title: Bioinformatic Analyses of Unique (Orphan) Core Genes of the GenusAcidithiobacillus: 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 genusAcidithiobacillusof the classAcidithiobacillia. These core gene families are absent in the closest extant genusThermithiobacillus tepidariusthat subtends theAcidithiobacillusgenus 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 ofAcidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to theAcidithiobacillusgenus, 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).
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.
authors.forename: Carolina
authors.initials: C
authors.lastname: González
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Lazcano
authors.affiliation: Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor Santiago, Chile.
authors.forename: Jorge
authors.initials: J
authors.lastname: Valdés
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia & VidaSantiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile.
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
keywords: Acidithiobacillus; Orphan (ORFan) genes; Thermithiobacillus; acid resistance; biomining bioleaching and acid mine drainage (AMD); extreme acidophile; horizontal gene transfer (HGT); metagenome and metatranscriptome