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Genome Announc. 2017 July; 5(29): e00654-17.
Published online 2017 July 20. doi:  10.1128/genomeA.00654-17
PMCID: PMC5522936

Multiple Genome Sequences of Lactobacillus plantarum Strains

ABSTRACT

We report here the genome sequences of four Lactobacillus plantarum strains which vary in surface hydrophobicity. Bioinformatic analysis, using additional genomes of Lactobacillus plantarum strains, revealed a possible correlation between the cell wall teichoic acid-type and cell surface hydrophobicity and provide the basis for consecutive analyses.

GENOME ANNOUNCEMENT

Cell wall teichoic acids (WTA) are inter alia suggested to influence cell adhesion (1, 2). The species Lactobacillus plantarum was shown to be unique among this genus to produce either poly(glycerol-3-phosphate) [poly(Gro-P)] or poly(ribitol-3-phosphate) [poly(Rbo-P)] WTA molecules, depending on the strain’s gene equipment, possibly resulting in different alditol-polymer-dependent cell surface characteristics (3,6). Testing the surface hydrophobicity of different L. plantarum strains by the MATH test, large differences in surface hydrophobicity could be determined (T. A. Kafka, D. Reitermayer, C. A. Lenz, and R. F. Vogel, unpublished data). In order to gain insights into the role of WTA type on cell surface hydrophobicity, we sequenced the complete genomes of four strains that vary in cell surface hydrophobicity.

Surface hydrophobicity was determined by a modified version of the MATH test (7). High-molecular-weight DNA was purified from de Man-Rogosa-Sharpe (MRS) liquid cultures using the Genomic-tip 100/G kit (Qiagen, Hilden, Germany). Using NanoDrop (Thermo Fisher Scientific) and agarose gel electrophoresis, the quality and quantity of isolated genomic DNA were checked. Single-molecule real-time sequencing (PacBio RSII) was carried out at GATC Biotech (Constance, Germany) (8). An insert size of 8 to 12 kb was selected for library creation, resulting in at least 200 Mb of raw data from 1 to 2 SMRT cells (1 × 120-min movies), applying P4-C2 chemistry. Assembly was done with SMRT Analysis version 2.2.0.p2, using the Hierarchical Genome Assembly Process (HGAP) (9), and completed by manual curation (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Finishing-Bacterial-Genomes). Genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (10).

Strain characteristics, sequencing statistics, genome information, and accession numbers are listed in Table 1.

TABLE 1
Strain characteristics, sequencing statistics, genome information, and accession numbers

The chromosome sizes range from 3.09 Mb to 3.14 Mb, with G+C contents of 44.6% to 44.7%. We found four to 10 plasmids (per strain), with G+C contents ranging from 35.0% to 55.0%. Plasmid sizes range from 0.8 to 67.9 kb, resulting in genome sizes of 3.24 to 3.40 Mb. The chromosomes encode 64 to 69 tRNAs.

The analysis of all four L. plantarum genomes, considering additional genomes of already sequenced L. plantarum strains, revealed conserved differences in WTA biosynthesis clusters, resulting in two different WTA types possibly correlating with specific surface hydrophobicities. In hydrophobic and hydrophilic stains, we could determine the tar locus, which is necessary for the biosynthesis of poly(Rbo-P) WTAs (3). Thereby, we could prove that the tar loci of hydrophilic and hydrophobic strains differ by sharing gene sequence identities of only 65 to 87% and that these differences are conserved among these two groups (99% sequence similarity, 99% coverage to each other). Comparing the genomes of both groups by BADGE and following bioinformatic analysis, we could determine the genes tagD1-tagF1-tagF2 (tag locus) in hydrophilic strains, which were lacking in the genomes of hydrophobic strains (11). In line with that finding, hydrophilic strains are supposed to synthesize poly(Gro-P) while hydrophobic strains are supposed to synthesize poly(Rbo-P) WTAs (3, 4).

The availability of these L. plantarum genome sequences provides the basis for consecutive analyses (e.g., wall teichoic acid isolation and transcriptomics) with the objective to obtain new insights regarding the role of WTAs on surface hydrophobicity or adhesive properties to biotic and abiotic materials.

Accession number(s).

The four complete L. plantarum genomes have been deposited in DDBJ/EMBL/GenBank under the accession numbers stated in Table 1.

ACKNOWLEDGMENTS

This work was supported by the German Research Foundation (DFG) and the Technische Universität München within the funding program Open Access Publishing. Parts of this work were funded by the German Ministry of Economics and Technology (via AiF), project AiF 17463N. None of the funding sources had any influence on the study design, the collection, analysis, or interpretation of data, the writing of the report, or the decision to submit the article for publication.

Footnotes

Citation Kafka TA, Geissler AJ, Vogel RF. 2017. Multiple genome sequences of Lactobacillus plantarum strains. Genome Announc 5:e00654-17. https://doi.org/10.1128/genomeA.00654-17.

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Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)