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Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. Th...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036050/ https://www.ncbi.nlm.nih.gov/pubmed/22452844 http://dx.doi.org/10.1264/jsme2.ME11321 |
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author | Okubo, Takashi Tsukui, Takahiro Maita, Hiroko Okamoto, Shinobu Oshima, Kenshiro Fujisawa, Takatomo Saito, Akihiro Futamata, Hiroyuki Hattori, Reiko Shimomura, Yumi Haruta, Shin Morimoto, Sho Wang, Yong Sakai, Yoriko Hattori, Masahira Aizawa, Shin-ichi Nagashima, Kenji V. P. Masuda, Sachiko Hattori, Tsutomu Yamashita, Akifumi Bao, Zhihua Hayatsu, Masahito Kajiya-Kanegae, Hiromi Yoshinaga, Ikuo Sakamoto, Kazunori Toyota, Koki Nakao, Mitsuteru Kohara, Mitsuyo Anda, Mizue Niwa, Rieko Jung-Hwan, Park Sameshima-Saito, Reiko Tokuda, Shin-ichi Yamamoto, Sumiko Yamamoto, Syuji Yokoyama, Tadashi Akutsu, Tomoko Nakamura, Yasukazu Nakahira-Yanaka, Yuka Hoshino, Yuko Takada Hirakawa, Hideki Mitsui, Hisayuki Terasawa, Kimihiro Itakura, Manabu Sato, Shusei Ikeda-Ohtsubo, Wakako Sakakura, Natsuko Kaminuma, Eli Minamisawa, Kiwamu |
author_facet | Okubo, Takashi Tsukui, Takahiro Maita, Hiroko Okamoto, Shinobu Oshima, Kenshiro Fujisawa, Takatomo Saito, Akihiro Futamata, Hiroyuki Hattori, Reiko Shimomura, Yumi Haruta, Shin Morimoto, Sho Wang, Yong Sakai, Yoriko Hattori, Masahira Aizawa, Shin-ichi Nagashima, Kenji V. P. Masuda, Sachiko Hattori, Tsutomu Yamashita, Akifumi Bao, Zhihua Hayatsu, Masahito Kajiya-Kanegae, Hiromi Yoshinaga, Ikuo Sakamoto, Kazunori Toyota, Koki Nakao, Mitsuteru Kohara, Mitsuyo Anda, Mizue Niwa, Rieko Jung-Hwan, Park Sameshima-Saito, Reiko Tokuda, Shin-ichi Yamamoto, Sumiko Yamamoto, Syuji Yokoyama, Tadashi Akutsu, Tomoko Nakamura, Yasukazu Nakahira-Yanaka, Yuka Hoshino, Yuko Takada Hirakawa, Hideki Mitsui, Hisayuki Terasawa, Kimihiro Itakura, Manabu Sato, Shusei Ikeda-Ohtsubo, Wakako Sakakura, Natsuko Kaminuma, Eli Minamisawa, Kiwamu |
author_sort | Okubo, Takashi |
collection | PubMed |
description | Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere. |
format | Online Article Text |
id | pubmed-4036050 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-40360502014-07-24 Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs Okubo, Takashi Tsukui, Takahiro Maita, Hiroko Okamoto, Shinobu Oshima, Kenshiro Fujisawa, Takatomo Saito, Akihiro Futamata, Hiroyuki Hattori, Reiko Shimomura, Yumi Haruta, Shin Morimoto, Sho Wang, Yong Sakai, Yoriko Hattori, Masahira Aizawa, Shin-ichi Nagashima, Kenji V. P. Masuda, Sachiko Hattori, Tsutomu Yamashita, Akifumi Bao, Zhihua Hayatsu, Masahito Kajiya-Kanegae, Hiromi Yoshinaga, Ikuo Sakamoto, Kazunori Toyota, Koki Nakao, Mitsuteru Kohara, Mitsuyo Anda, Mizue Niwa, Rieko Jung-Hwan, Park Sameshima-Saito, Reiko Tokuda, Shin-ichi Yamamoto, Sumiko Yamamoto, Syuji Yokoyama, Tadashi Akutsu, Tomoko Nakamura, Yasukazu Nakahira-Yanaka, Yuka Hoshino, Yuko Takada Hirakawa, Hideki Mitsui, Hisayuki Terasawa, Kimihiro Itakura, Manabu Sato, Shusei Ikeda-Ohtsubo, Wakako Sakakura, Natsuko Kaminuma, Eli Minamisawa, Kiwamu Microbes Environ Regular Paper Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere. Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology 2012-09 2012-03-28 /pmc/articles/PMC4036050/ /pubmed/22452844 http://dx.doi.org/10.1264/jsme2.ME11321 Text en Copyright © 2012 by the Japanese Society of Microbial Ecology / the Japanese Society of Soil Microbiology http://creativecommons.org/licenses/by/3.0 This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Regular Paper Okubo, Takashi Tsukui, Takahiro Maita, Hiroko Okamoto, Shinobu Oshima, Kenshiro Fujisawa, Takatomo Saito, Akihiro Futamata, Hiroyuki Hattori, Reiko Shimomura, Yumi Haruta, Shin Morimoto, Sho Wang, Yong Sakai, Yoriko Hattori, Masahira Aizawa, Shin-ichi Nagashima, Kenji V. P. Masuda, Sachiko Hattori, Tsutomu Yamashita, Akifumi Bao, Zhihua Hayatsu, Masahito Kajiya-Kanegae, Hiromi Yoshinaga, Ikuo Sakamoto, Kazunori Toyota, Koki Nakao, Mitsuteru Kohara, Mitsuyo Anda, Mizue Niwa, Rieko Jung-Hwan, Park Sameshima-Saito, Reiko Tokuda, Shin-ichi Yamamoto, Sumiko Yamamoto, Syuji Yokoyama, Tadashi Akutsu, Tomoko Nakamura, Yasukazu Nakahira-Yanaka, Yuka Hoshino, Yuko Takada Hirakawa, Hideki Mitsui, Hisayuki Terasawa, Kimihiro Itakura, Manabu Sato, Shusei Ikeda-Ohtsubo, Wakako Sakakura, Natsuko Kaminuma, Eli Minamisawa, Kiwamu Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title | Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title_full | Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title_fullStr | Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title_full_unstemmed | Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title_short | Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs |
title_sort | complete genome sequence of bradyrhizobium sp. s23321: insights into symbiosis evolution in soil oligotrophs |
topic | Regular Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036050/ https://www.ncbi.nlm.nih.gov/pubmed/22452844 http://dx.doi.org/10.1264/jsme2.ME11321 |
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