Lecture 2: Describing Microbial Diversity: the ... - MCD Biology

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22 3. Changes must span the evolutionary distance inspected -- i.e., compared sequences must not be randomized. 4. No lateral transfer -- the evolution of the gene must reflect the evolution of the cells considered. a. Genes that are known to be derived from lateral transfer are called “xenologs.” If you are interested in metabolic genes, there is a good chance, at least among bacteria, that you are dealing with genes or pathways that potentially can move between different organisms. b. e.g. penicillinase and other commonly transferred antibiotic resistance genes (scary!). c. e.g. Rhizobium symbiotic (leguminous plants) N2-fixation. 5. Note the evident impact of lateral transfers throughout evolution. Much of microbial physiological diversity (probably) is dependent on laterally transferred genes. a. Note also that portions of genes can transfer (e.g. with “two- component” systems) so that “homologous” blocks of sequence can show-up in functionally unrelated genes. Formation of intralineage "gene families" also results in mixing-up functional modules of macromolecules. b. How to detect xenologs?
23 B. When “molecular phylogeny” first got started, considerable work was done with protein sequences, e.g. cytochrome C, hemoglobin. 1. But proteins are hard to get and sequence; it is now easier to isolate/sequence genes. 2. Most protein genes are “shallow” clocks, the result of relatively recent evolution; e.g. E. coli doesn’t have hemoglobin. 8. Choice of molecules for comprehensive (all organisms) phylogeny -- ribosomal RNAs (rRNAs). A. Ribosome -- carries out protein synthesis Small subunit Large subunit S L “23S” rRNA (LSU): 3000-5000nt “16S”-“18S” (SSU) rRNA: 1500-2000nt “5S” rRNA - 120 nt ca. 25 proteins ca. 30-40 proteins B. rRNAs present in all organisms and the major organelles (mitochondria and chloroplasts).
Page 1 and 2: Lecture 2: Describing Microbial Div
Page 3 and 4: 3 A. Slowly evolving molecules (e.g
Page 5 and 6: 5 B. Phylogenetic perspective allow
Page 7 and 8: 7 Indeed, the lexicon of biology st
Page 9 and 10: 9 A. Still, “monera” (mostly te
Page 11 and 12: 11 4) Supposition that the eucaryot
Page 13 and 14: 13 3) You cannot meaningfully compa
Page 15 and 16: Note that organism-to-node “dista
Page 17: 17 Vignette - Tree-reading - Baum,
Page 20 and 21: 20 A. Doesn’t really matter so lo
Page 24 and 25: 24 C. Highly conserved throughout e
Page 26 and 27: B. In essence, the tree is a quanti
Page 28 and 29: 28 Bacteria C. The eucaryote nuclea
Page 30 and 31: 30 H. Note how deeply divergent are
Page 32 and 33: 32 You can download trees, carry ou
Page 34 and 35: 34 C. Most of what we know about ba
Page 36 and 37: 36 B. Environmental sequences have
Page 38 and 39: 38 A. Note that the microbial eucs
Page 40 and 41: 19. The three-domain tree is seen f
Page 42: 42 D. Even enzymes in the same bios
Page 45: Gary Olsen edits the Doolittle tree

Lecture 2: Describing Microbial Diversity: the ... - MCD Biology

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