27 diciembre 2016

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

DOI : 10.3389/fmicb.2016.02035

Jorge Valdés, David S. Holmes

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).

Investigadores Participantes del Centro

Biocomputing and Applied Genomics Laboratory

Doctor en Biotecnología, Universidad Andrés Bello, Chile.


Extremophile Genomics and Astrobiology Laboratory

Doctor en Bioquímica, California Institute of Technology, USA.



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