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INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH
Nadadur, S. S. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH. Presented at Nat'l Symp on Molecular Maneuverings in Biological Defense Systems, Prasanthi Nilayam, India, August 8-10, 2003.
Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and functional genomics. Understanding the number of genes, coding genes, sequence homology, their expression, regulation and protein function can only be achieved by a comparative analysis. The most interesting aspect of this field is its contribution to our understanding of how various species are related and different from others in the evolution tree at the molecular level.
All our understanding of basic metabolic pathways and cell cycle regulation has came from elegant studies carried out using model organisms such as yeast and worm. Comparative sequence homology of worm/yeast cDNA/protein sequences led to the identification of homologous genes for specific cell cycle proteins and signaling mediators for this process. With the availability of complete genome sequences for the worm, yeast, fly (Drosophila melanogaster) and human, the efforts to identify homologous genes/proteins is carried out at the genome level instead of gene to gene homology searches. Along with the genome sequencing efforts, we have made strides in developing and integrating high throughput technologies to screen for the expression of thousands of genes in one single experiment. Incorporating the genome efforts, with expression profiling along with the evolutionary biology, has led to new branch of biology called comparative genomics.
Two classical comparative genomics studies convincingly demonstrated conservation of genome elements for basic essential components of cell as well as certain specialized functions in human.
Yeast vs Worm: Comparison of 6,217 yeast open reading frames (ORFs) with 19,099 ORFs of worm suggested that the core biological processes of the two organisms are carried out by a similar number of proteins (1). This degree of conservation was observed not just for intermediary metabolism, DNA/RNA metabolism, protein folding and degradation but also in proteins for signal transduction. This was not a surprise as the worm RAS homolog let-60 is involved in a variety of signaling is homologous to yeast RAS1 and RAS2 genes (2). Similarly the yeast CDC28 and worm ncc-1 form an orthologous pair in the cyclin-dependent kinase family and are demonstrated to be interchangeable illustrating functional conservation in vivo (3).
Fly, Yeast and Worm Vs Human: Using the genome comparison of three eukaryotic model organisms Rubin et al., (4) have carried out an exploratory search to identify the possible orthologs for human disease genes in these genome. When a set of 289 genes that are implicated in the disease process either due to mutation, alteration, amplification or deletion were selected and searched 61% of genes (177) had orthologs in Drosophila. About 68% of cancer genes had orthologs in the fly. Most of the genes implicated in human neurological diseases had an ortholog in fly and worm and some even in the yeast (4).
These and many other studies clearly indicated the importance of our understanding on orthologs their identification and study in model organisms to gain insights into their function in human. Makalowski and Boguski (5) made an extensive survey on well characterized human-rodent orthologs and as expected found high conservation in both amino acid and corresponding DNA coding sequences. Along with this a very high degree of conservation in the untranslated regions (UTRs) flanking the coding sequences have been observed. This observation has opened up opportunities to explore the more than eight million expressed sequence tag (EST) sequences for identification of orthologs across the species even though they might not have been functionally characterized. The Institute of Genome Research (TIGR) is utilizing this approach to develop a database for orthologous gene alignments (6). The conservation of orthologs observed in essential components may also be preserved. If so, orthologous genes for the signaling pathways mediating stress response pathways shared across the species can provide insights into similar pathways that are implicated in many pathological conditions. With this hypothesis we have initiated studies to identify orthologous gene index for oxidative stress response using global gene expression analysis.
Major research emphasis of our laboratory is to identify the toxic constituents and molecular mechanisms of action for ambient particulate matter (PM) supporting the US EPA's mission on Clean Air Act. As with many environmental toxicology studies, PM health effects research also suffer from the lack of suitable molecular markers derived from laboratory animal studies and this problem is much more complicated in the case of PM as it's a complex pollutant. Preliminary comparative in vitro studies using human and rodent endothelial cells and global gene expression profiling analysis indicated some interesting observations supporting the usefulness of such an approach (7).
This abstract has been reviewed by the National Health and Environmental Effects Research Laboratory and approved for presentation. Approval does not signify that the contents reflect
Record Details:Record Type: DOCUMENT (PRESENTATION/ABSTRACT)
Organization:U.S. ENVIRONMENTAL PROTECTION AGENCY
OFFICE OF RESEARCH AND DEVELOPMENT
NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY
EXPERIMENTAL TOXICOLOGY DIVISION
PULMONARY TOXICOLOGY BRANCH