{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T18:21:23Z","timestamp":1790360483522,"version":"4.1.0"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T00:00:00Z","timestamp":1510531200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["15-14-00063"],"award-info":[{"award-number":["15-14-00063"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0188037","type":"journal-article","created":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T18:38:09Z","timestamp":1510598289000},"page":"e0188037","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":47,"title":["Comparison of histone-like HU protein DNA-binding properties and HU\/IHF protein sequence alignment"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4158-5300","authenticated-orcid":true,"given":"Dmitri","family":"Kamashev","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulia","family":"Agapova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey","family":"Rastorguev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna A.","family":"Talyzina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin M.","family":"Boyko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitry A.","family":"Korzhenevskiy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Vlaskina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raif","family":"Vasilov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir I.","family":"Timofeev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana V.","family":"Rakitina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,11,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.ympev.2016.11.014","article-title":"Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF","volume":"107","author":"D Dey","year":"2017","journal-title":"Mol Phylogenet Evol"},{"key":"ref3","first-page":"207","article-title":"Biological and Medical Physics, Biomedical Engineering","author":"D Charif","year":"2017"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0022-2836(66)80258-9","article-title":"An improved method of testing for evolutionary homology","volume":"16","author":"WM Fitch","year":"1966","journal-title":"J Mol Biol"},{"key":"ref5","unstructured":"Adler D, Murdoch D, Nenadic O, Urbanek S, Chen M, Gebhardt A, et al. (2017) 3D Visualization Using OpenGL: R package version 0.98.1. CRANR-projectorg\/package."},{"key":"ref6","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1134\/S1063774515060231","article-title":"Isolation, purification, crystallization, and preliminary X-ray diffraction study of the crystals of HU protein from M. Gallisepticum","volume":"60","author":"A Nikolaeva","year":"2015","journal-title":"Crystallography Reports"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"221","DOI":"10.3103\/S0027131416040027","article-title":"Preparation of the recombinant HU-proteins from S. melliferum and M. gallisepticum and of their complexes with ds-dna for structural NMR experiments","volume":"71","author":"D Altukhov","year":"2016","journal-title":"Moscow University \u0421hemistry Bulletin"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/07391102.2016.1264893","article-title":"Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum","author":"DA Altukhov","year":"2016","journal-title":"J Biomol Struct Dyn"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/S0300-9084(00)01151-2","article-title":"Overproduction and improved strategies to purify the threenative forms of nuclease-free HU protein","volume":"82","author":"O Pellegrini","year":"2000","journal-title":"Biochimie"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1107\/S2053230X14025333","article-title":"Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the histone-like HU protein from Spiroplasma melliferum KC3","volume":"71","author":"K Boyko","year":"2015","journal-title":"Acta Crystallogr F Struct Biol Commun"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/S1357-4310(95)91170-7","article-title":"Comparative protein modeling by satisfaction of spatial restraints","volume":"1","author":"A Sali","year":"1995","journal-title":"Mol Med Today"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"5434","DOI":"10.1093\/emboj\/18.19.5434","article-title":"The binding motif recognized by HU on both nicked and cruciform DNA","volume":"18","author":"D Kamashev","year":"1999","journal-title":"EMBO J"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/nar\/gkm667","article-title":"HU binds and folds single-stranded DNA","volume":"36","author":"D Kamashev","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"27622","DOI":"10.1074\/jbc.M201978200","article-title":"The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids","volume":"277","author":"A Balandina","year":"2002","journal-title":"J Biol Chem"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1111\/j.1432-1033.1992.tb17095.x","article-title":"Determination of DNA-binding parameters for the Bacillus subtilis histone-like HBsu protein through introduction of fluorophores by site-directed mutagenesis of a synthetic gene","volume":"207","author":"N Groch","year":"1992","journal-title":"Eur J Biochem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"6527","DOI":"10.1093\/emboj\/19.23.6527","article-title":"The histone-like protein HU binds specifically to DNA recombination and repair intermediates","volume":"19","author":"D Kamashev","year":"2000","journal-title":"EMBO J"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1128\/MMBR.51.3.301-319.1987","article-title":"Histonelike proteins of bacteria","volume":"51","author":"K Drlica","year":"1987","journal-title":"Microbiol Rev"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1111\/j.1365-2958.2005.04598.x","article-title":"The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin","volume":"56","author":"RT Dame","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/nrmicro2261","article-title":"Bacterial nucleoid-associated proteins, nucleoid structure and gene expression","volume":"8","author":"SC Dillon","year":"2010","journal-title":"Nat Rev Microbiol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e4367","DOI":"10.1371\/journal.pone.0004367","article-title":"The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction","volume":"4","author":"J Oberto","year":"2009","journal-title":"PLoS One"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/embor.2009.232","article-title":"Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU","volume":"11","author":"M Berger","year":"2010","journal-title":"EMBO Rep"},{"key":"ref22","first-page":"1","article-title":"Functional evolution of bacterial histone-like HU proteins","volume":"13","author":"A Grove","year":"2011","journal-title":"Curr Issues Mol Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/0378-1119(86)90129-0","article-title":"Genetic characterization of the gene hupB encoding the HU-1 protein of Escherichia coli","volume":"45","author":"Y Kano","year":"1986","journal-title":"Gene"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1006\/jmbi.1999.2631","article-title":"Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA","volume":"287","author":"V Pinson","year":"1999","journal-title":"J Mol Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3749","DOI":"10.1093\/emboj\/cdg351","article-title":"Flexible DNA bending in HU-DNA cocrystal structures","volume":"22","author":"KK Swinger","year":"2003","journal-title":"EMBO J"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1107\/S0907444999000578","article-title":"The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus","volume":"55","author":"SW White","year":"1999","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/0378-1119(92)90026-L","article-title":"Histone-like proteins are required for cell growth and constraint of supercoils in DNA","volume":"122","author":"K Yasuzawa","year":"1992","journal-title":"Gene"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/0300-9084(92)90136-3","article-title":"The DNA-binding protein HBsu is essential for normal growth and development in Bacillus subtilis","volume":"74","author":"B Micka","year":"1992","journal-title":"Biochimie"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1073\/pnas.0510013103","article-title":"Essential genes of a minimal bacterium","volume":"103","author":"JI Glass","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.mib.2010.09.013","article-title":"Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression","volume":"13","author":"DF Browning","year":"2010","journal-title":"Curr Opin Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.sbi.2003.12.003","article-title":"IHF and HU: flexible architects of bent DNA","volume":"14","author":"KK Swinger","year":"2004","journal-title":"Curr Opin Struct Biol"},{"key":"ref32","first-page":"365","article-title":"Bacterial Chromatin","author":"A Mu\u00f1oz","year":"2010"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1002\/j.1460-2075.1991.tb07998.x","article-title":"HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments","volume":"10","author":"E Bonnefoy","year":"1991","journal-title":"EMBO J"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1111\/j.1365-2958.1993.tb01126.x","article-title":"Protein HU binds specifically to kinked DNA","volume":"7","author":"A Pontiggia","year":"1993","journal-title":"Mol Microbiol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"10291","DOI":"10.1074\/jbc.270.17.10291","article-title":"HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps","volume":"270","author":"B Castaing","year":"1995","journal-title":"J Biol Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/0300-9084(94)90014-0","article-title":"Histones, HMG, HU, IHF: Meme combat","volume":"76","author":"J Oberto","year":"1994","journal-title":"Biochimie"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1007\/s00792-016-0859-1","article-title":"HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses","volume":"20","author":"AC Papageorgiou","year":"2016","journal-title":"Extremophiles"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"36366","DOI":"10.1038\/srep36366","article-title":"Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3","volume":"6","author":"KM Boyko","year":"2016","journal-title":"Sci Rep"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/MMBR.62.4.1094-1156.1998","article-title":"Molecular biology and pathogenicity of mycoplasmas","volume":"62","author":"S Razin","year":"1998","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1093\/nar\/30.9.2031","article-title":"Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution","volume":"30","author":"EP Rocha","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"8692","DOI":"10.1021\/bi2009097","article-title":"Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA","volume":"50","author":"D Kamashev","year":"2011","journal-title":"Biochemistry"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1016\/j.biocel.2011.06.012","article-title":"Multivariate geometrical analysis of catalytic residues in the penicillin-binding proteins","volume":"43","author":"S Bobba","year":"2011","journal-title":"Int J Biochem Cell Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"6489","DOI":"10.1128\/JB.00709-09","article-title":"One of the two genes encoding nucleoid-associated HU proteins in Streptomyces coelicolor is developmentally regulated and specifically involved in spore maturation","volume":"191","author":"P Salerno","year":"2009","journal-title":"J Bacteriol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"8744","DOI":"10.1021\/bi800010s","article-title":"The C-terminal domain of HU-related histone-like protein Hlp from Mycobacterium smegmatis mediates DNA end-joining","volume":"47","author":"A Mukherjee","year":"2008","journal-title":"Biochemistry"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0022-2836(03)00725-3","article-title":"Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure","volume":"331","author":"J Ramstein","year":"2003","journal-title":"J Mol Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1042\/BJ20040938","article-title":"Substrate specificity of Helicobacter pylori histone-like HU protein is determined by insufficient stabilization of DNA flexure points","volume":"383","author":"C Chen","year":"2004","journal-title":"Biochem J"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1016\/j.biochi.2011.03.005","article-title":"Purification and functional analysis of recombinant Acholeplasma laidlawii histone-like HU protein","volume":"93","author":"SA Levitskiy","year":"2011","journal-title":"Biochimie"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0188037","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T19:35:27Z","timestamp":1603308927000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0188037"}},"subtitle":[],"editor":[{"given":"Dipankar","family":"Chatterji","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,11,13]]},"references-count":47,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2017,11,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0188037","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,13]]}}}