Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Talwar, Chandni; Nagar, Shekhar; Kumar, Roshan; Scaria, Joy; Lal, Rup; Negi, Ram Krishan

doi:10.1038/s41598-020-58163-8

Title: Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Journal Article · 23 January 2020 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-58163-8 · OSTI ID:1629661

Talwar, Chandni ^[1]; Nagar, Shekhar ^[2]; Kumar, Roshan ^[3]; Scaria, Joy ^[4]; Lal, Rup ^[5]; Negi, Ram Krishan ^[2]

Univ. of Delhi, New Delhi (India). Dept. of Zoology; DOE/OSTI
Univ. of Delhi, New Delhi (India). Dept. of Zoology
Magadh Univ., Bihar (India). P.G. Dept. of Zoology
South Dakota State Univ., Brookings, SD (United States). Dept. of Veterinary and Biomedical Sciences; South Dakota Center for Biologics Research and Commercialization, Brookings, SD (United States)
The Energy and Resources Inst., New Delhi (India). NASI Senior Scientist Platinum Jubilee Fellow

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7±19.1 and 36.5±10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1629661

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 10; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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