Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus: Functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation

Carolina González, Marcelo Lazcano, Jorge Valdés, David S. Holmes

Resultado de la investigación: Article

4 Citas (Scopus)

Resumen

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-offof 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).

Idioma originalEnglish
Número de artículo2035
PublicaciónFrontiers in Microbiology
Volumen7
N.ºDEC
DOI
EstadoPublished - 1 ene 2016

Huella dactilar

Acidithiobacillus
Molecular Probes
Metagenomics
Computational Biology
Genes
Metagenome
Proteins
Cell Division
Proteomics
Drainage
Amino Acid Sequence
Nucleotides
Chromosomes
Genome
Databases
Acids
Membranes

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Citar esto

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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-offof 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).",
keywords = "Acid resistance, Acidithiobacillus, Biomining bioleaching and acid mine drainage (AMD), Extreme acidophile, Horizontal gene transfer (HGT), Metagenome and metatranscriptome, Orphan (ORFan) genes, Thermithiobacillus",
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Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus : Functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation. / González, Carolina; Lazcano, Marcelo; Valdés, Jorge; Holmes, David S.

En: Frontiers in Microbiology, Vol. 7, N.º DEC, 2035, 01.01.2016.

Resultado de la investigación: Article

TY - JOUR

T1 - Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus

T2 - Functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation

AU - González, Carolina

AU - Lazcano, Marcelo

AU - Valdés, Jorge

AU - Holmes, David S.

PY - 2016/1/1

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N2 - 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-offof 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).

AB - 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-offof 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).

KW - Acid resistance

KW - Acidithiobacillus

KW - Biomining bioleaching and acid mine drainage (AMD)

KW - Extreme acidophile

KW - Horizontal gene transfer (HGT)

KW - Metagenome and metatranscriptome

KW - Orphan (ORFan) genes

KW - Thermithiobacillus

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DO - 10.3389/fmicb.2016.02035

M3 - Article

AN - SCOPUS:85009354564

VL - 7

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - DEC

M1 - 2035

ER -