Cell, Vol. 63, 451-453,
November
2, 1990, Copyright
0 1990 by Cell Press
More Than Just ‘Histone-like” Proteins Molly 8. Schmid Department of Molecular Biology Princeton University Princeton, New Jersey 08544 Like eukaryotes, prokaryotes compact their DNA within the cell. As a naked DNA molecule, the Escherichia coli genome (5 x 108 bp) should form a random coil with a radius of gyration (Ro) of about 5 km. Packed into an average E. coli cell with dimensions of 0.75 pm x 2 pm, the volume of the DNA must compact by about lOOO-fold. This DNA condensation is opposed by the electrostatic repulsion of the negative charges on the phosphates. As the importance of the positively charged histones in eukaryotic DNA compaction became clear, the search for prokaryotic histone-like proteins began. From the results of Worcel, Pettijohn, and their coworkers, the E. coli genome is known to be organized into about 40 independently supercoiled domains, and at this level, the organization of prokaryotic DNA seems similar to that of eukaryotic chromatin. However, the local structure of DNA seems different. In vivo, prokaryotic DNA is torsionally strained, while eukaryotes convert most of the torsional strain into writhe using the nucleosome. Thus, either the roles or the relative amounts of the eukaryotic histones and prokaryotic histone-like proteins must differ. In addition, while eukaryotes may store negative superhelicity through use of the nucleosome, prokaryotes possess the enzyme DNA gyrase that can produce negative superhelicity at the expense of ATl? Several characteristics of eukaryotic histones made the search for prokaryotic histone-like proteins appear tantalizingly easy. The eukaryotic histones are abundant, of low molecular weight, acid soluble, and basic; each of these properties can serve as the basis for a protein purification step. In addition, binding of histones to DNA is relatively salt insensitive and the amino acid sequences of these proteins are evolutionarily conserved. Unfortunately, the search for prokaryotic histone-like proteins proved far more difficult than initially imagined. In prokaryotes, the inability to cleanly separate DNA from ribosomes has proven especially troubling. Ribosomal proteins are abundant (there are about 20,000 ribosomes per cell), most are small (49 of the 52 proteins have molecular weights between 5 and 25 kd), and many bind RNA and thus show general nucleic acid binding affinity. In addition, the prokaryotic histone-like proteins fail to exhibit many of the histone properties. The binding of prokaryotic histone-like proteins to DNA is relatively salt sensitive; one of the histone-like proteins (H-NS) has a neutral pl, and none of them are as abundant (per base pair) as their eukaryotic counterparts. Many of the proteins now considered histone-like were first identified by functional criteria. The HU protein was identified as a transcription factor by in vitro assays, the H protein inhibited an in vitro DNA replication system, and the HLPI protein (the product of the firA gene) was identi-
Minireview
fied by a mutation that suppressed a rifampicin-resistant mutation of RNA polymerase. In each of these cases, the relevant proteins were purified, found to be of low molecular weight and abundant, and deemed histone-like because their general amino acid composition resembled that of the histones. In the case of H, the resemblance to eukaryotic H2A is sufficiently strong that anti-H2A antibodies cross-react with it. Simultaneously, several groups purified proteins based on their h&tone-like traits, and after innumerable nomenclatures and some remaining confusion about which proteins are identical, the four proteins HU, H-NS, HLPI, and H have emerged as the prokaryotic proteins most like the eukaryotic histones (Drlica and Rouviere-Yaniv, 1987). In addition to these four proteins, two others, integration host factor (IHF) and factor for inversion stimulation (FIS), have emerged with potentially important roles in prokaryotic DNA organization. While these proteins resemble histones in many respects, great debate remains about the in vivo roles of the proteins and whether they are indeed histone-like in function. Recent results have begun to provide clues for the histone-like proteins H-NS, HU, IHF, and FIS. H-NS The H-NS protein (also widely known as Hla) is a neutral protein with strong DNA binding affinity and a wellconserved amino acid sequence between the E. coli and Salmonellatyphimurium proteins. Although overall a neutral protein, the sequence includes many patches of basic and acidic amino acids. H-NS does not wrap DNA in vitro; no change in linking number of circular DNA is seen in topological assays after H-NS binding. However, H-NS binding compacts DNA significantly, as measured by a large increase in sedimentation velocity of the DNA-protein complex. Recent data have pointed to the importance of the H-NS protein in DNA compaction and transcription in vivo. First, regulatory mutations in a large number of different genes (drdX, bgly, osmZ, pi/G, virf?) appear likely to be allelic (Gdransson et al., 1990). The DNA encoding this regulatory gene was cloned and sequenced and was found to
Prokaryotic
DNA Compacting
Proteins
Protein
Gene
MW
Monomers/Cell
H-NS
15,500
20,000
HU-2
hns/osmZ/ bg/Y hupA
9,500
60,000
w-1 IHF-a IHF-6 FIS
hupB himA hip fis
11,200 10,600 11,200
ND ND Variable
H
rpsC
26,000
20,000-120,000
HLPI
firA
17,000
ND, no data.
4,000
Reference
Thompson et al., 1967 Bruckner and Cox, 1969 Aasland et al., 1966
Cdl 452
encode the H-NS protein (based on protein size and sequence of the first 19 amino acids). In all of the cases studied to date, loss of the H-NS protein causes an increase in transcription, so that in the wild-type form, H-NS presumably acts as a negative regulator of transcription. The effect is somewhat complicated by the fact that not all hns mutations that derepress one of these unlinked genes derepress the others. H-NS is not an essential protein for growth under most standard laboratory conditions. However, the wild-type hns gene cannot be tolerated on a high copy vector, and filamentation of cells is seen even when hns is cloned into lower copy vectors. Overexpression of H-NS may cause improper expression (or nonexpression) of genes essential for cell viability. The H-NS protein also affects the frequency of some types of illegitimate recombination events. Removal of the hns gene increases the frequency of spontaneous deletions by IO- to lOO-fold (Lejeune and Danchin, 1990) and the frequency of site-specific inversion in the pili phase variation system of E. coli. The illegitimate recombination phenotypes, as well as the transcriptional phenotypes, are consistent with a role for the H-NS protein in DNA “inactivation:’ That is, H-NS may make DNA inaccessible to other DNA binding proteins. Consistent with this simplistic interpretation is the 5-fold accumulation of H-NS during stationary phase (Spassky et al., 1984). Mutations in the hns gene alter the superhelicity of reporter plasmids, but these effects are complex, as superhelicity increases in some mutant strains and decreases in others. Potential interactions between hns and gyrase, or effects of hns on transcription with subsequent direct or indirect effects on superhelicity, make the in vivo hns effects on transcription and illegitimate recombination problematic. HU The HU protein is a dimer of two very similar, but nonidentical, subunits in the enteric bacteria E. coli and S. typhimurium, but a homodimer in many other prokaryotic species. Other than this difference, the HU amino acid sequence is highly conserved in prokaryotes. The genes encoding the two HU subunits (hop4 and hupB) have been cloned and sequenced from both E. coli and S. typhimurium. Null mutations in either of the hup genes have little phenotype. Presumably, each of the HU subunits can substitute for the other, requiring the double mutant to display an HU- phenotype. A strain lacking both of the HU proteins shows a cold-sensitive phenotype, instability of F’ plasmids, and relaxation of reporter plasmid superhelicity, phenotypes also associated with some mutant alleles of DNA gyrase (Hillyard et al., 1990). Upon binding, HU can wrap DNA and relieve torsional strain as writhe. At lower protein concentrations, HU induces bends in DNA. This was shown by the ability to stimulate the rate of circularization of very short (99-126 bp) DNA fragments. Without the HU protein, these fragments do not circularize; when HU is added, these short fragments can be ligated into circles (Hodges-Garcia et al., 1989).
In vitro, HU acts as an accessory factor in several reactions and may achieve this through DNA bending. The HU protein stimulates initiation of replication from 0riC in vitro, and prevents the initiation of I. replication without the transcriptional activation that is required in vivo (MensaWilmot et al., 1989). Addition of HU stimulates the binding of lac repressor and CAP protein, but inhibits binding of trp repressor, to their respective binding sites (Flashner and Gralla, 1988). In addition, HU protein is required for both the in vivo and in vitro reaction of bin-mediated sitespecific inversion, which controls phase variation in S. typhimurium (Johnson et al., 1986). All of these effects have been explained by the formation of productive or unproductive DNA bends. What is the role of HU in vivo? The viability of double HU mutant strains (hupA- hupB-) suggests either that the HU proteins serve a nonessential function for growth under laboratory conditions or that other molecules (other proteins or the polyamines) can substitute. The hupAhupE mutant strain does not show aberrant initiation of replication in vivo, as in vitro results would have suggested (Ogawa et al., 1989). The secondary phenotypes shown by HU mutants (instability of F’, cold sensitivity, and altered superhelicity of reporter plasmids) are sufficiently complex that they give little clue to the normal physiological role of the HU protein. There is even question about which nucleic acid HU protein binds in vivo. In situ microscopy of E. coli cells shows that anti-HU antibodies stain the cytoplasm, not the nucleoid DNA region (Durrenberger et al., 1988). Kellenberger and colleagues propose that HU’s role is in RNA association, not DNA association, which is consistent with the greater affinity of HU for single-stranded nucleic acids. IHF and F/S The IHF and FIS proteins were originally discovered as host factors required for in vitro site-specific recombination events (Johnson et al., 1986; Friedman, 1988). IHF is required for li integration and excision both in vivo and in vitro, while FIS is required in vivo and in vitro to stimulate hin-mediated inversion. Both IHF and FIS show sitespecific binding; IHF binds to a consensus sequence that is somewhat context dependent, while FIS binds to specific sites that differ in sequence but appear to be naturally bent. The IHF proteins organize DNA and the h integrase protein into a tight complex that has been termed the “intasome.” IHF’s role in this complex is DNA bending, since a properly positioned bent DNA segment can substitute for the IHF requirement (Goodman and Nash, 1989). Recent results have expanded IHF’s role from formation of the h integration complex to include formation of protein-DNA complexes necessary for initiation of transcription (Hoover et al., 1990). Evidence suggests that IHF and FIS are members of different DNA binding protein families. By amino acid sequence, the IHF proteins are related to the HU proteins. However, IHF and HU differ markedly, as the binding of IHF is strongly sequence specific, while that of HU shows very weak sequence specificity. The FIS protein has
Minireview 453
amino acid sequence homology with the DNA binding protein NtrC, which activates transcription of a54-dependent promoters (Johnson et al., 1988). Concluslons Although the search for proteins that compact prokaryotic DNA began with the assumption that they would be histone-like, the current candidates display unanticipated characteristics, such as DNA bending and roles in illegitimate recombination, that may provide a route to identify other prokaryotic DNA compacting proteins. The set of prokaryotic DNA organizing proteins may be larger than is now apparent. While the H-NS and HU proteins may play a generalized compacting role, the sequence specificity of IHF and FIS may foreshadow a set of prokaryotic DNA compacting proteins that organize specific DNA regions. The roles of these proteins in vivo are now clouded by their interconnections with DNA topoisomerases, and perhaps with each other. Do these proteins, or subsets of them, substitute for one another? Clearly, this seems true for HU-a and HU-9, but do other interrelationships exist? Why does loss of some proteins cause altered DNA superhelicity? Many of the in vivo effects that are observed in mutants lacking one of these proteins may arise from altered DNA superhelicity. In contrast, the absence of some phenotypes may arise from functional redundancy between different proteins. Lessons have been learned from IHF, where an in vitro role for the protein was assigned and is now undergoing expansion as the in vivo effects of himA and hip mutations are reexplored. In several respects, the prokaryotic proteins that bend DNA and organize nucleoprotein complexes resemble eukaryotic transcription factors more than the histones. The presence of torsional strain in prokaryotes may arise from the absence of proteins to fulfill the histone role. Whether other proteins play a h&tone-like role in stationary phase, or in spores, remains to be seen.
Aasland, Ft., Coleman, and Kleppe, K. (1988). Bruckner, 3145-3161. Drlica,
Ft. C.,
and
J., Holck, A. L., Smith, C. L., Raetz, J, Bacterial. 770, 5916-5918. Cox,
K., and Rouviere-Yaniv,
M. M.
(1989).
Nucl.
J. (1987). Microbial.
Durrenberger, M., Bjornsti, M. A., Uetz, T., Hobot, berger, E. (1968). J. Bacterial. 770, 4757-4788. Flashner,
Y., and Gralla,
J. D. (1988).
Friedman,
D. I. (1968).
Cell 55, 545-554.
Goodman,
S D., and Nash,
Acids
C. R. H., Res.
Rev. 51, 301-305. J. A., and Kellen-
Cell 54, 713-721.
H. A. (1989).
Nature
347, 251-254.
Gijransson, M., Sonden, B., Nilsson, P, Dagberg. B., Forsman, Emanuelsson, K., and Uhlin, B E. (1990). Nature 344, 662-885. Hillyard, D. R., Edlund, M., Hughes, K. T., Marsh, N. i? (1990). J. Bacterial. 172, 5402-5407. Hodges-Garcia, Y., Hagerman, Chem. 264, 14621-14823. Hoover, 11-22.
T. R., Santero,
Johnson,
R. C., Bruist,
P J., and Pettijohn,
E., Porter,
17,
S., and Kustu,
M. F., and Simon,
K.,
M., and Higgins, D. E. (1989). J. Biol. S. (1990).
Cell 63,
M. I. (1986). Cell 46,531-+X39.
Johnson, R. C., Ball, C. A., Pfeffer, D., and Simon, Natl. Acad. Sci. USA 85, 3484-3488.
M. I. (1988). Proc.
Lejeune, 380-383.
P., and Danchin,
Mensa-Wilmot, 2393-2402.
K., Carroll,
A. (1990).
Proc.
K., and McMacken,
Ogawa, T., Wada, M., Kano, Y., Imamoto, Bacterial. 177, 5872-5679. Spassky, A., Rimsky, Res. 12, 5321-5340.
S., Garreau,
Thompson, J. F., de Vargas, A. (1987). Cell 50, 901-908.
Natl. Acad.
Sci. USA 87,
R. (1989).
F., and Okazaki,
H., and But, H. (1984).
L. M., Koch, C., Kahmann,
EMBO
J. 8,
T. (1989). J. Nucl. Acids
R., and Landy,
November
2, 1990, Copyright
0 1990 by Cell Press
More Than Just ‘Histone-like” Proteins Molly 8. Schmid Department of Molecular Biology Princeton University Princeton, New Jersey 08544 Like eukaryotes, prokaryotes compact their DNA within the cell. As a naked DNA molecule, the Escherichia coli genome (5 x 108 bp) should form a random coil with a radius of gyration (Ro) of about 5 km. Packed into an average E. coli cell with dimensions of 0.75 pm x 2 pm, the volume of the DNA must compact by about lOOO-fold. This DNA condensation is opposed by the electrostatic repulsion of the negative charges on the phosphates. As the importance of the positively charged histones in eukaryotic DNA compaction became clear, the search for prokaryotic histone-like proteins began. From the results of Worcel, Pettijohn, and their coworkers, the E. coli genome is known to be organized into about 40 independently supercoiled domains, and at this level, the organization of prokaryotic DNA seems similar to that of eukaryotic chromatin. However, the local structure of DNA seems different. In vivo, prokaryotic DNA is torsionally strained, while eukaryotes convert most of the torsional strain into writhe using the nucleosome. Thus, either the roles or the relative amounts of the eukaryotic histones and prokaryotic histone-like proteins must differ. In addition, while eukaryotes may store negative superhelicity through use of the nucleosome, prokaryotes possess the enzyme DNA gyrase that can produce negative superhelicity at the expense of ATl? Several characteristics of eukaryotic histones made the search for prokaryotic histone-like proteins appear tantalizingly easy. The eukaryotic histones are abundant, of low molecular weight, acid soluble, and basic; each of these properties can serve as the basis for a protein purification step. In addition, binding of histones to DNA is relatively salt insensitive and the amino acid sequences of these proteins are evolutionarily conserved. Unfortunately, the search for prokaryotic histone-like proteins proved far more difficult than initially imagined. In prokaryotes, the inability to cleanly separate DNA from ribosomes has proven especially troubling. Ribosomal proteins are abundant (there are about 20,000 ribosomes per cell), most are small (49 of the 52 proteins have molecular weights between 5 and 25 kd), and many bind RNA and thus show general nucleic acid binding affinity. In addition, the prokaryotic histone-like proteins fail to exhibit many of the histone properties. The binding of prokaryotic histone-like proteins to DNA is relatively salt sensitive; one of the histone-like proteins (H-NS) has a neutral pl, and none of them are as abundant (per base pair) as their eukaryotic counterparts. Many of the proteins now considered histone-like were first identified by functional criteria. The HU protein was identified as a transcription factor by in vitro assays, the H protein inhibited an in vitro DNA replication system, and the HLPI protein (the product of the firA gene) was identi-
Minireview
fied by a mutation that suppressed a rifampicin-resistant mutation of RNA polymerase. In each of these cases, the relevant proteins were purified, found to be of low molecular weight and abundant, and deemed histone-like because their general amino acid composition resembled that of the histones. In the case of H, the resemblance to eukaryotic H2A is sufficiently strong that anti-H2A antibodies cross-react with it. Simultaneously, several groups purified proteins based on their h&tone-like traits, and after innumerable nomenclatures and some remaining confusion about which proteins are identical, the four proteins HU, H-NS, HLPI, and H have emerged as the prokaryotic proteins most like the eukaryotic histones (Drlica and Rouviere-Yaniv, 1987). In addition to these four proteins, two others, integration host factor (IHF) and factor for inversion stimulation (FIS), have emerged with potentially important roles in prokaryotic DNA organization. While these proteins resemble histones in many respects, great debate remains about the in vivo roles of the proteins and whether they are indeed histone-like in function. Recent results have begun to provide clues for the histone-like proteins H-NS, HU, IHF, and FIS. H-NS The H-NS protein (also widely known as Hla) is a neutral protein with strong DNA binding affinity and a wellconserved amino acid sequence between the E. coli and Salmonellatyphimurium proteins. Although overall a neutral protein, the sequence includes many patches of basic and acidic amino acids. H-NS does not wrap DNA in vitro; no change in linking number of circular DNA is seen in topological assays after H-NS binding. However, H-NS binding compacts DNA significantly, as measured by a large increase in sedimentation velocity of the DNA-protein complex. Recent data have pointed to the importance of the H-NS protein in DNA compaction and transcription in vivo. First, regulatory mutations in a large number of different genes (drdX, bgly, osmZ, pi/G, virf?) appear likely to be allelic (Gdransson et al., 1990). The DNA encoding this regulatory gene was cloned and sequenced and was found to
Prokaryotic
DNA Compacting
Proteins
Protein
Gene
MW
Monomers/Cell
H-NS
15,500
20,000
HU-2
hns/osmZ/ bg/Y hupA
9,500
60,000
w-1 IHF-a IHF-6 FIS
hupB himA hip fis
11,200 10,600 11,200
ND ND Variable
H
rpsC
26,000
20,000-120,000
HLPI
firA
17,000
ND, no data.
4,000
Reference
Thompson et al., 1967 Bruckner and Cox, 1969 Aasland et al., 1966
Cdl 452
encode the H-NS protein (based on protein size and sequence of the first 19 amino acids). In all of the cases studied to date, loss of the H-NS protein causes an increase in transcription, so that in the wild-type form, H-NS presumably acts as a negative regulator of transcription. The effect is somewhat complicated by the fact that not all hns mutations that derepress one of these unlinked genes derepress the others. H-NS is not an essential protein for growth under most standard laboratory conditions. However, the wild-type hns gene cannot be tolerated on a high copy vector, and filamentation of cells is seen even when hns is cloned into lower copy vectors. Overexpression of H-NS may cause improper expression (or nonexpression) of genes essential for cell viability. The H-NS protein also affects the frequency of some types of illegitimate recombination events. Removal of the hns gene increases the frequency of spontaneous deletions by IO- to lOO-fold (Lejeune and Danchin, 1990) and the frequency of site-specific inversion in the pili phase variation system of E. coli. The illegitimate recombination phenotypes, as well as the transcriptional phenotypes, are consistent with a role for the H-NS protein in DNA “inactivation:’ That is, H-NS may make DNA inaccessible to other DNA binding proteins. Consistent with this simplistic interpretation is the 5-fold accumulation of H-NS during stationary phase (Spassky et al., 1984). Mutations in the hns gene alter the superhelicity of reporter plasmids, but these effects are complex, as superhelicity increases in some mutant strains and decreases in others. Potential interactions between hns and gyrase, or effects of hns on transcription with subsequent direct or indirect effects on superhelicity, make the in vivo hns effects on transcription and illegitimate recombination problematic. HU The HU protein is a dimer of two very similar, but nonidentical, subunits in the enteric bacteria E. coli and S. typhimurium, but a homodimer in many other prokaryotic species. Other than this difference, the HU amino acid sequence is highly conserved in prokaryotes. The genes encoding the two HU subunits (hop4 and hupB) have been cloned and sequenced from both E. coli and S. typhimurium. Null mutations in either of the hup genes have little phenotype. Presumably, each of the HU subunits can substitute for the other, requiring the double mutant to display an HU- phenotype. A strain lacking both of the HU proteins shows a cold-sensitive phenotype, instability of F’ plasmids, and relaxation of reporter plasmid superhelicity, phenotypes also associated with some mutant alleles of DNA gyrase (Hillyard et al., 1990). Upon binding, HU can wrap DNA and relieve torsional strain as writhe. At lower protein concentrations, HU induces bends in DNA. This was shown by the ability to stimulate the rate of circularization of very short (99-126 bp) DNA fragments. Without the HU protein, these fragments do not circularize; when HU is added, these short fragments can be ligated into circles (Hodges-Garcia et al., 1989).
In vitro, HU acts as an accessory factor in several reactions and may achieve this through DNA bending. The HU protein stimulates initiation of replication from 0riC in vitro, and prevents the initiation of I. replication without the transcriptional activation that is required in vivo (MensaWilmot et al., 1989). Addition of HU stimulates the binding of lac repressor and CAP protein, but inhibits binding of trp repressor, to their respective binding sites (Flashner and Gralla, 1988). In addition, HU protein is required for both the in vivo and in vitro reaction of bin-mediated sitespecific inversion, which controls phase variation in S. typhimurium (Johnson et al., 1986). All of these effects have been explained by the formation of productive or unproductive DNA bends. What is the role of HU in vivo? The viability of double HU mutant strains (hupA- hupB-) suggests either that the HU proteins serve a nonessential function for growth under laboratory conditions or that other molecules (other proteins or the polyamines) can substitute. The hupAhupE mutant strain does not show aberrant initiation of replication in vivo, as in vitro results would have suggested (Ogawa et al., 1989). The secondary phenotypes shown by HU mutants (instability of F’, cold sensitivity, and altered superhelicity of reporter plasmids) are sufficiently complex that they give little clue to the normal physiological role of the HU protein. There is even question about which nucleic acid HU protein binds in vivo. In situ microscopy of E. coli cells shows that anti-HU antibodies stain the cytoplasm, not the nucleoid DNA region (Durrenberger et al., 1988). Kellenberger and colleagues propose that HU’s role is in RNA association, not DNA association, which is consistent with the greater affinity of HU for single-stranded nucleic acids. IHF and F/S The IHF and FIS proteins were originally discovered as host factors required for in vitro site-specific recombination events (Johnson et al., 1986; Friedman, 1988). IHF is required for li integration and excision both in vivo and in vitro, while FIS is required in vivo and in vitro to stimulate hin-mediated inversion. Both IHF and FIS show sitespecific binding; IHF binds to a consensus sequence that is somewhat context dependent, while FIS binds to specific sites that differ in sequence but appear to be naturally bent. The IHF proteins organize DNA and the h integrase protein into a tight complex that has been termed the “intasome.” IHF’s role in this complex is DNA bending, since a properly positioned bent DNA segment can substitute for the IHF requirement (Goodman and Nash, 1989). Recent results have expanded IHF’s role from formation of the h integration complex to include formation of protein-DNA complexes necessary for initiation of transcription (Hoover et al., 1990). Evidence suggests that IHF and FIS are members of different DNA binding protein families. By amino acid sequence, the IHF proteins are related to the HU proteins. However, IHF and HU differ markedly, as the binding of IHF is strongly sequence specific, while that of HU shows very weak sequence specificity. The FIS protein has
Minireview 453
amino acid sequence homology with the DNA binding protein NtrC, which activates transcription of a54-dependent promoters (Johnson et al., 1988). Concluslons Although the search for proteins that compact prokaryotic DNA began with the assumption that they would be histone-like, the current candidates display unanticipated characteristics, such as DNA bending and roles in illegitimate recombination, that may provide a route to identify other prokaryotic DNA compacting proteins. The set of prokaryotic DNA organizing proteins may be larger than is now apparent. While the H-NS and HU proteins may play a generalized compacting role, the sequence specificity of IHF and FIS may foreshadow a set of prokaryotic DNA compacting proteins that organize specific DNA regions. The roles of these proteins in vivo are now clouded by their interconnections with DNA topoisomerases, and perhaps with each other. Do these proteins, or subsets of them, substitute for one another? Clearly, this seems true for HU-a and HU-9, but do other interrelationships exist? Why does loss of some proteins cause altered DNA superhelicity? Many of the in vivo effects that are observed in mutants lacking one of these proteins may arise from altered DNA superhelicity. In contrast, the absence of some phenotypes may arise from functional redundancy between different proteins. Lessons have been learned from IHF, where an in vitro role for the protein was assigned and is now undergoing expansion as the in vivo effects of himA and hip mutations are reexplored. In several respects, the prokaryotic proteins that bend DNA and organize nucleoprotein complexes resemble eukaryotic transcription factors more than the histones. The presence of torsional strain in prokaryotes may arise from the absence of proteins to fulfill the histone role. Whether other proteins play a h&tone-like role in stationary phase, or in spores, remains to be seen.
Aasland, Ft., Coleman, and Kleppe, K. (1988). Bruckner, 3145-3161. Drlica,
Ft. C.,
and
J., Holck, A. L., Smith, C. L., Raetz, J, Bacterial. 770, 5916-5918. Cox,
K., and Rouviere-Yaniv,
M. M.
(1989).
Nucl.
J. (1987). Microbial.
Durrenberger, M., Bjornsti, M. A., Uetz, T., Hobot, berger, E. (1968). J. Bacterial. 770, 4757-4788. Flashner,
Y., and Gralla,
J. D. (1988).
Friedman,
D. I. (1968).
Cell 55, 545-554.
Goodman,
S D., and Nash,
Acids
C. R. H., Res.
Rev. 51, 301-305. J. A., and Kellen-
Cell 54, 713-721.
H. A. (1989).
Nature
347, 251-254.
Gijransson, M., Sonden, B., Nilsson, P, Dagberg. B., Forsman, Emanuelsson, K., and Uhlin, B E. (1990). Nature 344, 662-885. Hillyard, D. R., Edlund, M., Hughes, K. T., Marsh, N. i? (1990). J. Bacterial. 172, 5402-5407. Hodges-Garcia, Y., Hagerman, Chem. 264, 14621-14823. Hoover, 11-22.
T. R., Santero,
Johnson,
R. C., Bruist,
P J., and Pettijohn,
E., Porter,
17,
S., and Kustu,
M. F., and Simon,
K.,
M., and Higgins, D. E. (1989). J. Biol. S. (1990).
Cell 63,
M. I. (1986). Cell 46,531-+X39.
Johnson, R. C., Ball, C. A., Pfeffer, D., and Simon, Natl. Acad. Sci. USA 85, 3484-3488.
M. I. (1988). Proc.
Lejeune, 380-383.
P., and Danchin,
Mensa-Wilmot, 2393-2402.
K., Carroll,
A. (1990).
Proc.
K., and McMacken,
Ogawa, T., Wada, M., Kano, Y., Imamoto, Bacterial. 177, 5872-5679. Spassky, A., Rimsky, Res. 12, 5321-5340.
S., Garreau,
Thompson, J. F., de Vargas, A. (1987). Cell 50, 901-908.
Natl. Acad.
Sci. USA 87,
R. (1989).
F., and Okazaki,
H., and But, H. (1984).
L. M., Koch, C., Kahmann,
EMBO
J. 8,
T. (1989). J. Nucl. Acids
R., and Landy,
