The Clostridia are a diverse group of Gram-positive bacteria that include several pathogens and many terrestrial species that
produce solvents and organic acids through fermentation of a variety of carbon sources. However, the knowledge about
carbohydrate utilization pathways and their regulation in
spp. is rather limited. Accurate projection of known
carbohydrate catabolic pathways across diverse bacteria with complete genomes is quite challenging due to frequent variations
in components of these pathways.
In this study we combine comparative genomics with experimental techniques to reconstruct sugar utilization pathways
species directly from their genome sequences. The subsystems-based comparative genomic approach was
used, which integrates the analysis of conserved operons and regulons with pathway reconstruction across a large variety of
genomes. This approach allows us to significantly improve the accuracy of genomic annotations and to identify previously
uncharacterized genes involved in clostridial sugar metabolism. The predicted gene functions are then experimentally verified
through a combination of genetic and biochemical techniques. Comparison of the reconstructed catabolic pathways with
identified substantial variations including non-orthologous gene replacements and families of paralogous
proteins with different susbtrate specificity. Our long-term goal is to build a comprehensive knowledge base of carbohydrate
utilization pathways in various
species. This knowledge base is important for bioengineering and biomedical
spp. as well as for analysis of metagenomic data.
Chen Yang is a professor in the Key Laboratory of Synthetic Biology, Chinese Academy of Sciences. She completed her B.S. in biochemical
engineering from Zhejiang University in 1994 and Ph.D. in biochemical engineering and science from Kyushu Institute of Technology, Japan, in
2001. From 2001 to 2008 she was a postdoctoral fellow in Keio University, Japan, and then in Burnham Institute for Medical Research, USA. Dr.
Yang has published over 20 papers in prestigious journals. Her current research is focused on comparative genomics and metabolic flux analysis
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