RESUMEN
Sigma factors are bacterial transcription factors that bind the core RNA polymerase and direct transcription initiation at a specific promoter site. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions and selectively increase the transcription of those genes. Here, we attempt to identify sigma factors in 5 genomes belonging to the Enterobacter cloacae complex (Ecc), a group of gram-negative bacteria that are important nosocomial pathogens. This process includes the identification of orthologous sequences, conserved motifs, domains, families, phylogenetic profiles, and protein-protein associations of these components. Based on the reference genome, genome-wide comparison revealed that the genomes of Enterobacter asburiae JCM6051, Enterobacter nimipressuralis CIP 104980, Enterobacter hormaechei ATCC49162, Enterobacter kobei JCM 8580, and Enterobacter ludwigii EN-119 encode 10 sigma factors that exist in the reference strain Enterobacter cloacae subsp cloacae ATCC13047. Moreover, the sequence similarity, protein domains and families of the sigma factors, protein-protein association, and phylogenetic profile indicate that the sigma factor proteins of these 5 strains may have evolutionary relatedness and functional characteristics important to their various environmental niches. Interestingly, the absence of RpoS in E kobei, which contributes to bacterial survival under environmental stress conditions, indicates that RpoS might have been independently acquired and may play different roles relating to pathogenicity, host range determination, and/or niche adaptation. Future work such as RNA sequencing will be directed towards investigating the roles that these sigma factors play in the biology of the Ecc.
RESUMEN
OBJECTIVES: Multidrug-resistant Mycobacterium tuberculosis poses a global threat, particularly in developing countries such as Pakistan. Genome sequencing, comparative genomic analysis and drug resistance gene analysis could be beneficial for understanding and monitoring M. tuberculosis disease severity in Pakistan by elucidating the biology of M. tuberculosis. METHODS: Here the draft genome of M. tuberculosis strain SWLPK was sequenced, assembled and annotated using an Illumina MiSeq system. De novo genomic assembly was conducted using Geneious Pro™ v.10. The assembled genome of strain SWLPK was annotated using the Rapid Annotation using Subsystem Technology (RAST) server, tRNAscan-SE 1.21 and RNAmmer v.1.2, which provide high-quality functional annotation. RESULTS: Mycobacterium tuberculosis strain SWLPK yielded an average read depth of 68.5-fold, which covered 97% of the genome of reference strain H37Rv. The genome contains 4305 protein-coding genes, including key drug resistance and virulence-associated genes such as type seven secretion systems. Additionally, it has a 65.6% GC content and contains 48 RNAs and 12 contigs. We determined that all proteins encoded by this strain contain conserved domains, except OxyR, which is associated with first-line antituberculosis drugs such as ethambutol, rifampicin, streptomycin, pyrazinamide and isoniazid. CONCLUSIONS: This genome sequence provides information regarding the drug resistance genes and virulence propensity of M. tuberculosis strain SWLPK. Strain SWLPK appears to be multidrug-resistant, similar to the Beijing genotype, as it clusters in the same group. These findings will pave the way for genomic characterisation, which will provide further insights into adaptation and evolution in human hosts by transcriptome studies and gene manipulation.