publication . Article . 2018

Corrigendum: Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology

Yiqin Deng; Yiqin Deng; Youlu Su; Songlin Liu; Zhixun Guo; Changhong Cheng; Hongling Ma; Jinjun Wu; Juan Feng; Chang Chen; ...
Open Access English
  • Published: 01 Oct 2018 Journal: Frontiers in Microbiology (issn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media S.A.
Abstract
Small non-coding RNAs (sRNAs) are important modulators of gene expression and are involved in the pathogenesis and survival of prokaryotes. However, few studies have been conducted with Vibrio alginolyticus, which limits our ability to probe the regulation of virulence and environmental adaptation by sRNAs in this opportunistic pathogen. In this study, the sRNA candidate srvg23535 was identified in V. alginolyticus ZJ-T. The precise transcript end, secondary structure, and sequence conservation were determined. A srvg23535 null mutant was constructed and characterized by using Phenotype MicroArray (PM) technology. In silico target prediction was conducted by Int...
Subjects
free text keywords: small non-coding RNAs, srvg23535, Vibrio alginolyticus, identification, Phenotype MicroArray technology, Microbiology, QR1-502, Correction, Original Research, Microbiology (medical), Vibrio, biology.organism_classification, biology, In silico, Mutant, Phenotype microarray, Vibrio harveyi, Vibrio parahaemolyticus, Gene expression
Related Organizations
63 references, page 1 of 5

Argaman L.Hershberg R.Vogel J.Bejerano G.Wagner E. G.Margalit H. (2001). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11 941–950. 10.1016/S0960-9822(01)00270-6 11448770 [OpenAIRE] [PubMed] [DOI]

Bishop D. H.Claybrook J. R.Spiegelman S. (1967). Electrophoretic separation of viral nucleic acids on polyacrylamide gels. J. Mol. Biol. 26 373–387. 10.1016/0022-2836(67)90310-5 5339793 [OpenAIRE] [PubMed] [DOI]

Blumenstein K.Macayasanz D.Martín J. A.Albrectsen B. R.Witzell J. (2015). Phenotype microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes. Front. Microbiol. 6:1033. 10.3389/fmicb.2015.01033 26441951 [OpenAIRE] [PubMed] [DOI]

Bochner B. (2009). Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33 191–205. 10.1016/j.apmr.2008.10.013 19054113 [OpenAIRE] [PubMed] [DOI]

Bochner B. R.Gadzinski P.Panomitros E. (2001). Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 11 1246–1255. 10.1101/gr.186501 11435407 [OpenAIRE] [PubMed] [DOI]

Browning D. F.Cole J. A.Busby S. J. (2004). Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol. Microbiol. 53 203–215. 10.1006/jmaa.1999.6641 15225315 [OpenAIRE] [PubMed] [DOI]

Chang C.Jin X.Chaoqun H. (2009). Phenotypic and genetic differences between opaque and translucent colonies of Vibrio alginolyticus. Biofouling 25 525–531. 10.1080/08927010902964578 19408137 [OpenAIRE] [PubMed] [DOI]

Chen S.Lesnik E. A.Hall T. A.Sampath R.Griffey R. H.Ecker D. J. (2002). A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65 157–177. 10.1016/S0303-2647(02)00013-8 12069726 [OpenAIRE] [PubMed] [DOI]

Citil B. E.Derin S.Sankur F.Sahan M.Citil M. U. (2015). Vibrio alginolyticus associated chronic myringitis acquired in mediterranean waters of turkey. Case Rep. Infect. Dis. 2015:187212–187215. 10.1155/2015/187212 26605095 [OpenAIRE] [PubMed] [DOI]

Davis B. M.Waldor M. K. (2007). RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol. Microbiol. 65 373–385. 10.1111/j.1365-2958.2007.05796.x 17590231 [OpenAIRE] [PubMed] [DOI]

De L. N.Gottesman S. (2009). The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J. Bacteriol. 191 461–476. 10.1128/JB.01157-08 18978044 [OpenAIRE] [PubMed] [DOI]

Duan R.Pak C.Jin P. (2007). Single nucleotide polymorphism associated with mature mir-125a alters the processing of pri-mirna. Hum. Mol. Genet. 16 1124–1131. 10.1093/hmg/ddm062 17400653 [OpenAIRE] [PubMed] [DOI]

Erwin D. P.Nydam S. D.Call D. R. (2012). Vibrio parahaemolyticus ExsE is requisite for initial adhesion and subsequent type III secretion system 1-dependent autophagy in Hela cells. Microbiology 158 2303–2314. 10.1099/mic.0.059931-0 22767546 [OpenAIRE] [PubMed] [DOI]

Gough E. J.Gough N. M. (1984). Diect calaon of the szes of DNA fragments separated by gel electrophoresis using programmes witten for a pocket caculator. Nucleic Acids Res. 12 845–853. 10.1093/nar/12.1Part2.845 6320110 [OpenAIRE] [PubMed] [DOI]

Griffithsjones S.Bateman A.Marshall M.Khanna A.Eddy S. R. (2003). Rfam: an RNA family database. Nucleic Acids Res. 31 439–441. 10.1093/nar/gkg006 12520045 [OpenAIRE] [PubMed] [DOI]

63 references, page 1 of 5
Abstract
Small non-coding RNAs (sRNAs) are important modulators of gene expression and are involved in the pathogenesis and survival of prokaryotes. However, few studies have been conducted with Vibrio alginolyticus, which limits our ability to probe the regulation of virulence and environmental adaptation by sRNAs in this opportunistic pathogen. In this study, the sRNA candidate srvg23535 was identified in V. alginolyticus ZJ-T. The precise transcript end, secondary structure, and sequence conservation were determined. A srvg23535 null mutant was constructed and characterized by using Phenotype MicroArray (PM) technology. In silico target prediction was conducted by Int...
Subjects
free text keywords: small non-coding RNAs, srvg23535, Vibrio alginolyticus, identification, Phenotype MicroArray technology, Microbiology, QR1-502, Correction, Original Research, Microbiology (medical), Vibrio, biology.organism_classification, biology, In silico, Mutant, Phenotype microarray, Vibrio harveyi, Vibrio parahaemolyticus, Gene expression
Related Organizations
63 references, page 1 of 5

Argaman L.Hershberg R.Vogel J.Bejerano G.Wagner E. G.Margalit H. (2001). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11 941–950. 10.1016/S0960-9822(01)00270-6 11448770 [OpenAIRE] [PubMed] [DOI]

Bishop D. H.Claybrook J. R.Spiegelman S. (1967). Electrophoretic separation of viral nucleic acids on polyacrylamide gels. J. Mol. Biol. 26 373–387. 10.1016/0022-2836(67)90310-5 5339793 [OpenAIRE] [PubMed] [DOI]

Blumenstein K.Macayasanz D.Martín J. A.Albrectsen B. R.Witzell J. (2015). Phenotype microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes. Front. Microbiol. 6:1033. 10.3389/fmicb.2015.01033 26441951 [OpenAIRE] [PubMed] [DOI]

Bochner B. (2009). Global phenotypic characterization of bacteria. FEMS Microbiol. Rev. 33 191–205. 10.1016/j.apmr.2008.10.013 19054113 [OpenAIRE] [PubMed] [DOI]

Bochner B. R.Gadzinski P.Panomitros E. (2001). Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 11 1246–1255. 10.1101/gr.186501 11435407 [OpenAIRE] [PubMed] [DOI]

Browning D. F.Cole J. A.Busby S. J. (2004). Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol. Microbiol. 53 203–215. 10.1006/jmaa.1999.6641 15225315 [OpenAIRE] [PubMed] [DOI]

Chang C.Jin X.Chaoqun H. (2009). Phenotypic and genetic differences between opaque and translucent colonies of Vibrio alginolyticus. Biofouling 25 525–531. 10.1080/08927010902964578 19408137 [OpenAIRE] [PubMed] [DOI]

Chen S.Lesnik E. A.Hall T. A.Sampath R.Griffey R. H.Ecker D. J. (2002). A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65 157–177. 10.1016/S0303-2647(02)00013-8 12069726 [OpenAIRE] [PubMed] [DOI]

Citil B. E.Derin S.Sankur F.Sahan M.Citil M. U. (2015). Vibrio alginolyticus associated chronic myringitis acquired in mediterranean waters of turkey. Case Rep. Infect. Dis. 2015:187212–187215. 10.1155/2015/187212 26605095 [OpenAIRE] [PubMed] [DOI]

Davis B. M.Waldor M. K. (2007). RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol. Microbiol. 65 373–385. 10.1111/j.1365-2958.2007.05796.x 17590231 [OpenAIRE] [PubMed] [DOI]

De L. N.Gottesman S. (2009). The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J. Bacteriol. 191 461–476. 10.1128/JB.01157-08 18978044 [OpenAIRE] [PubMed] [DOI]

Duan R.Pak C.Jin P. (2007). Single nucleotide polymorphism associated with mature mir-125a alters the processing of pri-mirna. Hum. Mol. Genet. 16 1124–1131. 10.1093/hmg/ddm062 17400653 [OpenAIRE] [PubMed] [DOI]

Erwin D. P.Nydam S. D.Call D. R. (2012). Vibrio parahaemolyticus ExsE is requisite for initial adhesion and subsequent type III secretion system 1-dependent autophagy in Hela cells. Microbiology 158 2303–2314. 10.1099/mic.0.059931-0 22767546 [OpenAIRE] [PubMed] [DOI]

Gough E. J.Gough N. M. (1984). Diect calaon of the szes of DNA fragments separated by gel electrophoresis using programmes witten for a pocket caculator. Nucleic Acids Res. 12 845–853. 10.1093/nar/12.1Part2.845 6320110 [OpenAIRE] [PubMed] [DOI]

Griffithsjones S.Bateman A.Marshall M.Khanna A.Eddy S. R. (2003). Rfam: an RNA family database. Nucleic Acids Res. 31 439–441. 10.1093/nar/gkg006 12520045 [OpenAIRE] [PubMed] [DOI]

63 references, page 1 of 5
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publication . Article . 2018

Corrigendum: Identification of a Novel Small RNA srvg23535 in Vibrio alginolyticus ZJ-T and Its Characterization With Phenotype MicroArray Technology

Yiqin Deng; Yiqin Deng; Youlu Su; Songlin Liu; Zhixun Guo; Changhong Cheng; Hongling Ma; Jinjun Wu; Juan Feng; Chang Chen; ...