BK 초청세미나 (한국생명공학연구원, 김지현박사)
생명과학과
2011-10-14
세미나 장소 : j311
세미나 일시 : 2011.11.10. (16:30)
세미나 발표자 : 한국생명공학연구원 김지현박사
세미나 일시 : 2011.11.10. (16:30)
세미나 발표자 : 한국생명공학연구원 김지현박사
Genome Dynamics and Evolution of Escherichia coli - Friend or Foe
Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We determined the complete genome sequences of E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the λ attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have 99% sequence identity over ∼92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagellar genes in B, due to a 41-kb IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal gene transfer. Comparative analysis of 32 E. coli and Shigella genomes, both commensals and pathogenic strains, identified a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome. Pathogens such as EAEC, ETEC, EPEC, EHEC, EIEC, UPEC, APEC, and Shigella strains possess various pathogenicity/virulence factors and toxins encoded in pathogenicity islands, virulence plasmids, and prophages. On the other hand, the relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. We thus sequenced genomes sampled through 40,000 generations from a laboratory population of E. coli REL606. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.
Biography: Dr. Jihyun F. Kim is a principal research scientist at the Systems and Synthetic Biology Research Center of the Korea Research Institute of Bioscience and Biotechnology (KRIBB). He served as the director of the center between 2008 and 2011, and provides leadership overseeing matters among others pertaining to the investigation of microbiology, genomic sciences, systems/synthetic biology, and next-generation biotechnology. He got his bachelor's and master's degrees at Seoul National University. He then served as an agricultural researcher at Rural Development Administration in Korea for a year. With a doctorate in Molecular Plant Pathology at Cornell University in 1997 partly supported by Korean Government's Overseas Scholarship, Dr. Kim was employed as a postdoctoral associate at the same institution for three years. He began his career as a professional scientist in microbial genomics at KRIBB in 2000, and is affiliated with the University of Science and Technology (UST) and more recently the Korea Advanced Institute of Science and Technology (KAIST) as an adjunct professor. Among many scientific accomplishments, including several awards and a number of highly cited publications on evolution, genomes and pathogenicity of bacterial systems, he is proud of filing patents for his study when he was still a graduate student. As a project leader, he continually seeks innovative approaches for his research, a position in which he finds great satisfaction.