Complete genome sequence of Lactobacillus plantarum WCFS1

Kleerebezem, Michiel; Boekhorst, Jos; van Kranenburg, Richard; Molenaar, Douwe; Kuipers, Oscar P.; Leer, Rob; Tarchini, Renato; Peters, Sander A.; Sandbrink, Hans M.; Fiers, Mark W. E. J.; Stiekema, Willem; Lankhorst, René M. Klein; Bron, Peter A.; Hoffer, Sally M.; Groot, Masja N. Nierop; Kerkhoven, Robert; de Vries, Maaike; Ursing, Björn; de Vos, Willem M.; Siezen, Roland J.

doi:10.1073/pnas.0337704100

Cited by 1,472Probiotics and Fermented FoodsBacterial Genetics and BiotechnologyGenomics and Phylogenetic Studies

Complete genome sequence of Lactobacillus plantarum WCFS1

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Kleerebezem, Michiel, Boekhorst, Jos, van Kranenburg, Richard, Molenaar, Douwe, Kuipers, Oscar P., Leer, Rob, Tarchini, Renato, Peters, Sander A. +12 more·2003·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.0337704100PMC PMC149946

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Abstract

The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single colony isolate of strain NCIMB8826 that was originally isolated from human saliva, has been determined, and contains 3,052 predicted protein-encoding genes. Putative biological functions could be assigned to 2,120 (70%) of the predicted proteins. Consistent with the classification of L. plantarum as a facultative heterofermentative lactic acid bacterium, the genome encodes all enzymes required for the glycolysis and phosphoketolase pathways, all of which appear to belong to the class of potentially highly expressed genes in this organism, as was evident from the codon-adaptation index of individual genes. Moreover, L. plantarum encodes a large pyruvate-dissipating potential, leading to various end-products of fermentation. L. plantarum is a species that is encountered in many different environmental niches, and this flexible and adaptive behavior is reflected by the relatively large number of regulatory and transport functions, including 25 complete PTS sugar transport systems. Moreover, the chromosome encodes >200 extracellular proteins, many of which are predicted to be bound to the cell envelope. A large proportion of the genes encoding sugar transport and utilization, as well as genes encoding extracellular functions, appear to be clustered in a 600-kb region near the origin of replication. Many of these genes display deviation of nucleotide composition, consistent with a foreign origin. These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome.

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Authors: Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O. P., Leer, R., Tarchini, R., Peters, S. A., Sandbrink, H. M., Fiers, M. W. E. J., Stiekema, W., Lankhorst, R. M. K., Bron, P. A., Hoffer, S. M., Groot, M. N. N., Kerkhoven, R., de Vries, M., Ursing, B., de Vos, W. M., & Siezen, R. J.
Affiliations: Radboud University Nijmegen (NL)
Wageningen Centre for Food Sciences, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Greenomics, Plant Research International, P.O. Box 16, 6700 AA Wageningen, The Netherlands; and Center for Molecular and Biomolecular Informatics, University of Nijmegen, P.O. Box 9010, 6500GL Nijmegen, The Netherlands
ORCID: Kleerebezem, Michiel
Boekhorst, Jos
Kuipers, Oscar P.
Peters, Sander A.
Fiers, Mark W. E. J.
Bron, Peter A.
Siezen, Roland J.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2003-02-03
Volume: 100
Issue: 4
Pages: 1990-1995
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.0337704100
PMC: PMC149946
OpenAlex: W2102672175
Cited by: 1,472
References: 49
Citations by year: 2026: 41 · 2025: 47 · 2024: 44 · 2023: 45 · 2022: 57 · 2021: 55 · 2020: 57 · 2019: 68 · 2018: 62 · 2017: 53 · 2016: 60 · 2015: 64 · 2014: 69 · 2013: 70 · 2012: 66
FWCI: 126.46
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Socio-Environmental Systems Modeling (acceptedVersion)
University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
Radboud Repository (Radboud University) (submittedVersion)
VU Research Portal (submittedVersion)
Data Archiving and Networked Services (DANS) (submittedVersion)
Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
Topics: Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: Lactobacillus plantarum WCFS1, complete genome sequence, lactic acid bacteria, heterofermentative metabolism, glycolysis, phosphoketolase pathway, extracellular proteins, cell envelope, gene clusters, nucleotide composition, foreign DNA, gene function annotation
MeSH terms: Biological Transport, Carbon, Lactobacillus, Molecular Sequence Data, Open Reading Frames, Genome, Bacterial, Replication Origin, Carbohydrate Metabolism

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