Complete plasmid sequence carrying type IV-like and type VII secretion systems from an atypical mycobacteria strain

Morgado, Sérgio; Abanto, Michel; Freitas, Fernanda; Fonseca, Érica L.; Vicente, Ana Carolina Paulo

doi:10.1590/0074-02760160546

Cited by 3 publications

(3 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, despite several reports of Mycolicibacterium genomes [15][16][17][18][19][20][21][22][23][24][25][26], these studies rarely survey plasmids among their contigs. Thus, only a few plasmids have been reported in this genus, mainly from unrecognized genomes [2,14,[27][28][29][30]. Despite the reclassification of Mycobacterium, some Mycobacterium sp.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Morgado

Moreno-Vicente

2021

Microbial Genomics

Self Cite

View full text Add to dashboard Cite

The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family Mycobacteriaceae , including the genus Mycolicibacterium , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the Mycobacteriaceae mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus Mycobacterium . To fill in the gaps in these issues, we performed a systematic in silico study of these mobile elements based on 242 available genomes of the genus Mycolicibacterium . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family Mycobacteriaceae , this study showed an abundance of these genetic elements in a dozen species of the genus Mycolicibacterium .

show abstract

Section: Introductionmentioning

confidence: 99%

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Morgado

Moreno-Vicente

2021

Microbial Genomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…This can be seen in the T7SS phylogeny, where pCBMA213_2 branched at the root of the ESX-2 tree (). The analysis of pCBMA213_2 ESX system was presented in a previous study [29].…”

Section: Resultsmentioning

confidence: 99%

“…Conversely, plasmids are supposed to be rare [15, 16]. So far, only dozens of plasmids have been characterized (https://www.ncbi.nlm.nih.gov/genome/plasmids), most of them in clinical strains [17–30], despite hundreds of species in the Mycobacteriaceae family. Plasmids have primarily been associated with the evolution and dissemination of a specialized secretion system, termed ESX or type-VII secretion system (T7SS), among the mycobacteria.…”

Section: Introductionmentioning

confidence: 99%

Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS

Morgado

Vicente

2020

Microbial Genomics

Self Cite

View full text Add to dashboard Cite

Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focusing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.

show abstract

Insights into ancestry and adaptive evolution of theMycobacterium tuberculosiscomplex from analysis of the emerging pathogenMycobacterium riyadhense

Guan

Garbati

Mfarrej

et al. 2019

Preprint

View full text Add to dashboard Cite

Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis, the deadliest bacterial pathogen for humans globally, from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense is a novel non-tuberculous mycobacterium (NTM) that is being increasingly isolated from human clinical cases with tuberculosis (TB)-like symptoms in various parts of the world. We provide evidence here that M. riyadhense is likely a ‘missing link’ in our understanding of the evolution of M. tuberculosis. To elucidate the genomic hallmarks that define the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the Mycobacterium tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologues with the MTBC; contains linear and circular plasmids carrying type IV and type VII secretion systems; and shows expansion of toxin/anti-toxin pairs. We conclude that M. riyadhense is an emerging mycobacterial pathogen that shares a common ancestor with members of the MTBC and that can serve as an experimental model to study the evolution and pathogenesis of tubercle bacilli.Author summaryMycobacterium tuberculosis is one of the most prolific infectious killers in humans and is a member of the Mycobacterium tuberculosis complex (MTBC) - a group of genetically related pathogens that cause tuberculosis (TB) in mammalian species. It is postulated that MTBC has evolved from a free-living environmental ancestor into an obligate pathogen. In this evolutionary context, a comprehensive understanding of the genomic hallmarks of the free-living environmental ancestors of the MTBC is of particular scientific interest for better understanding of the evolution of the MTBC. Mycobacterium riyadhense is a novel environmental mycobacterium, first isolated in 2009 in a hospital in Riyadh, that is increasingly being isolated from clinical cases with typical tuberculosis (TB)-like symptoms in humans. In this study, we report the characterization of eight clinical isolates of M. riyadhense, compare their genomes to members of the MTBC, and provide a comprehensive insight into the adaptive changes associated with the evolution of the MTBC from environmental mycobacteria. We show that M. riyadhense is one of the closest known environmental mycobacteria related to the MTBC, and we provide several lines of molecular evidence that M. riyadhense is likely the ‘missing link’ in the evolution of M. tuberculosis. It shares a common ancestor with members of the MTBC that have evolved through a process of genome reduction, expansion of toxin/antitoxin (T/A) gene systems, and ultimately host adaptation.

show abstract

Complete plasmid sequence carrying type IV-like and type VII secretion systems from an atypical mycobacteria strain

Cited by 3 publications

References 16 publications

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS

Insights into ancestry and adaptive evolution of theMycobacterium tuberculosiscomplex from analysis of the emerging pathogenMycobacterium riyadhense

Contact Info

Product

Resources

About