Prediction Expression Analysis and Target Validation of Bacterial Small RNAs

  • Puneet Kaur
  • Praveen P. Balgir


In the past few years, researchers from all over the world have unveiled a large number of small noncoding RNAs (sRNAs) in a wide variety of bacterial species. They play a central role in gene expression regulation of critical cellular processes in response to environmental changes. Most of them have been identified by predictive computational searches, while some have been detected through experimental approaches. The chapter reviews different computational studies available for predictive searches and various experimental strategies that have contributed for the detection and validation of sRNAs and their targets like microarrays, next-generation sequencing, and co-immunoprecipitation with Hfq. Although these approaches have led to the discovery of numerous sRNAs, regulatory roles of many of them are yet to be investigated.



This work was supported by grant from the DBT-Punjabi University Interdisciplinary Life Science Programme for advanced research and education (DBT-IPLS Project) No. BT/PR-4548/INF/22/146/2012.


  1. Acebo P, Martin-Galiano AJ, Navarro S, Zaballos A, Amblar M (2012) Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae. RNA 18:530–546CrossRefPubMedPubMedCentralGoogle Scholar
  2. Antal M, Bordeau V, Douchin V, Felden B (2005) A small bacterial RNA regulates a putative ABC transporter. J BiolChem 280:7901–7908Google Scholar
  3. Argaman L, Hershberg R, Vogel J, Bejerano G et al (2001) Novel small RNA encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11:941–950CrossRefPubMedGoogle Scholar
  4. Babu MM, Sridhar J, Gunasekaran P (2011) Global transcriptome analysis of Bacillus cereus ATCC 14579 in response to silver nitrate stress. J Nanobiotechnol 9(1):1–2CrossRefGoogle Scholar
  5. Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G (2009) Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides. Mol Microbiol 74(6):1497–1512CrossRefPubMedGoogle Scholar
  6. Busch A, Richter AS, Backofen R (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24:2849–2856CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cao Y, Zhao Y, Cha L, Ying X et al (2009) sRNATarget: a web server for prediction of bacterial sRNA targets. Bioinformation 3:364–366CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cao Y, Wu J, Liu Q, Zhao Y et al (2010) sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA 16(11):2051–2057CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chen S, Zhang A, Blyn LB, Storz G (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186:6689–6697CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chen Y, Indurthi DC, Jones SW, Papoutsakis ET (2011) Small RNAs in the genus clostridium. MBio 2(1):e00340–e00310CrossRefPubMedPubMedCentralGoogle Scholar
  11. Cho SH, Lei R, Henninger TD, Contreras LM (2014) Discovery of ethanol-responsive small RNAs in Zymomonas mobilis. Appl Environ Microbiol 80(14):4189–4198CrossRefPubMedPubMedCentralGoogle Scholar
  12. Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P et al (2006) Identification of small Hfq-binding RNAs in Listeria monocytogenes. RNA 12:1383–1396CrossRefPubMedPubMedCentralGoogle Scholar
  13. Coenye T, Drevinek P, Mahenthiralingam E, Shah SA et al (2007) Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiol Letter 276(1):83–92CrossRefGoogle Scholar
  14. del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI (2007) Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics. Mol Microbiol 66:1080–1091CrossRefPubMedPubMedCentralGoogle Scholar
  15. Dequivre M, Diel B, Villard C, Sismeiro O et al (2015) Small RNA deep-sequencing analyses reveal a new regulator of virulence in Agrobacterium fabrum C58. Mol Plant-Microbe Interact 28(5):580–589CrossRefPubMedGoogle Scholar
  16. Dong H, Peng X, Wang N, Wu Q (2014) Identification of novel sRNAs in Brucella abortus 2308. FEMS Microbiol Lett 354:119–125CrossRefPubMedGoogle Scholar
  17. Douchin V, Bohn C, Bouloc P (2006) Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli. J BiolChem 281:12253–12259Google Scholar
  18. Durand S, Braun F, Lioliou E, Romilly C et al (2015) A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis. PLoS Genet 11(2):e1004957CrossRefPubMedPubMedCentralGoogle Scholar
  19. Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 39:W149–W154CrossRefPubMedPubMedCentralGoogle Scholar
  20. Fischer S, Benz J, Späth B, Jellen-Ritter A et al (2011) Regulatory RNAs in Haloferax volcanii. Biochem Soc Trans 39(1):159–162CrossRefPubMedGoogle Scholar
  21. Gierga G, Voss B, Hess WR (2012) Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions. ISME J 6(8):1544–1557CrossRefPubMedPubMedCentralGoogle Scholar
  22. Gottesman S (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58:303–328CrossRefPubMedGoogle Scholar
  23. Gottesman S, McCullen CA, Guillier M, Vanderpool CK et al (2006) Small RNA regulators and the bacterial response to stress. Cold Spring Harbor Symp Quant Biol 71:1–11CrossRefPubMedGoogle Scholar
  24. Hébrard M, Kröger C, Srikumar S, Colgan A et al (2012) sRNAs and the virulence of Salmonella enterica serovar typhimurium. RNA Biol 9(4):437–445CrossRefPubMedPubMedCentralGoogle Scholar
  25. Herbig A, Nieselt K (2011) nocoRNAc: characterization of non-coding RNAs in prokaryotes. BMC Bioinforma 12(1):1CrossRefGoogle Scholar
  26. Huang HY, Chang HY, Chou CH, Tseng CP et al (2009) sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 37(suppl 1):D150–D154CrossRefPubMedGoogle Scholar
  27. Jiang R-P, Tang D-J, Chen X-L, He Y-Q, Feng J-X, Jiang B-L, Lu G-T, Lin M, Tang J-L (2010) Identification of four novel small non-coding RNAs from Xanthomonas campestris pathovar campestris. BMC Genomics 11(1):316CrossRefPubMedPubMedCentralGoogle Scholar
  28. Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005) Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 33:1040–1050CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kery MB, Feldman M, Livny J, Tjaden B (2014) TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res 42(W1):W124–W129CrossRefPubMedPubMedCentralGoogle Scholar
  30. Khoo JS, Chai SF, Mohamed R et al (2012) Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs. BMC Genomics 13(Suppl 7):S13PubMedPubMedCentralGoogle Scholar
  31. Koo JT, Alleyne TM, Schiano CA et al (2011) Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci U S A 108(37):E709–E717CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kumar R, Shah P, Swiatlo E, Burgess SC et al (2010) Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics 11:350CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kwenda S, Gorshkov V, Ramesh AM, Naidoo S et al (2016) Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. BMC Genomics 17(1):1Google Scholar
  34. Landt SG, Abeliuk E, McGrath PT, Lesley JA et al (2008) Small non-coding RNAs in Caulobacter crescentus. Mol Microbiol 68(3):600–614CrossRefPubMedGoogle Scholar
  35. Li L, Huang D, Cheung MK, Nong W et al (2013) BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Res 41(D1):D233–D238CrossRefPubMedGoogle Scholar
  36. Liu JM, Camilli A (2010) A broadening world of bacterial small RNAs. Curr Opin Microbiol 13:18–23CrossRefPubMedGoogle Scholar
  37. Liu JM, Livny J, Lawrence MS, Kimball MD et al (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37(6):e46CrossRefPubMedPubMedCentralGoogle Scholar
  38. Liu WB, Shi Y, Yao LL, Zhou Y, Ye BC (2013) Prediction and characterization of small non-coding RNAs related to secondary metabolites in Saccharopolyspora erythraea. PLoS One 8(11):e80676CrossRefPubMedPubMedCentralGoogle Scholar
  39. Livny J, Fogel MA, Davis BM, Waldor MK (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 13:4096–4105CrossRefGoogle Scholar
  40. Livny J, Brencic A, Lory S, Waldor MK (2006) 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(12):3484–3493CrossRefPubMedPubMedCentralGoogle Scholar
  41. Livny J, Teonadi H, Livny M, Waldor MK (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 3(9):e3197CrossRefPubMedPubMedCentralGoogle Scholar
  42. Lorenz C, von Pelchrzim F, Schroeder R (2006) Genomic systematic evolution of ligands by exponential enrichment (genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels. Nat Protoc 1:2204–2212CrossRefPubMedGoogle Scholar
  43. Madhugiri R, Pessi G, Voss B, Hahn J et al (2012) Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol 9(1):47–58CrossRefPubMedGoogle Scholar
  44. Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D (2009) Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 19(6):1084–1092CrossRefPubMedPubMedCentralGoogle Scholar
  45. Masse E, Vanderpool CK, Gottesman S (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187(20):6962–6971CrossRefPubMedPubMedCentralGoogle Scholar
  46. McClure R, Tjaden B, Genco C (2014) Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions. Front Microbiol 5:456CrossRefPubMedPubMedCentralGoogle Scholar
  47. McKenzie AT, Pomerantsev AP, Sastalla I, Martens C et al (2014) Transcriptome analysis identifies Bacillus anthracis genes that respond to CO 2 through an AtxA-dependent mechanism. BMC Genomics 15(1):1CrossRefGoogle Scholar
  48. Mentz A, Neshat A, Pfeifer-Sancar K, Pühler A et al (2013) Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics 14(1):714CrossRefPubMedPubMedCentralGoogle Scholar
  49. Michaux C, Hartke A, Martini C, Reiss S et al (2014a) Involvement of Enterococcus faecalis small RNAs in stress response and virulence. Infect Immun 82(9):3599–3611CrossRefPubMedPubMedCentralGoogle Scholar
  50. Michaux C, Verneuil N, Hartke A, Giard JC (2014b) Physiological roles of small RNA molecules. Microbiology 160:1007–1019CrossRefPubMedGoogle Scholar
  51. Mraheil MA, Billion A, Mohamed W, Mukherjee K et al (2011) The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res 39:4235–4248CrossRefPubMedPubMedCentralGoogle Scholar
  52. Panek J, Bobek J, Mikulik K, Basler M, Vohradsky J (2008) Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics 9:217CrossRefPubMedPubMedCentralGoogle Scholar
  53. Park SH, Bao Z, Butcher BG et al (2014) Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology 160(5):941–953CrossRefPubMedGoogle Scholar
  54. Patenge N, Billion A, Raasch P, Normann J et al (2012) Identification of novel growth phase-and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays. BMC Genomics 13(1):1CrossRefGoogle Scholar
  55. Pellin D, Miotto P, Ambrosi A, Cirillo DM, Di Serio C (2012) A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis. PloS ONE 7(3):e32723CrossRefPubMedPubMedCentralGoogle Scholar
  56. Peng J, Yang J, Jin Q (2011) An integrated approach for finding overlooked genes in Shigella. PLoS One 6(4):e18509CrossRefPubMedPubMedCentralGoogle Scholar
  57. Perez N, Trevino J, Liu Z, Ho SC et al (2009) A genome-wide analysis of small regulatory RNAs in the human pathogen group a Streptococcus. PLoS One 4:e7668CrossRefPubMedPubMedCentralGoogle Scholar
  58. Phillips P, Progulske-Fox A, Grieshaber S, Grieshaber N (2014) Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis. FEMS Microbiol Lett 351(2):202–208CrossRefPubMedGoogle Scholar
  59. Pichon C, Felden B (2003) Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics 19:1707–1709CrossRefPubMedGoogle Scholar
  60. Pichon C, Felden B (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci U S A 102(40):14249–14254CrossRefPubMedPubMedCentralGoogle Scholar
  61. Pischimarov J, Kuenne C, Billion A, Hemberger J et al (2012) sRNAdb: a small non-coding RNA database for gram-positive bacteria. BMC Genomics 13(1):384CrossRefPubMedPubMedCentralGoogle Scholar
  62. Raasch P, Schmitz U, Patenge N, Vera J et al (2010) Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinformatics 11:491CrossRefPubMedPubMedCentralGoogle Scholar
  63. Rivas E, Klein RJ, Jones TA, Eddy SR (2001) Computational identification of noncoding RNAs in Escherichia coli by comparative genomics. Curr Biol 11:1369–1373CrossRefPubMedGoogle Scholar
  64. Rivers AR, Burns AS, Chan LK, Moran MA (2016) Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3. Front Microbiol 7:380CrossRefPubMedPubMedCentralGoogle Scholar
  65. Schlüter JP, Reinkensmeier J, Daschkey S et al (2010) A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 11(1):1CrossRefPubMedPubMedCentralGoogle Scholar
  66. Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J et al (2011) Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 40(5):gkr904Google Scholar
  67. Schroeder CL, Narra HP, Rojas M, Sahni A et al (2015) Bacterial small RNAs in the genus Rickettsia. BMC Genomics 16(1):1CrossRefGoogle Scholar
  68. Schuster CF, Park JH, Prax M, Herbig A et al (2013) Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum. J Bacteriol 195(1):115–125CrossRefPubMedPubMedCentralGoogle Scholar
  69. Shioya K, Michaux C, Kuenne C, Hain T et al (2011) Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583. PLoSONE 6(9):e23948CrossRefGoogle Scholar
  70. Silvaggi JM, Perkins JB, Losick R (2006) Genes for small noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol 188:532–541CrossRefPubMedPubMedCentralGoogle Scholar
  71. Sittka A, Lucchini S, Papenfort K, Sharma CM et al (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global posttranscriptional regulator, Hfq. PLoS Genet 4(8):e1000163CrossRefPubMedPubMedCentralGoogle Scholar
  72. Sittka A, Sharma CM, Rolle K, Vogel J (2009) 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 6(3):266–275CrossRefPubMedGoogle Scholar
  73. Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S et al (2008) Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology 154:3175–3187CrossRefPubMedGoogle Scholar
  74. Soutourina OA, Monot M, Boudry P, Saujet L et al (2013) Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile. PLoS Genet 9(5):e1003493CrossRefPubMedPubMedCentralGoogle Scholar
  75. Sridhar J, Ramkumar S, Narmada Sabarinathan R, Hong-Yu O (2010) sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes. PLoS ONE5 8:e11970CrossRefGoogle Scholar
  76. Stubben CJ, Micheva-Viteva SN, Shou Y, Buddenborg SK et al (2014) Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions. BMC Genomics 15(1):1CrossRefGoogle Scholar
  77. Tesorero RA, Yu N, Wright JO, Svencionis JP et al (2013) Novel regulatory small RNAs in Streptococcus pyogenes. PLoS One 8(6):e64021CrossRefPubMedPubMedCentralGoogle Scholar
  78. Tjaden B (2008) TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 36:W109–W113CrossRefPubMedPubMedCentralGoogle Scholar
  79. Tsai CH, Liao R, Chou B, Contreras LM (2015) Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation. Appl Environ Microbiol 81(5):1754–1764CrossRefPubMedPubMedCentralGoogle Scholar
  80. Tsui HC, Mukherjee D, Ray VA, Sham LT et al (2010) Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39. J Bacteriol 192:264–279CrossRefPubMedGoogle Scholar
  81. Valverde C, Livny J, Schluter JP, Reinkensmeier J et al (2008) Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics 9:416CrossRefPubMedPubMedCentralGoogle Scholar
  82. van der Meulen SB, de Jong A, Kok J (2016) Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biol 13(3):353–366CrossRefPubMedPubMedCentralGoogle Scholar
  83. Vercruysse M, Fauvart M, Cloots L, Engelen K et al (2011) 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(1):53CrossRefGoogle Scholar
  84. Vogel J, Bartels V, Tang TH, Churakov G et al (2003) RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 31:6435–6443CrossRefPubMedPubMedCentralGoogle Scholar
  85. Voss B, Georg J, Schön V, Ude S, Hess WR (2009) Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 10:123CrossRefPubMedPubMedCentralGoogle Scholar
  86. Wang L, Yang G, Qi L, Li X et al (2016) A novel small RNA regulates tolerance and virulence in Shigella flexneri by responding to acidic environmental changes. Front Cell Infect Microbiol 6:24PubMedPubMedCentralGoogle Scholar
  87. Washietl S, Hofacker IL, Stadler PF (2005) Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 102:2454–2459CrossRefPubMedPubMedCentralGoogle Scholar
  88. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15:1637–1651CrossRefPubMedPubMedCentralGoogle Scholar
  89. Weissenmayer BA, Prendergast JGD, Lohan AJ, Loftus BJ (2011) Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. PLoS One 6(3):e17570CrossRefPubMedPubMedCentralGoogle Scholar
  90. 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):492–506CrossRefPubMedGoogle Scholar
  91. Wright PR, Richter AS, Papenfort K, Mann M et al (2013) Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A 110(37):E3487–E3496CrossRefPubMedPubMedCentralGoogle Scholar
  92. Wurtzel O, Sesto N, Mellin JR, Karunker I et al (2012) Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8(1):583PubMedPubMedCentralGoogle Scholar
  93. Xia L, Xia W, Li S, Li W et al (2012) Identification and expression of small non-coding RNA, L10-Leader, in different growth phases of Streptococcus mutans. Nucleic Acid Ther 22:177–186PubMedCrossRefGoogle Scholar
  94. Yan Y, Su S, Meng X, Ji X et al (2013) Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in vitro and during infection. PLoS One 8(9):e74495CrossRefPubMedPubMedCentralGoogle Scholar
  95. Ying X, Cao Y, Wu J, Liu Q et al (2011) STarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS One 6:e22705CrossRefPubMedPubMedCentralGoogle Scholar
  96. Zeng Q, Sundin GW (2014) Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function. BMC Genomics 15(1):1CrossRefGoogle Scholar
  97. Zeng L, Choi SC, Danko CG, Siepel A et al (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One 8(3):e60465CrossRefPubMedPubMedCentralGoogle Scholar
  98. Zhang A, Wassarman KM, Rosenow C, Tjaden BC et al (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Puneet Kaur
    • 1
  • Praveen P. Balgir
    • 1
  1. 1.Department of BiotechnologyPunjabi UniversityPatialaIndia

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