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Title: Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.

Abstract

In this study, Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus , based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp. As a result, Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position. In conclusion, the present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specificmore » niches.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [3];  [7];  [8];  [4];  [9]
  1. Tokyo Univ. of Agriculture, Abashiri, Hokkaido (Japan). Dept. of Food and Cosmetic Science, Faculty of Bioindustry
  2. The Univ. of Tokyo Kashiwa, Chiba (Japan). Dept. of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences; Center for Information Biology, National Institute of Genetics, Mishima (Japan)
  3. Tokyo Univ. of Agriculture, Tokyo (Japan). NODAI Culture Collection Centre
  4. Tokyo Univ. of Agriculture, Tokyo (Japan). Dept. of Food and Cosmetic Science, Faculty of Bioindustry
  5. Univ. of Turku, Turku (Finland). Functional Foods Forum
  6. Tokyo Univ. of Agriculture, Tokyo (Japan). NODAI Culture Collection Centre, Genome Research Center
  7. Tokyo Univ. of Agriculture, Tokyo (Japan). NODAI Culture Collection Centre, Genome Research Center, Dept. of Bioscience
  8. Univ. of Stellenbosch, Stellenbosch (South Africa). Dept. of Microbiology
  9. Center for Information Biology, National Institute of Genetics Mishima (Japan); RIKEN Center for Sustainable Resource Science Yokohama (Japan)
Publication Date:
Research Org.:
Tokyo Univ. of Agriculture, Abashiri, Hokkaido (Japan)
Sponsoring Org.:
USDOE Office of Science (SC); MEXT; National Institute of Genetics (NIG)
OSTI Identifier:
1268306
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Fructobacillus; Leuconostoc; comparative genomics; Fructophilic lactic acid bacteria; niche-specific evolution; metabolism

Citation Formats

Endo, Akihito, Tanizawa, Yasuhiro, Tanaka, Naoto, Maeno, Shintaro, Kumar, Himanshu, Shiwa, Yuh, Okada, Sanae, Yoshikawa, Hirofumi, Dicks, Leon, Nakagawa, Junichi, and Arita, Masanori. Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.. United States: N. p., 2015. Web. doi:10.1186/s12864-015-2339-x.
Endo, Akihito, Tanizawa, Yasuhiro, Tanaka, Naoto, Maeno, Shintaro, Kumar, Himanshu, Shiwa, Yuh, Okada, Sanae, Yoshikawa, Hirofumi, Dicks, Leon, Nakagawa, Junichi, & Arita, Masanori. Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.. United States. doi:https://doi.org/10.1186/s12864-015-2339-x
Endo, Akihito, Tanizawa, Yasuhiro, Tanaka, Naoto, Maeno, Shintaro, Kumar, Himanshu, Shiwa, Yuh, Okada, Sanae, Yoshikawa, Hirofumi, Dicks, Leon, Nakagawa, Junichi, and Arita, Masanori. Tue . "Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.". United States. doi:https://doi.org/10.1186/s12864-015-2339-x. https://www.osti.gov/servlets/purl/1268306.
@article{osti_1268306,
title = {Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.},
author = {Endo, Akihito and Tanizawa, Yasuhiro and Tanaka, Naoto and Maeno, Shintaro and Kumar, Himanshu and Shiwa, Yuh and Okada, Sanae and Yoshikawa, Hirofumi and Dicks, Leon and Nakagawa, Junichi and Arita, Masanori},
abstractNote = {In this study, Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus , based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp. As a result, Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position. In conclusion, the present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.},
doi = {10.1186/s12864-015-2339-x},
journal = {BMC Genomics},
number = 1,
volume = 16,
place = {United States},
year = {2015},
month = {12}
}

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Figures / Tables:

Table 1 Table 1: General genome characteristics of the strains analyzed

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