Riboregulation in plant-associated α-proteobacteria

References

• Kuykendall LD, Elkan GH. Rhizobium japonicum derivatives differing in nitrogen-fixing efficiency and carbohydrate utilization. Appl Environ Microbiol 1976; 32:511 - 9; PMID: 988784
   PubMed Web of Science ®Google Scholar
• Segovia L, Young JP, Martínez-Romero E. Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int J Syst Bacteriol 1993; 43:374 - 7; http://dx.doi.org/10.1099/00207713-43-2-374; PMID: 8494746
   PubMedGoogle Scholar
• Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC. How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat Rev Microbiol 2007; 5:619 - 33; http://dx.doi.org/10.1038/nrmicro1705; PMID: 17632573
   PubMed Web of Science ®Google Scholar
• Gelvin SB. Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol Mol Biol Rev 2003; 67:16 - 37; http://dx.doi.org/10.1128/MMBR.67.1.16-37.2003; PMID: 12626681
   PubMed Web of Science ®Google Scholar
• del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics. Mol Microbiol 2007; 66:1080 - 91; http://dx.doi.org/10.1111/j.1365-2958.2007.05978.x; PMID: 17971083
   PubMed Web of Science ®Google Scholar
• Ulvé VM, Sevin EW, Chéron A, Barloy-Hubler F. Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics 2007; 8:467; http://dx.doi.org/10.1186/1471-2164-8-467; PMID: 18093320
   PubMed Web of Science ®Google Scholar
• Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G. Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 2008; 9:416; http://dx.doi.org/10.1186/1471-2164-9-416; PMID: 18793445
   PubMed Web of Science ®Google Scholar
• Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.. BMC Genomics 2010; 11:245; http://dx.doi.org/10.1186/1471-2164-11-245; PMID: 20398411
   PubMed Web of Science ®Google Scholar
• Vercruysse M, Fauvart M, Cloots L, Engelen K, Thijs IM, Marchal K, Michiels J. Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array. BMC Genomics 2010; 11:53; http://dx.doi.org/10.1186/1471-2164-11-53; PMID: 20089193
   PubMed Web of Science ®Google Scholar
• Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E. Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol 2012; 9:47 - 58; http://dx.doi.org/10.4161/rna.9.1.18008; PMID: 22258152
   PubMed Web of Science ®Google Scholar
• Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.. RNA Biol 2012; 9:446 - 57; http://dx.doi.org/10.4161/rna.17212; PMID: 22336765
   PubMed Web of Science ®Google Scholar
• Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens.. PLoS One 2013; 8:e70720; http://dx.doi.org/10.1371/journal.pone.0070720; PMID: 23950988
   PubMedGoogle Scholar
• Fischer HM. Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 1994; 58:352 - 86; PMID: 7968919
   PubMedGoogle Scholar
• Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 2002; 99:13148 - 53; http://dx.doi.org/10.1073/pnas.192319099; PMID: 12271122
   PubMed Web of Science ®Google Scholar
• Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, et al. The composite genome of the legume symbiont Sinorhizobium meliloti.. Science 2001; 293:668 - 72; http://dx.doi.org/10.1126/science.1060966; PMID: 11474104
   PubMed Web of Science ®Google Scholar
• Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, et al. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 2001; 294:2323 - 8; http://dx.doi.org/10.1126/science.1066803; PMID: 11743194
   PubMed Web of Science ®Google Scholar
• Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF Jr., et al. The genome of the natural genetic engineer Agrobacterium tumefaciens C58.. Science 2001; 294:2317 - 23; http://dx.doi.org/10.1126/science.1066804; PMID: 11743193
   PubMed Web of Science ®Google Scholar
• Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K, et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.. DNA Res 2002; 9:189 - 97; http://dx.doi.org/10.1093/dnares/9.6.189; PMID: 12597275
   PubMed Web of Science ®Google Scholar
• González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, et al. The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci U S A 2006; 103:3834 - 9; http://dx.doi.org/10.1073/pnas.0508502103; PMID: 16505379
   PubMed Web of Science ®Google Scholar
• Morita T, Maki K, Aiba H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 2005; 19:2176 - 86; http://dx.doi.org/10.1101/gad.1330405; PMID: 16166379
   PubMed Web of Science ®Google Scholar
• Vogel J, Luisi BF. Hfq and its constellation of RNA. Nat Rev Microbiol 2011; 9:578 - 89; http://dx.doi.org/10.1038/nrmicro2615; PMID: 21760622
   PubMed Web of Science ®Google Scholar
• Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton JC, Vogel J. SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay. Mol Microbiol 2006; 62:1674 - 88; http://dx.doi.org/10.1111/j.1365-2958.2006.05524.x; PMID: 17427289
   PubMed Web of Science ®Google Scholar
• Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.. Cell 2004; 118:69 - 82; http://dx.doi.org/10.1016/j.cell.2004.06.009; PMID: 15242645
   PubMed Web of Science ®Google Scholar
• Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, et al. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev 2007; 21:1353 - 66; http://dx.doi.org/10.1101/gad.423507; PMID: 17545468
   PubMed Web of Science ®Google Scholar
• Heroven AK, Böhme K, Rohde M, Dersch P. A Csr-type regulatory system, including small non-coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM. Mol Microbiol 2008; 68:1179 - 95; http://dx.doi.org/10.1111/j.1365-2958.2008.06218.x; PMID: 18430141
   PubMed Web of Science ®Google Scholar
• Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, et al. The primary transcriptome of the major human pathogen Helicobacter pylori.. Nature 2010; 464:250 - 5; http://dx.doi.org/10.1038/nature08756; PMID: 20164839
   PubMed Web of Science ®Google Scholar
• Schlüter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A. Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021. BMC Genomics 2013; 14:156; http://dx.doi.org/10.1186/1471-2164-14-156; PMID: 23497287
   PubMed Web of Science ®Google Scholar
• Torres-Quesada O, Reinkensmeier J, Schlüter J-P, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jiménez-Zurdo JI. Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti.. RNA Biol 2014; 11; In press http://dx.doi.org/10.4161/rna.28239; PMID: 24786641
   PubMed Web of Science ®Google Scholar
• Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F. Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein. Mol Microbiol 2011; 80:492 - 506; http://dx.doi.org/10.1111/j.1365-2958.2011.07589.x; PMID: 21320185
   PubMed Web of Science ®Google Scholar
• Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 2005; 6:R70; http://dx.doi.org/10.1186/gb-2005-6-8-r70; PMID: 16086852
   PubMed Web of Science ®Google Scholar
• Voss B, Hölscher M, Baumgarth B, Kalbfleisch A, Kaya C, Hess WR, Becker A, Evguenieva-Hackenberg E. Expression of small RNAs in Rhizobiales and protection of a small RNA and its degradation products by Hfq in Sinorhizobium meliloti.. Biochem Biophys Res Commun 2009; 390:331 - 6; http://dx.doi.org/10.1016/j.bbrc.2009.09.125; PMID: 19800865
   PubMed Web of Science ®Google Scholar
• Wassarman KM, Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell 2000; 101:613 - 23; http://dx.doi.org/10.1016/S0092-8674(00)80873-9; PMID: 10892648
   PubMed Web of Science ®Google Scholar
• Wassarman KM, Saecker RM. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 2006; 314:1601 - 3; http://dx.doi.org/10.1126/science.1134830; PMID: 17158328
   PubMed Web of Science ®Google Scholar
• Reinkensmeier J, Schlüter JP, Giegerich R, Becker A. Conservation and occurrence of trans-encoded sRNAs in the Rhizobiales. Genes (Basel) 2011; 2:925 - 56; http://dx.doi.org/10.3390/genes2040925; PMID: 24710299
   PubMed Web of Science ®Google Scholar
• Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335 - 7; http://dx.doi.org/10.1093/bioinformatics/btp157; PMID: 19307242
   PubMed Web of Science ®Google Scholar
• Reeder J, Reeder J, Giegerich R. Locomotif: from graphical motif description to RNA motif search. Bioinformatics 2007; 23:i392 - 400; http://dx.doi.org/10.1093/bioinformatics/btm179; PMID: 17646322
   PubMedGoogle Scholar
• Sauthoff G, Möhl M, Janssen S, Giegerich R. Bellman’s GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics 2013; 29:551 - 60; http://dx.doi.org/10.1093/bioinformatics/btt022; PMID: 23355290
   PubMed Web of Science ®Google Scholar
• del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N, Jiménez-Zurdo JI. A survey of sRNA families in α-proteobacteria. RNA Biol 2012; 9:119 - 29; http://dx.doi.org/10.4161/rna.18643; PMID: 22418845
   PubMed Web of Science ®Google Scholar
• Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 2006; 7:R34; http://dx.doi.org/10.1186/gb-2006-7-4-r34; PMID: 16640791
   PubMed Web of Science ®Google Scholar
• Torres-Quesada O, Millán V, Nisa-Martínez R, Bardou F, Crespi M, Toro N, Jiménez-Zurdo JI. Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti.. PLoS One 2013; 8:e68147; http://dx.doi.org/10.1371/journal.pone.0068147; PMID: 23869210
   PubMed Web of Science ®Google Scholar
• Caswell CC, Gaines JM, Ciborowski P, Smith D, Borchers CH, Roux CM, Sayood K, Dunman PM, Roop Ii RM. Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol 2012; 85:345 - 60; http://dx.doi.org/10.1111/j.1365-2958.2012.08117.x; PMID: 22690807
   PubMed Web of Science ®Google Scholar
• Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G. Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.. Mol Microbiol 2011; 80:1479 - 95; http://dx.doi.org/10.1111/j.1365-2958.2011.07658.x; PMID: 21535243
   PubMed Web of Science ®Google Scholar
• Babitzke P, Romeo T. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 2007; 10:156 - 63; http://dx.doi.org/10.1016/j.mib.2007.03.007; PMID: 17383221
   PubMed Web of Science ®Google Scholar
• Watson RJ, Heys R. Replication regions of Sinorhizobium meliloti plasmids. Plasmid 2006; 55:87 - 98; http://dx.doi.org/10.1016/j.plasmid.2005.08.003; PMID: 16202450
   PubMed Web of Science ®Google Scholar
• Sobrero P, Valverde C. The bacterial protein Hfq: much more than a mere RNA-binding factor. Crit Rev Microbiol 2012; 38:276 - 99; http://dx.doi.org/10.3109/1040841X.2012.664540; PMID: 22435753
   PubMed Web of Science ®Google Scholar
• Kaminski PA, Desnoues N, Elmerich C. The expression of nifA in Azorhizobium caulinodans requires a gene product homologous to Escherichia coli HF-I, an RNA-binding protein involved in the replication of phage Q beta RNA. Proc Natl Acad Sci U S A 1994; 91:4663 - 7; http://dx.doi.org/10.1073/pnas.91.11.4663; PMID: 8197116
   PubMed Web of Science ®Google Scholar
• Sobrero P, Valverde C. Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011. Arch Microbiol 2011; 193:629 - 39; http://dx.doi.org/10.1007/s00203-011-0701-1; PMID: 21484295
   PubMed Web of Science ®Google Scholar
• Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880 - 91; http://dx.doi.org/10.1016/j.molcel.2011.08.022; PMID: 21925377
   PubMed Web of Science ®Google Scholar
• Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008; 4:e1000163; http://dx.doi.org/10.1371/journal.pgen.1000163; PMID: 18725932
   PubMed Web of Science ®Google Scholar
• Sittka A, Sharma CM, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol 2009; 6:266 - 75; http://dx.doi.org/10.4161/rna.6.3.8332; PMID: 19333007
   PubMed Web of Science ®Google Scholar
• Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 2010; 38:3794 - 808; http://dx.doi.org/10.1093/nar/gkq032; PMID: 20348540
   PubMed Web of Science ®Google Scholar
• Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J. An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 2012; 31:4005 - 19; http://dx.doi.org/10.1038/emboj.2012.229; PMID: 22922465
   PubMed Web of Science ®Google Scholar
• Dambach M, Irnov I, Winkler WC. Association of RNAs with Bacillus subtilis Hfq. PLoS One 2013; 8:e55156; http://dx.doi.org/10.1371/journal.pone.0055156; PMID: 23457461
   PubMed Web of Science ®Google Scholar
• Vytvytska O, Moll I, Kaberdin VR, von Gabain A, Bläsi U. Hfq (HF1) stimulates ompA mRNA decay by interfering with ribosome binding. Genes Dev 2000; 14:1109 - 18; PMID: 10809669
   PubMed Web of Science ®Google Scholar
• Mohanty BK, Maples VF, Kushner SR. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli.. Mol Microbiol 2004; 54:905 - 20; http://dx.doi.org/10.1111/j.1365-2958.2004.04337.x; PMID: 15522076
   PubMed Web of Science ®Google Scholar
• Barra-Bily L, Pandey SP, Trautwetter A, Blanco C, Walker GC. The Sinorhizobium meliloti RNA chaperone Hfq mediates symbiosis of S. meliloti and alfalfa. J Bacteriol 2010; 192:1710 - 8; http://dx.doi.org/10.1128/JB.01427-09; PMID: 20081033
   PubMed Web of Science ®Google Scholar
• Wilms I, Möller P, Stock AM, Gurski R, Lai EM, Narberhaus F. Hfq influences multiple transport systems and virulence in the plant pathogen Agrobacterium tumefaciens.. J Bacteriol 2012; 194:5209 - 17; http://dx.doi.org/10.1128/JB.00510-12; PMID: 22821981
   PubMed Web of Science ®Google Scholar
• Kaminski PA, Elmerich C. The control of Azorhizobium caulinodans nifA expression by oxygen, ammonia and by the HF-I-like protein, NrfA. Mol Microbiol 1998; 28:603 - 13; http://dx.doi.org/10.1046/j.1365-2958.1998.00823.x; PMID: 9632262
   PubMed Web of Science ®Google Scholar
• Zhang Y, Hong G. Post-transcriptional regulation of NifA expression by Hfq and RNase E complex in Rhizobium leguminosarum bv. viciae.. Acta Biochim Biophys Sin (Shanghai) 2009; 41:719 - 30; http://dx.doi.org/10.1093/abbs/gmp060; PMID: 19727520
   PubMed Web of Science ®Google Scholar
• Barra-Bily L, Fontenelle C, Jan G, Flechard M, Trautwetter A, Pandey SP, Walker GC, Blanco C. Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq. J Bacteriol 2010; 192:1719 - 29; http://dx.doi.org/10.1128/JB.01429-09; PMID: 20081032
   PubMed Web of Science ®Google Scholar
• Gao M, Barnett MJ, Long SR, Teplitski M. Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis. Mol Plant Microbe Interact 2010; 23:355 - 65; http://dx.doi.org/10.1094/MPMI-23-4-0355; PMID: 20192823
   PubMed Web of Science ®Google Scholar
• Torres-Quesada O, Oruezábal RI, Peregrina A, Jofré E, Lloret J, Rivilla R, Toro N, Jiménez-Zurdo JI. The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa. BMC Microbiol 2010; 10:71; http://dx.doi.org/10.1186/1471-2180-10-71; PMID: 20205931
   PubMed Web of Science ®Google Scholar
• Sobrero P, Schlüter JP, Lanner U, Schlosser A, Becker A, Valverde C. Quantitative proteomic analysis of the Hfq-regulon in Sinorhizobium meliloti 2011. PLoS One 2012; 7:e48494; http://dx.doi.org/10.1371/journal.pone.0048494; PMID: 23119037
   PubMedGoogle Scholar
• Drepper T, Raabe K, Giaourakis D, Gendrullis M, Masepohl B, Klipp W. The Hfq-like protein NrfA of the phototrophic purple bacterium Rhodobacter capsulatus controls nitrogen fixation via regulation of nifA and anfA expression. FEMS Microbiol Lett 2002; 215:221 - 7; http://dx.doi.org/10.1111/j.1574-6968.2002.tb11394.x; PMID: 12399038
   PubMed Web of Science ®Google Scholar
• Mulley G, White JP, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole PS. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol 2011; 80:149 - 67; http://dx.doi.org/10.1111/j.1365-2958.2011.07565.x; PMID: 21276099
   PubMed Web of Science ®Google Scholar
• Robertson GT, Roop RM 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 1999; 34:690 - 700; http://dx.doi.org/10.1046/j.1365-2958.1999.01629.x; PMID: 10564509
   PubMed Web of Science ®Google Scholar
• Roop RM 2nd, Robertson GT, Ferguson GP, Milford LE, Winkler ME, Walker GC. Seeking a niche: putative contributions of the hfq and bacA gene products to the successful adaptation of the brucellae to their intracellular home. Vet Microbiol 2002; 90:349 - 63; http://dx.doi.org/10.1016/S0378-1135(02)00220-1; PMID: 12414155
   PubMed Web of Science ®Google Scholar
• Pandey SP, Minesinger BK, Kumar J, Walker GC. A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res 2011; 39:4691 - 708; http://dx.doi.org/10.1093/nar/gkr060; PMID: 21325267
   PubMed Web of Science ®Google Scholar
• Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 2014; 15:121; http://dx.doi.org/10.1186/1471-2164-15-121; PMID: 24511998
   PubMed Web of Science ®Google Scholar
• Davies BW, Köhrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol Microbiol 2010; 78:506 - 18; http://dx.doi.org/10.1111/j.1365-2958.2010.07351.x; PMID: 20807199
   PubMed Web of Science ®Google Scholar
• Grinwald M, Ron EZ. The Escherichia coli translation-associated heat shock protein YbeY is involved in rRNA transcription antitermination. PLoS One 2013; 8:e62297; http://dx.doi.org/10.1371/journal.pone.0062297; PMID: 23638028
   PubMed Web of Science ®Google Scholar
• Jacob AI, Köhrer C, Davies BW, RajBhandary UL, Walker GC. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 2013; 49:427 - 38; http://dx.doi.org/10.1016/j.molcel.2012.11.025; PMID: 23273979
   PubMed Web of Science ®Google Scholar
• Wassarman KM. 6S RNA: a regulator of transcription. Mol Microbiol 2007; 65:1425 - 31; http://dx.doi.org/10.1111/j.1365-2958.2007.05894.x; PMID: 17714443
   PubMed Web of Science ®Google Scholar
• Egea PF, Stroud RM, Walter P. Targeting proteins to membranes: structure of the signal recognition particle. Curr Opin Struct Biol 2005; 15:213 - 20; http://dx.doi.org/10.1016/j.sbi.2005.03.007; PMID: 15837181
   PubMed Web of Science ®Google Scholar
• Altman S. A view of RNase P. Mol Biosyst 2007; 3:604 - 7; http://dx.doi.org/10.1039/b707850c; PMID: 17700860
   PubMed Web of Science ®Google Scholar
• http://rfam.sanger.ac.uk/
   Google Scholar
• Ebeling S, Kündig C, Hennecke H. Discovery of a rhizobial RNA that is essential for symbiotic root nodule development. J Bacteriol 1991; 173:6373 - 82; PMID: 1717438
   PubMed Web of Science ®Google Scholar
• Keiler KC, Shapiro L, Williams KP. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter.. Proc Natl Acad Sci U S A 2000; 97:7778 - 83; http://dx.doi.org/10.1073/pnas.97.14.7778; PMID: 10884408
   PubMed Web of Science ®Google Scholar
• Williams KP. The tmRNA Website: invasion by an intron. Nucleic Acids Res 2002; 30:179 - 82; http://dx.doi.org/10.1093/nar/30.1.179; PMID: 11752287
   PubMed Web of Science ®Google Scholar
• MacLellan SR, Smallbone LA, Sibley CD, Finan TM. The expression of a novel antisense gene mediates incompatibility within the large repABC family of α-proteobacterial plasmids. Mol Microbiol 2005; 55:611 - 23; http://dx.doi.org/10.1111/j.1365-2958.2004.04412.x; PMID: 15659174
   PubMed Web of Science ®Google Scholar
• Chai Y, Winans SC. A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol 2005; 56:1574 - 85; http://dx.doi.org/10.1111/j.1365-2958.2005.04636.x; PMID: 15916607
   PubMed Web of Science ®Google Scholar
• Chevrot R, Rosen R, Haudecoeur E, Cirou A, Shelp BJ, Ron E, Faure D. GABA controls the level of quorum-sensing signal in Agrobacterium tumefaciens.. Proc Natl Acad Sci U S A 2006; 103:7460 - 4; http://dx.doi.org/10.1073/pnas.0600313103; PMID: 16645034
   PubMed Web of Science ®Google Scholar
• Planamente S, Moréra S, Faure D. In planta fitness-cost of the Atu4232-regulon encoding for a selective GABA-binding sensor in Agrobacterium. Commun Integr Biol 2013; 6:e23692; http://dx.doi.org/10.4161/cib.23692; PMID: 23710277
   PubMedGoogle Scholar
• Overlöper A, Kraus A, Gurski R, Wright PR, Georg J, Hess WR, Narberhaus F. Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region. RNA Biol 2014; 11; http://dx.doi.org/10.4161/rna.29145; PMID: 24921646
   PubMed Web of Science ®Google Scholar
• Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J. Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A 2013; 110:E3487 - 96; http://dx.doi.org/10.1073/pnas.1303248110; PMID: 23980183
   PubMed Web of Science ®Google Scholar
• Urban JH, Vogel J. Translational control and target recognition by Escherichia coli small RNAs in vivo.. Nucleic Acids Res 2007; 35:1018 - 37; http://dx.doi.org/10.1093/nar/gkl1040; PMID: 17264113
   PubMed Web of Science ®Google Scholar
• McIntosh M, Meyer S, Becker A. Novel Sinorhizobium meliloti quorum sensing positive and negative regulatory feedback mechanisms respond to phosphate availability. Mol Microbiol 2009; 74:1238 - 56; http://dx.doi.org/10.1111/j.1365-2958.2009.06930.x; PMID: 19889097
   PubMed Web of Science ®Google Scholar
• McIntosh M, Czuppon P, Best K, Becker A, Pfaffelhuber P. Modeling quorum sensing in Sinorhizobium meliloti.. International Journal of Biomathematics and Biostatistics 2013; 2:59 - 74
   Google Scholar
• Chen S, Zhang A, Blyn LB, Storz G. MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli.. J Bacteriol 2004; 186:6689 - 97; http://dx.doi.org/10.1128/JB.186.20.6689-6697.2004; PMID: 15466019
   PubMed Web of Science ®Google Scholar
• Dühring U, Axmann IM, Hess WR, Wilde A. An internal antisense RNA regulates expression of the photosynthesis gene isiA.. Proc Natl Acad Sci U S A 2006; 103:7054 - 8; http://dx.doi.org/10.1073/pnas.0600927103; PMID: 16636284
   PubMed Web of Science ®Google Scholar
• Basineni SR, Madhugiri R, Kolmsee T, Hengge R, Klug G. The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its target rpoS in E. coli is growth phase dependent. RNA Biol 2009; 6:584 - 94; http://dx.doi.org/10.4161/rna.6.5.10082; PMID: 20016254
   PubMed Web of Science ®Google Scholar
• Madhugiri R, Basineni SR, Klug G. Turn-over of the small non-coding RNA RprA in E. coli is influenced by osmolarity. Mol Genet Genomics 2010; 284:307 - 18; http://dx.doi.org/10.1007/s00438-010-0568-x; PMID: 20717695
   PubMed Web of Science ®Google Scholar
• Kim KS, Lee Y. Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res 2004; 32:6057 - 68; http://dx.doi.org/10.1093/nar/gkh939; PMID: 15550566
   PubMed Web of Science ®Google Scholar
• Papenfort K, Said N, Welsink T, Lucchini S, Hinton JC, Vogel J. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74:139 - 58; http://dx.doi.org/10.1111/j.1365-2958.2009.06857.x; PMID: 19732340
   PubMed Web of Science ®Google Scholar
• Massé E, Escorcia FE, Gottesman S. Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli.. Genes Dev 2003; 17:2374 - 83; http://dx.doi.org/10.1101/gad.1127103; PMID: 12975324
   PubMed Web of Science ®Google Scholar
• Rasmussen AA, Eriksen M, Gilany K, Udesen C, Franch T, Petersen C, Valentin-Hansen P. Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control. Mol Microbiol 2005; 58:1421 - 9; http://dx.doi.org/10.1111/j.1365-2958.2005.04911.x; PMID: 16313626
   PubMed Web of Science ®Google Scholar
• Afonyushkin T, Vecerek B, Moll I, Bläsi U, Kaberdin VR. Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res 2005; 33:1678 - 89; http://dx.doi.org/10.1093/nar/gki313; PMID: 15781494
   PubMed Web of Science ®Google Scholar
• Viegas SC, Silva IJ, Saramago M, Domingues S, Arraiano CM. Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway. Nucleic Acids Res 2011; 39:2918 - 30; http://dx.doi.org/10.1093/nar/gkq1239; PMID: 21138960
   PubMed Web of Science ®Google Scholar
• Bandyra KJ, Said N, Pfeiffer V, Górna MW, Vogel J, Luisi BF. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 2012; 47:943 - 53; http://dx.doi.org/10.1016/j.molcel.2012.07.015; PMID: 22902561
   PubMed Web of Science ®Google Scholar
• Mackie GA. Ribonuclease E is a 5′-end-dependent endonuclease. Nature 1998; 395:720 - 3; http://dx.doi.org/10.1038/27246; PMID: 9790196
   PubMed Web of Science ®Google Scholar
• Evguenieva-Hackenberg E, Klug G. New aspects of RNA processing in prokaryotes. Curr Opin Microbiol 2011; 14:587 - 92; http://dx.doi.org/10.1016/j.mib.2011.07.025; PMID: 21945217
   PubMed Web of Science ®Google Scholar
• Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Bläsi U. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 2003; 9:1308 - 14; http://dx.doi.org/10.1261/rna.5850703; PMID: 14561880
   PubMed Web of Science ®Google Scholar
• Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res 2007; 35:7651 - 64; http://dx.doi.org/10.1093/nar/gkm916; PMID: 17982174
   PubMed Web of Science ®Google Scholar
• Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, et al. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883 - 923; PMID: 20659169
   PubMed Web of Science ®Google Scholar
• Mathy N, Bénard L, Pellegrini O, Daou R, Wen T, Condon C. 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 2007; 129:681 - 92; http://dx.doi.org/10.1016/j.cell.2007.02.051; PMID: 17512403
   PubMed Web of Science ®Google Scholar
• Pobigaylo N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A. Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti.. Appl Environ Microbiol 2006; 72:4329 - 37; http://dx.doi.org/10.1128/AEM.03072-05; PMID: 16751548
   PubMed Web of Science ®Google Scholar
• Baumgardt K, Charoenpanich P, McIntosh M, Schikora A, Stein E, Thalmann S, Kogel KH, Klug G, Becker A, Evguenieva-Hackenberg E. RNase E affects the expression of the acyl-homoserine lactone synthase gene sinI in Sinorhizobium meliloti.. J Bacteriol 2014; 196:1435 - 47; http://dx.doi.org/10.1128/JB.01471-13; PMID: 24488310
   PubMed Web of Science ®Google Scholar
• Madhugiri R, Evguenieva-Hackenberg E. RNase J is involved in the 5′-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti.. FEBS Lett 2009; 583:2339 - 42; http://dx.doi.org/10.1016/j.febslet.2009.06.026; PMID: 19540834
   PubMed Web of Science ®Google Scholar
• Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nat Rev Microbiol 2012; 10:618 - 30; http://dx.doi.org/10.1038/nrmicro2852; PMID: 22890146
   PubMed Web of Science ®Google Scholar
• Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res 2008; 36:W70-4; http://dx.doi.org/10.1093/nar/gkn188; PMID: 18424795
   PubMedGoogle Scholar