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Evolutionary studies of Corynebacteria by comparative genomics.
https://ir.soken.ac.jp/records/1016
https://ir.soken.ac.jp/records/10167a725bcb-5682-4983-9b8e-3088dd5135e7
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要旨・審査要旨 (264.6 kB)
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本文 (7.7 MB)
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| Item type | 学位論文 / Thesis or Dissertation(1) | |||||
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| 公開日 | 2010-02-22 | |||||
| タイトル | ||||||
| タイトル | Evolutionary studies of Corynebacteria by comparative genomics. | |||||
| タイトル | ||||||
| タイトル | Evolutionary studies of Corynebacteria by comparative genomics. | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_46ec | |||||
| 資源タイプ | thesis | |||||
| 著者名 |
西尾, 陽介
× 西尾, 陽介 |
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| フリガナ |
ニシオ, ヨウスケ
× ニシオ, ヨウスケ |
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| 著者 |
NISHIO, Yousuke
× NISHIO, Yousuke |
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| 学位授与機関 | ||||||
| 学位授与機関名 | 総合研究大学院大学 | |||||
| 学位名 | ||||||
| 学位名 | 博士（理学） | |||||
| 学位記番号 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | 総研大乙第148号 | |||||
| 研究科 | ||||||
| 値 | 生命科学研究科 | |||||
| 専攻 | ||||||
| 値 | 18 遺伝学専攻 | |||||
| 学位授与年月日 | ||||||
| 学位授与年月日 | 2005-09-30 | |||||
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| 値 | 2005 | |||||
| 要旨 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | Corynebacterium efficiens is a gram-positive non-pathogenic bacterium previously known as Corynebacterium thermoaminogenes. This strain has recently been shown to be a near relative of Corynebacterium glutamicum and Corynebacterium callunae, both of which are recognized as glutamic acid-producing Corynebactetrium. The optimal temperature for glutamate production by C. glutamicum is around 30℃, and this microorganism can neither grow nor produce glutamate at 40℃ or above. On the other hand, C. efficiens can grow and produce glutamate above 40℃. The glutamic-acid-producing species of corynebacteria are known to overproduce glutamic acid under a variety of conditions, such as biotin limitation, although the mechanism of this phenomenon remains unclear. Another member of this genus, Corynebacterium diphtheriae, is a well-known pathogen that does not produce glutamic acid. The purpose of the present study is to elucidate the mechanism underlying the thermal stability of C. efficiens and to investigate the evolutionary processes that are related to the glutamic-acid-overproduction mechanisms in C. glutamicum and C. efficiens through considering the genome evolution of Corynebacterium. In order to describe the mechanisms, I conducted a comparative genomics study using a genome-wide comparison of amino-acid substitutions and metabolic pathways using whole genome sequences.<br /> This thesis comprises five chapters. In chapter 1, I describe the research background on this study, placing particular emphasis on the relationship between thermostability and fermentation. I noted that the industrial fermentation process could be carried out at a higher temperature; it might be possible to reduce the electric power consumption and carbon dioxide generation <br /> In chapter 2, I describe the thermostability mechanism of C. efficiens revealed by the complete genome sequence comparison between C. efficiens and C. glutomicum. Differences in the growth temperature, protein stability and GC content between C. efficiens and C. glutamicum can be investigated through comparative genomics using the complete genome sequences of these bacteria. Because these two species are phylogenetically closely related, more than 1,000 orthologous genes with 60-95% amino-acid sequence identity can be compared. Taking an advantage of comparative genomic studies, I found that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that tree substitutions from lysine to arginine, serine to alanin, and serine to threonine, are important for the thermostability of the C. efficiens proteins. On the basis of these findings, I suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens. <br /> In chapter 3, I make an attempt to understand the evolutionary process involved in the ability of amino acid production in Corynebacterium. To attain this purpose, I analyzed the differentiation of metabolic pathways based on a comparative genome analysis of high GC Gram-positive bacteria, including Mycobacterium and Streptomyces. When Mycobacterium and Streptomyces were used as outgroups, the comparative study suggested that the common ancestor of Corynebacteria already possessed almost all of the gene sets necessary for amino acid production. However, C. diphtheriae was found to have lost the genes responsible for amino acid production. Moreover, I found that the common ancestor of C. efficiens and C. glutamicum have acquired some of genes responsible for amino acid production by horizontal gene transfer. Thus, I show that the evolutionary events of gene loss and horizontal gene transfer must have been responsible for functional differentiation in amino acid biosynthesis of the three species of Corynebacteria. <br /> In chapter 4, I discuss the evolutionary process for glutamic acid overproduction mechanism under the biotin limitation condition in C. glutamicum. To attain this pupose, I compared between the biotin biosynthesis related genes in high GC Gram-positive bacteria. I found that the complete biotin biosynthesis pathnay was inherited in C. diphtheriae, while C. glutamicum and C. efficiens only possessed an incomplete pathway. Furthermore the complete biotin biosynthesis pathway in C. diphtheriae suggested to be achieved by the horizontal gene transfer. I conclude that this evolutionary event may have affected metabolic regulation in corynebacteria following the loss of the glutamic acid overproduction mechanism in C. diphtheriae. <br /> Finally, in chapter 5, I describe the summary and the conclusion of the present study. This study acquired significant knowledge of the protein thermostabilization mechanism and evolutionary process for amino acid production mechanism in Corynebacterium by conducting whole genome comparisons. I conclude that this study gives significant insight to the evolutionary process of bacterial diversity from view point of genome evolution. <br /> | |||||
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| 値 | 有 | |||||
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| 内容記述タイプ | Other | |||||
| 内容記述 | application/pdf | |||||
