Cell Host & Microbe
Previews Engen, P.A., Green, S.J., Voigt, R.M., Forsyth, C.B., and Keshavarzian, A. (2015). Alcohol Res. 37, 223–236. Llopis, M., Cassard, A.M., Wrzosek, L., Boschat, L., Bruneau, A., Ferrere, G., Puchois, V., Martin, J.C., Lepage, P., Le Roy, T., et al. (2015). Gut. http://dx.doi.org/10.1136/gutjnl-2015-310585. Szabo, G., Dolganiuc, A., Dai, Q., and Pruett, S.B. (2007). J. Immunol. 178, 1243–1249.
Vaishnava, S., Yamamoto, M., Severson, K.M., Ruhn, K.A., Yu, X., Koren, O., Ley, R., Wakeland, E.K., and Hooper, L.V. (2011). Science 334, 255–258. van Ampting, M.T., Loonen, L.M., Schonewille, A.J., Konings, I., Vink, C., Iovanna, J., Chamaillard, M., Dekker, J., van der Meer, R., Wells, J.M., and Bovee-Oudenhoven, I.M. (2012). Infect. Immun. 80, 1115–1120.
Wang, L., Fouts, D.E., Sta¨rkel, P., Hartmann, P., Chen, P., Llorente, C., DePew, J., Moncera, K., Ho, S.B., Brenner, D.A., et al. (2016). Cell Host Microbe 19, this issue, 227–239. Zakhari, S. (2013). Alcohol Res. 35, 6–16. Zindl, C.L., Lai, J.F., Lee, Y.K., Maynard, C.L., Harbour, S.N., Ouyang, W., Chaplin, D.D., and Weaver, C.T. (2013). Proc. Natl. Acad. Sci. USA 110, 12768–12773.
Microbes without Borders: Decompartmentalization of the Aging Gut Erin S. Keebaugh1 and William W. Ja1,* 1Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, FL 33458, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chom.2016.01.016
The microbiota supports intestinal homeostasis in developing animals. With increased age, gut maintenance declines and microbes can stray from traditional zones, negatively impacting host health. In this issue of Cell Host & Microbe, Li et al. (2016) detail the mechanisms leading to the decline in intestinal health in aged flies. Flies often feed on rotting fruits teeming with microbes, most of which are tolerated by, or are even beneficial to, the developing host. Early-life studies comparing conventionally raised and axenic (germ-free) Drosophila showed that the presence of commensal bacteria supports normal growth. In some circumstances, consumed microbes provide nutritional support or protect the host by outcompeting pathogenic bacteria (Buchon et al., 2013a; Yamada et al., 2015). Other bacteria are actively controlled by a network of immune pathways within the intestinal epithelia. The immune deficiency (Imd) pathway, which generates antimicrobial peptides, is perhaps the most well-defined line of enteric defense. Imd pathway genes are differentially expressed across the fly intestine, which has at least ten different intestinal compartments with unique sets of molecular and anatomical features (Figure 1; Buchon et al., 2013b; Marianes and Spradling, 2013). The Imd pathway is activated by pattern recognition receptors that recognize a peptidoglycan motif possessed by both pathogenic and commensal species common to the fly (Buchon et al., 2013a). Within the intestine,
Imd-negative regulators attenuate the response to less-invasive commensal species, whereas Imd induction is stronger in response to invasive, pathogenic bacteria, which also generate higher levels of immune elicitors. The different levels of immune activation induced by commensal and pathogenic bacteria aid in the appropriate regulation of enteric microbes. With age, however, flies experience a loss of intestinal homeostasis; two hallmarks of aging include alterations in the composition and quantity of gut commensal populations and a decline in barrier function (Clark et al., 2015; Guo et al., 2014). At the molecular level, a decrease in activity of Imd-negative regulators ultimately leads to intestinal stem cell hyperproliferation, failure of barrier function, and organismal death. Blocking Imd deregulation, or raising flies axenically, can prevent some of these effects and extend life, suggesting that agerelated dysbiosis is a major factor in mortality (Clark et al., 2015; Guo et al., 2014). In this issue of Cell Host & Microbe, Li et al. (2016) explore the onset of intestinal pathologies in aging flies, and show that intestinal compartmentalization and the proper maintenance of enteric microbiota
are closely aligned. To determine if intestinal partitions are involved in controlling luminal constituents, Li and colleagues first disrupted compartmentalization in the fly intestine, focusing on the ‘‘copper cells,’’ which form an acidic region that shares similarities to our stomach. When copper cells are intact, microbes are mostly associated with anterior portions of the fly gut (Figure 1). When copper cells are ablated, the discrete acidic region of the gut is lost and commensal numbers increase throughout the intestine, with the largest increase seen in the posterior gut. This suggests that the copper cells—and their corresponding acidic region—are normally responsible for partitioning microbes within the intestinal lumen and lowering commensal counts in posterior intestines. Furthermore, Li et al. (2016) found that disruption of copper cells drove Imd activation and epithelial proliferation, demonstrating a crucial link between compartmentalization and commensal homeostasis, and highlighting the possibility that decompartmentalization may be a primary factor driving intestinal abnormalities in aged animals. Consistent with this idea, knocking down transcription
Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc. 133
Cell Host & Microbe
Previews
factors involved in intestinal ingly acidic intestine in some compartmentalization phenoaged flies. Approximately copies some symptoms of 40% of old flies, however, do aging (Buchon et al., 2013b). not show an increase in Li and colleagues further acidity throughout their intessupport this hypothesis by tinal tract. It remains unknown finding that, in old flies, the whether animals possessing cellular makeup of the copper acidic versus nonacidic intescell region undergoes metatines are simply at different plasia, whereby conventional stages of age-related decline copper cells are replaced or if there are more complex by cell types characteristic host and/or microbial factors of other portions of the fly that drive individual variation. gut. Importantly, they also Future studies might also observed these changes in focus on other ways that germ-free animals, supportcell-type alterations of the ing the idea that age-related intestinal epithelia influence alterations of the copper host health. Li et al. (2016) cell region initiate intestinal found that decreasing JAK/ pathologies. Stat signaling, and thus What are the molecular preserving compartmentalizamechanisms of age-related intion, extended axenic fly lifetestinal decompartmentalizaspan. This finding highlights tion? To answer this question, that dysbiosis alone cannot Li et al. (2016) investigated explain all of the mal-effects pathways previously shown of aging, and that the destrucFigure 1. Representation of the Microbial Content and Broad to be deregulated with age tion of gut compartmentalizaCompartmentalization of Human and Drosophila Digestive Tracts (Guo et al., 2014) and found tion itself is detrimental to Shown are the human (left) and Drosophila (right) digestive tracts. Note that the that JAK/Stat pathway activity host health. While the benefit fly midgut has at least ten distinct sections within these broad compartments (dashed lines) based on molecular and morphological markers (Buchon et al., increases throughout the inof sustained gut structure in 2013b; Marianes and Spradling, 2013). Unlike in mammals, the fly host does testine of older flies. A series the absence of microbes renot harbor a stable microbiota without constant reintroduction of commensals of experiments activating sysmains unknown, it could be through ingestion, highlighting some of the differences in how microbes are temic and enteric JAK/Stat that sectioning of the gut is distributed throughout the human and fly guts (Li et al., 2016). signaling drove transformasupportive of proper nutrient tive changes in the copper processing and absorption. cell region. Furthermore, tracing the origin 2016). Furthermore, these animals were Ultimately, how much will the fly model of metaplastic cells within the copper cell long-lived, revealing that mis-regulation teach us about human health and how region revealed both mis-differentiated of JAK/Stat signaling within a specific gastrointestinal compartmentalization inintestinal stem cells and trans-differenti- intestinal region sparks the intestinal fluences our wellbeing? Previous findings demonstrated that disruption of regional ated existing copper cells; these cells and organismal decline of aging flies. were formed by parallel modulation of Further studies will be useful to deter- identity across the fly midgut negatively morphogen signaling and transcription mine how microbes are influenced by the impacted host fitness (Buchon et al., factors. Overall, these data demonstrate stages of decompartmentalization, and 2013b) and could induce features of that JAK/Stat activation can drive a break- how the host responds when microbes metabolic syndrome (Lin et al., 2015). The down in intestinal partitions, whereby both are no longer held within more permissive current study by Li et al. (2016) reveals that mis- and trans-differentiated cells replace regions of the gut. For example, how intestinal decompartmentalization is a natudoes decompartmentalization impact the ral occurrence that underlies diminished canonical copper cells. Finally, Li and colleagues tested if spatial distribution of specific microbial physiological state with age. Together, reducing JAK/Stat signaling specifically species? In the current report, the distribu- these findings establish a link between within the intestinal region containing tion of the common commensal Lactoba- the maintenance of intestinal partitioning copper cells can offset the suite of cillus plantarum was analyzed, but it will and health, and identify a new focus for age-related pathologies seen in previous be of interest to track other species, research on metabolism and aging studies (Clark et al., 2015; Guo et al., especially given that specific species of (Buchon et al., 2013b; Li et al., 2016). Inter2014). Knockdown of different JAK/Stat commensals can elicit unique effects on estingly, the intestinal microbiota of aged components in adult flies resulted in Drosophila health (Lee and Hase, 2014; humans is markedly different from that of lower counts of commensal bacteria Yamada et al., 2015). By focusing on younger individuals (Claesson et al., 2011), and proliferating intestinal stem cells, L. plantarum, Li and colleagues deter- and the fly and human gastrointestinal both characteristics of younger animals mined that the expansion of these acid- tracts share other key similarities (Figure 1; possessing a homeostatic gut (Li et al., producing bacteria may cause an increas- Buchon et al., 2013b; Marianes and 134 Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc.
Cell Host & Microbe
Previews Spradling, 2013). As such, fast-paced studies using the genetically tractable fly model are poised to provide great insight into the pathobiology of declining health upon age or gastrointestinal decline. REFERENCES Buchon, N., Broderick, N.A., and Lemaitre, B. (2013a). Nat. Rev. Microbiol. 11, 615–626. Buchon, N., Osman, D., David, F.P., Fang, H.Y., Boquete, J.P., Deplancke, B., and Lemaitre, B. (2013b). Cell Rep. 3, 1725–1738.
Claesson, M.J., Cusack, S., O’Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J.R., Falush, D., Dinan, T., Fitzgerald, G., et al. (2011). Proc. Natl. Acad. Sci. USA 108 (Suppl 1 ), 4586–4591. Clark, R.I., Salazar, A., Yamada, R., Fitz-Gibbon, S., Morselli, M., Alcaraz, J., Rana, A., Rera, M., Pellegrini, M., Ja, W.W., and Walker, D.W. (2015). Cell Rep. 12, 1656–1667. Guo, L., Karpac, J., Tran, S.L., and Jasper, H. (2014). Cell 156, 109–122. Lee, W.J., and Hase, K. (2014). Nat. Chem. Biol. 10, 416–424.
Li, H., Qi, Y., and Jasper, H. (2016). Cell Host Microbe 19, this issue, 240–253. Lin, W.S., Huang, C.W., Song, Y.S., Yen, J.H., Kuo, P.C., Yeh, S.R., Lin, H.Y., Fu, T.F., Wu, M.S., Wang, H.D., and Wang, P.Y. (2015). PLoS ONE 10, e0139722. Marianes, A., and Spradling, A.C. (2013). eLife 2, e00886. Yamada, R., Deshpande, S.A., Bruce, K.D., Mak, E.M., and Ja, W.W. (2015). Cell Rep. 10, 865–872.
CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done Rachel J. Whitaker1,* and Carin K. Vanderpool1 1Department of Microbiology, University of Illinois at Urbana-Champaign *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chom.2016.01.015
Microbial CRISPR-Cas acts as a defense, but also as a gatekeeper controlling the flow of new genes into microbial genomes. In a recent Cell paper, Jiang et al. (2016) uncover the functional importance of transcription-dependent RNA targeting in type III-A CRISPR-Cas antiviral defense and provide insight into the co-evolution of virus-host symbioses. Discoveries of novel molecular mechanisms in diverse microbial CRISPR-Cas systems continue, despite the intense public focus on patent rights and the ethics of using this technology for human genetic engineering. While potential applications for CRISPR-Cas are exciting, let us not forget that this exquisite adaptive immune system evolved in microorganisms to recognize, and ostensibly defend against, genetic symbionts like viruses. Though development of the simple, single effector endonuclease Cas9 has made the type II CRISPR-Cas systems famous, the more complex and diverse type I and type III systems are much more common in bacteria and archaea (Makarova et al., 2015). Exploring the diversity of type I and type III systems promises a gold mine for new discoveries that will take years to understand even at the current rapid pace of exploration. As with all basic discoveries, these mechanisms will need to be integrated into models of microbial evolution and will likely shape our understanding of
virus-host interactions and immunity across all domains of life. An excellent example of furthering our understanding of CRISPR-Cas function is the contribution of Jiang et al. (2016), which uncovers the functional importance of transcription-dependent RNA targeting in type III CRISPR-Cas immunity. Type III CRISPR-Cas systems are the only ones demonstrated to target and cleave both viral genomic DNA and viral RNA transcripts (Makarova et al., 2015), thereby inhibiting completion of the virus life cycle. Adding to their intrigue, some of these systems have been demonstrated to be dependent upon viral transcription for successful immune interference (Deng et al., 2013; Goldberg et al., 2014). The RNA and DNA targeting functions work together in multi-protein effector complexes. A core DNA-cleaving component Cas10 acts on the non-template strand of DNA during transcription (Goldberg et al., 2014). This core protein is associated with a diversity of variable components for RNA process-
ing (Hale et al., 2012; Samai et al., 2015; Staals et al., 2014; Tamulaitis et al., 2014) whose function is less well understood. Previously, it had been shown in Staphylococcus epidermidis that the Csm3 protein in the type III-A CRISPRCas system functions in CRISPR RNA (crRNA)-guided mRNA degradation (Samai et al., 2015; Staals et al., 2014; Tamulaitis et al., 2014). However, the biological relevance for this function was unclear because inactivating Csm3 did not impact immunity to virus infection in this system (Samai et al., 2015). Jiang et al. (2016) uncovered an important clue to the underlying biological relevance of RNA targeting with the characterization of a second ribonuclease activity, encoded by the last gene of unknown function in the type III-A CRISPRCas system of S. epidermidis: csm6. They show that Csm6 is a sequence-nonspecific ribonuclease that can (but does not seem to) function independently of the Cas10-Csm complex. Inactivation of
Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc. 135
Previews Engen, P.A., Green, S.J., Voigt, R.M., Forsyth, C.B., and Keshavarzian, A. (2015). Alcohol Res. 37, 223–236. Llopis, M., Cassard, A.M., Wrzosek, L., Boschat, L., Bruneau, A., Ferrere, G., Puchois, V., Martin, J.C., Lepage, P., Le Roy, T., et al. (2015). Gut. http://dx.doi.org/10.1136/gutjnl-2015-310585. Szabo, G., Dolganiuc, A., Dai, Q., and Pruett, S.B. (2007). J. Immunol. 178, 1243–1249.
Vaishnava, S., Yamamoto, M., Severson, K.M., Ruhn, K.A., Yu, X., Koren, O., Ley, R., Wakeland, E.K., and Hooper, L.V. (2011). Science 334, 255–258. van Ampting, M.T., Loonen, L.M., Schonewille, A.J., Konings, I., Vink, C., Iovanna, J., Chamaillard, M., Dekker, J., van der Meer, R., Wells, J.M., and Bovee-Oudenhoven, I.M. (2012). Infect. Immun. 80, 1115–1120.
Wang, L., Fouts, D.E., Sta¨rkel, P., Hartmann, P., Chen, P., Llorente, C., DePew, J., Moncera, K., Ho, S.B., Brenner, D.A., et al. (2016). Cell Host Microbe 19, this issue, 227–239. Zakhari, S. (2013). Alcohol Res. 35, 6–16. Zindl, C.L., Lai, J.F., Lee, Y.K., Maynard, C.L., Harbour, S.N., Ouyang, W., Chaplin, D.D., and Weaver, C.T. (2013). Proc. Natl. Acad. Sci. USA 110, 12768–12773.
Microbes without Borders: Decompartmentalization of the Aging Gut Erin S. Keebaugh1 and William W. Ja1,* 1Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, FL 33458, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chom.2016.01.016
The microbiota supports intestinal homeostasis in developing animals. With increased age, gut maintenance declines and microbes can stray from traditional zones, negatively impacting host health. In this issue of Cell Host & Microbe, Li et al. (2016) detail the mechanisms leading to the decline in intestinal health in aged flies. Flies often feed on rotting fruits teeming with microbes, most of which are tolerated by, or are even beneficial to, the developing host. Early-life studies comparing conventionally raised and axenic (germ-free) Drosophila showed that the presence of commensal bacteria supports normal growth. In some circumstances, consumed microbes provide nutritional support or protect the host by outcompeting pathogenic bacteria (Buchon et al., 2013a; Yamada et al., 2015). Other bacteria are actively controlled by a network of immune pathways within the intestinal epithelia. The immune deficiency (Imd) pathway, which generates antimicrobial peptides, is perhaps the most well-defined line of enteric defense. Imd pathway genes are differentially expressed across the fly intestine, which has at least ten different intestinal compartments with unique sets of molecular and anatomical features (Figure 1; Buchon et al., 2013b; Marianes and Spradling, 2013). The Imd pathway is activated by pattern recognition receptors that recognize a peptidoglycan motif possessed by both pathogenic and commensal species common to the fly (Buchon et al., 2013a). Within the intestine,
Imd-negative regulators attenuate the response to less-invasive commensal species, whereas Imd induction is stronger in response to invasive, pathogenic bacteria, which also generate higher levels of immune elicitors. The different levels of immune activation induced by commensal and pathogenic bacteria aid in the appropriate regulation of enteric microbes. With age, however, flies experience a loss of intestinal homeostasis; two hallmarks of aging include alterations in the composition and quantity of gut commensal populations and a decline in barrier function (Clark et al., 2015; Guo et al., 2014). At the molecular level, a decrease in activity of Imd-negative regulators ultimately leads to intestinal stem cell hyperproliferation, failure of barrier function, and organismal death. Blocking Imd deregulation, or raising flies axenically, can prevent some of these effects and extend life, suggesting that agerelated dysbiosis is a major factor in mortality (Clark et al., 2015; Guo et al., 2014). In this issue of Cell Host & Microbe, Li et al. (2016) explore the onset of intestinal pathologies in aging flies, and show that intestinal compartmentalization and the proper maintenance of enteric microbiota
are closely aligned. To determine if intestinal partitions are involved in controlling luminal constituents, Li and colleagues first disrupted compartmentalization in the fly intestine, focusing on the ‘‘copper cells,’’ which form an acidic region that shares similarities to our stomach. When copper cells are intact, microbes are mostly associated with anterior portions of the fly gut (Figure 1). When copper cells are ablated, the discrete acidic region of the gut is lost and commensal numbers increase throughout the intestine, with the largest increase seen in the posterior gut. This suggests that the copper cells—and their corresponding acidic region—are normally responsible for partitioning microbes within the intestinal lumen and lowering commensal counts in posterior intestines. Furthermore, Li et al. (2016) found that disruption of copper cells drove Imd activation and epithelial proliferation, demonstrating a crucial link between compartmentalization and commensal homeostasis, and highlighting the possibility that decompartmentalization may be a primary factor driving intestinal abnormalities in aged animals. Consistent with this idea, knocking down transcription
Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc. 133
Cell Host & Microbe
Previews
factors involved in intestinal ingly acidic intestine in some compartmentalization phenoaged flies. Approximately copies some symptoms of 40% of old flies, however, do aging (Buchon et al., 2013b). not show an increase in Li and colleagues further acidity throughout their intessupport this hypothesis by tinal tract. It remains unknown finding that, in old flies, the whether animals possessing cellular makeup of the copper acidic versus nonacidic intescell region undergoes metatines are simply at different plasia, whereby conventional stages of age-related decline copper cells are replaced or if there are more complex by cell types characteristic host and/or microbial factors of other portions of the fly that drive individual variation. gut. Importantly, they also Future studies might also observed these changes in focus on other ways that germ-free animals, supportcell-type alterations of the ing the idea that age-related intestinal epithelia influence alterations of the copper host health. Li et al. (2016) cell region initiate intestinal found that decreasing JAK/ pathologies. Stat signaling, and thus What are the molecular preserving compartmentalizamechanisms of age-related intion, extended axenic fly lifetestinal decompartmentalizaspan. This finding highlights tion? To answer this question, that dysbiosis alone cannot Li et al. (2016) investigated explain all of the mal-effects pathways previously shown of aging, and that the destrucFigure 1. Representation of the Microbial Content and Broad to be deregulated with age tion of gut compartmentalizaCompartmentalization of Human and Drosophila Digestive Tracts (Guo et al., 2014) and found tion itself is detrimental to Shown are the human (left) and Drosophila (right) digestive tracts. Note that the that JAK/Stat pathway activity host health. While the benefit fly midgut has at least ten distinct sections within these broad compartments (dashed lines) based on molecular and morphological markers (Buchon et al., increases throughout the inof sustained gut structure in 2013b; Marianes and Spradling, 2013). Unlike in mammals, the fly host does testine of older flies. A series the absence of microbes renot harbor a stable microbiota without constant reintroduction of commensals of experiments activating sysmains unknown, it could be through ingestion, highlighting some of the differences in how microbes are temic and enteric JAK/Stat that sectioning of the gut is distributed throughout the human and fly guts (Li et al., 2016). signaling drove transformasupportive of proper nutrient tive changes in the copper processing and absorption. cell region. Furthermore, tracing the origin 2016). Furthermore, these animals were Ultimately, how much will the fly model of metaplastic cells within the copper cell long-lived, revealing that mis-regulation teach us about human health and how region revealed both mis-differentiated of JAK/Stat signaling within a specific gastrointestinal compartmentalization inintestinal stem cells and trans-differenti- intestinal region sparks the intestinal fluences our wellbeing? Previous findings demonstrated that disruption of regional ated existing copper cells; these cells and organismal decline of aging flies. were formed by parallel modulation of Further studies will be useful to deter- identity across the fly midgut negatively morphogen signaling and transcription mine how microbes are influenced by the impacted host fitness (Buchon et al., factors. Overall, these data demonstrate stages of decompartmentalization, and 2013b) and could induce features of that JAK/Stat activation can drive a break- how the host responds when microbes metabolic syndrome (Lin et al., 2015). The down in intestinal partitions, whereby both are no longer held within more permissive current study by Li et al. (2016) reveals that mis- and trans-differentiated cells replace regions of the gut. For example, how intestinal decompartmentalization is a natudoes decompartmentalization impact the ral occurrence that underlies diminished canonical copper cells. Finally, Li and colleagues tested if spatial distribution of specific microbial physiological state with age. Together, reducing JAK/Stat signaling specifically species? In the current report, the distribu- these findings establish a link between within the intestinal region containing tion of the common commensal Lactoba- the maintenance of intestinal partitioning copper cells can offset the suite of cillus plantarum was analyzed, but it will and health, and identify a new focus for age-related pathologies seen in previous be of interest to track other species, research on metabolism and aging studies (Clark et al., 2015; Guo et al., especially given that specific species of (Buchon et al., 2013b; Li et al., 2016). Inter2014). Knockdown of different JAK/Stat commensals can elicit unique effects on estingly, the intestinal microbiota of aged components in adult flies resulted in Drosophila health (Lee and Hase, 2014; humans is markedly different from that of lower counts of commensal bacteria Yamada et al., 2015). By focusing on younger individuals (Claesson et al., 2011), and proliferating intestinal stem cells, L. plantarum, Li and colleagues deter- and the fly and human gastrointestinal both characteristics of younger animals mined that the expansion of these acid- tracts share other key similarities (Figure 1; possessing a homeostatic gut (Li et al., producing bacteria may cause an increas- Buchon et al., 2013b; Marianes and 134 Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc.
Cell Host & Microbe
Previews Spradling, 2013). As such, fast-paced studies using the genetically tractable fly model are poised to provide great insight into the pathobiology of declining health upon age or gastrointestinal decline. REFERENCES Buchon, N., Broderick, N.A., and Lemaitre, B. (2013a). Nat. Rev. Microbiol. 11, 615–626. Buchon, N., Osman, D., David, F.P., Fang, H.Y., Boquete, J.P., Deplancke, B., and Lemaitre, B. (2013b). Cell Rep. 3, 1725–1738.
Claesson, M.J., Cusack, S., O’Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J.R., Falush, D., Dinan, T., Fitzgerald, G., et al. (2011). Proc. Natl. Acad. Sci. USA 108 (Suppl 1 ), 4586–4591. Clark, R.I., Salazar, A., Yamada, R., Fitz-Gibbon, S., Morselli, M., Alcaraz, J., Rana, A., Rera, M., Pellegrini, M., Ja, W.W., and Walker, D.W. (2015). Cell Rep. 12, 1656–1667. Guo, L., Karpac, J., Tran, S.L., and Jasper, H. (2014). Cell 156, 109–122. Lee, W.J., and Hase, K. (2014). Nat. Chem. Biol. 10, 416–424.
Li, H., Qi, Y., and Jasper, H. (2016). Cell Host Microbe 19, this issue, 240–253. Lin, W.S., Huang, C.W., Song, Y.S., Yen, J.H., Kuo, P.C., Yeh, S.R., Lin, H.Y., Fu, T.F., Wu, M.S., Wang, H.D., and Wang, P.Y. (2015). PLoS ONE 10, e0139722. Marianes, A., and Spradling, A.C. (2013). eLife 2, e00886. Yamada, R., Deshpande, S.A., Bruce, K.D., Mak, E.M., and Ja, W.W. (2015). Cell Rep. 10, 865–872.
CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done Rachel J. Whitaker1,* and Carin K. Vanderpool1 1Department of Microbiology, University of Illinois at Urbana-Champaign *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chom.2016.01.015
Microbial CRISPR-Cas acts as a defense, but also as a gatekeeper controlling the flow of new genes into microbial genomes. In a recent Cell paper, Jiang et al. (2016) uncover the functional importance of transcription-dependent RNA targeting in type III-A CRISPR-Cas antiviral defense and provide insight into the co-evolution of virus-host symbioses. Discoveries of novel molecular mechanisms in diverse microbial CRISPR-Cas systems continue, despite the intense public focus on patent rights and the ethics of using this technology for human genetic engineering. While potential applications for CRISPR-Cas are exciting, let us not forget that this exquisite adaptive immune system evolved in microorganisms to recognize, and ostensibly defend against, genetic symbionts like viruses. Though development of the simple, single effector endonuclease Cas9 has made the type II CRISPR-Cas systems famous, the more complex and diverse type I and type III systems are much more common in bacteria and archaea (Makarova et al., 2015). Exploring the diversity of type I and type III systems promises a gold mine for new discoveries that will take years to understand even at the current rapid pace of exploration. As with all basic discoveries, these mechanisms will need to be integrated into models of microbial evolution and will likely shape our understanding of
virus-host interactions and immunity across all domains of life. An excellent example of furthering our understanding of CRISPR-Cas function is the contribution of Jiang et al. (2016), which uncovers the functional importance of transcription-dependent RNA targeting in type III CRISPR-Cas immunity. Type III CRISPR-Cas systems are the only ones demonstrated to target and cleave both viral genomic DNA and viral RNA transcripts (Makarova et al., 2015), thereby inhibiting completion of the virus life cycle. Adding to their intrigue, some of these systems have been demonstrated to be dependent upon viral transcription for successful immune interference (Deng et al., 2013; Goldberg et al., 2014). The RNA and DNA targeting functions work together in multi-protein effector complexes. A core DNA-cleaving component Cas10 acts on the non-template strand of DNA during transcription (Goldberg et al., 2014). This core protein is associated with a diversity of variable components for RNA process-
ing (Hale et al., 2012; Samai et al., 2015; Staals et al., 2014; Tamulaitis et al., 2014) whose function is less well understood. Previously, it had been shown in Staphylococcus epidermidis that the Csm3 protein in the type III-A CRISPRCas system functions in CRISPR RNA (crRNA)-guided mRNA degradation (Samai et al., 2015; Staals et al., 2014; Tamulaitis et al., 2014). However, the biological relevance for this function was unclear because inactivating Csm3 did not impact immunity to virus infection in this system (Samai et al., 2015). Jiang et al. (2016) uncovered an important clue to the underlying biological relevance of RNA targeting with the characterization of a second ribonuclease activity, encoded by the last gene of unknown function in the type III-A CRISPRCas system of S. epidermidis: csm6. They show that Csm6 is a sequence-nonspecific ribonuclease that can (but does not seem to) function independently of the Cas10-Csm complex. Inactivation of
Cell Host & Microbe 19, February 10, 2016 ª2016 Elsevier Inc. 135
