The Fundamental Similarity of All Living Things

1. Microbial Ecology 138023 Oded Beja The Fundamental Similarity of All Living Things

2. All cells encode information on the form of DNA • DNA in all cells is composed of -the same four bases adenine, guanine, cytosine, thymine -the same sugar (D-ribose) -assembled in the same chemical structure and stereochemistry

3. All cells encode information on the form of DNA • DNA in all cells is composed of -the same four bases adenine, guanine, cytosine, thymine -the same sugar (D-ribose) -assembled in the same chemical structure and stereochemistry •Information in DNA is stored using a Universal 3-letter code

4. All cells encode information on the form of DNA • DNA in all cells is composed of -the same four bases adenine, guanine, cytosine, thymine -the same sugar (D-ribose) -assembled in the same chemical structure and stereochemistry •Information in DNA is stored using a Universal 3-letter code •DNA synthesis is handled the same way in all organisms

5. All cells encode information on the form of DNA • DNA in all cells is composed of -the same four bases adenine, guanine, cytosine, thymine -the same sugar (D-ribose) -assembled in the same chemical structure and stereochemistry •Information in DNA is stored using a Universal 3-letter code •DNA synthesis is handled the same way in all organisms •The function of DNA is carried out via transcription into RNA using RNA polymerases

6. RNA is used to direct protein synthesis based on information in DNA •RNA in all cells has the same structure -same 4 bases (ACGU)and sugar, -same structure and stereochemistry •All cells have the same types of RNA:rRNA, tRNA, These RNAs are very much alike in sequence and structure in all cells ex:The rRNA in all organisms are greater than 50% identical in sequence and 80% in structure

8. Proteins direct most of the cell catalysis and structure •Proteins in all cells use the same 20 amino acids, synthesized in the same way,and use the same post-translation modification

10. Proteins direct most of the cell catalysis and structure •Proteins in all cells use the same 20 amino acids, synthesized in the same way,and use the same post-translation modification •Protein synthesis is carried out via translation in the same way in all organisms

11. Proteins direct most of the cell catalysis and structure •Proteins in all cells use the same 20 amino acids, synthesized in the same way,and use the same post-translation modification •Protein synthesis is carried out via translation in the same way in all organisms •Most of the reactions catalyzed by these proteins are the same and the enzymes that carry them out are very-much alike in amino acid sequence and 3- dimensional structure, and mechanism of action

12. All cells are bound by a lipoprotein membrane •strictly control what goes in and come out of the cell (transport systems) •defines the cell, separating inside and outside

13. So,all cells are pretty-much alike What does this means? 1-All organisms share a common ancestry 2-The last common ancestor of all living things was a complex organism 3-The last common ancestor had all the biochemistry that is now universal The diversity of extant life (modern life) is in peripheral biochemistry details!

14. Microbial Ecology 138023 Oded Beja Phylogenetics and the Trees of Life

18. Prokaryotic species: A prokaryote whose 16S rRNA sequence differs by more than 3% (or is less than 97% identical) from that of all other organisms should be considered a new species (3% of 1500 nucleotides = 45 nucleotides). The DNA from 2 bacteria whose 16S rRNA sequences are less than 97%identical usually hybridize to less than 70%, a minimal value for organisms to be considered being of the same species.

19. Molecular Phylogenetics is the study of evolutionary relationships among organisms by using molecular data such as DNA and protein sequences A phylogenetic classification (cladistics) is based upon evolutionary relationships i .e. upon common ancestry, in contrast to a phenetic classification (phenetics, numerical taxonomy) which is based upon overall similarity

20. Nomenclature of trees •Trees can be made with nucleotide or protein Sequences •Homologs are genes/proteins with a common evolutionary ancestor reflected by sequence Similarity •Orthologs are homologs that diverged due to Speciation •Paralogs are homologs that diverged due to duplication

21. Homology is... the similarity that is the result of inheritance from a common ancestor - identification and analysis of homologies is central to phylogenetics Two sequences are homologous if they share a common evolutionary ancestry. THERE ARE NO DEGREES OF HOMOLOGY

22. A phylogenetic tree represents the evolutionary / geneological relationships between a collection of organisms (or molecular sequences). It is composed of branches and nodes Only one branch connects any two nodes.There are internal branches (-----) and external branches (_). Branches define the topology of the tree, that is the relationships among taxa in terms of ancestry

23. Two alternative representation of a phylogenetic tree: (a) Unscaled branches (phenogram): terminal nodes are lined up and nodes are positioned proportionally to time of divergence (b)Scaled branches (dendrogram): lengths of branches are proportional to number of molecular changes along them (e.g. nucleotide or aa substitution). The evolutionary distance between two organisms is the total length of all the branches that connect them

24. Other methods for determining phylogenetic relationships 1-DNA:DNA hybridization 2-DNA base composition 3-Serology 4-Lipid profiling 5-RFLP analysis 6-rRNA spacer sequence analysis 7-Ribotyping 8-Phenotypic markers

25. Lateral gene transfer In prokaryotes

26. Standart model of the universal SSU rRNA tree

27. זיהוי • דרגת דמיון גבוהה בין התורם למקבל עבור התכונה הנבדקת. • חלוקה פילוגנטית עבור התכונה בין המקבל לזנים הקרובים אליו אבולציונית. • מה בין convergent evolutionלבין lateral gene transfer • ניתוח גנטי-מולקולרי של רצפי DNA

28. שיטות זיהוי • ניתוח מידע ממאגרים לגבי הומולוגיות בין גנים • חיפוש רצפיםבעלי הרכב לא אופיני • GC content • codon usage • שרידי רצפים הקשורים לאינטגרציה של LGT

29. מנגנונים נפוצים למעבר של חומר גנטי בין חיידקים

31. Gene transfer agents (GTAs) GTAs discovered in the purple nonsulfur bacterium Rhodobacter capsulatus are host-encoded viruslike elements that package random fragments of the host chromosome and are found in the genome of almost every sequenced member of the alpharoteobacteria order Rhodobacterales

33. תפוצת DNA ממקור לטרלי בגנומים בקטריאלים

35. Standart model of the universal SSU rRNA tree