REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
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REVIEW THE STATUS OF GENOME ANALYSIS OF CULTURED ARCHAEA
- 2. GENOME Entirety of an organism's hereditary information Includes both the genes and the non-coding sequences of the DNA/RNA The genome is vast in terms of its informational content. Composed of chemical symbols designated by a four-letter alphabet of A's, T's, C's, and G's, the human genome is some 3.2 billion letters in length Availability of genome sequences provides opportunity to explore genetic variability both between organisms and within the individual organism
- 3. Background Biologists have organized living things into large groups called kingdoms. There are six of them: Archaebacteria Eubacteria Protista Fungi Plantae Animalia
- 4. Some recent findings… In 1996, scientists decided to split Monera into two groups of bacteria: Archaebacteria and Eubacteria Because these two groups of bacteria were different in many ways scientists created a new level of classification called a DOMAIN. Now we have 3 domains 1. Bacteria 2. Archaea 3. Eukarya
- 5. The domain ARCHAEA “Ancient” bacteria Some of the first archaebacteria were discovered in Yellowstone National Park’s hot springs and geysers. Numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle.
- 6. Basic Facts They live in extreme environments (like hot springs or salty lakes) and normal environments (like soil and ocean water). All are unicellular (each individual is only one cell). No peptidoglycan in their cell wall. Some have a flagella that aids in their locomotion.
- 8. Why to study ARCHAEA? As one of the most ancient lineages of living organisms, the archaea set a boundary for evolutionary diversity and have the potential to offer key insights into the early evolution of life, including the origin of the eukaryotes. Many archaea are also extremophiles that flourish at high temperature, low or high pH, or high salt and delineate another boundary for life, the biochemical and geochemical boundary, which sets the physical limits of the biosphere. Finally, some archaea are fundamental components of the biogeochemical cycles on earth or dominate special ecosystems that are of great interest (such as the methanogens).
- 9. Archaea with sequenced genome or ongoing genome projects
- 11. Published studies involving genomic analyses
- 12. Genome analysis of some cultivated archaea published in NCBI a. Methanobrevibacter smithii (Human gut methanogen) b. Sulfolobus islandicus (Hyperthermophilic acidophilic sulfur-metabolizing archeon)
- 14. A genomic analysis of the archaeal system Ignicoccus hospitalisNanoarchaeum equitans
- 15. The crenarchaeaote Ignicoccus hospitalis is a specific host for Nanoarchaeum equitans. Both the organisms represent hyperthermophilic lineages and inhabit types of ecosystems that are often considered to be ancient. The genome of I. hospitalis consists of a single circular chromosome
- 16. General features of I. hospitalis genome
- 18. Genome sequencing and functional annotation DNA isolation proteinase K digestion method Sequencing & assembly Automated gene prediction Sequence translation tRNAScanSE tool tRNA genes were fined BLASTn rRNA genes were fined
- 19. Comparative genomic analysis Analysis of the I. hospitalis and N. equitans genomes IMG system operons were identified Phyre tool Structure fold prediction blastclust analyses frequency of paralogs
- 20. Phylogenetic analysis protein sequence was blasted sequences with significant hits were retrieved CLUSTALW and aligned with the query sequence PAUP tool Phylogenetic trees were then constructed
- 21. Conclusion….. Pioneering groundwork in the archaeal research field has been the isolation and cultivation of hyperthermophilic organisms and other extremophiles. This has not only led to the discovery of novel metabolisms and special adaptations of archaea, but also to a more fundamental understanding of the features that unify the organisms of this third domain of life. It will be as exciting and important to isolate species of those archaeal groups that have so far solely been studied by molecular techniques. In particular, some of the organisms that are commonly found in moderate, aerobic environments should eventually be brought into culture, perhaps assisted by predictions made in metagenomic studies.
- 22. Although the study of model organisms remains crucial, it has become clear over the past years of archaeal research that cultivation independent techniques, including population genomics, will be indispensable if we want to fully understand the diversity and ecological impact of archaea.