Complete genome sequence of <em>Lactobacillus plantarum</em> WCFS1

Michiel Kleerebezem

Jos Boekhorst

Richard van Kranenburg

Douwe Molenaar

Hans Sandbrink+11 authors

^{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}

^{To whom correspondence should be addressed. E-mail:}ln.SFCW@emoneg.

^{Deceased May 10, 2002.}

Communicated by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC

Received 2002 Aug 8; Accepted 2002 Dec 18.

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.

Abstract

Lactic acid bacteria are used for the preservation of food and feed raw materials such as milk, meat, and vegetables or other plant materials. Research carried out in recent years has led to the conviction that certain strains of lactic acid bacteria, in particular strains from the genera Lactobacillus, may promote health in man and animals (1). The genus Lactobacillus encompasses a considerable number of different species that display a relatively large degree of diversity (2). Among these, Lactobacillus plantarum is a flexible and versatile species that is encountered in a variety of environmental niches, including some dairy, meat, and many vegetable or plant fermentations. Moreover, L. plantarum is frequently encountered as a natural inhabitant of the human gastrointestinal (GI) tract (3), and a selected strain, L. plantarum 299v, is marketed as a probiotic that may confer various health beneficial effects to the consumer (4, 5). The ecological flexibility of L. plantarum is reflected by the observation that this species has one of the largest genomes known among lactic acid bacteria (6). Several strains of L. plantarum are genetically accessible, and genetic tools have been developed for this species, including (controlled) gene expression systems (7, 8) and vectors that can be used for the construction of gene disruption or deletion variants (9, 10). The ability to persist in the human GI tract has stimulated research aimed at the use of L. plantarum as a delivery vehicle for therapeutic compounds, including vaccines (11). Here we present the complete genomic sequence of L. plantarum WCFS1, a single colony isolate from L. plantarum NCIMB8826, which was originally isolated from human saliva (National Collection of Industrial and Marine Bacteria, Aberdeen, U.K.) (12). It has been shown to survive the passage of the stomach in an active form and is able to persist for >6 days in the human GI tract (13).

SP, signal peptide; NLP, N-terminal lipoprotein anchor; N-SA, N-terminal signal anchor sequence. The number of SP-containing proteins that also have a cell-wall binding domain is indicated in parentheses.

Acknowledgments

This paper is dedicated to the fond memory of our dear friend and colleague Dr. Hans Sandbrink, who passed away during the course of this research. We thank Frank van Enckevort, Jakub Rychter, Maud le Coq, Maarten Arends, Nico Penninkhof, Jornt Bek, Michiel Wels, Ingeborg Boels, Wilbert Sybesma, Patrick van de Boogaard, Elaine Vaughan, Armand Hermans, Bart Pieterse, Mariët van der Werf, Bernadet Renckens, and Mark Sturme for their contribution to annotation. We thank Marleen Abma-Henkens, Marjo van Staveren, and Paul Mooijman for their skillful technical assistance. We thank Harald Brüssow for preliminary analysis of the prophages, and Torsten Stachelhaus for preliminary analysis of the nonribosomal peptide biosynthesis gene cluster. We thank James Brown for identification of the RNase P RNA region.

Acknowledgments

Abbreviations

ABC	ATP-binding cassette
PHX	potentially highly expressed
EMP	Embden–Meyerhoff–Parnas
PTS	phosphotransferase system

Abbreviations

Footnotes

Data deposition: The sequence reported in this paper has been deposited in the EMBL database (accession no. {"type":"entrez-nucleotide","attrs":{"text":"AL935263","term_id":"342240345","term_text":"AL935263"}}AL935263).

Footnotes

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