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. 2012 Jan;194(1):195–196. doi: 10.1128/JB.06275-11

Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome

Roland J Siezen a,b,c,d,✉, Christof Francke a,b,c, Bernadet Renckens b,c, Jos Boekhorst a,b,c,d, Michiel Wels a,b,c,d, Michiel Kleerebezem a,c,d, Sacha A F T van Hijum a,b,c,d
PMCID: PMC3256602  PMID: 22156394

Abstract

There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated proteins.

GENOME ANNOUNCEMENT

Lactobacillus plantarum is a versatile facultative heterofermentative lactic acid bacterium (LAB) found in vegetables, meat, fish, and dairy products (2–4, 14, 19, 20, 32) and the gastrointestinal tract (1). L. plantarum WCFS1 has become one of the model strains in LAB research since the initial genome publication (25). Bioinformatics tools have been used to predict the function of its genes (7, 39, 42), reconstruct metabolic pathways (18, 43–45) and gene regulatory networks (17, 49, 51), and compare its genome with genomes of other LAB (6, 26, 52). The genomic, phenotypic, and metabolic diversity of L. plantarum has been previously described (31, 40, 41). L. plantarum has been employed as a model for LAB interactions with mammalian gut tissues in studies that provided insights into the microbial adaptation to that habitat (8–10, 27–29) and identified candidate probiotic genes (21, 22, 30, 34, 46, 47).

Resequencing performed with a Solexa GAIIx genome analyzer (BaseClear, The Netherlands) resulted in 10,783,316 reads of 50 bp (5-kb mated pairs), totaling 550 Mb (∼160× coverage). RoVar software (http://trac.nbic.nl/rovar) was used to align Solexa reads to the L. plantarum WCFS1 genome sequence by the use of BLAT (24). Read alignment was allowed provided that structural variations (SVs) in the form of single nucleotide polymorphisms (SNPs) or small indels were at least 4 bp from the end of a read. SVs were allowed with a maximum of one read mismatch and a sequence depth of at least 20 reads that unanimously identified a genotype.

Improved manual annotation of encoded functions was performed using Artemis and ACT (12, 13, 36), RAST (5), ISGA (23), Pfam (15, 16), InterProScan (35), BRENDA (38), CAZy (11), TCDB (37), and ERGO (33) software and experimental evidence. L. plantarum supermotifs (LPSMs) (48), T-boxes (48, 50), and extracellular protein functions were as previously predicted (7, 52).

The circular chromosome (3,308,273 bp; 44.5% GC content) contains 3,042 protein-encoding genes (of which 18 are pseudogenes), 70 tRNA-encoding genes, 5 rRNA operons, 8 miscellaneous RNAs, 32 T-boxes, and 27 LPSMs. Resequencing showed 116 differences (97 single nucleotide corrections and 19 single nucleotide indels) from the published sequence (25). Thirty-eight corrections are in intergenic regions, and 78 corrections are within protein-coding sequences, leading to 55 amino acid changes and 10 corrections of the N or C terminus of encoded proteins.

Compared to the originally published L. plantarum WCFS1 genome (25), 27 coding sequences (CDS) or fragments have now been deleted and 34 CDS or fragments added. Annotations were improved for nearly 1,200 encoded proteins; the improvements included the addition of family information for most transcriptional regulators (n = 190), transporters (n = 79), and oxidoreductases (n = 44). Comparative analysis of putative secreted and cell surface-associated proteins (7, 26, 52) has led to improved annotation of 74 putative extracellular proteins (see the LAB-Secretome database at www.cmbi.ru.nl/lab_secretome/) (52). Originally, 740 CDS were annotated as corresponding to a hypothetical (membrane) protein (25), but 24 of those CDS have now been deleted and 366 have been given a general family assignment (n = 229) or a very specific function assignment (n = 137). We hope that the comprehensive curated annotation of this model LAB will be of significant use to the many L. plantarum researchers worldwide.

Nucleotide sequence accession number.

The sequence and the annotation were deposited in EMBL/GenBank at AL935263.2 (GI:342240345), replacing versions AL935263.1 and AL935252 to AL935262.

ACKNOWLEDGEMENTS

We thank Paul de Vos for continued support of this project and all authors of L. plantarum literature who provided experimental evidence to support our reannotation.

This project was funded by the Top Institute Food and Nutrition, Wageningen, The Netherlands.

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