Research Progress on Small Non-coding RNA of the Xanthomonas spp.

doi:10.13560/j.cnki.biotech.bull.1985.2017.03.004

Abstract

Abstract: The gram-negative plant-pathogenic bacterium of the genus Xanthomonas infects a variety of monocotyledonous plants and dicotyledonous plants,such as rice,cabbage,tomato,citrus and other economic crops. Type III secretion system and other virulence determinants contribute to the infection and proliferation of Xanthomonas. The majority of bacterial small non-coding RNAs（sRNAs）modulates the expression of target mRNAs by base pairing mechanisms,or affects various physiological functions of the cell by binding directly with the protein. This review summarizes the recent study advances in the classification and the effects of sRNA on bacterial protein regulation,metabolism,transcription and virulence regulation,focusing on the identified sRNAs of Xanthomonas and their biological functions,which aims at providing new ideas for controlling crop’s diseases caused by Xanthomonas.

Key words: Xanthomonas, small non-coding RNA, protein regulation, metabolism, virulence regulation

YAN Yu-ping, ZHONG Xi, WANG Xue-feng. Research Progress on Small Non-coding RNA of the Xanthomonas spp.[J]. Biotechnology Bulletin, 2017, 33(3): 22-28.

References

[1] Livny J, Waldor MK. Identification of small RNAs in diverse bacter-ial species[J]. Current Opinion in Microbiology, 2007, 10（2）：96-101.
[2] Chao Y, Kai P, Reinhardt R, et al. An atlas of Hfq-bound transcripts reveals 3'UTRs as a genomic reservoir of regulatory small RNAs[J]. EMBO Journal, 2012, 31：4005-4019.
[3] Oliva G, Sahr T, Buchrieser C. Small RNAs, 5'UTR elements and RNA-binding proteins in intracellular bacteria：impact on metabolism and virulence[J]. FEMS Microbiology Reviews, 2015, 39（3）：331-349.
[4] Gottesman S, Storz G. Bacterial small RNA regulators：versatile roles and rapidly evolving variations[J]. Cold Spring Harbor Perspectives in Biology, 2011, 3（12）：723-729.
[5] Sievers S, Lillebæk EMS, Jacobsen K, et al. A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB[J]. Nucleic Acids Research, 2014, 42（14）：9383-9398.
[6] Da Silva AR, Ferro JA, Reinach F, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities[J]. Nature, 2002, 417（6887）：459-463.
[7] Afolabi O, Milan B, Amoussa R, et al. First report of Xanthomonas oryzae pv. oryzicola causing bacterial leaf streak of rice in Burundi[J]. Applied and Environmental Microbiology, 2015, 81：688-698.
[8] Leyns F, Cleene MD, Swings JG, et al. The host range of the genus Xanthomonas[J]. Botanical Review, 1984, 50（3）：308-356.
[9] 龙海, 李一农, 李芳荣, 等. 植物病原菌黄单胞菌的分类研究进展[J]. 植物保护, 2010, 36（5）：11-16.
[10] Mikulík K, Palečková P, Felsberg J, et al. SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation[J]. Proteomics, 2008, 8（7）：1429-1441.
[11] Eddy SR. Non-coding RNA genes and the modern RNA world[J]. Nature Reviews Genetics, 2001, 2（12）：919-929.
[12] Romeo T. Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB[J]. Molecular Microbiology, 1998, 29（6）：1321-1330.
[13] Kazantsev AV, Pace NR. Bacterial RNase P：a new view of an ancient enzyme[J]. Nature Reviews Microbiology, 2006, 4（10）：729-740.
[14] Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs[J]. Current Opinion in Microbiology, 2007, 10（2）：102-109.
[15] Aiba H. Mechanism of RNA silencing by Hfq-binding small RNAs[J]. Current Opinion in Microbiology, 2007, 10（2）：134-139.
[16] Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria[J]. Microbiology and Molecular Biology Reviews, 2011, 75（2）：286-300.
[17] Chambers JR, Sauer K. Small RNAs and their role in biofilm formation[J]. Trends in Microbiology, 2013, 21（1）：39-49.
[18] Prévost K, Desnoyers G, Jacques JF, et al. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage[J]. Genes & Development, 2011, 25（4）：385-396.
[19] Brennan RG, Link TM. Hfq structure, function and ligand binding[J]. Current Opinion in Microbiology, 2007, 10（2）：125-133.
[20] Warrier I, Hicks LD, Battisti JM, et al. Identification of novel small RNAs and characterization of the 6S RNA of Coxiella burnetii[J]. PLoS One, 2014, 9（6）：e100147.
[21] Kulkarni PR, Cui X, Williams JW, et al. Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri[J]. Nucleic Acids Research, 2006, 34（11）：3361-3369.
[22] Wadler CS, Vanderpool CK. A dual function for a bacterial small RNA：SgrS performs base pairing-dependent regulation and encodes a functional polypeptide[J]. Proceedings of the National Academy of Sciences, 2007, 104（51）：20454-20459.
[23] Vanderpool CK, Balasubramanian D, Lloyd CR. Dual-function RNA regulators in bacteria[J]. Biochimie, 2011, 93（11）：1943-1949.
[24] Grabowicz M, Koren D, Silhavy TJ. The CpxQ sRNA negatively regulates skp to prevent mistargeting of β-Barrel outer membrane proteins into the cytoplasmic membrane[J]. Microbiology, 2016, 7（2）：312-328.
[25] Song T, Mika F, Lindmark B, et al. A new Vibrio cholerae, sRNA modulates colonization and affects release of outer membrane vesicles[J]. Molecular Microbiology, 2008, 70（1）：100-111.
[26] Hoe CH, Raabe CA, Rozhdestvensky TS, et al. Bacterial sRNAs：regulation in stress[J]. International Journal of Medical Microbiology, 2013, 303（5）：217-229.
[27] Pfeiffer V, Papenfort K, Lucchini S, et al. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation[J]. Nature Structural & Molecular Biology, 2009, 16（8）：840-846.
[28] Pfeiffer V, Sittka A, Tomer R, et al. A small non-coding RNA of the invasion gene island（SPI-1）represses outer membrane protein synthesis from the Salmonella core genome[J]. Molecular Microbiology, 2007, 66（5）：1174-1191.
[29] Wassarman KM, Storz G. 6S RNA regulates E. coli RNA polymerase activity[J]. Cell, 2000, 101（6）：613-623.
[30] Leng Y, Vakulskas CA, Zere TR, et al. Regulation of CsrB/C sRNA decay by EIIA Glc of the phosphoenolpyruvate：carbohydrate phosphotransferase system[J]. Molecular Microbiology, 2015, 99（4）：627-639.
[31] Holmqvist E, Vogel J. A small RNA serving both the Hfq and CsrA regulons[J]. Genes & Development, 2013, 27（10）：1073-1081.
[32] Kimata K, Tanaka Y, Inada T, et al. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli[J]. The EMBO Journal, 2001, 20（13）：3587-3595.
[33] Maki K, Otaka MH, Aiba H. A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA[J]. Molecular Microbiology, 2010, 76（3）：782-792.
[34] Semsey S, Andersson AM, Krishna S, et al. Genetic regulation of fluxes：iron homeostasis of Escherichia coli[J]. Nucleic Acids Research, 2006, 34（17）：4960-4967.
[35] Jacques JF, Jang S, Prévost K, et al. RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli[J]. Molecular Microbiology, 2006, 62（4）：1181-1190.
[36] Schellhorn HE. Elucidating the function of the RpoS regulon[J]. Future Microbiology, 2014, 9（4）：497-507.
[37] Dalia AB. RpoS is required for natural transformation of Vibrio cholerae, through regulation of chitinases[J]. Environmental Microbiology, 2016, doi:10. 1111/1462-2920. 13302.
[38] Mccullen CA, Benhammou JN, Majdalani N, et al. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs：pairing increases translation and protects rpoS mRNA from degradation[J]. Journal of Bacteriology, 2010, 192（21）：5559-5571.
[39] Wilf NM, Salmond GP. The stationary phase sigma factor, RpoS, regulates the production of a carbapenem antibiotic, a bioactive prodigiosin and virulence in the enterobacterial pathogen Serratia sp. ATCC 39006[J]. Microbiology, 2012, 158（Pt 3）：648-658.
[40] Mandin P, Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA[J]. The EMBO Journal, 2010, 29（18）：3094-3107.
[41] Chevalier C, Boisset S, Romilly C, et al. Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation[J]. PLoS Pathogens, 2010, 6（3）：e1000809.
[42] Huntzinger E, Boisset S, Saveanu C, et al. Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression[J]. The EMBO Journal, 2005, 24（4）：824-835.
[43] Jones JB, Lacy GH, Bouzar H, et al. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper[J]. Systematic & Applied Microbiology, 2004, 27（6）：755-762.
[44] Zimaro T, Thomas L, Marondedze C, et al. The type III protein secretion system contributes to Xanthomonas citri subsp. citri biofilm formation[J]. BMC Microbiology, 2014, 14（1）：50-57.
[45] Ryan RP, Vorhölter FJ, Potnis N, et al. Pathogenomics of Xanthomonas：understanding bacterium-plant interactions[J]. Nature Reviews Microbiology, 2011, 9（5）：344-355.
[46] Abendroth U, Schmidtke C, Bonas U. Small non-coding RNAs in plant-pathogenic Xanthomonas spp.[J]. RNA Biology, 2014, 11（5）：457-463.
[47] Findeiss S, Schmidtke C, Stadler PF, et al. A novel family of plasmid-transferred anti-sense ncRNAs[J]. RNA Biology, 2010, 7（2）：120-124.
[48] Schmidtke C, Findeiss S, Sharma CM, et al. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions[J]. Nucleic Acids Research, 2012, 40（5）：2020-2031.
[49] Schmidtke C, Abendroth U, Brock J, et al. Small RNA sX13：a multifaceted regulator of virulence in the plant pathogen Xanthomonas[J]. PLoS Pathogens, 2013, 9（9）：e1003626.
[50] Liang H, Zhao YT, Zhang JQ, et al. Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae[J]. BMC Genomics, 2011, 12（1）：87-101.
[51] Jiang RP, Tang DJ, Chen XL, et al. Identification of four novel small non-coding RNAs from Xanthomonas campestris pathovar campestris[J]. BMC Genomics, 2010, 11（1）：316-325.
[52] An SQ, Febrer M, Mccarthy Y, et al. High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis[J]. Molecular Microbiology, 2013, 88（6）：1058-1069.
[53] 周莲, 王杏雨, 何亚文. 植物病原黄单胞菌DSF信号依赖的群体感应机制及调控网络[J]. 中国农业科学, 2013, 46（14）：2910-2922.
[54] Chen XL, Tang DJ, Jiang RP, et al. sRNA-Xcc1, an integron-encoded transposon-and plasmid-transferred trans-acting sRNA, is under the positive control of the key virulence regulators HrpG and HrpX of Xanthomonas campestris pathovarcampestris[J]. RNA Biology, 2011, 8（6）：947-953.
[55] Shao W, Price MN, Deutschbauer AM, et al. Conservation of transcription start sites within genes across a bacterial genus[J]. Microbiology, 2014, 5（4）：01398-01412.
[56] Cohen O, Doron S, Wurtzel O, et al. Comparative transcriptomics across the prokaryotic tree of life[J]. Nucleic Acids Research, 2016, doi:10. 1093/nar/gkw394.