Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation

ISME J. 2016 Feb;10(2):310-20. doi: 10.1038/ismej.2015.113. Epub 2015 Jul 3.

Abstract

Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biodegradation, Environmental
  • Cytochrome c Group / metabolism*
  • Electron Transport
  • Ferric Compounds / metabolism
  • Geobacter / classification
  • Geobacter / genetics
  • Geobacter / isolation & purification
  • Geobacter / metabolism*
  • Groundwater / microbiology
  • Molecular Sequence Data
  • Oxidation-Reduction
  • Phylogeny
  • Proteomics
  • Sequence Alignment
  • Uranium / metabolism*

Substances

  • Bacterial Proteins
  • Cytochrome c Group
  • Ferric Compounds
  • Uranium