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).
