The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

HU, a major component of the bacterial nucleoid, shares properties with histones, high mobility group proteins (HMGs), and other eukaryotic proteins. HU, which participates in many major pathways of the bacterial cell, binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates. Here we demonstrate that HU binds to double-stranded DNA, double-stranded RNA, and linear DNA-RNA duplexes with a similar low affinity. In contrast to this nonspecific binding to total cellular RNA and to supercoiled DNA, HU specifically recognizes defined structures common to both DNA and RNA. In particular HU binds specifically to nicked or gapped DNA-RNA hybrids and to composite RNA molecules such as DsrA, a small non-coding RNA. HU, which modulates DNA architecture, may play additional key functions in the bacterial machinery via its RNA binding capacity. The simple, straightforward structure of its binding domain with two highly flexible β-ribbon arms and an α-helical platform is an alternative model for the elaborate binding domains of the eukaryotic proteins that display dual DNA- and RNA-specific binding capacities. HU, a major component of the bacterial nucleoid, shares properties with histones, high mobility group proteins (HMGs), and other eukaryotic proteins. HU, which participates in many major pathways of the bacterial cell, binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates. Here we demonstrate that HU binds to double-stranded DNA, double-stranded RNA, and linear DNA-RNA duplexes with a similar low affinity. In contrast to this nonspecific binding to total cellular RNA and to supercoiled DNA, HU specifically recognizes defined structures common to both DNA and RNA. In particular HU binds specifically to nicked or gapped DNA-RNA hybrids and to composite RNA molecules such as DsrA, a small non-coding RNA. HU, which modulates DNA architecture, may play additional key functions in the bacterial machinery via its RNA binding capacity. The simple, straightforward structure of its binding domain with two highly flexible β-ribbon arms and an α-helical platform is an alternative model for the elaborate binding domains of the eukaryotic proteins that display dual DNA- and RNA-specific binding capacities. double-stranded single-stranded small cytoplasmic RNA RNA recognition motif integration host factor The Escherichia coli HU protein is a major component of the bacterial nucleoid (1Rouviere-Yaniv J. Gros F. Proc. Natl. Acad. Sci. U. S. A. 1975; 72: 3428-3432Crossref PubMed Scopus (250) Google Scholar, 2Rouviere-Yaniv J. Cold Spring Harbor Symp. Quant. Biol. 1978; 42: 439-447Crossref PubMed Google Scholar, 3Wery M. Woldringh C. Rouviere-Yaniv J. Biochimie (Paris). 2001; 83: 193-200Crossref PubMed Scopus (53) Google Scholar). This small basic histone-like protein that can introduce negative supercoiling into a close circular DNA molecule in the presence of topoisomerase I is highly conserved and found in all bacterial species (4Rouviere-Yaniv J. Yaniv M. Germond J.E. Cell. 1979; 17: 265-274Abstract Full Text PDF PubMed Scopus (329) Google Scholar, 5Haselkorn R. Rouviere-Yaniv J. Proc. Natl. Acad. Sci. U. S. A. 1976; 73: 1917-1920Crossref PubMed Scopus (60) Google Scholar, 6Grove A. Galeone A. Maryol L. Geiduschek E.P. J. Mol. Biol. 1996; 260: 196-206Crossref PubMed Scopus (38) Google Scholar, 7Oberto J. Rouviere-Yaniv J. J. Bacteriol. 1996; 178: 293-297Crossref PubMed Google Scholar). HU plays a role in DNA replication, recombination, and repair (8Bramhill D. Kornberg A. Cell. 1988; 54: 915-918Abstract Full Text PDF PubMed Scopus (333) Google Scholar, 9Boubrik F. Rouviere-Yaniv J. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3958-3962Crossref PubMed Scopus (100) Google Scholar, 10Li S. Waters R. J. Bacteriol. 1998; 180: 3750-3756Crossref PubMed Google Scholar). It participates in Mu transposition (11Lavoie B.D. Shaw G.S. Millner A. Chaconas G. Cell. 1996; 85: 761-771Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar) and regulation of gene transcription (12Aki T. Adhya S. EMBO J. 1997; 16: 3666-3674Crossref PubMed Scopus (154) Google Scholar). HU has been shown to be important for optimal survival of cells in the stationary phase and under various stress conditions (13Claret L. Rouviere-Yaniv J. J. Mol. Biol. 1997; 273: 93-104Crossref PubMed Scopus (149) Google Scholar). HU belongs to the family of architectural nuclear proteins that control DNA topology by introducing bends into double-stranded (ds)1 DNA and stabilize higher-order nucleoprotein complexes. HU resembles eukaryotic proteins of the high mobility group (HMG) class in its DNA binding properties because it binds dsDNA with low affinity and no sequence specificity. In contrast, it displays high affinity for some altered DNA structures such as junctions, nicks, gaps, forks, and overhangs even under stringent salt conditions (14Pontiggia A. Negri A. Beltrame M. Bianchi M.E. Mol. Microbiol. 1993; 7: 343-350Crossref PubMed Scopus (169) Google Scholar, 15Bonnefoy E. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1994; 242: 116-129Crossref PubMed Scopus (125) Google Scholar, 16Castaing B. Zelwer C. Laval J. Boiteux S. J. Biol. Chem. 1995; 270: 10291-10296Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar, 17Kamashev D. Balandina A. Rouviere-Yaniv J. EMBO J. 1999; 18: 5434-5444Crossref PubMed Scopus (81) Google Scholar, 18Pinson V. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1999; 287: 485-497Crossref PubMed Scopus (102) Google Scholar). The DNA structural motif for HU recognition consists of either two dsDNA modules with propensity to be inclined or one dsDNA module adjacent to a ssDNA binding module (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). X-ray crystallography and NMR studies have established the structure of HU dimer in the absence of DNA (20Tanaka I. Appelt K. Dijk J. White S.W. PubMed Scopus Google Scholar, S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar, M. R. R. J. Mol. Biol. 1995; PubMed Scopus Google Scholar). The two to a α-helical with two β-ribbon studies that HU duplex DNA via the with its flexible the high affinity binding to its binding motif an additional with the HU (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). to histones, HU has been shown to to but the role of this protein in RNA binding we have shown that HU binds with high affinity to the stress factor of RNA and its A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar). in to this it shown that the HU protein of specifically binds the domain of a small cytoplasmic RNA a of recognition RNA K. S. T. K. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar). In the eukaryotic a of that a of proteins or RNA recognition to specifically to both DNA and RNA Cell. 19: Full Text PDF PubMed Scopus Google Scholar, Proc. Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar, Cell. Full Text PDF PubMed Scopus Google Scholar, A. A. M. G. I. A. Proc. Natl. Acad. Sci. U. S. A. 1996; PubMed Scopus Google Scholar, V. F. E. M. M. Mol. Cell. Biol. 1997; 17: PubMed Scopus Google Scholar, S. 1998; PubMed Scopus Google Scholar, J. L. G. Mol. Cell. Biol. 1995; PubMed Google Scholar, E.P. T. 1999; PubMed Scopus Google Scholar, A. B. Mol. Cell. Biol. 1997; 17: PubMed Scopus Google Scholar). HU sequence or structural to RNA recognition or its small domain two β-ribbon arms and an α-helical is to with high specificity to (20Tanaka I. Appelt K. Dijk J. White S.W. PubMed Scopus Google Scholar, S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar, M. R. R. J. Mol. Biol. 1995; PubMed Scopus Google Scholar, A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar). In this we the RNA binding of HU affinity to total cellular RNA and found that HU binds to RNA as as to supercoiled DNA, to be the for the HU J. Cold Spring Harbor Symp. Quant. Biol. 1978; 42: 439-447Crossref PubMed Google Scholar). The of binding to double-stranded RNA and DNA as as to linear DNA-RNA hybrids shown to be In contrast, HU binding to DNA-RNA structures is that to DNA and RNA duplexes and displays the affinity as with nicked DNA, one of the structures that HU binds for the structural of recognition RNA, a small RNA that modulates the of key such or D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar, D. A. S. EMBO J. 1996; PubMed Scopus Google Scholar, C. D. T. S. Proc. Natl. Acad. Sci. U. S. A. 1998; PubMed Scopus Google Scholar, M.E. M. Proc. Natl. Acad. Sci. U. S. A. 1998; PubMed Scopus Google Scholar, M. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google Scholar). found that RNA is one of the for HU of RNA that HU with high affinity an RNA structure similar to that of a DNA one of its DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). The DNA to RNA and RNA and by the by S. D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar) as a and In the of the two DNA The under the control of the into the and of The a with by in the by for and of the RNA duplex the DNA and with DNA and under the control of the into the and of The and RNA with in by for by the of the DNA-RNA the DNA with RNA in as The and RNA RNA, DNA and a DNA a and D. and C. DNA-RNA and as DNA but with the and and with or in by for by The and G. as (20Tanaka I. Appelt K. Dijk J. White S.W. PubMed Scopus Google Scholar) in high salt or in low salt which the but either in or for low or high salt RNA by of E. coli cells in to E. coli a A. The supercoiled of the an and the linear DNA the HU protein a of with of nicked DNA, and of in of high salt as A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar). the of the by one molecule and one HU dimer is by is the of HU to is the of the protein binding is the of the molecules by the and and of protein binding a DNA that is the of binding for the that is DNA The and in the to the of and in The of the to and by of the for of the of the is shown in that this is for nonspecific binding the affinity of the protein is the for binding of an a molecule one binding nonspecific is we have The protein as an of HU for the of the HU dimer be by the that can be by the factor of The factor is as and the of the and binding of HU to double-stranded DNA, RNA, and the DNA-RNA the has been as E. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1994; 242: 116-129Crossref PubMed Scopus (125) Google Scholar, 18Pinson V. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1999; 287: 485-497Crossref PubMed Scopus (102) Google Scholar). The of HU to as in is the of that binding is nonspecific and that the is a protein binding is to the of of is the of the and is the of the protein to The protein in the is the of the protein to nicked nicked DNA is that of The of total is is the of the binding of the protein in L. The of HU with nicked DNA and to the of and nicked DNA, and the of the to and by of and we have or as in that the of binding is to the of the This is the DNA is with the The of the DNA can be to the J. Mol. Biol. PubMed Scopus Google Scholar). that under the conditions DNA is in the of the is one HU HU is one of the proteins in the bacterial In contrast to its low affinity binding to duplex linear DNA, HU binds with high affinity to DNA and repair under high salt conditions (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). have found that HU specifically recognizes the and its A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar). HU affinity to is as high as that to nicked DNA, which is that for double-stranded it that HU is to DNA and RNA, both may as HU binding in the This to the RNA binding properties of the affinity of HU to the major DNA and RNA species in the bacterial HU binding to supercoiled and linear DNA as as to total cellular RNA and mobility can be to and high because DNA is to be by HU, and total RNA is in to in the the we an which one of with nicked DNA for HU HU a with the nicked DNA with an of under stringent salt conditions B. Zelwer C. Laval J. Boiteux S. J. Biol. Chem. 1995; 270: 10291-10296Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar, 17Kamashev D. Balandina A. Rouviere-Yaniv J. EMBO J. 1999; 18: 5434-5444Crossref PubMed Scopus (81) Google Scholar, 18Pinson V. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1999; 287: 485-497Crossref PubMed Scopus (102) Google Scholar). HU with nicked DNA, and the with of the of The in DNA in the of DNA or RNA a in the of HU in the as a of binding to the The of the of and nicked in the absence or presence of the the of HU to the the of the can be the of the of the DNA as under a control of this the nicked DNA as a of the nicked DNA The of HU to nicked DNA found in this is a close to the of the protein B. Zelwer C. Laval J. Boiteux S. J. Biol. Chem. 1995; 270: 10291-10296Abstract Full Text Full Text PDF PubMed Scopus (125) Google Scholar, 17Kamashev D. Balandina A. Rouviere-Yaniv J. EMBO J. 1999; 18: 5434-5444Crossref PubMed Scopus (81) Google Scholar, 18Pinson V. Takahashi M. Rouviere-Yaniv J. J. Mol. Biol. 1999; 287: 485-497Crossref PubMed Scopus (102) Google Scholar). this we the for linear and supercoiled and total RNA the the of HU to supercoiled DNA to be under stringent conditions as an of The to the affinity of HU for linear DNA, and a of under the high salt This for the of HU binding and of HU HU protein binds supercoiled DNA linear DNA of the This is in with studies with HU which supercoiled DNA DNA K. B. Chaconas G. J. Mol. Biol. 1999; PubMed Scopus Google Scholar). RNA may as a HU we total bacterial RNA and the affinity of HU the The of as under the affinity of HU affinity to E. coli to be HU binds the major species of in bacterial cells with a similar affinity. the of nicked DNA the of the that the of the species to the nicked DNA with the RNA and DNA as as a DNA-RNA of of the binding to HU the mobility that the of the duplexes of the of and the of the to be to the salt high salt the DNA-RNA the in low salt dsDNA is both of duplex RNA is the In of binding to HU, under high salt conditions no with duplex This for dsDNA because under high salt conditions a is because of the of nonspecific HU linear DNA in the (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). In contrast, a defined be under low salt conditions with dsDNA an of for the and a of HU dimer that HU with the dsDNA E. Rouviere-Yaniv J. EMBO J. PubMed Scopus Google Scholar). that HU can be by and by the HU dimer of in a similar to the HU binding The of the is It is that for but the of binding is for the for dsDNA and RNA and The in the for the and in that HU binds dsDNA This is in with the of in studies under stringent salt which that HU binds linear DNA as as total RNA DNA-RNA of the sequence for HU of with the with to the binding model of one HU dimer to The of the is the as for the HU is to and DNA-RNA hybrids with similar The of and to DNA-RNA hybrids shown to an M. 1993; PubMed Scopus Google Scholar). HU to both the and of RNA and DNA This of binding can be by the high of HU arms S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar). HU particular DNA but it binds stringent with high affinity to some altered DNA The DNA structure that HU binds even in the presence of of dsDNA is either a DNA a single-stranded or a DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). The specificity of HU DNA binding by the of the HU arms with the double-stranded of the molecule and the of HU with the flexible which can be either a or single-stranded DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). we have that under low salt conditions HU binds an with a similar affinity to which it binds DNA duplex we HU specifically both and structures in which one of the DNA is with RNA. structures of particular because DNA A. T. DNA and Scholar). In the DNA-RNA is in the repair of the double-stranded A. Microbiol. Mol. Biol. 1999; PubMed Google Scholar). that HU binds structures under stringent conditions and a with The and for nicked RNA and RNA, to the found for nicked DNA and DNA and that for double-stranded this binding is have that HU is to with an affinity similar to that with which it binds nicked DNA, one of its A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar). The of this RNA is in RNA with a and structure to the HU to the RNA of E. which has both and negative such as or the factor the and stress D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar, D. A. S. EMBO J. 1996; PubMed Scopus Google Scholar). under the control of in and for mobility with HU The structure of this small RNA, which consists of D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar, M. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google is in A. The shown is or and M. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google Scholar). that HU binds this RNA and under high salt conditions with an of for the the structural by HU this small RNA, we RNA its to two by a single-stranded RNA of HU two with this RNA, and in the structure which one to a of This structure by HU, one the of can be the of two one RNA and one has the RNA have shown that the DNA the DNA is in contrast to the DNA a for HU (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). The that the RNA as as the DNA-RNA with a similar high affinity to the DNA that HU recognizes the motif in both RNA and DNA the that HU specifically binds to RNA an RNA by of its HU binds this structure with the of one as as it binds the RNA of its that the HU is one the binding of HU to DNA and RNA. In contrast to binding to DNA, HU recognizes RNA as as HU has a high affinity for RNA in contrast to the DNA we the DNA-RNA shown in and the binding of HU to a DNA-RNA to that of the DNA this we that HU binds to the DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar) but binds to the DNA-RNA high salt conditions HU one with the DNA-RNA with an of It is to that this DNA structure is in DNA replication, as is its DNA-RNA that the protein HU is an found that under conditions HU affinity to total bacterial RNA is that for supercoiled DNA, which is of the bacterial and for the DNA and RNA of the bacterial cell, we that the of HU DNA and RNA be In that the affinity we that the and of HU binding to DNA or RNA duplexes as as to DNA-RNA hybrids with one dimer This that HU is to both the and of because of the high of its which have been shown to the of DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar, S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar). a is in the binding of HU to dsDNA and The for the RNA is found for HU binding to dsDNA This a of HU molecules the for It is that HU in its binding to DNA-RNA hybrids to dsDNA for even the DNA-RNA the M. 1993; PubMed Scopus Google Scholar). the domain of to as as and to stabilize the K. C. A. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google Scholar). The motif by for with T. K. A. A. 1999; PubMed Scopus Google Scholar). is to to both and similar It to be HU with its motif a binding HU is as a protein that binds to DNA with low affinity and without sequence specificity but that recognizes with high the other DNA structures such as nicked DNA or HU binds DNA-RNA hybrids as as it binds dsDNA it of to it with nicked and DNA-RNA we the binding of HU to DNA and RNA duplexes and to DNA-RNA HU such DNA-RNA structures under stringent conditions with an affinity similar to that for DNA the nicked RNA and the RNA, as of DNA via the in which the RNA to the DNA the DNA-RNA is in and in repair of DNA A. Microbiol. Mol. Biol. 1999; PubMed Google Scholar). the HU in E. coli to be which the of HU is its for which in the low This that binding This may the role of HU in DNA and repair (8Bramhill D. Kornberg A. Cell. 1988; 54: 915-918Abstract Full Text PDF PubMed Scopus (333) Google Scholar, 9Boubrik F. Rouviere-Yaniv J. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3958-3962Crossref PubMed Scopus (100) Google Scholar). HU is the bacterial protein that a dual DNA and RNA binding such proteins have been in of proteins DNA- and some of the found in RNA and two transcription an for binding to double-stranded DNA J. L. G. Mol. Cell. Biol. 1995; PubMed Google Scholar, E.P. T. 1999; PubMed Scopus Google Scholar, A. B. Mol. Cell. Biol. 1997; 17: PubMed Scopus Google and the of protein recognizes both dsDNA and A. B. Mol. Cell. Biol. 1997; 17: PubMed Scopus Google Scholar). The the which is to specifically with RNA. The domains of and proteins binding to both RNA and dsDNA Cell. 19: Full Text PDF PubMed Scopus Google Scholar, Proc. Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar, Cell. Full Text PDF PubMed Scopus Google Scholar, A. A. M. G. I. A. Proc. Natl. Acad. Sci. U. S. A. 1996; PubMed Scopus Google Scholar, V. F. E. M. M. Mol. Cell. Biol. 1997; 17: PubMed Scopus Google Scholar). of the is the transcription which modules for either DNA or RNA of modules the of the protein binding affinity for DNA, the with RNA F. U. T. Cell. Full Text PDF PubMed Scopus Google Scholar, V. 1993; 260: PubMed Scopus Google Scholar, D. A. J. Mol. Biol. 2000; PubMed Scopus Google Scholar). in to to DNA and RNA. The HU protein an to this DNA and RNA binding The structure of HU consists of the of β-ribbon arms and an α-helical (20Tanaka I. Appelt K. Dijk J. White S.W. PubMed Scopus Google Scholar, S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar, M. R. R. J. Mol. Biol. 1995; PubMed Scopus Google Scholar). HU and domains be HU, in a similar to it binds its DNA- and domains protein a structural with the HU family of proteins White S.W. V. 1997; Full Text Full Text PDF PubMed Scopus Google Scholar, A. I. K. M. M. S. 1997; Full Text Full Text PDF PubMed Scopus Google Scholar). have a similar the double-stranded and a of that of the HU The structure of the of to via the F. A. R. J. M. D. A. I. F. A. Cell. 2000; Full Text Full Text PDF PubMed Scopus Google Scholar) to the that the HU arms in a similar It has been shown that the shares with integration host factor and HU Cell. Full Text PDF PubMed Scopus Google Scholar). The highly structure of a DNA binding module a that the DNA J. A. A. M. PubMed Scopus Google similar to the by the flexible arms and the platform of the HU (20Tanaka I. Appelt K. Dijk J. White S.W. PubMed Scopus Google Scholar, S.W. Appelt K. I. D. 1999; PubMed Scopus Google Scholar, M. R. R. J. Mol. Biol. 1995; PubMed Scopus Google Scholar). It be to as HU, with RNA or DNA-RNA have that HU binds to RNA, the structure of which has been as D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar, M. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google Scholar). the structural of HU we HU with RNA HU be two by a and one HU dimer to one with the can be as the of two RNA and one RNA have shown that DNA that a DNA is It that HU recognizes the motif in RNA a model for binding of HU to DNA (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). The specificity of binding by the of HU flexible arms with a in the of the and of HU with the ssDNA that HU binds double-stranded DNA and RNA with the similar affinity as as the of HU to RNA structures to a similar model for the of HU with RNA The of HU arms with the double-stranded of RNA and the of HU with the single-stranded of the molecule the binding and of HU arms with the DNA HU binding to DNA because the the to the HU (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). HU is of with both RNA and we that HU is to with the it for but with the RNA major of both and major RNA is an proteins. that HU binds to DNA-RNA This is because of the of DNA-RNA of the of the which is to the RNA the HU in B. has been as a component of the recognition that specifically with the domain of K. S. T. K. J. Biol. Chem. 1999; Full Text Full Text PDF PubMed Scopus Google Scholar). The domain of is of two by an double-stranded It that the is an for binding to the have shown that HU has a high affinity to the DNA the (19Kamashev D. Rouviere-Yaniv J. EMBO J. 2000; 19: 6527-6535Crossref PubMed Scopus (148) Google Scholar). This is that HU the for recognition with its RNA and DNA and that the motif for HU binding consists of two double-stranded or and single-stranded modules to be RNA many and it is that HU recognizes this structural motif a of of such an RNA is DsrA, a of the as of cellular in as an small RNA that transcription of by D. S. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: PubMed Scopus Google Scholar). is a transcription of for It is to that of HU E. E. S. Rouviere-Yaniv J. J. Mol. Biol. 1993; Scopus Google Scholar). In A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, D. A. S. EMBO J. 1996; PubMed Scopus Google Scholar, C. D. T. S. Proc. Natl. Acad. Sci. U. S. A. 1998; PubMed Scopus Google Scholar, M.E. M. Proc. Natl. Acad. Sci. U. S. A. 1998; PubMed Scopus Google Scholar, M. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google Scholar). binding to the A. L. R. Rouviere-Yaniv J. Mol. Microbiol. 2001; PubMed Scopus Google Scholar) and to HU may major in the bacterial the stress and bacterial for the of to for the of E. coli to for the HU to for a of the to and for and to an for

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