Non-Coding RNAs are Differentially Expressed by Nocardia brasiliensis in Vitro and in Experimental Actinomycetoma

Josué S. Cruz-Rabadán1, Juan Miranda-Ríos2, Guadalupe Espín-Ocampo3, Luis J. Méndez-Tovar4, Héctor Rubén Maya-Pineda1, Francisca Hernández-Hernández1, *
1 Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México.
2 Unidad de Genética de la Nutrición, Instituto Nacional de Pediatría and Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM, Ciudad de México, México.
3 Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, México.
4 Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.

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Creative Commons License
© 2017 Cruz-Rabadán et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Microbiology and Parasitology, Facultad de Medicina, Ciudad Universitaria, Av Universidad 3000, Coyoacán, Copilco Universidad, C.P. 04510, México; Tel: 52 (55) 56232559; Fax: 52 (55) 56232458; E-mails:,



Nocardia 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. Nocardia brasiliensis is the main aetiological agent of actinomycetoma in various countries. Many bacterial non-coding RNAs are regulators of genes associated with virulence factors.


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

Methods and Result:

The N. brasiliensis 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 (tRNAsCys, Met, Thr), 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 N. brasiliensis infection compared with the in vitro conditions.


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

Keywords: Nocardia brasiliensis, Non-coding RNAs, Small RNA, Actinomycetoma, RNA-Seq, Actinomycetes, Mycetoma.