Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge?
| Autor: | Pushplata Prasad, Akanksha Jaiswar, Alok Adholeya, Deepti Varshney |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Chromium Candidate gene Protein family lcsh:QH426-470 lcsh:Biotechnology 030106 microbiology Aspergillus flavus Protein-ligand interaction Biology Ligands Polymorphism Single Nucleotide DNA sequencing Fungal Proteins 03 medical and health sciences Drug Resistance Fungal lcsh:TP248.13-248.65 Genetic variation Genetics Adaptation Indel DNA Fungal Whole genome sequencing Binding Sites Sewage Genetic Variation High-Throughput Nucleotide Sequencing Sequence Analysis DNA biology.organism_classification Adaptation Physiological Major facilitator superfamily Molecular Docking Simulation Kinetics lcsh:Genetics 030104 developmental biology Non synonymous SNPs (nsSNPs) Mutation Protein structure and function Genome Fungal Biotechnology Research Article |
| Zdroj: | BMC Genomics, Vol 19, Iss 1, Pp 1-16 (2018) BMC Genomics |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/s12864-018-5244-2 |
| Popis: | Background Environmental stress induced genetic polymorphisms have been suggested to arbitrate functional modifications influencing adaptations in microbes. The relationship between the genetic processes and concomitant functional adaptation can now be investigated at a genomic scale with the help of next generation sequencing (NGS) technologies. Using a NGS approach we identified genetic variations putatively underlying chromium tolerance in a strain of Aspergillus flavus isolated from a tannery sludge. Correlation of nsSNPs in the candidate genes (n = 493) were investigated for their influence on protein structure and possible function. Whole genome sequencing of chromium tolerant A. flavus strain (TERIBR1) was done (Illumina HiSeq2000). The alignment of quality trimmed data of TERIBR1 with reference NRRL3357 (accession number EQ963472) strain was performed using Bowtie2 version 2.2.8. SNP with a minimum read depth of 5 and not in vicinity (10 bp) of INDEL were filtered. Candidate genes conferring chromium resistance were selected and SNPs were identified. Protein structure modeling and interpretation for protein-ligand (CrO4− 2) docking for selected proteins harbouring non-synonymous substitutions were done using Phyre2 and PatchDock programs. Results High rate of nsSNPs (approximately 11/kb) occurred in selected candidate genes for chromium tolerance. Of the 16 candidate genes selected for studying effect of nsSNPs on protein structure and protein-ligand interaction, four proteins belonging to the Major Facilitator Superfamily (MFS) and recG protein families showed significant interaction with chromium ion only in the chromium tolerant A. flavus strain TERIBR1. Conclusions Presence of nsSNPs and subsequent amino-acid alterations evidently influenced the 3D structures of the candidate proteins, which could have led to improved interaction with (CrO4− 2) ion. Such structural modifications might have enhanced chromium efflux efficiency of A. flavus (TERIBR1) and thereby offered the adaptation benefits in counteracting chromate stress. Our findings are of fundamental importance to the field of heavy-metal bio-remediation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5244-2) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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