Non-Coding RNAs Are Differentially Expressed by and in Experimental Actinomycetoma

Overview

Journal Open Microbiol J

Publisher Bentham Open

Specialty Microbiology

Date 2017 Aug 26

PMID 28839491

Citations 3

Authors

Josue S Cruz-Rabadan

Juan Miranda-Rios

Guadalupe Espin-Ocampo

Luis J Mendez-Tovar

Hector Ruben Maya-Pineda

Francisca Hernandez-Hernandez

Affiliations

Soon will be listed here.

Abstract

Introduction: spp. are common soil-inhabiting bacteria that frequently infect humans through traumatic injuries or inhalation routes and cause infections, such as actinomycetoma and nocardiosis, respectively. is the main aetiological agent of actinomycetoma in various countries. Many bacterial non-coding RNAs are regulators of genes associated with virulence factors.

Objective: The aim of this work was to identify non-coding RNAs (ncRNAs) expressed during infection conditions and in free-living form () in .

Methods And Result: The transcriptome (predominately < 200 nucleotides) was determined by RNA next-generation sequencing in both conditions. A total of seventy ncRNAs were identified in both conditions. Among these ncRNAs, 18 were differentially expressed, 12 were located within intergenic regions, and 2 were encoded as antisense of 2 different genes. Finally, 10 of these ncRNAs were studied by rapid amplification of cDNA ends and/or quantitative reverse transcription polymerase chain reaction. Interestingly, 3 transcripts corresponded to tRNA-derived fragments (tRNAs), and one transcript was overlapped between an intergenic region and the 5´end of the 23S rRNA. Expression of these last four transcripts was increased during infection compared with the conditions.

Conclusion: The results of this work suggest a possible role for these transcripts in the regulation of virulence genes in actinomycetoma pathogenesis.

Citing Articles

causing pulmonary nocardiosis: a case report and its review of the literature.

Srivastava S, Samaddar A, Khan S, Tak V, Bohra G, Sharma D Access Microbiol. 2024; 6(2).

PMID: 38482345 PMC: 10928402. DOI: 10.1099/acmi.0.000530.v5.

Microbial risk assessment of in polluted environments, case of urban rainfall water.

Vautrin F, Pujic P, Paquet C, Bergeron E, Mouniee D, Marchal T Comput Struct Biotechnol J. 2021; 19:384-400.

PMID: 33489008 PMC: 7787915. DOI: 10.1016/j.csbj.2020.12.017.

High Intraspecific Genetic Diversity of , a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Using and Genes.

Kosova-Maali D, Bergeron E, Maali Y, Durand T, Gonzalez J, Mouniee D Biomed Res Int. 2018; 2018:7314054.

PMID: 29888277 PMC: 5985140. DOI: 10.1155/2018/7314054.

References

Vera-Cabrera L, Ortiz-Lopez R, Elizondo-Gonzalez R, Ocampo-Candiani J . Complete genome sequence analysis of Nocardia brasiliensis HUJEG-1 reveals a saprobic lifestyle and the genes needed for human pathogenesis. PLoS One. 2013; 8(6):e65425. PMC: 3670865. DOI: 10.1371/journal.pone.0065425. View

Bahl C, Morisseau C, Bomberger J, Stanton B, Hammock B, OToole G . Crystal structure of the cystic fibrosis transmembrane conductance regulator inhibitory factor Cif reveals novel active-site features of an epoxide hydrolase virulence factor. J Bacteriol. 2010; 192(7):1785-95. PMC: 2838060. DOI: 10.1128/JB.01348-09. View

de la Cruz M, Calva E . The complexities of porin genetic regulation. J Mol Microbiol Biotechnol. 2010; 18(1):24-36. DOI: 10.1159/000274309. View

Heyer R, Dorr M, Jellen-Ritter A, Spath B, Babski J, Jaschinski K . High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii. RNA Biol. 2012; 9(7):1011-8. PMC: 3495736. DOI: 10.4161/rna.20826. View

Toledo-Arana A, Repoila F, Cossart P . Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol. 2007; 10(2):182-8. DOI: 10.1016/j.mib.2007.03.004. View

Cozen A, Quartley E, Holmes A, Hrabeta-Robinson E, Phizicky E, Lowe T . ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat Methods. 2015; 12(9):879-84. PMC: 4553111. DOI: 10.1038/nmeth.3508. View

Ramos J, Martinez-Bueno M, Molina-Henares A, Teran W, Watanabe K, Zhang X . The TetR family of transcriptional repressors. Microbiol Mol Biol Rev. 2005; 69(2):326-56. PMC: 1197418. DOI: 10.1128/MMBR.69.2.326-356.2005. View

Vockenhuber M, Sharma C, Statt M, Schmidt D, Xu Z, Dietrich S . Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol. 2011; 8(3):468-77. PMC: 3218513. DOI: 10.4161/rna.8.3.14421. View

Sydor T, von Bargen K, Becken U, Spuerck S, Nicholson V, Prescott J . A mycolyl transferase mutant of Rhodococcus equi lacking capsule integrity is fully virulent. Vet Microbiol. 2007; 128(3-4):327-41. DOI: 10.1016/j.vetmic.2007.10.020. View

10.

Zheng G, Qin Y, Clark W, Dai Q, Yi C, He C . Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015; 12(9):835-837. PMC: 4624326. DOI: 10.1038/nmeth.3478. View

11.

Storz G, Vogel J, Wassarman K . Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 2011; 43(6):880-91. PMC: 3176440. DOI: 10.1016/j.molcel.2011.08.022. View

12.

Fahal A, Mahgoub E, El Hassan A, Abdel-Rahman M . Mycetoma in the Sudan: an update from the Mycetoma Research Centre, University of Khartoum, Sudan. PLoS Negl Trop Dis. 2015; 9(3):e0003679. PMC: 4376889. DOI: 10.1371/journal.pntd.0003679. View

13.

Lopez-Martinez R, Mendez-Tovar L, Bonifaz A, Arenas R, Mayorga J, Welsh O . [Update on the epidemiology of mycetoma in Mexico. A review of 3933 cases]. Gac Med Mex. 2013; 149(5):586-92. View

14.

Bonifaz A, Tirado-Sanchez A, Calderon L, Saul A, Araiza J, Hernandez M . Mycetoma: experience of 482 cases in a single center in Mexico. PLoS Negl Trop Dis. 2014; 8(8):e3102. PMC: 4140667. DOI: 10.1371/journal.pntd.0003102. View

15.

Pederson T . Regulatory RNAs derived from transfer RNA?. RNA. 2010; 16(10):1865-9. PMC: 2941095. DOI: 10.1261/rna.2266510. View

16.

Kosono S, Haga K, Tomizawa R, Kajiyama Y, Hatano K, Takeda S . Characterization of a multigene-encoded sodium/hydrogen antiporter (sha) from Pseudomonas aeruginosa: its involvement in pathogenesis. J Bacteriol. 2005; 187(15):5242-8. PMC: 1196046. DOI: 10.1128/JB.187.15.5242-5248.2005. View

17.

Romero-Silva M, Mendez V, Agullo L, Seeger M . Genomic and functional analyses of the gentisate and protocatechuate ring-cleavage pathways and related 3-hydroxybenzoate and 4-hydroxybenzoate peripheral pathways in Burkholderia xenovorans LB400. PLoS One. 2013; 8(2):e56038. PMC: 3572157. DOI: 10.1371/journal.pone.0056038. View

18.

Busch A, Richter A, Backofen R . IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics. 2008; 24(24):2849-56. PMC: 2639303. DOI: 10.1093/bioinformatics/btn544. View

19.

Hemm M, Paul B, Miranda-Rios J, Zhang A, Soltanzad N, Storz G . Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies. J Bacteriol. 2009; 192(1):46-58. PMC: 2798279. DOI: 10.1128/JB.00872-09. View

20.

Millan-Chiu B, Hernandez-Hernandez F, Perez-Torres A, Mendez-Tovar L, Lopez-Martinez R . In situ TLR2 and TLR4 expression in a murine model of mycetoma caused by Nocardia brasiliensis. FEMS Immunol Med Microbiol. 2011; 61(3):278-87. DOI: 10.1111/j.1574-695X.2010.00775.x. View