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Cited by 342Fungal and yeast genetics researchGenomics and Phylogenetic StudiesAntifungal resistance and susceptibility

A Human-Curated Annotation of the Candida albicans Genome

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Braun, Burkhard R, van het Hoog, Marco, d'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, Inglis, Diane O, Uhl, M. Andrew +35 more·2005·PLoS Genetics
DOI 10.1371/journal.pgen.0010001PMC PMC1183520
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Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

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  • The ALS gene family encodes eight GPI-linked cell surface proteins that mediate binding to diverse host substrates.

    “This gene family encodes eight GPI-linked cell surface proteins that mediate binding to diverse host substrates [20][21][22][23][24][25].”

    From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [21]

    The Results/Discussion section, under “Multigene Families” (page unavailable), says the ALS family has eight genes encoding cell-surface glycoproteins involved in host–pathogen interactions; it also reports adhesive capability for an Als3p variant. Our copy does not establish that all eight proteins are GPI-linked or that they bind diverse host substrates. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • The Als family of proteins contains six members in addition to Als1 and Als3.

    “The Als family of proteins contains six members in addition to Als1 and Als3 [20][21][22][23][24][25].”

    From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [21]

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Authors
Braun, B. R., van het Hoog, M., d'Enfert, C., Martchenko, M., Dungan, J., Kuo, A., Inglis, D. O., Uhl, M. A., Hogues, H., Berriman, M., Lorenz, M., Levitin, A., Oberholzer, U., Bachewich, C., Harcus, D., Marcil, A., Dignard, D., Iouk, T., Zito, R., Frangeul, L., Tekaia, F., Rutherford, K., Wang, E., Munro, C. A., Bates, S., Gow, N. A., Hoyer, L. L., Köhler, G., Morschhäuser, J., Newport, G., Znaidi, S., Raymond, M., Turcotte, B., Sherlock, G., Costanzo, M., Ihmels, J., Berman, J., Sanglard, D., Agabian, N., Mitchell, A. P., Johnson, A. D., Whiteway, M., & Nantel, A.
Affiliations
  • University of California, San Francisco (US)
  • Biotechnology Research Institute (CA)
  • Wellcome Sanger Institute (GB)
  • The University of Texas Health Science Center at Houston (US)
  • Institut Pasteur (FR)
  • University of Aberdeen (GB)
  • University of Illinois Urbana-Champaign (US)
  • University of Würzburg (DE)
  • Montreal Clinical Research Institute (CA)
  • Royal Victoria Hospital (CA)
  • Stanford Medicine (US)
  • Weizmann Institute of Science (IL)
  • University of Minnesota (US)
  • Centre Hospitalier Universitaire Vaudois (CH)
  • New York University (US)
Corresponding author
Nantel, André
ORCID
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2005-06-17
Volume
1
Issue
1
Pages
e1
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.0010001
PMC
PMC1183520
OpenAlex
W2060322845
Cited by
342
References
12
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FWCI
12.85
Type
journal article
Language
en
Open access
Licence
cc-by
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  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
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Funders
  • Burroughs Wellcome Fund
  • Massachusetts Institute of Technology
  • North Carolina State University
  • Wellcome Trust
  • Broad Institute
  • Incyte
  • National Institutes of Health
  • University of California, San Francisco
  • Canadian Institutes of Health Research (MOP42516)
  • National Research Council Canada
  • National Institute of Allergy and Infectious Diseases (R01AI049187)
  • National Institute of Dental and Craniofacial Research (P01DE007946)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
Keywords
Candida albicans, genome annotation, gene identification, fungal pathogens, antifungal drug targets, short sequence repeats, gene family, comparative genomics, catabolic genes, oxidative enzymes, amino acid catabolism, lipase, proteolytic enzymes, transporters, sequencing errors

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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