Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

Abstract

Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e−5. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).

Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C

“…ferrooxidans BY0502 may have been misidentified, as it showed more relatedness with A . ferrivora ns on the basis of ANI and TETRA analysis 16 . Variants with a predicted high impact in A .…”

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

“…Intraspecific variations can be accounted for by diverse plasmids present [31], and by a highly diverse set of integrated mobile genetic elements [32][33][34]. Recently, pangenomic studies have provided additional insights into the core and exclusive functions of certain species of Acidithiobacillus [35,36]. However, studies performed so far have (i) overlooked the existence of different taxonomic ranks within the class Acidithiobacillia, (ii) involved few representative strains of each species, and/or (iii) undertaken biased sampling efforts, recovering strains from a limited range of habitats or geographical origins.…”

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes

“…In this core genome, five highly conserved gene families specific to the Acidithiobacillus spp. have been recently described ( Gonzalez et al, 2016 ).…”