Lecture 6: The World of Omics PDF

Lecture 6: The World of Omics Genomics and Metagenomics What is Omics? A collective term for disciplines in biology focusing on large-scale data (genomics, proteomics, transcriptomics, etc.) Studies molecules comprehensively to understand structure, function, and dynamics in living sy...

Lecture 6: The World of Omics Genomics and Metagenomics What is Omics? A collective term for disciplines in biology focusing on large-scale data (genomics, proteomics, transcriptomics, etc.) Studies molecules comprehensively to understand structure, function, and dynamics in living systems. Types of Omics Genomics: Study of an organism’s complete DNA sequence (genome) Transcriptomics: Focus on RNA transcripts (gene expression patterns) Proteomics: Analysis of the structure, function, and interactions of proteins Metabolomics: Study of small molecule metabolites (chemical fingerprints) Epigenomics: Analysis of epigenetic changes, such as DNA methylation Polyesters Bacteria differ from one another - reserve material - with unbalanced supplies of nutrients The nature of the reserve material depends upon the genotype of the organism the kind of limitation. If the carbon-to-nitrogen ratio is high if nitrogen, phosphorus, or oxygen are limiting many bacteria will accumulate glycogen and/or aliphatic polyesters, polyhydroxyalkanoates (PHAs), in amounts up to 80% or more of their cellular dry weight. Sequencing of genomes Genome sequencing of viruses began in the late 1970s. The random sequencing of fragments by the Sanger dideoxy termination method The complete sequencing of bacteriophage DNAs, notably that of phage λ in 1980 Sequencing of genomes The first attempt to obtain a complete genome sequence of a cellular organism was geared toward Escherichia coli 1989 - a set of λ-based clones, each containing up to 20 kb DNA, with overlapping ends randomly cut into much smaller fragments cloned into an M13 vector and Sequenced and the sequences were assembled by looking for overlaps “clone-by-clone shotgun”- the shotgun approach could not be used for larger segments of DNA or for an entire genome. Sequencing of genomes Craig Venter - successfully used the random shotgun approach for the entire 1.8-megabase (Mb) genome of Haemophilus influenza Genome sequence -24,000 “reads-about 400 bases or slightly longer The total sequences used for assembly were almost 12 Mb long Human genome – at about 3 Gb, more than 1600 times larger than that of H. influenzae. The International Human Genome Sequencing Consortium used the clone- by-clone shotgun approach, and the “first draft” was published in 2001. Prokaryotic genomes H. influenzae genome (1.8 Mb) Chlamydia trachomatis (1.0 Mb) Mycoplasma genitalum (0.6 Mb) E. coli (4.6 Mb) Pseudomonas aeruginosa (6.3 Mb) Streptomyces coelicolor (8.7 Mb) Bradyrhizobium japonicum (9.1 Mb) Most archeal genomes have a rather small size, between 1.5 and 3 Mb Prokaryotic genomes What is the minimal set of genes that allow simple cellular organism to grow and replicate? Classify genes, and the proteins coded by these genes, on the basis of homology. BLAST Orthologs: Homologous proteins in two different organisms, where they developed independently of each other Paralogs: Homologous proteins that exist in the same species, presumably created originally by gene duplication and often differentiated later in terms of functions M. genitalum (coding for 468 proteins) and H. influenzae -“minimal gene set” of about 300 genes The set of genes needed for an independent survival -about 1500 genes. Prokaryotic genomes What do larger genomes contain in addition to the minimal set just mentioned? H. influenza -- the upper respiratory tract of animals E. coli - intestinal tract and in natural waters, contains many more genes (often paralogs) needed for adaptation P. aeruginosa - a resident of soil and water but can also cause severe infection in humans, has a larger genome filled with a more complex array of genes. S. coelicolor - several antibiotics and undergoes differentiation into aerial spores - This genome is equipped for very complex regulatory responses-, 55 sigma factors (E. coli 7 sigma factors ) Prokaryotic genomes Another major mechanism - horizontal transfer from other organisms of large genomic islands. In Salmonella, “pathogenicity islands” B. japonicum, an N2-fixing symbiont of the soybean root, contains a very large (610-kb) “symbiosis island” Prokaryotic genomes How do the genomes of organisms of limited habitat become smaller? Salmonella typhi is a pathogen specializing in infecting humans and cannot cause major diseases in other animals Salmonella typhimurium, which can infect many animal species In S. typhi, more than 200 genes have been converted into pseudogenes Mycobacterium leprae (3.3 Mb)- only 50% of the genome contains protein-coding genes, and 27% is occupied by 1116 pseudogenes that have functional orthologs in Mycobacterium tuberculosis (4.4 Mb). Metagenomics Biotechnology - expression of a foreign gene coding for a useful product in a suitable host organism, such as E. coli or yeast Direct cloning - extremely valuable - not yet been cultured Soil samples from a diverse range of environments is likely to supply genes that code for proteins with widely different properties Thus, it has now become a standard approach in the industry to maintain such samples for the direct cloning of useful genes Metagenomics Genomes of the entire community of microorganisms, many of which may be currently uncultured – metagenomics Biofilm from acid mine drainage -the large surface of pyrite (FeS2) becomes exposed to air and water, causing large-scale leaching of Metal through oxidation by Fe(II)-oxidizing bacteria-sulfuric acid The pH of the effluent was 0.83 and the temperature was 42◦C. Prediction of metabolic pathways Leptospirillum group II (2.23Mb, a eubacterium, high GC) can fix carbon and Ferroplasma (1.82 Mb, an archeon, low GC), Leptospirillum group III - N2-fixing genes