The Methylome and Deep RNome in Clostridium: New Gadgets Uncover Larger Cellular Complexity
Event details
| Date | 12.12.2014 |
| Hour | 12:30 |
| Speaker | Prof. Eleftherios Terry Papoutsakis, University of Delaware, Newark, DE (USA) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
New technologies now enable a considerably more detailed picture of the state of nucleic acids in organisms, and notably of the DNA methylation and the deep, strand-specific RNome. Here we examined the methylome (state of DNA methylation) of Clostridium acetobutylicum and C. pasterianum under normal and, for C. acetobutylicum, metabolite stress conditions. We also used Illumina-based strand-specific RNAseq to probe the deep RNome of C. acetobutylicum under both normal and stress conditions.
Several strains of C. acetobutylicum and C. pasterianum were sequenced and assembled via Single Molecule Real-Time (SMRT; PacBio) sequencing. The WT C. pasterianum type was assembled into 2 contigs (4.4 Mb) and was compared to the previously published version of the same strain, which exists in 37 contigs with a total length of 4.28 Mb. Mutations introduced to an evolved, more tolerant to crude glycerol C. pasterianum strain were identified by sequence comparison to the WT. DNA methylation patterns identified with SMRT sequencing were used to aid in optimization of transformation efficiency of plasmid DNA. The DNA methylome of C. acetobutylicum under normal versus metabolite stress conditions was also compared aiming to understand the impact of stress on DNA methylation and if this is possibly related to cell survival and gene expression. Strand-specific RNAseq was employed to explore the complex transcriptome of these two organisms, with emphasis on identifying strand-specific expression of small RNAs (both cis and trans), unknown genes, and also transcriptional start sites to probe the impact of culture conditions on the rich RNome of these organisms. The results demonstrate a much richer RNome that could anticipated, to the point in fact that the expected RNome based on the genome is only a small fraction of the experimentally observed strand-specific RNome. The information that can be extracted from such data leads to new ways to solve old problems, and significantly provides a much deeper understanding of the inner workings of the cells.
Bio:
Dr. Papoutsakis comes to UD from Northwestern University, where he served as Walter P. Murphy Professor of Chemical and Biological Engineering and also was a member of the Lurie Comprehensive Cancer Center of the Northwestern University Medical School. Before that, he was a member of the Rice University faculty.
His research focuses on areas of systems biology, metabolic engineering, experimental and computational genomics with applications in stem-cell biology and prokaryotic biology for the production of biofuels and chemicals from biomass.
A fellow of the American Academy of Microbiology and the American Association for the Advancement of Science and a founding fellow of the American Institute of Medical and Biological Engineers, Papoutsakis also has received several awards, including the Amgen Biochemical Engineering Award and the Merck Cell Culture Engineering Award, both from the from Engineering Conferences International; the Alpha Chi Sigma Award and the Food, Pharmaceutical and Bioengineering Award, both from the American Institute of Chemical Engineers; and the Marvin Johnson Award and the Van Lanen Award, both from the Biochemical Technology Division of the American Chemical Society. Papoutsakis has published extensively in his field and served as editor-in-chief of Biotechnology and Bioengineering. He also serves on the advisory boards of four journals in the field of biotechnology and tissue engineering, and on the organizing committees or advisory boards of many international meetings. He has authored several issued and pending patents. He has served or serves on the Scientific Advisory Boards (SAB) of four biotechnology companies. He consults regularly and offers expert witness services in the field of biotechnology, and biomedical sciences more broadly.
A graduate of the National Technical University of Athens, Greece, Papoutsakis received his Master's and Doctoral degrees from Purdue University.
Abstract:
New technologies now enable a considerably more detailed picture of the state of nucleic acids in organisms, and notably of the DNA methylation and the deep, strand-specific RNome. Here we examined the methylome (state of DNA methylation) of Clostridium acetobutylicum and C. pasterianum under normal and, for C. acetobutylicum, metabolite stress conditions. We also used Illumina-based strand-specific RNAseq to probe the deep RNome of C. acetobutylicum under both normal and stress conditions.
Several strains of C. acetobutylicum and C. pasterianum were sequenced and assembled via Single Molecule Real-Time (SMRT; PacBio) sequencing. The WT C. pasterianum type was assembled into 2 contigs (4.4 Mb) and was compared to the previously published version of the same strain, which exists in 37 contigs with a total length of 4.28 Mb. Mutations introduced to an evolved, more tolerant to crude glycerol C. pasterianum strain were identified by sequence comparison to the WT. DNA methylation patterns identified with SMRT sequencing were used to aid in optimization of transformation efficiency of plasmid DNA. The DNA methylome of C. acetobutylicum under normal versus metabolite stress conditions was also compared aiming to understand the impact of stress on DNA methylation and if this is possibly related to cell survival and gene expression. Strand-specific RNAseq was employed to explore the complex transcriptome of these two organisms, with emphasis on identifying strand-specific expression of small RNAs (both cis and trans), unknown genes, and also transcriptional start sites to probe the impact of culture conditions on the rich RNome of these organisms. The results demonstrate a much richer RNome that could anticipated, to the point in fact that the expected RNome based on the genome is only a small fraction of the experimentally observed strand-specific RNome. The information that can be extracted from such data leads to new ways to solve old problems, and significantly provides a much deeper understanding of the inner workings of the cells.
Bio:
Dr. Papoutsakis comes to UD from Northwestern University, where he served as Walter P. Murphy Professor of Chemical and Biological Engineering and also was a member of the Lurie Comprehensive Cancer Center of the Northwestern University Medical School. Before that, he was a member of the Rice University faculty.
His research focuses on areas of systems biology, metabolic engineering, experimental and computational genomics with applications in stem-cell biology and prokaryotic biology for the production of biofuels and chemicals from biomass.
A fellow of the American Academy of Microbiology and the American Association for the Advancement of Science and a founding fellow of the American Institute of Medical and Biological Engineers, Papoutsakis also has received several awards, including the Amgen Biochemical Engineering Award and the Merck Cell Culture Engineering Award, both from the from Engineering Conferences International; the Alpha Chi Sigma Award and the Food, Pharmaceutical and Bioengineering Award, both from the American Institute of Chemical Engineers; and the Marvin Johnson Award and the Van Lanen Award, both from the Biochemical Technology Division of the American Chemical Society. Papoutsakis has published extensively in his field and served as editor-in-chief of Biotechnology and Bioengineering. He also serves on the advisory boards of four journals in the field of biotechnology and tissue engineering, and on the organizing committees or advisory boards of many international meetings. He has authored several issued and pending patents. He has served or serves on the Scientific Advisory Boards (SAB) of four biotechnology companies. He consults regularly and offers expert witness services in the field of biotechnology, and biomedical sciences more broadly.
A graduate of the National Technical University of Athens, Greece, Papoutsakis received his Master's and Doctoral degrees from Purdue University.
Practical information
- Informed public
- Free