{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:46:47Z","timestamp":1765486007520},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,4,26]],"date-time":"2016-04-26T00:00:00Z","timestamp":1461628800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,4,26]],"date-time":"2016-04-26T00:00:00Z","timestamp":1461628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p><jats:italic>Brucella<\/jats:italic> is the causative agent of brucellosis, a worldwide epidemic zoonosis. Small noncoding RNAs (sRNAs) are important modulators of gene expression and involved in pathogenesis and stress adaptation of <jats:italic>Brucella<\/jats:italic>. In this study, using a strand-specific RNA deep-sequencing approach, we identified a global set of sRNAs expressed by <jats:italic>B. melitensis<\/jats:italic> 16M. In total, 1321 sRNAs were identified, ranging from 100 to 600 nucleotides. These sRNAs differ in their expression levels and strand and chromosomal distributions. The role of BSR0441, one of these sRNAs, in the virulence of <jats:italic>B. melitensis<\/jats:italic> 16M was further characterized. BSR0441 was highly induced during the infection of macrophages and mice. The deletion mutant of BSR0441 showed significantly reduced spleen colonization in the middle and late phases of infection. The expression of the BSR0441 target mRNA genes was also altered in the BSR0441 mutant strain during macrophage and mice infection, which is consistent with its reduced intracellular survival capacity. In summary, <jats:italic>Brucella<\/jats:italic> encodes a large number of sRNAs, which may be involved in the stress adaptation and virulence of <jats:italic>Brucella<\/jats:italic>. Further investigation of these regulators will extend our understanding of the <jats:italic>Brucella<\/jats:italic> pathogenesis mechanism and the interactions between <jats:italic>Brucella<\/jats:italic> and its hosts.<\/jats:p>","DOI":"10.1038\/srep25123","type":"journal-article","created":{"date-parts":[[2016,4,26]],"date-time":"2016-04-26T09:24:58Z","timestamp":1461662698000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Large-scale identification of small noncoding RNA with strand-specific deep sequencing and characterization of a novel virulence-related sRNA in Brucella melitensis"],"prefix":"10.1038","volume":"6","author":[{"given":"Zhijun","family":"Zhong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyang","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinran","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiwei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuangshuang","family":"Lei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingjuan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuxuan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuyun","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuehua","family":"Ke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinying","family":"Du","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhoujia","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhihua","family":"Ren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangneng","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zeliang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,4,26]]},"reference":[{"key":"BFsrep25123_CR1","doi-asserted-by":"publisher","first-page":"213","DOI":"10.3201\/eid0302.970219","volume":"3","author":"MJ Corbel","year":"1997","unstructured":"Corbel, M. J. Brucellosis: an overview. Emerg. Infect. Dis. 3, 213\u2013221 (1997).","journal-title":"Emerg. Infect. Dis."},{"key":"BFsrep25123_CR2","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1051\/vetres:2005003","volume":"36","author":"J Godfroid","year":"2005","unstructured":"Godfroid, J. et al. From the discovery of the Malta fever\u2019s agent to the discovery of a marine mammal reservoir, brucellosis has continuously been a re-emerging zoonosis. Vet. Res. 36, 313\u2013326 (2005).","journal-title":"Vet. Res."},{"key":"BFsrep25123_CR3","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/s00430-009-0123-8","volume":"198","author":"RM Roop 2nd","year":"2009","unstructured":"Roop, R. M. 2nd, Gaines, J. M., Anderson, E. S., Caswell, C. C. & Martin, D. W. Survival of the fittest: how Brucella strains adapt to their intracellular niche in the host. Med Microbiol Immunol. 198, 221\u2013238 (2009).","journal-title":"Med Microbiol Immunol."},{"key":"BFsrep25123_CR4","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1016\/j.cell.2009.01.043","volume":"136","author":"LS Waters","year":"2009","unstructured":"Waters, L. S. & Storz, G. Regulatory RNAs in bacteria. Cell. 136, 615\u2013628 (2009).","journal-title":"Cell."},{"key":"BFsrep25123_CR5","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1126\/science.1072249","volume":"296","author":"G Storz","year":"2002","unstructured":"Storz, G. An expanding universe of noncoding RNAs. Science. 296, 1260\u20131263 (2002).","journal-title":"Science."},{"key":"BFsrep25123_CR6","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.molcel.2014.05.006","volume":"55","author":"JJ Tree","year":"2014","unstructured":"Tree, J. J., Granneman, S., McAteer, S. P., Tollervey, D. & Gally, D. L. Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli. Mol Cell. 55, 199\u2013213 (2014).","journal-title":"Mol Cell."},{"key":"BFsrep25123_CR7","doi-asserted-by":"publisher","first-page":"15287","DOI":"10.1038\/srep15287","volume":"5","author":"G Bak","year":"2015","unstructured":"Bak, G. et al. Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli. Sci Rep. 5, 15287 (2015).","journal-title":"Sci Rep."},{"key":"BFsrep25123_CR8","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1093\/nar\/gkl453","volume":"34","author":"J Livny","year":"2006","unstructured":"Livny, J., Brencic, A., Lory, S. & Waldor, M. K. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res. 34, 3484\u20133493 (2006).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep25123_CR9","doi-asserted-by":"publisher","first-page":"2459","DOI":"10.1093\/nar\/gkn077","volume":"36","author":"S Muller","year":"2008","unstructured":"Muller, S. et al. Combined in silico and experimental identification of the Pyrococcus abyssi H\/ACA sRNAs and their target sites in ribosomal RNAs. Nucleic Acids Res. 36, 2459\u20132475 (2008).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep25123_CR10","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/978-1-61779-346-2_5","volume":"799","author":"Y Pannekoek","year":"2012","unstructured":"Pannekoek, Y. & van der Ende, A., Identification and functional characterization of sRNAs in Neisseria meningitidis. Methods Mol Biol. 799, 73\u201389 (2012).","journal-title":"Methods Mol Biol."},{"key":"BFsrep25123_CR11","doi-asserted-by":"publisher","first-page":"535","DOI":"10.2217\/fmb.12.13","volume":"7","author":"Y Qu","year":"2012","unstructured":"Qu, Y. et al. Identification by cDNA cloning of abundant sRNAs in a human-avirulent Yersinia pestis strain grown under five different growth conditions. Future Microbiol. 7, 535\u2013547 (2012).","journal-title":"Future Microbiol."},{"key":"BFsrep25123_CR12","doi-asserted-by":"publisher","first-page":"e79411","DOI":"10.1371\/journal.pone.0079411","volume":"8","author":"CH Tsai","year":"2013","unstructured":"Tsai, C. H. et al. Identification of novel sRNAs in mycobacterial species. Plos One. 8, e79411 (2013).","journal-title":"Plos One."},{"key":"BFsrep25123_CR13","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1046\/j.1365-2958.1999.01629.x","volume":"34","author":"GT Robertson","year":"1999","unstructured":"Robertson, G. T. & Roop, R. M. Jr. The Brucella abortus host factor I (HF-I) protein contributes to stress resistance during stationary phase and is a major determinant of virulence in mice. Mol Microbiol. 34, 690\u2013700 (1999).","journal-title":"Mol Microbiol."},{"key":"BFsrep25123_CR14","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1111\/j.1365-2958.2012.08117.x","volume":"85","author":"CC Caswell","year":"2012","unstructured":"Caswell, C. C. et al. Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol. 85, 345\u2013360 (2012).","journal-title":"Mol Microbiol."},{"key":"BFsrep25123_CR15","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1111\/1574-6968.12433","volume":"354","author":"H Dong","year":"2014","unstructured":"Dong, H., Peng, X., Wang, N. & Wu, Q. Identification of novel sRNAs in Brucella abortus 2308. FEMS Microbiol Lett. 354, 119\u2013125 (2014).","journal-title":"FEMS Microbiol Lett."},{"key":"BFsrep25123_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/femsle\/fnu017","volume":"362","author":"X Peng","year":"2015","unstructured":"Peng, X., Dong, H. & Wu, Q. A new cis-encoded sRNA, BsrH, regulating the expression of hemH gene in Brucella abortus 2308. FEMS Microbiol Lett. 362, 1\u20137 (2015).","journal-title":"FEMS Microbiol Lett."},{"key":"BFsrep25123_CR17","first-page":"164","volume":"6","author":"Y Wang","year":"2015","unstructured":"Wang, Y. et al. Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis. Front Microbiol. 6, 164 (2015).","journal-title":"Front Microbiol."},{"key":"BFsrep25123_CR18","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1128\/JB.00711-15","volume":"198","author":"B Saadeh","year":"2015","unstructured":"Saadeh, B. et al. Transcriptome-wide identification of Hfq-associated RNAs in Brucella suis by deep sequencing. J Bacteriol. 198, 427\u2013435 (2015).","journal-title":"J Bacteriol."},{"key":"BFsrep25123_CR19","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1016\/j.chom.2010.06.008","volume":"8","author":"K Papenfort","year":"2010","unstructured":"Papenfort, K. & Vogel, J. Regulatory RNA in bacterial pathogens. Cell Host Microbe. 8, 116\u2013127 (2010).","journal-title":"Cell Host Microbe."},{"key":"BFsrep25123_CR20","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1007\/s00018-009-0162-8","volume":"67","author":"P Romby","year":"2010","unstructured":"Romby, P. & Charpentier, E. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci. 67, 217\u2013237 (2010).","journal-title":"Cell Mol Life Sci."},{"key":"BFsrep25123_CR21","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.cell.2013.03.003","volume":"153","author":"K Papenfort","year":"2013","unstructured":"Papenfort, K., Sun, Y., Miyakoshi, M., Vanderpool, C. K. & Vogel, J. Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell. 153, 426\u2013437 (2013).","journal-title":"Cell."},{"key":"BFsrep25123_CR22","doi-asserted-by":"publisher","first-page":"3569","DOI":"10.1128\/JB.01767-08","volume":"191","author":"AR Wattam","year":"2009","unstructured":"Wattam, A. R. et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 191, 3569\u20133579 (2009).","journal-title":"J Bacteriol."},{"key":"BFsrep25123_CR23","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1128\/JB.01779-08","volume":"191","author":"SC Slater","year":"2009","unstructured":"Slater, S. C. et al. Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol. 191, 2501\u20132511 (2009).","journal-title":"J Bacteriol."},{"key":"BFsrep25123_CR24","doi-asserted-by":"publisher","first-page":"e1002342","DOI":"10.1371\/journal.ppat.1002342","volume":"7","author":"KB Arnvig","year":"2011","unstructured":"Arnvig, K. B. et al. Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. Plos Pathog. 7, e1002342 (2011).","journal-title":"Plos Pathog."},{"key":"BFsrep25123_CR25","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1146\/annurev-micro-090110-102946","volume":"65","author":"A Battesti","year":"2011","unstructured":"Battesti, A., Majdalani, N. & Gottesman, S. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol. 65, 189\u2013213 (2011).","journal-title":"Annu Rev Microbiol."},{"key":"BFsrep25123_CR26","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1016\/j.molcel.2011.08.022","volume":"43","author":"G Storz","year":"2011","unstructured":"Storz, G., Vogel, J. & Wassarman, K. M. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 43, 880\u2013891 (2011).","journal-title":"Mol Cell."},{"key":"BFsrep25123_CR27","doi-asserted-by":"publisher","first-page":"e75736","DOI":"10.1371\/journal.pone.0075736","volume":"8","author":"JK Salazar","year":"2013","unstructured":"Salazar, J. K. et al. Roles of a novel Crp\/Fnr family transcription factor Lmo0753 in soil survival, biofilm production and surface attachment to fresh produce of Listeria monocytogenes. Plos One. 8, e75736 (2013).","journal-title":"Plos One."},{"key":"BFsrep25123_CR28","doi-asserted-by":"publisher","first-page":"e71933","DOI":"10.1371\/journal.pone.0071933","volume":"8","author":"M Cui","year":"2013","unstructured":"Cui, M. et al. Impact of Hfq on global gene expression and intracellular survival in Brucella melitensis. Plos One. 8, e71933 (2013).","journal-title":"Plos One."},{"key":"BFsrep25123_CR29","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1111\/j.1365-2958.2004.04337.x","volume":"54","author":"BK Mohanty","year":"2004","unstructured":"Mohanty, B. K., Maples, V. F. & Kushner, S. R. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol. 54, 905\u2013920 (2004).","journal-title":"Mol Microbiol."},{"key":"BFsrep25123_CR30","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.mib.2007.03.015","volume":"10","author":"RG Brennan","year":"2007","unstructured":"Brennan, R. G. & Link, T. M. Hfq structure, function and ligand binding. Curr Opin Microbiol. 10, 125\u2013133 (2007).","journal-title":"Curr Opin Microbiol."},{"key":"BFsrep25123_CR31","doi-asserted-by":"publisher","first-page":"E709","DOI":"10.1073\/pnas.1101655108","volume":"108","author":"JT Koo","year":"2011","unstructured":"Koo, J. T., Alleyne, T. M., Schiano, C. A., Jafari, N. & Lathem, W. W. Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci USA 108, E709\u2013717 (2011).","journal-title":"Proc Natl Acad Sci USA"},{"key":"BFsrep25123_CR32","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1006\/plas.1995.1006","volume":"33","author":"PH Elzer","year":"1995","unstructured":"Elzer, P. H. et al. In vivo and in vitro stability of the broad-host-range cloning vector pBBR1MCS in six Brucella species. Plasmid. 33, 51\u201357 (1995).","journal-title":"Plasmid."},{"key":"BFsrep25123_CR33","doi-asserted-by":"publisher","first-page":"e123","DOI":"10.1093\/nar\/gkp596","volume":"37","author":"D Parkhomchuk","year":"2009","unstructured":"Parkhomchuk, D. et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123 (2009).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep25123_CR34","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1038\/nmeth.1491","volume":"7","author":"JZ Levin","year":"2010","unstructured":"Levin, J. Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods. 7, 709\u2013715 (2010).","journal-title":"Nat Methods."},{"key":"BFsrep25123_CR35","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1093\/nar\/gku317","volume":"42","author":"MB Kery","year":"2014","unstructured":"Kery, M. B., Feldman, M., Livny, J. & Tjaden, B. TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res. 42, 124\u2013129 (2014).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep25123_CR36","doi-asserted-by":"publisher","first-page":"e147","DOI":"10.1093\/nar\/gkq437","volume":"38","author":"BM Beckmann","year":"2010","unstructured":"Beckmann, B. M., Grunweller, A., Weber, M. H. & Hartmann, R. K. Northern blot detection of endogenous small RNAs (approximately14 nt) in bacterial total RNA extracts. Nucleic Acids Res. 38, e147 (2010).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep25123_CR37","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 25, 402\u2013408 (2001).","journal-title":"Methods."},{"key":"BFsrep25123_CR38","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1016\/j.vetmic.2011.03.031","volume":"151","author":"Y Wang","year":"2011","unstructured":"Wang, Y. et al. The 16MDeltavjbR as an ideal live attenuated vaccine candidate for differentiation between Brucella vaccination and infection. Vet Microbiol. 151, 354\u2013362 (2011).","journal-title":"Vet Microbiol."},{"key":"BFsrep25123_CR39","doi-asserted-by":"publisher","first-page":"e5368","DOI":"10.1371\/journal.pone.0005368","volume":"4","author":"Y Wang","year":"2009","unstructured":"Wang, Y. et al. Comparative proteomics analyses reveal the virB of B. melitensis affects expression of intracellular survival related proteins. Plos One. 4, e5368 (2009).","journal-title":"Plos One."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep25123.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep25123","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep25123.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T04:15:13Z","timestamp":1672892113000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep25123"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,26]]},"references-count":39,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,4,29]]}},"alternative-id":["BFsrep25123"],"URL":"https:\/\/doi.org\/10.1038\/srep25123","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,26]]},"assertion":[{"value":"4 February 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 April 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 April 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"25123"}}