Conserved small mRNA with an unique, extended Shine-Dalgarno sequence

References

• Sharma CM, Vogel J. Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol 2014; 19:97-105 PMID:25024085; https://doi.org/10.1016/j.mib.2014.06.010
   PubMed Web of Science ®Google Scholar
• Prasse D, Thomsen J, De Santis R, Muntel J, Becher D, Schmitz RA. First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1. Biochimie 2015; 117:138-48; PMID:25890157; https://doi.org/10.1016/j.biochi.2015.04.007
   PubMed Web of Science ®Google Scholar
• Storz G, Wolf YI, Ramamurthi, KS Small proteins can no longer be ignored. Annu Rev Biochem 2014; 83:753-77; PMID:24606146; https://doi.org/10.1146/annurev-biochem-070611-102400
   PubMed Web of Science ®Google Scholar
• Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol 2010; 76:990-1009; PMID:20444087; https://doi.org/10.1111/j.1365-2958.2010.07158.x
   PubMed Web of Science ®Google Scholar
• Shine J, Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 1974; 71:1342-6; PMID:4598299; https://doi.org/10.1073/pnas.71.4.1342
   PubMedGoogle Scholar
• Omotajo D, Tate T, Cho H, Choudhary M. Distribution and diversity of ribosome binding sites in prokaryotic genomes. BMC Genomics 2015; 16:604; PMID:26268350; https://doi.org/10.1186/s12864-015-1808-6
   PubMed Web of Science ®Google Scholar
• Warren AS, Archuleta J, Feng WC, Setubal JC. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics 2010; 11:131; PMID:20230630; https://doi.org/10.1186/1471-2105-11-131
   PubMed Web of Science ®Google Scholar
• Kuroda H, Suzuki H, Kusumegi T, Hirose T, Yukawa Y, Sugiura M. Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts. Plant Cell Physiol 2007; 48:1374-78; PMID:17664183; https://doi.org/10.1093/pcp/pcm097
   PubMed Web of Science ®Google Scholar
• Komarova AV, Tchufistova LS, Supina EV, Boni IV. Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 2002; 8:1137-47; PMID:12358433; https://doi.org/10.1017/S1355838202029990
   PubMed Web of Science ®Google Scholar
• Osterman IA, Evfratov SA, Sergiev PV, Dontsova OA. Comparison of mRNA features affecting translation initiation and reinitiation. Nucleic Acids Res 2013; 41:474-86; PMID:23093605; https://doi.org/10.1093/nar/gks989
   PubMed Web of Science ®Google Scholar
• Ramamurthi KS, Storz G. The small protein floodgates are opening; now the functional analysis begins. BMC Biol 2014; 12:96; PMID:25475548; https://doi.org/10.1186/s12915-014-0096-y
   PubMed Web of Science ®Google Scholar
• Tenson T, DeBlasio A, Mankin A. A functional peptide encoded in the Escherichia coli 23S rRNA. Proc Natl Acad Sci U S A 1996; 93:5641-6; PMID:8643630; https://doi.org/10.1073/pnas.93.11.5641
   PubMed Web of Science ®Google Scholar
• Edwards A, Frederix M, Wisniewski-Dyé F, Jones J, Zorreguieta A, Downie JA. The cin and rai quorum-sensing regulatory systems in Rhizobium leguminosarum are coordinated by ExpR and CinS, a small regulatory protein coexpressed with CinI. J Bacteriol 2009; 191:3059-67; PMID:19270098; https://doi.org/10.1128/JB.01650-08
   PubMed Web of Science ®Google Scholar
• Vogel J, Argaman L, Wagner EG, Altuvia S. The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr Biol 2004; 14:2271-6; PMID:15620655; https://doi.org/10.1016/j.cub.2004.12.003
   PubMed Web of Science ®Google Scholar
• Fozo EM, Kawano M, Fontaine F, Kaya Y, Mendieta KS, Jones KL, Ocampo A, Rudd KE, Storz G. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol Microbiol 2008; 70:1076-93; PMID:18710431; https://doi.org/10.1111/j.1365-2958.2008.06394.x
   PubMed Web of Science ®Google Scholar
• Lewis K. Persister cells. Annu Rev Microbiol 2010; 64:357-72; PMID:20528688; https://doi.org/10.1146/annurev.micro.112408.134306
   PubMed Web of Science ®Google Scholar
• Desbrosses GJ, Stougaard J. Root nodulation: a paradigm for how plant-microbe symbiosis influences host developmental pathways. Cell Host Microbe 2011; 10:348-58; PMID:22018235; https://doi.org/10.1016/j.chom.2011.09.005
   PubMed Web of Science ®Google Scholar
• Fischer HM. Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 1994; 58:352-86; PMID:7968919.
   PubMedGoogle Scholar
• Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimo, N, Goebel M, Pessi G, Fischer HM, Ahrens CH, et al. Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 2016; 17:302; PMID:27107716; https://doi.org/10.1186/s12864-016-2602-9
   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; PMID:12597275; https://doi.org/10.1093/dnares/9.6.189
   PubMed Web of Science ®Google Scholar
• Regensburger B, Hennecke H. RNA polymerase from Rhizobium japonicum. Arch Microbiol 1983; 135:103-9; PMID:6639271; https://doi.org/10.1007/BF00408017
   PubMed Web of Science ®Google Scholar
• Delamuta JR, Ribeiro RA, Ormeño-Orrillo E, Melo IS, Martínez-Romero E, Hungria M. Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov. Int J Syst Evol Microbiol. 2013; 63:3342-51; PMID:23504968; https://doi.org/10.1099/ijs.0.049130-0
   PubMed Web of Science ®Google Scholar
• Mesa S, Hauser F, Friberg M, Malaguti E, Fischer HM, Hennecke H. Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum. J Bacteriol 2008; 190:6568-79; PMID:18689489; https://doi.org/10.1128/JB.00748-08
   PubMed Web of Science ®Google Scholar
• Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 1985; 33:103-19; PMID:2985470; https://doi.org/10.1016/0378-1119(85)90120-9
   PubMed Web of Science ®Google Scholar
• Simon R, Priefer U, Pühler A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Biotechnology 1982; 1:784-91; https://doi.org/10.1038/nbt1183-784
   Web of Science ®Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: A laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
   Google Scholar
• Alvarez-Morales A, Betancourt-Alvarez M, Kaluza K, Hennecke, H. Activation of the Bradyrhizobium japonicum nifH and nifDK operons is dependent on promoter-upstream DNA sequences. Nucleic Acids Res 1986; 14:4207-27; PMID:3086837; https://doi.org/10.1093/nar/14.10.4207
   PubMed Web of Science ®Google Scholar
• Rudolph G, Semini G, Hauser F, Lindemann A, Friberg M, Hennecke H, Fischer HM. The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein. J Bacteriol 2006; 188:733-44; PMID:16385063; https://doi.org/10.1128/JB.188.2.733-744.2006
   PubMed Web of Science ®Google Scholar
• Ledermann R, Bartsch I, Remus-Emsermann MN, Vorholt JA, Fischer HM. Stable Fluorescent and Enzymatic Tagging of Bradyrhizobium diazoefficiens to Analyze Host-Plant Infection and Colonization. Mol Plant Microbe Interact 2015; 28:959-67; PMID:26035130; https://doi.org/10.1094/MPMI-03-15-0054-TA
   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; PMID:22258152; https://doi.org/10.4161/rna.9.1.18008
   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; PMID:19540834; https://doi.org/10.1016/j.febslet.2009.06.026
   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; PMID:19800865; https://doi.org/10.1016/j.bbrc.2009.09.125
   PubMed Web of Science ®Google Scholar
• Rheinberger HJ, Geigenmüller U, Wedd, M, Nierhaus KH. Parameters for the preparation of Escherichia coli ribosomes and ribosomal subunits active in tRNA binding. Methods Enzymol 1988; 164:658-70; PMID:3071687; https://doi.org/10.1016/S0076-6879(88)64076-6
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10; PMID:2231712; https://doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Smith C, Heyne S, Richter AS, Will S, Backofen R. Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res 2010; 38:W373-7; PMID:20444875; https://doi.org/10.1093/nar/gkq316
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947-48; PMID:17846036; https://doi.org/10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 2015; 10:845-58; PMID:25950237; https://doi.org/10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar
• Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature 2006; 444:391-4; PMID:17051149; https://doi.org/10.1038/nature05281
   PubMed Web of Science ®Google Scholar
• Liang W, Rudd KE, Deutscher MP. A role for REP sequences in regulating translation. Mol Cell 2015; 58:431-9; PMID:25891074; https://doi.org/10.1016/j.molcel.2015.03.019
   PubMed Web of Science ®Google Scholar
• Zahn K, Inui M, Yukawa H. Characterization of a separate small domain derived from the 5′ end of 23S rRNA of an alpha-proteobacterium. Nucleic Acids Res 1999; 27:4241-50; PMID:10518617; https://doi.org/10.1093/nar/27.21.4241
   PubMed Web of Science ®Google Scholar
• Evguenieva-Hackenberg E. Bacterial ribosomal RNA in pieces. Mol Microbiol 2005; 57:318-25; PMID:15978067; https://doi.org/10.1111/j.1365-2958.2005.04662.x
   PubMed Web of Science ®Google Scholar