Norman, Calcium signalling in bacteria, J. Bacteriol. 178 (1996) 3677–3682. V. Norris, M. Chen, M. Goldberg, J. Voskuil, G. McGurk, I.B. Holland, Calcium in bacteria: a solution to which problem? Mol. Microbiol. 5 (1991) 775–778. R.J. Smith, Calcium and bacteria, Adv. Microb. Physiol. 37 (1995) 83–133. J.A. Killian, M.C. Koorengevel, J.A. Bouwstra, G. Gooris, W. Dowhan, B. de Kruijff, Effect of divalent cations on lipid organization of cardiolipin isolated from Escherichia coli strain AH930, Biochim. Biophys. Acta 1189 (1994) 225–232. K. Kierek, P.I. Watnick, The Vibrio cholerae O139 O-antigen polysaccharide is essential for Ca2+ -dependent biofilm development in sea water, Proc. Natl. Acad. Sci. U S A 100 (2003) 14357–14362. D. Lu, G. Shang, H. Zhang, Q. Yu, X. Cong, J. Yuan, F. He, C. Zhu, Y. Zhao, K. Yin, Y. Chen, J. Hu, X. Zhang, Z. Yuan, S. Xu, W. Hu, H. Cang, L. Gu, Structural

[152]

[153]

[154]

[155]

[156]

[157]

[158]

[159]

[160]

[161]

[162]

[163]

[164]

[165]

[166] [167]

[168]

[169]

[170]

[171]

[172] [173]

[174]

[175]

[176]

[177]

insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex from Pseudomonas aeruginosa reveal a calcium-dependent membrane-binding mechanism, Mol. Microbiol. 92 (2014) 1092–1112. E. Josefsson, D. O’Connell, T.J. Foster, I. Durussel, J.A. Cox, The binding of calcium to the B-repeat segment of SdrD, a cell surface protein of Staphylococcus aureus, J. Biol. Chem. 273 (1998) 31145–31152. D.P. O’Connell, T. Nanavaty, D. McDevitt, S. Gurusiddappa, M. Hook, T.J. Foster, The fibrinogen-binding MSCRAMM (clumping factor) of Staphylococcus aureus has a Ca2+ -dependent inhibitory site, J. Biol. Chem. 273 (1998) 6821–6829. D. Ni Eidhin, S. Perkins, P. Francois, P. Vaudaux, M. Hook, T.J. Foster, Clumping factor B (ClfB), a new surface-located fibrinogen-binding adhesin of Staphylococcus aureus, Mol. Microbiol. 30 (1998) 245–257. M.J. Arrizubieta, A. Toledo-Arana, B. Amorena, J.R. Penades, I. Lasa, Calcium inhibits bap-dependent multicellular behavior in Staphylococcus aureus, J. Bacteriol. 186 (2004) 7490–7498. A.G. Torres, N.T. Perna, V. Burland, A. Ruknudin, F.R. Blattner, J.B. Kaper, Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli, Mol. Microbiol. 45 (2002) 951–966. M.C. Wolfgang, V.T. Lee, M.E. Gilmore, S. Lory, Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway, Dev. Cell 4 (2003) 253–263. M.Y. Sherman, A.L. Goldberg, Heat shock of Escherichia coli increases binding of dnaK (the hsp70 homolog) to polypeptides by promoting its phosphorylation, Proc. Natl. Acad. Sci. U S A 90 (1993) 8648–8652. A.K. Saha, J.N. Dowling, N.K. Mukhopadhyay, R.H. Glew, Demonstration of two protein kinases in extracts of Legionella micdadei, J. Gen. Microbiol. 134 (1988) 1275–1281. D. Flego, M. Pirhonen, H. Saarilahti, T.K. Palva, E.T. Palva, Control of virulence gene expression by plant calcium in the phytopathogen Erwinia carotovora, Mol. Microbiol. 25 (1997) 831–838. S. Ramstad, C.M. Futsaether, A. Johnsson, Porphyrin sensitization and intracellular calcium changes in the prokaryote Propionibacterium acnes, J. Photochem. Photobiol. B 40 (1997) 141–148. M. Werthen, T. Lundgren, Intracellular Ca(2+) mobilization and kinase activity during acylated homoserine lactone-dependent quorum sensing in Serratia liquefaciens, J. Biol. Chem. 276 (2001) 6468–6472. N.J. Watkins, M.R. Knight, A.J. Trewavas, A.K. Campbell, Free calcium transients in chemotactic and non-chemotactic strains of Escherichia coli determined by using recombinant aequorin, Biochem. J. 306 (Pt 3) (1995) 865–869. A.K. Campbell, R. Naseem, I.B. Holland, S.B. Matthews, K.T. Wann, Methylglyoxal and other carbohydrate metabolites induce lanthanum-sensitive Ca2+ transients and inhibit growth in E. coli, Arch. Biochem. Biophys. 468 (2007) 107–113. R. Naseem, S.R. Davies, H. Jones, K.T. Wann, I.B. Holland, A.K. Campbell, Cytosolic Ca2+ regulates protein expression in E. coli through release from inclusion bodies, Biochem. Biophys. Res. Commun. 360 (2007) 33–39. L.R. Prost, S.I. Miller, The Salmonellae PhoQ sensor: mechanisms of detection of phagosome signals, Cell. Microbiol. 10 (2008) 576–582. E.G. Vescovi, Y.M. Ayala, E. Di Cera, E.A. Groisman, Characterization of the bacterial sensor protein PhoQ. Evidence for distinct binding sites for Mg2+ and Ca2+ , J. Biol. Chem. 272 (1997) 1440–1443. M.C. Theodorou, C.A. Panagiotidis, C.H. Panagiotidis, A.A. Pantazaki, D.A. Kyriakidis, Involvement of the AtoS-AtoC signal transduction system in poly(R)-3-hydroxybutyrate biosynthesis in Escherichia coli, Biochim. Biophys. Acta 1760 (2006) 896–906. R.N. Reusch, R. Huang, L.L. Bramble, Poly-3-hydroxybutyrate/polyphosphate complexes form voltage-activated Ca2+ channels in the plasma membranes of Escherichia coli, Biophys. J. 69 (1995) 754–766. M.C. Theodorou, E. Tiligada, D.A. Kyriakidis, Extracellular Ca2+ transients affect poly-(R)-3-hydroxybutyrate regulation by the AtoS-AtoC system in Escherichia coli, Biochem. J. 417 (2009) 667–672. H.Y. Kwon, S.N. Kim, S.N. Pyo, D.K. Rhee, Ca2+ -dependent expression of the CIRCE regulon in Streptococcus pneumoniae, Mol. Microbiol. 55 (2005) 456–468. M. Ikura, Calcium binding and conformational response in EF-hand proteins, Trends Biochem. Sci. 21 (1996) 14–17. T. Yonekawa, Y. Ohnishi, S. Horinouchi, A calcium-binding protein with four EF-hand motifs in Streptomyces ambofaciens, Biosci. Biotech. Biochem. 65 (2001) 156–160. R. Utsumi, R.E. Brissette, A. Rampersaud, S.A. Forst, K. Oosawa, M. Inouye, Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate, Science 245 (1989) 1246–1249. A. Rampersaud, R. Utsumi, J. Delgado, S.A. Forst, M. Inouye, Ca2(+) -enhanced phosphorylation of a chimeric protein kinase involved with bacterial signal transduction, J. Biol. Chem. 266 (1991) 7633–7637. V. Checchetto, E. Formentin, L. Carraretto, A. Segalla, G.M. Giacometti, I. Szabo, E. Bergantino, Functional characterization and determination of the physiological role of a calcium-dependent potassium channel from cyanobacteria, Plant Physiol. 162 (2013) 953–964. Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, Crystal structure and mechanism of a calcium-gated potassium channel, Nature 417 (2002) 515–522.

D.C. Domínguez et al. / Cell Calcium 57 (2015) 151–165 [178] L.V. Parfenova, K. Abarca-Heidemann, B.M. Crane, B.S. Rothberg, Molecular architecture and divalent cation activation of TvoK, a prokaryotic potassium channel, J. Biol. Chem. 282 (2007) 24302–24309. [179] H. Hoi, T. Matsuda, T. Nagai, R.E. Campbell, Highlightable Ca2+ indicators for live cell imaging, J. Am. Chem. Soc. 135 (2013) 46–49. [180] A.N. Holder, A.L. Ellis, J. Zou, N. Chen, J.J. Yang, Facilitating chromophore formation of engineered Ca(2+) binding green fluorescent proteins, Arch. Biochem. Biophys. 486 (2009) 27–34. [181] A.M. Gambel, M.G. Desrosiers, D.R. Menick, Characterization of a P-type Ca(2+ )-ATPase from Flavobacterium odoratum, J. Biol. Chem. 267 (1992) 15923–15931. [182] J.L. Andersen, P. Gourdon, J.V. Moller, J.P. Morth, P. Nissen, Crystallization and preliminary structural analysis of the Listeria monocytogenes Ca(2+) ATPase LMCA1, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 (2011) 718–722. [183] R. Henderson, J.M. Baldwin, T.A. Ceska, F. Zemlin, E. Beckmann, K.H. Downing, Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy, J. Mol. Biol. 213 (1990) 899–929. [184] J.A. Stuart, B.W. Vought, C.F. Zhang, R.R. Birge, The active-site of bacteriorhodopsin—2-photon spectroscopic evidence for a positively charged chromophore binding-site mediated by calcium, Biospectroscopy 1 (1995) 9–28. [185] A.J.M. Driessen, K.J. Hellingwerf, W.N. Konings, Light-induced generation of a protonmotive force and Ca-2+ -transport in membrane-vesicles of Streptococcus cremoris fused with bacteriorhodopsin proteoliposomes, Biochim. Biophys. Acta 808 (1985) 1–12. [186] M. Wu, S. Tong, S. Waltersperger, K. Diederichs, M. Wang, L. Zheng, Crystal structure of Ca2+ /H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation, Proc. Natl. Acad. Sci. U S A 110 (2013) 11367–11372. [187] D.G. Swan, J. Cortes, R.S. Hale, P.F. Leadlay, Cloning, characterization, and heterologous expression of the Saccharopolyspora erythraea (Streptomyces

[188]

[189] [190]

[191]

[192]

[193]

[194]

[195]

[196]

165

erythraeus) gene encoding an EF-hand calcium-binding protein, J. Bacteriol. 171 (1989) 5614–5619. A. Roujeinikova, C. Raasch, S. Sedelnikova, W. Liebl, D.W. Rice, Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis, J. Mol. Biol. 321 (2002) 149–162. C. Petosa, R.J. Collier, K.R. Klimpel, S.H. Leppla, R.C. Liddington, Crystal structure of the anthrax toxin protective antigen, Nature 385 (1997) 833–838. N.K. Vyas, M.N. Vyas, F.A. Quiocho, A novel calcium binding site in the galactose-binding protein of bacterial transport and chemotaxis, Nature 327 (1987) 635–638. U. Baumann, S. Wu, K.M. Flaherty, D.B. McKay, Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif, EMBO J. 12 (1993) 3357–3364. L. Sadeghi, K. Khajeh, N. Mollania, B. Dabirmanesh, B. Ranjbar, Extra EF hand unit (DX) mediated stabilization and calcium independency of alpha-amylase, Mol. Biotechnol. 53 (2013) 270–277. S. Bagby, T.S. Harvey, S.G. Eagle, S. Inouye, M. Ikura, NMR-derived threedimensional solution structure of protein S complexed with calcium, Structure 2 (1994) 107–122. E. Garcia Vescovi, F.C. Soncini, E.A. Groisman, Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence, Cell 84 (1996) 165–174. J.S. Gunn, S.I. Miller, PhoP-PhoQ activates transcription of pmrAB, encoding a two-component regulatory system involved in Salmonella typhimurium antimicrobial peptide resistance, J. Bacteriol. 178 (1996) 6857–6864. A.J. Scotter, M. Guo, M.M. Tomczak, M.E. Daley, R.L. Campbell, R.J. Oko, D.A. Bateman, A. Chakrabartty, B.D. Sykes, P.L. Davies, Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides, BMC Struct. Biol. 7 (2007) 63, http://dx.doi.org/10.1186/1472-6807-7-63.