Outer membrane pore protein prediction in mycobacteria using genomic comparison

Publication type:
Journal article
Metadata:
Autoren
  • Nancy Mah
  • Carolina Perez-Iratxeta
  • Miguel A Andrade-Navarro
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000281239600023&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1099/mic.0.040089-0
eISSN
1465-2080
Externe Identifier
  • Clarivate Analytics Document Solution ID: 642TA
  • PubMed Identifier: 20466765
ISSN
1350-0872
Zeitschrift
MICROBIOLOGY-SGM
Paginierung
2506 - 2515
Datum der Veröffentlichung
2010
Status
Published
Titel
Outer membrane pore protein prediction in mycobacteria using genomic comparison
Sub types
  • Article
Ausgabe der Zeitschrift
156

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:p>Proteins responsible for outer membrane transport across the unique membrane structure of <jats:italic>Mycobacterium</jats:italic> spp. are attractive drug targets in the treatment of human diseases caused by the mycobacterial pathogens, <jats:italic>Mycobacterium tuberculosis</jats:italic>, <jats:italic>M. bovis</jats:italic>, <jats:italic>M. leprae</jats:italic> and <jats:italic>M. ulcerans</jats:italic>. In contrast with <jats:italic>Escherichia coli</jats:italic>, relatively few outer-membrane proteins (OMPs) have been identified in <jats:italic>Mycobacterium</jats:italic> spp., largely due to the difficulties in isolating mycobacterial membrane proteins and our incomplete understanding of secretion mechanisms and cell wall structure in these organisms. To further expand our knowledge of these elusive proteins in mycobacteria, we have improved upon our previous method of OMP prediction in mycobacteria by taking advantage of genomic data from seven mycobacteria species. Our improved algorithm suggests 4333 sequences as putative OMPs in seven species with varying degrees of confidence. The most virulent pathogenic mycobacterial species are slightly enriched in these selected sequences. We present examples of predicted OMPs involved in horizontal transfer and paralogy expansion. Analysis of local secondary structure content allowed identification of small domains predicted to perform as OMPs; some examples show their involvement in events of tandem duplication and domain rearrangements. We discuss the taxonomic distribution of these discovered families and architectures, often specific to mycobacteria or the wider taxonomic class of <jats:italic>Actinobacteria</jats:italic>. Our results suggest that OMP functionality in mycobacteria is richer than expected and provide a resource to guide future research of these understudied proteins.</jats:p>
Autoren
  • Nancy Mah
  • Carolina Perez-Iratxeta
  • Miguel A Andrade-Navarro
DOI
10.1099/mic.0.040089-0
eISSN
1465-2080
ISSN
1350-0872
Ausgabe der Veröffentlichung
8
Zeitschrift
Microbiology
Sprache
en
Paginierung
2506 - 2515
Datum der Veröffentlichung
2010
Status
Published
Herausgeber
Microbiology Society
Herausgeber URL
http://dx.doi.org/10.1099/mic.0.040089-0
Datum der Datenerfassung
2020
Titel
Outer membrane pore protein prediction in mycobacteria using genomic comparison
Ausgabe der Zeitschrift
156

Data source: Crossref

Abstract
Proteins responsible for outer membrane transport across the unique membrane structure of Mycobacterium spp. are attractive drug targets in the treatment of human diseases caused by the mycobacterial pathogens, Mycobacterium tuberculosis, M. bovis, M. leprae and M. ulcerans. In contrast with Escherichia coli, relatively few outer-membrane proteins (OMPs) have been identified in Mycobacterium spp., largely due to the difficulties in isolating mycobacterial membrane proteins and our incomplete understanding of secretion mechanisms and cell wall structure in these organisms. To further expand our knowledge of these elusive proteins in mycobacteria, we have improved upon our previous method of OMP prediction in mycobacteria by taking advantage of genomic data from seven mycobacteria species. Our improved algorithm suggests 4333 sequences as putative OMPs in seven species with varying degrees of confidence. The most virulent pathogenic mycobacterial species are slightly enriched in these selected sequences. We present examples of predicted OMPs involved in horizontal transfer and paralogy expansion. Analysis of local secondary structure content allowed identification of small domains predicted to perform as OMPs; some examples show their involvement in events of tandem duplication and domain rearrangements. We discuss the taxonomic distribution of these discovered families and architectures, often specific to mycobacteria or the wider taxonomic class of Actinobacteria. Our results suggest that OMP functionality in mycobacteria is richer than expected and provide a resource to guide future research of these understudied proteins.
Addresses
  • Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.
Autoren
  • Nancy Mah
  • Carolina Perez-Iratxeta
  • Miguel A Andrade-Navarro
DOI
10.1099/mic.0.040089-0
eISSN
1465-2080
Externe Identifier
  • PubMed Identifier: 20466765
Open access
false
ISSN
1350-0872
Ausgabe der Veröffentlichung
Pt 8
Zeitschrift
Microbiology (Reading, England)
Schlüsselwörter
  • Mycobacterium
  • Bacterial Outer Membrane Proteins
  • Porins
  • DNA, Bacterial
  • Sequence Analysis, DNA
  • Species Specificity
  • Genome, Bacterial
  • Algorithms
  • Comparative Genomic Hybridization
Sprache
eng
Medium
Print-Electronic
Online publication date
2010
Paginierung
2506 - 2515
Datum der Veröffentlichung
2010
Status
Published
Datum der Datenerfassung
2010
Titel
Outer membrane pore protein prediction in mycobacteria using genomic comparison.
Sub types
  • Research Support, Non-U.S. Gov't
  • Journal Article
Ausgabe der Zeitschrift
156

Data source: Europe PubMed Central

Abstract
Proteins responsible for outer membrane transport across the unique membrane structure of Mycobacterium spp. are attractive drug targets in the treatment of human diseases caused by the mycobacterial pathogens, Mycobacterium tuberculosis, M. bovis, M. leprae and M. ulcerans. In contrast with Escherichia coli, relatively few outer-membrane proteins (OMPs) have been identified in Mycobacterium spp., largely due to the difficulties in isolating mycobacterial membrane proteins and our incomplete understanding of secretion mechanisms and cell wall structure in these organisms. To further expand our knowledge of these elusive proteins in mycobacteria, we have improved upon our previous method of OMP prediction in mycobacteria by taking advantage of genomic data from seven mycobacteria species. Our improved algorithm suggests 4333 sequences as putative OMPs in seven species with varying degrees of confidence. The most virulent pathogenic mycobacterial species are slightly enriched in these selected sequences. We present examples of predicted OMPs involved in horizontal transfer and paralogy expansion. Analysis of local secondary structure content allowed identification of small domains predicted to perform as OMPs; some examples show their involvement in events of tandem duplication and domain rearrangements. We discuss the taxonomic distribution of these discovered families and architectures, often specific to mycobacteria or the wider taxonomic class of Actinobacteria. Our results suggest that OMP functionality in mycobacteria is richer than expected and provide a resource to guide future research of these understudied proteins.
Autoren
  • Nancy Mah
  • Carolina Perez-Iratxeta
  • Miguel A Andrade-Navarro
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/20466765
DOI
10.1099/mic.0.040089-0
eISSN
1465-2080
Ausgabe der Veröffentlichung
Pt 8
Zeitschrift
Microbiology (Reading)
Schlüsselwörter
  • Algorithms
  • Bacterial Outer Membrane Proteins
  • Comparative Genomic Hybridization
  • DNA, Bacterial
  • Genome, Bacterial
  • Mycobacterium
  • Porins
  • Sequence Analysis, DNA
  • Species Specificity
Sprache
eng
Country
England
Paginierung
2506 - 2515
Datum der Veröffentlichung
2010
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2010
Titel
Outer membrane pore protein prediction in mycobacteria using genomic comparison.
Sub types
  • Journal Article
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
156

Data source: PubMed

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