Abstract
High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. These sRNAs act mostly by protein-assisted base-pairing with target mRNAs to fine-tune post-transcriptional reprogramming of gene expression underlying bacterial responses to changing environments. Riboregulation impacts virtually any physiological process, and has been shown to largely influence virulence of pathogenic bacteria. Here, we review our current knowledge on the structure, conservation and function of the noncoding transcriptome of the α-rhizobia Sinorhizobium meliloti, the nitrogen-fixing symbiotic partner of alfalfa and related medics. Several RNAseq-based surveys in S. meliloti have shown abundant transcription from hitherto regarded as noncoding intergenic regions (IGRs), strikingly high numbers of mRNA-derived RNAs and pervasive antisense transcription of protein-coding genes. sRNAs encoded within IGRs constitute the most extensively studied group of bacterial riboregulators. They are differentially expressed and modulate translation and/or stability of trans-encoded target mRNAs by short antisense interactions that, in enteric model bacteria, are facilitated by the RNA chaperone Hfq. Among symbiotic rhizobia, regulatory sRNAs have been functionally characterized only in S. meliloti to date. The trans-sRNAs AbcR1 and AbcR2 are examples of Hfq-dependent sRNAs whereas EcpR1 does not bind Hfq. We will provide insights into the transcriptional regulation and activity mechanisms of these sRNAs for the targeting and control of multiple mRNAs involved in nutrient uptake (AbcR1/2) and cell cycle progression (EcpR1).
Similar content being viewed by others
References
Altman S (2011) Ribonuclease P. Philos Trans R Soc B 366:2936–2941. doi:10.1098/rstb.2011.0142
Barnett MJ, Bittner AN, Toman CJ, Oke V, Long SR (2012) Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium. J Bacteriol 194:4983–4994
Barra-Bily L, Fontenelle C, Jan G, Flechard M, Trautwetter A, Pandey SP, Walker GC, Blanco C (2010a) Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq. J Bacteriol 192:1719–1729
Barra-Bily L, Pandey SP, Trautwetter A, Blanco C, Walker GC (2010b) The Sinorhizobium meliloti RNA chaperone Hfq mediates symbiosis of S. meliloti and alfalfa. J Bacteriol 192:1710–1718
Baumgardt K, Charoenpanich P, McIntosh M, Schikora A, Stein E, Thalmann S, Kogel K-H, Klug G, Becker A, Evguenieva-Hackenberg E (2014) RNase E affects the expression of the acyl-homoserine lactone synthase gene sinI in Sinorhizobium meliloti. J Bacteriol 196:1435–1447
Becker A, Overlöper A, Schlüter J-P, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E (2014) Riboregulation in plant-associated α-proteobacteria. RNA Biol 11:550–562
Caswell CC, Gaines JM, Ciborowski P, Smith D, Borchers CH, Roux CM, Sayood K, Dunman PM, Roop Ii RM (2012) Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol 85:345–360
Cavanagh AT, Wassarman KM (2014) 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond. Annu Rev Microbiol 68:45–60
Curtis PD, Brun YV (2010) Getting in the loop: regulation of development in Caulobacter crescentus. Microbiol Mol Biol Rev 74:13–41
del Val C, Rivas E, Torres-Quesada O, Toro N, Jiménez-Zurdo JI (2007) Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics. Mol Microbiol 66:1080–1091
del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N, Jiménez-Zurdo JI (2012) A survey of sRNA families in α-proteobacteria. RNA Biol 9:119–129
Dombrecht B, Marchal K, Vanderleyden J, Michelis J (2002) Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales. Genome Biol 3:RESEARCH0076
Drepper T, Raabe K, Giaourakis D, Gendrullis M, Masepohl B, Klipp W (2002) 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 215:221–227
Ebeling S, Kündig C, Hennecke H (1991) Discovery of a rhizobial RNA that is essential for symbiotic root nodule development. J Bacteriol 173:6373–6382
Egea PF, Stroud RM, Walter P (2005) Targeting proteins to membranes: structure of the signal recognition particle. Curr Opin Struct Biol 15:213–220
Flechard M, Fontenelle C, Blanco C, Goude R, Ermel G, Trautwetter A (2010) RpoE2 of Sinorhizobium meliloti is necessary for trehalose synthesis and growth in hyperosmotic media. Microbiology 156:1708–1718
Fröhlich KS, Vogel J (2009) Activation of gene expression by small RNA. Curr Opin Microbiol 12:674–682
Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Land M, Hauser L, Woyke T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi EG (2011) Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics 12:235
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668–672
Gao M, Barnett MJ, Long SR, Teplitski M (2010) Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis. Mol Plant Microbe Interact 23:355–365
Gibson KE, Kobayashi H, Walker GC (2008) Molecular determinants of a symbiotic chronic infection. Annu Rev Genet 42:413–441
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, Dávila G (2006) The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci U S A 103:3834–3839
Gottesman S, Storz G (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3. doi: 10.1101/cshperspect.a003798
Jacob AI, Köhrer C, Davies BW, Rajbhandary UL, Walker GC (2013) Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 49:427–438
Jiménez-Zurdo JI, Valverde C, Becker A (2013) Insights into the noncoding RNome of nitrogen-fixing endosymbiotic α-proteobacteria. Mol Plant Microbe Interact 26:160–167
Jonas K (2014) To divide or not to divide: control of the bacterial cell cycle by environmental cues. Curr Opin Microbiol 18:54–60
Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC (2007) How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat Rev Microbiol 5:619–633
Kaminski PA, Elmerich C (1998) The control of Azorhizobium caulinodans nifA expression by oxygen, ammonia and by the HF-I-like protein, NrfA. Mol Microbiol 28:603–613
Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7:331–338
Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K et al (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9:189–197
Krol E, Becker A (2011) ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome. Mol Microbiol 81:1233–1254
Lasa I, Toledo-Arana A, Gingeras TR (2012) An effort to make sense of antisense transcription in bacteria. RNA Biol 9:1039–1044
Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan J-B, Wang K (2013) A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PLoS One 8:e70720
MacLellan SR, Smallbone LA, Sibley CD, Finan TM (2005) The expression of a novel antisense gene mediates incompatibility within the large repABC family of α-proteobacterial plasmids. Mol Microbiol 55:611–623
Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer H-M, Evguenieva-Hackenberg E (2012) Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol 9:47–58
Mauchline TH, Fowler JE, East AK, Sartor AL, Zaheer R, Hosie AHF, Poole PS, Finan TM (2006) Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome. Proc Natl Acad Sci U S A 103:17933–17938
McIntosh M, Meyer S, Becker A (2009) Novel Sinorhizobium meliloti quorum sensing positive and negative regulatory feedback mechanisms respond to phosphate availability. Mol Microbiol 74:1238–1256
Moore SD, Sauer RT (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu Rev Biochem 76:101–124
Oke V, Rushing BG, Fisher EJ, Moghadam-Tabrizi M, Long SR (2001) Identification of the heat-shock sigma factor RpoH and a second RpoH-like protein in Sinorhizobium meliloti. Microbiology 147:2399–2408
Ono Y, Mitsui H, Sato T, Minamisawa K (2001) Two RpoH homologs responsible for the expression of heat shock protein genes in Sinorhizobium meliloti. Mol Gen Genet 264:902–912
Overlöper A, Kraus A, Gurski R, Wright PR, Georg J, Hess WR, Narberhaus F (2014) Two separate modules of the conserved regulatory RNA AbcR1 address multiple target mRNAs in and outside of the translation initiation region. RNA Biol 11:624–640
Pandey SP, Minesinger BK, Kumar J, Walker GC (2011) A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res 39:4691–4708
Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC (2014) Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15:121
Papenfort K, Vogel J (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8:116–127
Reinkensmeier J, Schlüter J-P, Giegerich R, Becker A (2011) Conservation and occurrence of trans-encoded sRNAs in the Rhizobiales. Genes 2:925–956
Robledo M, Frage B, Wright PR, Becker A (2015a) A stress-induced small RNA modulates alpha-rhizobial cell cycle progression. PLoS Genet 11:e1005153
Robledo M, Jiménez-Zurdo JI, Becker A (2015b) Antisense transcription of symbiotic genes in Sinorhizobium meliloti. Symbiosis. Under revision
Roop RM, Robertson GT, Ferguson GP, Milford LE, Winkler ME, Walker GC (2002) 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 90:349–363
Roux B, Rodde N, Jardinaud M-F, Timmers T, Sauviac L, Cottret L, Carrère S, Sallet E, Courcelle E, Moreau S, Debellé F, Capela D, de Carvalho-Niebel F, Gouzy J, Bruand C, Gamas P (2014) An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J 77:817–837
Sallet E, Roux B, Sauviac L, M-Fo J, Carrère S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D, Bruand C, Schiex T (2013) Next-Generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res 20:339–354
Sauviac L, Philippe H, Phok K, Bruand C (2007) An extracytoplasmic function sigma factor acts as a general stress response regulator in Sinorhizobium meliloti. J Bacteriol 189:4204–4216
Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A (2010) A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 11:245
Schlüter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A (2013) Global mapping of transcription start sites and promoter motifs in the symbiotic alpha-proteobacterium Sinorhizobium meliloti 1021. BMC Genomics 14:156
Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorholter FJ, Weidner S, Goesmann A, Puhler A, Schluter A (2011) The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J Biotechnol 155:20–33
Serganov A, Nudler E (2013) A decade of riboswitches. Cell 152:17–24
Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf H-J, Hinton JCD, Vogel J (2011) Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 81:1144–1165
Sobrero P, Valverde C (2011) Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011. Arch Microbiol 1–11
Sobrero P, Valverde C (2012) The bacterial protein Hfq: much more than a mere RNA-binding factor. Crit Rev Microbiol 38:276–299
Sobrero P, Schluter JP, Lanner U, Schlosser A, Becker A, Valverde C (2012) Quantitative proteomic analysis of the Hfq-regulon in Sinorhizobium meliloti 2011. PLoS One 7:e48494
Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9–16
Storz G (2002) An expanding universe of noncoding RNAs. Science 296:1260–1263
Storz G, Vogel J, Wassarman KM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43:880–891
Torres-Quesada O, Oruezabal RI, Peregrina A, Jofre E, Lloret J, Rivilla R, Toro N, Jimenez-Zurdo JI (2010) The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa. BMC Microbiol 10:71
Torres-Quesada O, Millán V, Nisa-Martínez R, Bardou F, Crespi M, Toro N, Jiménez-Zurdo JI (2013) Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti. PLoS One 8:e68147
Torres-Quesada O, Reinkensmeier J, Schlüter J-P, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jiménez-Zurdo JI (2014) Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti. RNA Biol 11:563–579
Tsokos CG, Laub MT (2012) Polarity and cell fate asymmetry in Caulobacter crescentus. Curr Opin Microbiol 15:744–750
Ulve VM, Sevin EW, Cheron A, Barloy-Hubler F (2007) Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics 8:467
Urban JH, Vogel J (2007) Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res 35:1018–1037
Valverde C, Livny J, Schluter JP, Reinkensmeier J, Becker A, Parisi G (2008) Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 9:416
Vercruysse M, Fauvart M, Cloots L, Engelen K, Thijs IM, Marchal K, Michiels J (2010) 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 11:53
Vogel J, Luisi BF (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9:578–589
Vogel J, Wagner EG (2007) Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol 10:262–270
Voss B, Holscher M, Baumgarth B, Kalbfleisch A, Kaya C, Hess WR, Becker A, Evguenieva-Hackenberg E (2009) 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 390:331–336
Wagner EG (2013) Cycling of RNAs on Hfq. RNA Biol 10:619–626
Wagner EG, Simons RW (1994) Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48:713–742
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615–628
Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F (2011) Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding protein. Mol Microbiol 80(2):492–506
Wilms I, Moller P, Stock AM, Gurski R, Lai EM, Narberhaus F (2012a) Hfq influences multiple transport systems and virulence in the plant pathogen Agrobacterium tumefaciens. J Bacteriol 194:5209–5217
Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F (2012b) Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 9:446–457
Wilusz CJ, Wilusz J (2005) Eukaryotic Lsm proteins: lessons from bacteria. Nat Struct Mol Biol 12:1031–1036
Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013) Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci 110:E3487–E3496
Young JP, Crossman L, Johnston A, Thomson N, Ghazoui Z, Hull K, Wexler M, Curson A, Todd J, Poole P, Mauchline T, East A, Quail M, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7:R34
Zhang Y, Hong G (2009) Post-transcriptional regulation of NifA expression by Hfq and RNase E complex in Rhizobium leguminosarum bv. viciae. Acta Biochim Biophys Sin (Shanghai) 41:719–730
Acknowledgments
Work at the laboratory of José I. Jiménez-Zurdo is currently funded by ERDF-cofinanced grants CSD2009-00006 and BFU2013-48282-C2-2-P from the Spanish Ministerio de Economía y Competitividad.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Jiménez-Zurdo, J.I., Robledo, M. Unraveling the universe of small RNA regulators in the legume symbiont Sinorhizobium meliloti . Symbiosis 67, 43–54 (2015). https://doi.org/10.1007/s13199-015-0345-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13199-015-0345-z