Preamble

Genomics has become the new paradigm in biology and takes a holistic approach to molecular biology and evolution by studying the complete genome and its protein expression patterns. The recent publications on the sequence and analysis of the human, plant, microbial and fungal genomes represent a hallmark in genomics and the flood of genome information will give rise to exciting opportunities in bioinformatics, proteomics, structural genomics and in silico drug discovery programmes. Nevertheless, despite the rapid advances in genomics, genome sequencing in Malaysia is still relatively a new discipline. To enable Malaysia to harness the vast potential of genomics, a post-genomics approach needs to be integrated into the national research infrastructure in order to leapfrog the current sequencing programmes. Herein, we proposed a genomics project on two model organisms ie locally important bacterial pathogen Burkholderia pseudomallei and local avian protozoan, Eimeria tenella.

Functional Genomics of Burkholderia pseudomallei

Burkholderia pseudomallei is a pathogenic bacterium that secretes various extracellular products implicated in the pathogenesis of the fulminating disease, melioidosis. The importance of melioidosis locally in not fully appreciated and this is disturbing as there is no licensed vaccine against melioidosis and the bacterium is resistant to many antibiotics. A substantial amount of biological information on the pathogenicity of this organism has accumulated as a result of extensive research by various groups locally and abroad. Genomic data will complement this biological information in understanding the evolution of pathogenicity, the development of new preventive and therapeutic strategies and the implementation of new diagnostic measures. A human strain of this organism is currently being sequenced at the Sanger Centre (UK).

Functional genomics dissects entire genomes to gain new insights into evolutionary, biochemical, genetic, metabolic, and physiological pathways. It offers clear opportunities to understand how species have responded to challenges in the environment and can point to genes that help us identify and characterise virulence factors and in vivo survival mechanisms of the invading microorganism. Hence, we propose to identify proteins that are responsible for virulence, pathogenesis, host specificity and survival and the induction of protective immune responses by utilizing information generated from the Sanger Centre B. pseudomallei sequencing efforts. This in turn will provide the basis for designing effective vaccines, antimicrobial agents and diagnostic reagents for this important pathogen. The data accumulated from this work should establish a knowledge base in which sequence data is linked usefully to other biological information about B. pseudomallei and related microorganisms. On-going current research in local universities and research institutions on vaccine production, host-pathogen interactions, immunology of melioidosis and pathogen can benefit enormously from the gene information and this should assist in promoting these research projects. Information on the extracellular virulent factors can be used to design novel vaccine candidates, particularly DNA vaccines. The work will provide a major advance in our understanding of an organism that is important in veterinary and biological science.

 

EXECUTIVE SUMMARY

Project Title:
MICROBIAL GENOMICS FOR GENE AND NATURAL
PRODUCT DISCOVERY

 

 

Derivation of the Eimeria tenella Genome Sequence

Eimeria species are protozoan parasites of huge significance in the agricultural industry where they cause coccidiosis in poultry, cattle and sheep. Genetic resistance to all the major classes of anticoccidial drugs is well documented and continues to increase. Placed in the phylum Apicomplexa, they are related to other protozoan parasites of medical and veterinary significance including Plasmodium, Toxoplasma and Cryptosporidium. Thus, comparative sequencing between different apicomplexans will prove invaluable for identifying fundamental mechanisms and pathways in these parasites and will dramatically increase the likelihood of developing new control strategies through gene discovery and functional post-genomic approaches. There is a high level of support within the international Apicomplexan research community for the sequencing of the highly pathogenic Eimeria tenella genome. An international scientific consortium (U.K., Brazil & Malaysia) has recently been formed to initiate such a project. This international consortium will provide an opportunity to contribute significantly in this field and serve as a platform for the transfer of technologies associated and critical for such projects of genomic scale.

Thus this project aims to acquire and utilise platform technologies to undertake functional genomics of two model pathogens in our effort to identify gene products and pathways responsible for virulence. Concomitantly, potential vaccine candidates and intervention protocols can be proposed for these locally and globally important pathogens. The research approach proposed will involve state-of-the-art technologies such as high-throughput cloning, sequencing, data analysis, data mining and expression profiling.

Period of the project : 3 Years (2001 - 2004)

Achievements

Progress/Achievements for year one

Discovery

1. Datamining of genes involved in virulence and carbon utilization pathways were completed (100 % achieved) 2. Cloning of putative ORFs identified in 1 are being undertaken (85% achieved) 3. Sequencing of chromosome 1 and 2 of Eimeria tenella were completed (100% achieved) 4. Sequence gap identification and closure were being undertaken (80% achieved)

Status

- On-going