Abstract
Pediococcus acidilactici strain S1, a lactic acid-fermenting bacterium, was isolated from makgeolli-a Korean traditional fermented alcoholic beverage. Here we report the 1,980,172 bp (G + C content, 42%) genome sequence of Pediococcus acidilactici strain S1 with 1,525 protein-coding sequences (CDS), of which 47% could be assigned to recognized functional genes. The genome sequence of the strain S1 might provide insights into the genetic basis of the lactic acid bacterium with alcohol-tolerant.
Keywords:
Pediococcus spp.; Lactic acid bacteria; Microbial genome; Alcohol-tolerant
Introduction
Pediococcus acidilactici strain S1 is a gram-positive, coccus-shaped, lactic acid- fermenting bacterium that belongs to the Lactobacillaceae family. Several lactic acid bacteria (LAB) belonging to the genus Pediococcus have been isolated and characterized.11 Stiles ME, Holzapfel WH. Lactic acid bacteria of foods and their current taxonomy. Int J Food Microbiol. 1997;36:1-29. Most of them are found in fermented foods and beverages such as makgeolli, which is a traditional Korean rice wine.22 Jung SE, Kim SH. Probiotic properties of lactic acid bacteria isolated from commercial raw makgeolli. Korean J Food Sci Technol. 2015;47:44-50.P. acidilactici strain S1 was also isolated from makgeolli with alcohol-tolerant. The strain can be used for makgeolli brewing as a starter or supplementation.33 Jang D, Lee H, Pyo S, et al. Fermentation and quality evaluation of makgeolli, Korean rice wine supplemented with alcohol-tolerant Pediococcus acidilactici K3. Korean J Microbiol Biotechnol. 2014;42:367-376. Here, we present a description of the genome sequence and its annotation results.
The genome sequence of P. acidilactici strain S1 was revealed by using an Ion Torrent semiconductor sequencing machine.44 Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475:348-352. A total of 3,959,807 reads were generated at an average read length of 298 bp. The whole genome was assembled de novo from short shotgun sequence reads by using Mimicking Intelligent Read Assembly (MIRA) 4.055 Chevreux B. MIRA: an automated genome and EST assembler. Heidelberg, Germany: Ruprecht-Karls University; 2005. and CLC Genomics Workbench version 8.0. The best assembly results comprised 59 contigs with 531x coverage. The draft genome size was 1,980,172 bp with a G + C content of 42%. The assembled contigs were annotated by using NCBI Prokaryotic Genomes Annotation Pipeline (PGAP) version 3.0.66 Angiuoli SV, Gussman A, Klimke W, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS. 2008;12:137-141. RAST server (http://rast.nmpdr.org/) was used for subsystem classification and functional annotation.77 Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. The annotation predicted 1,771 protein-coding sequences (CDS), of which 47% were assigned to recognized functional genes with 40 tRNA and 7 rRNA genes.
Among the protein coding genes alcohol-tolerance enzymes were identified such as aldehyde dehydrogenase (477 aa; locus tag ATO21_00425; accession number LNUM01000003, 456 aa; locus tag ATO21_02775; accession number LNUM01000010), malate transporter (296 aa; locus tag ATO21_00560; accession number LNUM01000003), alcohol dehydrogenase (385 aa; locus tag ATO21_04225; accession number LNUM01000015, 341 aa; locus tag ATO21_05320; accession number LNUM01000020) and aryl-alcohol dehydrogenase (373 aa; locus tag ATO21_06665; accession number LNUM01000025).88 Ram S. Role of alcohol dehydrogenase, malate dehydrogenase and malic enzyme in flooding tolerance in Brachiaria species. J Plant Biochem Biotechnol. 2000;9:45-47.
9 Eanes WF, Merritt TJS, Flowers JM, et al. Direct evidence that genetic variation in glycerol-3-phosphate and malate dehydrogenase genes (Gpdh and Mdh1) affects adult ethanol tolerance in Drosophila melanogaster. Genetics. 2009;181:607-614.-1010 Brown SD, Guss AM, Karpinets TV, et al. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A. 2011;108:13752-13757. The genome sequence of P. acidilactici strain S1 can provide the insights of genetic information for the alcohol-tolerance of Pediococcus spp. at genetic level.
Nucleotide sequence accession numbers
The draft sequence of P. acidilactici strain S1 obtained in this Whole Genome Shotgun project has been deposited to the GenBank under the accession no. LNUM00000000. The version described in this paper is the first version, with accession, no. LNUM01000000.
Acknowledgments
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), which is funded by the Ministry of Education, Science and Technology (NRF-2014R1A1A1006415).
References
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1Stiles ME, Holzapfel WH. Lactic acid bacteria of foods and their current taxonomy. Int J Food Microbiol 1997;36:1-29.
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2Jung SE, Kim SH. Probiotic properties of lactic acid bacteria isolated from commercial raw makgeolli. Korean J Food Sci Technol 2015;47:44-50.
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3Jang D, Lee H, Pyo S, et al. Fermentation and quality evaluation of makgeolli, Korean rice wine supplemented with alcohol-tolerant Pediococcus acidilactici K3. Korean J Microbiol Biotechnol. 2014;42:367-376.
-
4Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475:348-352.
-
5Chevreux B. MIRA: an automated genome and EST assembler Heidelberg, Germany: Ruprecht-Karls University; 2005.
-
6Angiuoli SV, Gussman A, Klimke W, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS. 2008;12:137-141.
-
7Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
-
8Ram S. Role of alcohol dehydrogenase, malate dehydrogenase and malic enzyme in flooding tolerance in Brachiaria species. J Plant Biochem Biotechnol. 2000;9:45-47.
-
9Eanes WF, Merritt TJS, Flowers JM, et al. Direct evidence that genetic variation in glycerol-3-phosphate and malate dehydrogenase genes (Gpdh and Mdh1) affects adult ethanol tolerance in Drosophila melanogaster. Genetics. 2009;181:607-614.
-
10Brown SD, Guss AM, Karpinets TV, et al. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A. 2011;108:13752-13757.
Publication Dates
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Publication in this collection
Jul-Sep 2017
History
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Received
13 June 2016 -
Accepted
18 Sept 2016