Transcriptional Landscape and Essential Genes of Neisseria Gonorrhoeae

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 Aug 22

PMID 25143534

Citations 58

Authors

Christian W Remmele

Yibo Xian

Marco Albrecht

Michaela Faulstich

Martin Fraunholz

Elisabeth Heinrichs

Marcus T Dittrich

Tobias Muller

Richard Reinhardt

Thomas Rudel

Affiliations

Soon will be listed here.

Abstract

The WHO has recently classified Neisseria gonorrhoeae as a super-bacterium due to the rapid spread of antibiotic resistant derivatives and an overall dramatic increase in infection incidences. Genome sequencing has identified potential genes, however, little is known about the transcriptional organization and the presence of non-coding RNAs in gonococci. We performed RNA sequencing to define the transcriptome and the transcriptional start sites of all gonococcal genes and operons. Numerous new transcripts including 253 potentially non-coding RNAs transcribed from intergenic regions or antisense to coding genes were identified. Strikingly, strong antisense transcription was detected for the phase-variable opa genes coding for a family of adhesins and invasins in pathogenic Neisseria, that may have regulatory functions. Based on the defined transcriptional start sites, promoter motifs were identified. We further generated and sequenced a high density Tn5 transposon library to predict a core of 827 gonococcal essential genes, 133 of which have no known function. Our combined RNA-Seq and Tn-Seq approach establishes a detailed map of gonococcal genes and defines the first core set of essential gonococcal genes.

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References

Overton T, Whitehead R, Li Y, Snyder L, Saunders N, Smith H . Coordinated regulation of the Neisseria gonorrhoeae-truncated denitrification pathway by the nitric oxide-sensitive repressor, NsrR, and nitrite-insensitive NarQ-NarP. J Biol Chem. 2006; 281(44):33115-26. DOI: 10.1074/jbc.M607056200. View

Householder T, Belli W, Lissenden S, Cole J, Clark V . cis- and trans-acting elements involved in regulation of aniA, the gene encoding the major anaerobically induced outer membrane protein in Neisseria gonorrhoeae. J Bacteriol. 1999; 181(2):541-51. PMC: 93408. DOI: 10.1128/JB.181.2.541-551.1999. View

Isabella V, Clark V . Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae. BMC Genomics. 2011; 12:51. PMC: 3032703. DOI: 10.1186/1471-2164-12-51. View

Chaudhuri R, Allen A, Owen P, Shalom G, Stone K, Harrison M . Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH). BMC Genomics. 2009; 10:291. PMC: 2721850. DOI: 10.1186/1471-2164-10-291. View

Huis in t Veld R, Willemsen A, van Kampen A, Bradley E, Baas F, Pannekoek Y . Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis. PLoS One. 2011; 6(12):e29002. PMC: 3240639. DOI: 10.1371/journal.pone.0029002. View

Burge S, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki E . Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2012; 41(Database issue):D226-32. PMC: 3531072. DOI: 10.1093/nar/gks1005. View

Fyfe J, Strugnell R, Davies J . Control of gonococcal pilin-encoding gene expression in Escherichia coli. Gene. 1993; 123(1):45-50. DOI: 10.1016/0378-1119(93)90537-d. View

Sharma C, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A . The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010; 464(7286):250-5. DOI: 10.1038/nature08756. View

de Reuse H, Taha M . RegF, an SspA homologue, regulates the expression of the Neisseria gonorrhoeae pilE gene. Res Microbiol. 1997; 148(4):289-303. DOI: 10.1016/S0923-2508(97)81585-9. View

10.

Carbonetti N, Simnad V, Seifert H, So M, Sparling P . Genetics of protein I of Neisseria gonorrhoeae: construction of hybrid porins. Proc Natl Acad Sci U S A. 1988; 85(18):6841-5. PMC: 282074. DOI: 10.1073/pnas.85.18.6841. View

11.

Dietrich M, Munke R, Gottschald M, Ziska E, Boettcher J, Mollenkopf H . The effect of hfq on global gene expression and virulence in Neisseria gonorrhoeae. FEBS J. 2009; 276(19):5507-20. DOI: 10.1111/j.1742-4658.2009.07234.x. View

12.

Elkins C, Thomas C, Seifert H, Sparling P . Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence. J Bacteriol. 1991; 173(12):3911-3. PMC: 208026. DOI: 10.1128/jb.173.12.3911-3913.1991. View

13.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

14.

Swanson J, Robbins K, Barrera O, Corwin D, Boslego J, CIAK J . Gonococcal pilin variants in experimental gonorrhea. J Exp Med. 1987; 165(5):1344-57. PMC: 2188307. DOI: 10.1084/jem.165.5.1344. View

15.

Wang J, Breaker R . Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol. 2008; 86(2):157-68. DOI: 10.1139/O08-008. View

16.

Altuvia S . Identification of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol. 2007; 10(3):257-61. DOI: 10.1016/j.mib.2007.05.003. View

17.

Laskos L, Dillard J, Seifert H, Fyfe J, Davies J . The pathogenic neisseriae contain an inactive rpoN gene and do not utilize the pilE sigma54 promoter. Gene. 1998; 208(1):95-102. DOI: 10.1016/s0378-1119(97)00664-1. View

18.

Felsenstein J . Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981; 17(6):368-76. DOI: 10.1007/BF01734359. View

19.

Carrick C, Fyfe J, Davies J . The normally silent sigma54 promoters upstream of the pilE genes of both Neisseria gonorrhoeae and Neisseria meningitidis are functional when transferred to Pseudomonas aeruginosa. Gene. 1997; 198(1-2):89-97. DOI: 10.1016/s0378-1119(97)00297-7. View

20.

Belland R, Morrison S, Carlson J, Hogan D . Promoter strength influences phase variation of neisserial opa genes. Mol Microbiol. 1997; 23(1):123-35. DOI: 10.1046/j.1365-2958.1997.1971556.x. View