Do environmentally induced DNA variations mediate adaptation in Aspergillus flavus exposed to chromium stress in tannery sludge?

BMC Genomics. 2018 Dec 4;19(1):868. doi: 10.1186/s12864-018-5244-2.


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.

Keywords: Adaptation; Mutation; Non synonymous SNPs (nsSNPs); Protein structure and function; Protein-ligand interaction.

MeSH terms

  • Adaptation, Physiological / drug effects*
  • Adaptation, Physiological / genetics
  • Aspergillus flavus / drug effects
  • Aspergillus flavus / genetics*
  • Binding Sites
  • Chromium / chemistry
  • Chromium / metabolism
  • Chromium / toxicity*
  • DNA, Fungal / chemistry
  • DNA, Fungal / isolation & purification
  • DNA, Fungal / metabolism*
  • Drug Resistance, Fungal / drug effects
  • Drug Resistance, Fungal / genetics
  • Fungal Proteins / chemistry
  • Fungal Proteins / metabolism
  • Genetic Variation
  • Genome, Fungal*
  • High-Throughput Nucleotide Sequencing
  • Kinetics
  • Ligands
  • Molecular Docking Simulation
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • Sewage / chemistry*


  • DNA, Fungal
  • Fungal Proteins
  • Ligands
  • Sewage
  • Chromium