Molecular Phylogeny - The Tree of Life - Lab 9 | BISP 194, Study notes of Biology

Download Molecular Phylogeny - The Tree of Life - Lab 9 | BISP 194 and more Study notes Biology in PDF only on Docsity! Lecture 9 Molecular Phylogeny The Tree of Life Where did we come from? What is the story? Major events in evolutionary speciation can be deduced from comparisons of gene sequences. The assumption is that most changes are neutral and occur at about the same rate in different organisms = the molecular clock. It is calibrated on speciation events with fossil records.This is good for the last 500 Myrs but has to be extrapolated to earlier events. Eukaryotes arose 2 Byrs ago from a fusion of two genomes from quite different bacterial organisms, a eubacterial and an archae. The eubacteria gave rise to mitochondria. Many genes from each set were retained in the nucleus. If this fact were not considered, it would appear that bacteria and eukaryotes are only 2 Billion years old. In fact, eubacteria and archae diverged at least 3 Billion years ago. The degree of divergence of a dozen or so orthologs in a range of species can be used to establish the distance- time relationship. They used Grishin’s equation: q = [ln(1+2D)]/2D where q is the fraction of unchanged residues and D is the evolutionary distance. They showed that D increases linearly with time established from the fossil record. They extrapolated to earlier times. The molecular clock Timing major events in evolution by the molecular clock The major bacterial kingdoms diverged soon after life arose on this planet. 3 to 3.8 Byrs ago. Crown organisms, plants, fungi and animals diverged about 1 Byrs ago. Eukaryotic enzymes that appear to have been derived from either a archaebacterial or eubacterial ancestor. archaebacterial orthologs eubacterial orthologs mixed orthologs Well represented clusters of orthologs available in 1996 (a sparse data set) used for establishing early events Dictyostelium malaria Plasmodium (wrong) Baldauf’s burst based on molecular and anatomical relationships from archaebacteria A program has been developed using 34 clocks and a single tree to compare related proteins from diverse organisms. Eukaryotic Clusters of Orthologs (ECOs) This is referred to as Multiple Alignment and can be used to increase the likelihood of a correct prediction concerning function. Implementation is a bit complicated. Eukaryotic phylogeny based on complete proteomes Analysis of 5,908 clusters of orthologous proteins Human Dictyostelium Rice Plasmodium Giardia Drosophila C. elegans Euglena Leishmania Chlamydomonas Arabidopsis Tetrahymena Maize Fugu Ciona C. merolae Trypanosoma Anopheles Cryptosporidium Archea 100 Darwins Animals Pombe S. cerevisiae Neurospora Fungi Plants Entamoeba Amoeba Nowadays Information stored in the sequences of nucleic acids is converted by aminoacyl-tRNAs into information in the sequences of proteins. The function of proteins is determined by the primary sequence of amino acids. The RNA World When life first arose, all information resided in the sequences of RNAs. RNA sequences were copied into complementary RNA sequences. Modifications of some of the bases allowed specific RNAs to carry out catalytic functions. Protein Synthesis amino acid tRNA anticodon mRNA  Yeast phenylalanine tRNA Acceptor stem Anticocon stem, Feng, Cho and Doolittle (1997) suggested that in the RNA world, RNA “matchmakers” might have associated with some but not other amino acids, and brought them together with tRNA-like molecules that helped decode short, simple sequence RNAs. tRNA-like aa RNA matchmaker tRNA -like tRNA-like aa aa aa tRNA-like aa tRNA-like tRNA-like amino acid The “matchmaker” RNAs were gradually replaced, one at a time, by proteins that were the precursors to aminoacyl-tRNA synthetases. The increase in fidelity of tRNA charging resulted in more defined amino acid sequences in the proteins. By luck some proteins encoded by RNA facilitated the attachment of amino acids to the 3’ end of some tRNA precursors (hairpin RNAs). Two of these proteins were better than the others and their genes gave rise to all the aminoacyl-tRNA synthetases we see today. There may have been others but we know nothing about them. They did not survive in genomes. Back in the RNA world, they both bound AMP activated amino acids, but one of them attached the amino acid to the 2’ -OH of “tRNA” while the other attached the amino acid to the 3’ -OH of “tRNA”. Their descendents are referred to as Class I or Class II. 3 Billion Years Ago O O ADENINE OO H H 3’ 2’ Recognizing that there are two classes of enzymes made the problem solvable. The 3D structures of these enzymes are now known to be more similar among members of a class than between classes. The class I enzymes were aligned on a small shared motif: HIGH and then extending from that anchor point. Some of the class II enzymes were aligned on a motif related to GLER and then extended. The multiple alignment was then used to bring in the other members of this class. Class II enzymes were also aligned on a motif in another region GFxxxxxP and extended. Trees were built from the multiple alignment by distance matrix and parsimony techniques. Multiple Alignment of distantly related enzymes Class I Class II valine glutamine isoleucine glutamate tyrosine trytophan leucine methionine cysteine arginine threonine glycine proline phenylalanine histidine alanine serine aspartate asparagine lysine Using data available in 1994 from diverse bacteria and eukaryotes Nagel and Doolittle came up with consensus trees [GG] GA AG AA UG AC UC GG [AG] CA UA AU AUG CU GU UG CG CC CA GC AC GA UU Although each amino acid probably used 3 nucleotides, the third base was not used for discrimination until later. The code could have built up stepwise before the evolution of aminoacyl-tRNA synthetases. The conversion of life in the RNA world to life as we know it, is one of the more difficult steps in building a plausible story for the evolution of life. Understanding the evolutionary history of the critical aminoacyl-tRNA synthetases, fills a big gap. Until it was realized that there are two independent families of synthetases, attempts at alignment were never successful. Even then, multiple alignment was successful only when small, highly conserved motifs were used as anchors and the alignment built up step-wise. Multiple alignment of more highly similar proteins is much easier but is still a bit of an art unless the proteins are members of ECOs. Summary