Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a

crossmark
Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a
Human Vaginal Isolate
Shweta Malik,a,b Roland J. Siezen,c,d Bernadet Renckens,c Mario Vaneechoutte,e Jos Vanderleyden,a
Sarah Lebeera,b
KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg, Leuven, Belgiuma; University of Antwerp, Department of Bioscience Engineering,
Groenenborgerlaan, Antwerp, Belgiumb; Radboud University Nijmegen Medical Centre, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, The
Netherlandsc; Microbial Bioinformatics, Ede, The Netherlandsd; Ghent University, Laboratory of Bacteriology Research, Ghent, Belgiume
The draft genome of a highly auto-aggregating Lactobacillus plantarum strain isolated from a human vagina is reported. The
peculiar phenotype also provides an adhesive and co-aggregative potential with various pathogens, which could be of significance in the vaginal niche. Detailed genome analysis could aid in identifying the adhesins of the strain.
Received 25 September 2014 Accepted 6 October 2014 Published 13 November 2014
Citation Malik S, Siezen RJ, Renckens B, Vaneechoutte M, Vanderleyden J, Lebeer S. 2014. Draft genome sequence of Lactobacillus plantarum CMPG5300, a human vaginal
isolate. Genome Announc. 2(6):e01149-14. doi:10.1128/genomeA.01149-14.
Copyright © 2014 Malik et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Sarah Lebeer, [email protected]
L
actobacillus plantarum is a highly versatile species found in a
variety of environmental niches such as in the gastrointestinal
tract, and food products including dairy, meat, and vegetable fermentations (1, 2). There has been considerable interest in the
probiotic potential of this species (1, 3, 4), yet it has been restricted
to the intestinal isolates. Being a less commonly found species in
the vaginal niche (5, 6), there are no reports on the genomes of
vaginal L. plantarum isolates yet. Here, we report the draft genome
of a vaginal Lactobacillus plantarum strain CMPG5300 with a remarkably high auto-aggregative capacity and adhesive ability to
vaginal epithelial cell line VK2/E6E7 (7). The strong adhesive and
auto-aggregative property of the strain is related to proteinaceous
structures, as it can be abolished by proteinase treatment. A gene
deletion mutant of the sortase-encoding gene of the strain lost the
capacity to auto-aggregate and bind to mannose-rich conjugates
of yeast cells, suggesting a crucial role for sortase-dependent proteins for these characteristics (7). Further insight into the genome
of the strain may help the identification of putative adhesins imparting the exceptional features to the strain. This could particularly be of interest for targeted approaches that aim at evading
pathogens at the vaginal front.
The genomic DNA of the strain CMPG5300 was isolated as
described before (7) and whole-genome sequencing was performed using the 454 GS FLX⫹ sequencing platform (Genomics
Core, KU Leuven). The reads were assembled into contigs using
Roche GS De Novo Assembler software (version 2.5p1). The read
coverage within the contigs was 50-100⫻. The minimum overlap
length was set to 40 nucleotides, with a minimum overlap identity
of 90%. Open-reading frames were extracted using the getorf program from the EMBOSS suite v6.3.1 (8), automatically annotated
using the RAST server (9), and manually curated by comparison
against the published genome of L. plantarum WCFS1 (10) using
ACT (11).
The genome assembled into 48 contigs larger than 750 nt (containing a total 3,503,628 nt) of which at least six contigs represent
plasmids (size 2 to 40 kb; total ~143 kb), with a total G⫹C content
November/December 2014 Volume 2 Issue 6 e01149-14
of 44%. The genome contains 3,251 protein-encoding genes (at
least 140 are plasmid encoded). The scaffolded chromosome
(19 contigs) is highly syntenous to published L. plantarum chromosomes (10, 12–16) (accession no. AL935263.2, CP001617.1,
CP002222.1, CP004082.1, AGRI00000000.1, CP006033.1,
PRJNA203333). Large variations are found between all L. plantarum chromosomes, including CMPG5300, in gene clusters encoding prophages, exopolysaccharide biosynthesis, plantaricin biosynthesis, and sugar metabolism (17). The putative plasmids of
strain CMPG5300 encode a few sortase-dependent proteins,
which may be relevant for the auto-aggregating and adhesive
properties of this strain (7). These include a cell-envelope associated serine proteinase (Cmpg5300_3052) of 1,482 amino acids,
which is 99% identical to plasmid-encoded proteinases of L. plantarum strains 16 and P8. Furthermore, a mucus-binding protein
of 1,203 amino acids Cmpg5300.05_29 is encoded that is 98%
identical to a cell-surface protein of Lactobacillus antri, and 62%
identical to the mannose-specific adhesin (Msa) of L. plantarum
WCFS1.
Nucleotide sequence accession numbers. This whole-genome
shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AXZV00000000. The version described in
this paper is version AXZV01000000.
ACKNOWLEDGMENT
The genome sequencing was supported by the KU Leuven funding BOF
program financing (spokesman, Jan Balzarini). S.M. was supported by
Erasmus Mundus External Cooperation Window Lot 13 for her Ph.D.
research. S.L. also acknowledges support of FWO Vlaanderen for her
postdoc grant and a KaN grant.
REFERENCES
1. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers
OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema
W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de
Vries M, Ursing B, de Vos WM, Siezen RJ. 2003. Complete genome
sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U. S. A.
100:1990 –1995.
Genome Announcements
genomea.asm.org 1
Malik et al.
2. Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL,
Starrenburg MJ, Kleerebezem M, Molenaar D, van Hylckama Vlieg JE.
2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains
isolated from various environmental niches. Environ. Microbiol. 12:
758 –773. http://dx.doi.org/10.1111/j.1462-2920.2009.02119.x.
3. Connelly P. 2008. Lactobacillus plantarum—A literature review of therapeutic benefits. J. Aust. Tradit. Med. Soc. 14:79 – 82.
4. Klarin B, Molin G, Jeppsson B, Larsson A. 2008. Use of the probiotic
Lactobacillus plantarum 299 to reduce pathogenic bacteria in the oropharynx of intubated patients: a randomised controlled open pilot study. Crit.
Care 12:R136. http://dx.doi.org/10.1186/cc7109.
5. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL,
Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC,
Ault K, Peralta L, Forney LJ. 2011. Vaginal microbiome of reproductiveage women. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl 1):4680 – 4687.
http://dx.doi.org/10.1073/pnas.1002611107.
6. Gustafsson RJ, Ahrné S, Jeppsson B, Benoni C, Olsson C, Stjernquist
M, Ohlsson B. 2011. The Lactobacillus flora in vagina and rectum of fertile
and postmenopausal healthy Swedish women. BMC Womens Health 11:
17. http://dx.doi.org/10.1186/1472-6874-11-17.
7. Malik S, Petrova MI, Claes IJ, Verhoeven TL, Busschaert P,
Vaneechoutte M, Lievens B, Lambrichts I, Siezen RJ, Balzarini J,
Vanderleyden J, Lebeer S. 2013. The highly autoaggregative and adhesive
phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is
sortase dependent. Appl. Environ. Microbiol. 79:4576 – 4585. http://
dx.doi.org/10.1128/AEM.00926-13.
8. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular
biology open software suite. Trends Genet. 16:276 –277. http://dx.doi.org/
10.1016/S0168-9525(00)02024-2.
9. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA,
Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson
R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T,
Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V,
Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using
2 genomea.asm.org
10.
11.
12.
13.
14.
15.
16.
17.
Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/
1471-2164-9-75.
Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem
M, van Hijum SA. 2012. Complete resequencing and reannotation of the
Lactobacillus plantarum WCFS1 genome. J. Bacteriol. 194:195–196. http://
dx.doi.org/10.1128/JB.06275-11.
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG,
Parkhill J. 2005. ACT: the Artemis comparison tool. Bioinformatics 21:
3422–3423. http://dx.doi.org/10.1093/bioinformatics/bti553.
Zhang ZY, Liu C, Zhu YZ, Zhong Y, Zhu YQ, Zheng HJ, Zhao GP,
Wang SY, Guo XK. 2009. Complete genome sequence of Lactobacillus
plantarum JDM1. J. Bacteriol. 191:5020 –5021. http://dx.doi.org/10.1128/
JB.00587-09.
Wang Y, Chen C, Ai L, Zhou F, Zhou Z, Wang L, Zhang H, Chen W,
Guo B. 2011. Complete genome sequence of the probiotic Lactobacillus
plantarum ST-III. J. Bacteriol. 193:313–314. http://dx.doi.org/10.1128/
JB.01159-10.
Li X, Gu Q, Lou X, Zhang X, Song D, Shen L, Zhao Y. 2013. Complete
genome sequence of the probiotic Lactobacillus plantarum strain ZJ316.
Genome Announc. 1(2):e0009413. http://dx.doi.org/10.1128/
genomeA.00094-13.
Axelsson L, Rud I, Naterstad K, Blom H, Renckens B, Boekhorst J,
Kleerebezem M, van Hijum S, Siezen RJ. 2012. Genome sequence of the
naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG
61730). J. Bacteriol. 194:2391–2392. http://dx.doi.org/10.1128/JB.00141
-12.
Crowley S, Bottacini F, Mahony J, van Sinderen D. 2013. Complete
genome sequence of Lactobacillus plantarum strain 16, a broad-spectrum
antifungal-producing lactic acid bacterium. Genome Announc. 1(4):
e00533-13. http://dx.doi.org/10.1128/genomeA.00533-13.
Siezen RJ, van Hylckama Vlieg JE. 2011. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb.
Cell Fact. 10:S3. http://dx.doi.org/10.1186/1475-2859-10-S1-S3.
Genome Announcements
November/December 2014 Volume 2 Issue 6 e01149-14