题目：Genome scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis
时间：2013年6月25日(周二)上午10：00
地点：生物质能源研究所会议室
报告人简介：
William B. Whitman博士，美国佐治亚大学微生物系系主任，微生物学教授，同时兼任International Journal of Systematic Bacteriology副主编，Journal of Bacteriology编委，Bergey’s Manual责任主编，美国NIH，DOE,NSF等项目评审专家，并曾担任多个重要微生物国际会议的主席，在国际微生物学领域具有很高的学术地位和声誉。Whitman教授长期专注于微生物学研究，尤其在产甲烷菌的研究方面取得了杰出的研究成果，近3年在Nature, PNAS, JBC等国际顶级期刊发表研究论文30余篇。由于在微生物研究领域的突出贡献，Whitman博士被遴选为美国微生物科学院(American Academy of Microbiology, AAM)院士，美国科学促进会会士(The American Association for the Advancement of Science Fellow)，并荣获美国青年科学家总统奖，伯杰氏奖章等多个杰出奖项。
报告内容摘要：
Genome scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis
William B. Whitman, Department of Microbiology
University of Georgia, Athens GA 30602 USA
Methanogenic archaea are obligate anaerobic prokaryotes and widely distributed in O2-free environments where electron acceptors other than CO2 have been depleted. Methanogenesis is a highly specialized anaerobic respiration with a distinctive biochemistry composed of unusual coenzymes and catalysts whose roles are poorly understood. In anaerobic environments, it plays a key role, catalyzing the terminal step of carbon mineralization and maintaining an extremely low partial pressure of H2. Methane, the final product of this process, is also a significant greenhouse gas with about 80% of the atmospheric methane produced by these archaea .
Our understanding of the methanogenic archaea is far from complete. For instance, the methanogen Methanococcus maripaludis S2 possesses 1,728 protein coding genes, only a few of which have been characterized and an even smaller portion has been studied in detail. Close to 800 genes remain annotated as hypothetical proteins awaiting proper identification (1). Much of this uncertainty is shared with other archaea, where many of the fundamental life processes have not been investigated in the same detail as in bacteria and eukaryotes. To address these issues, the essentiality of methanococcal genes was evaluated by a saturation mutagenesis technique. Whole-genome libraries of Tn5 transposon mutants were constructed, and about 89,000 individual mutations were mapped following enrichment of the transposon-chromosomal DNA junctions and Illumina sequencing (Tn-seq). Because mutations in genes that are likely to be essential or strongly advantageous for growth are lethal or rapidly lost from the library, they may be identified by their low frequency in the libraries. Although definitive assignments of essentiality still require detailed analyses of each gene, the methodology generates hypotheses about the nature of specific genes and a great deal of insight into specific questions regarding methanogens as well as more general questions about the genetics, biochemistry and physiology of archaea.
By this methodology, about 30% of the genome appears to be possibly essential or strongly advantageous for growth. Many of these genes were homologous to eukaryotic genes that encode fundamental processes in replication, transcription, and translation, providing direct evidence for their importance in Archaea. Some genes classified as essential were unique to archaeal or methanococcal lineages, such as the genes encoding the DNA polymerase PolD. In contrast, the gene encoding the DNA polymerase B was not essential for growth, a conclusion which was confirmed by constructing an independent deletion mutant. Thus, PolD and not PolB is likely to play a fundamental role in DNA replication in methanococci. Similarly, 121 hypothetical ORFs were classified as possible essential and are likely to play fundamental roles in methanococcal information processing or metabolism that are not established outside this group of prokaryotes.
