Main theme of research: Microbial metabolism & diversity
The terms, Biodegradation, Biotransformation, and Biocatalysis (B3), which comprise the title of the conference held in San Juan, Puerto Rico, 2001, all deal with the same thing: microbial metabolism. Which term is used depends on the interest of researchers studying it. If their interest is in degrading environmental pollutants, they are said to study biodegradation. In contrast, industrialists using microbial metabolism are said to conduct biotransformation or biocatalysis. Microbial activities in the biosphere are a necessary prerequisite for the establishment of a carbon cycle. Microbial metabolism has been drawing increasing concerns with respect to its environmental and industrial applicability. One of the major interests of our lab is various kinds of microbial metabolism that occur in the natural environment. Microbial diversity has long been an important issue in the field of microbiology. Recent developments in the next generation sequencing technologies such as pyrosequencing and Illumina technology have been expanding our knowledge in microbial ecology. Microbial metabolism combined with ecological aspects would give us a better understanding of natural ecosystem.
Biodegradation and Bioremediation
One of the promising fields of microbial biotechnology is ‘bioremediation’, which develops for treating polluted environment by introducing biological agents in environmentally friendly manners. Bioremediation will apparently play an important role as a future methodology. The use of microbial cells or enzymes has tremendous effects upon contaminated soils and waste effluents. The principles of bioremediation technology are based on biodegradation by microorganisms. Microbial degradation varies from organism to organism and from compound to compound. Our lab is most interested in various chemistry, biochemistry and genetics involved in xenobiotic degradation to understand why particular compounds may not be susceptible to microbial degradation, and how microorganisms overcome these problems by evolving new catabolic activities. Studies have been focused on the elucidation of metabolic pathways related to biodegradation. Initial studies are aimed at isolating novel bacteria capable of degrading xenobiotic compounds such as environmental pollutants, endocrine disruptors and pharmaceutical drugs in the contaminated environments. A good combination of a variety of criteria, such as microbiology, ecology, chemistry, biochemistry and molecular biology, will result in better understanding of “biodegradation”.
: genomics, proteomics and bioinformatics in microbial metabolism research
A new paradigm of contemporary biological sciences is integrated “omics” based on the genome sequence of a given organism. Functional genomics approach is very useful to elucidate microbial metabolism of interest. Our lab has recently completed genome sequencing of some bacteria which show interesting metabolic activities. Analyses of transcriptome by RNA-Seq and proteome by LC-MS/MS are powerful tools to study microbial metabolism. By this approach, comparison of gene expression patterns can lead to a better understanding of up- or down regulated genes under various environmental stresses.
Biotransformation and novel biocatalysts
A promising field in microbial biotechnology is ‘biotransformations’. Microbial enzymes and metabolic pathways have been exploited by industry for many years for the production of primary and secondary metabolites. A variety of reactions catalyzed by microbial enzymes provide a wide selection of organic transformations. The use of enzymes or microbial cells is efficient as microbial enzymes are often chiral catalysts with rigid substrate binding properties, effecting reactions of high stereo- or enantiospecificity. Discovery of novel biocatalysts has a great potential for industrial applications. Our lab has been interested in the biotransformation of natural compounds such as plant secondary metabolites to produce highly value-added chemicals that have biological and pharmaceutical activities. These studies can be started from the isolation of microbes capable of such metabolic activities. Elucidation of metabolic pathway and the enzymes mediating the pathways will be the next.
Microbial enzyme developments: cellulases for bioethanol production
Cellulases are known as complex enzyme system which catalyzes saccharification of lignocellulosic biomass to glucose for bioethanol production. Our studies have been focused on molecular and biochemical studies on three major class of cellulases; exoglucanases, endoglucanases and b-glucosidases from the brown-rot fungus Fomitopsis palustris. Other types of glycosyl hydrolase family are also of interest.
Bacterial systematics (taxonomy)
One of our lab’s routine jobs is to isolate bacteria from the natural environments such as tidal flat sediments and soils etc. Characterization of such isolates can be done by using polyphasic taxonomy approach. Phylogenetic analyses are performed based on 16S rRNA gene sequences. Phenotypic characterization including chemotaxonomic properties is also carried out for the classification of bacterial isolates. Our lab recently reported a number of novel bacteria which were proposed as new taxa.
Microbial diversity: metagenomics & metaproteomics
Recent developments in the next generation sequencing technologies such as pyrosequencing enable in-depth knowledge in microbial ecology. Microbial community structure using metagenommic approach is now essential to explore any microbial ecosystems. Metaproteomic approach based on LC-MS/MS can also be a good tool to understand microbial ecosystems. Recent studies on microbial ecology in Korean traditional fermentation foods, animal intestines and soils are under progress.