Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees.

1. Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees. reading: Chapters 3, 5

2. Ernst Haeckel Textbook General Morphology 1866 Traces all of life to Moneren (Monera).Linear progress from Monera to Man.

3. Yet another version of Haeckel’s tree of life All eukaryotes descended from prokaryotes, culminating in man. Prokaryotes not all that interesting.

4. Zuckerkandl & Pauling Pauling: 1954 Nobel Prize, nature of the chemical bond Series of papers in 1962-1965: Mutations form the basis for disease. Disease has a molecular basis. Studying diseases that involve different forms of hemoglobin. Showed that: a. if you knew the genetic code, you could trace the mutations that caused disease b. there is buried history in protein (or gene) sequences (hold information) c. approximate time of the existence of an ancestral sequence d. can infer the probable sequence of the ancestor (AACGTTC) e. can infer “the lines of descent along which given changes in amino- acid sequence occurred”

5. Overall Scheme for Constructing a Phylogenetic Tree time cells/ culture DNA extraction phylogeny - development of a race or species clone tree reconstruction/inference algorithm sequence Thermus thermophilus GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG Synechocystis PCC 6301 GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG Micrococcus luteus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU Flexibacterium sp. GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU Agrobacterium tumefaciens GAC-ACGUGAA-AUCCUGUUC-GAACAU-GGGGAG--ACCA-CUC-U-CCA-AG-CCUA-AGUAC-UC-G-UG Escherichia coli GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG Pseudomonas cepacia GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG Aquifex aeolicus GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU Chloroflexus aurantiacus GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU

6. Example How to Construct a Phylogenetic Tree

7. Count the number ofdifferences. Correct formultiple mutations.

8. Construct a Tree that Best Explains the Distances Observed

9. Can also Build a Tree using Cladistics cladistics - reconstructing trees using shared, derived traits 1. chose which taxa 2. tabulate traits 3. identify synapomorphies = shared derived traits 4. build up a cladogram = tree showing evolutionary relationships good introductory resource: www.ucmp.berkeley.edu

10. The Importance of Having A Phylogenetic Tree

11. The Importance of Having A Phylogenetic Tree, cont.

12. Tree of Life Constructed by aligning a gene sequence common to all organisms. Common gene: ribosomal RNA gene. Three major lineages - these are called domains. Root is where the last common ancestor gave rise to the three domains. Root is placed at the base of the bacterial domain.

13. Ribosome Synthesizes Proteins in the Cell Large complex made of RNA and small proteins RNA catalyzes the reaction to make proteins RNAs called ribosomal RNAs

14. 1989: Rooting the Tree of Life three studies: Gogarten et al. ATPases Iwabe et al. tRNA synthetases Baldauf et al. elongation factors Archaea are more closely related to Eukaryotes than to Bacteria At first this was a big surprise - expected Bacteria and Archaea to be more similar to the exclusion of Eukaryotes

15. The Bacterial Domain At least 18 divisions - major lineages. Some divisions have never been cultured! Some have unique characteristics (e.g., the Cyanobacteria). Most lack unique characteristics. One major group Proteobacteria - have a large variety of different physiologies Bacterial tree is not well resolved at present

16. The Bacterial Domain, cont. Early lineages are hyperthermophiles. Deinococcus branches somewhat deep. E. coli is a member of the Proteobacteria, branches late. Cyanobacteria also branch late. Bacillus & Clostridium members of the Low G+C Gram Positive Bacteria. Are several lineages of photosynthetic phyla. Are Five Phyla Contain Photosynthetic Taxa: Green Non-Sulfur Bacteria Green Sulfur Bacteria Cyanobacteria Low G+C Gram Positives (Heliobacillus) Proteobacteria

17. Key Characteristics of Bacteria • 1. Cell walls made of a similar polymer (peptidoglycan) • 2. Lipids are made of similar compounds (fatty acids with ester linkages) 3. RNA polymerase (enzyme that makes mRNA copies of genes) made of 4 different proteins (’) • 4. Signature sequences tell RNA polymerase where to start making RNA • 5. All proteins begin with a modified amino acid formyl-Methionine

18. The Archaeal Domain Two major well-studied phyla are Euryarchaeota and Crenarchaeota. Two new phyla are Korarchaeota (no pure cultures yet) and Nanoarchaeota (is a symbiont of a Crenarchaeote). Not clear where these lineages branch. Most of the early branches are hyperthermophilic. Obsidian Pool, Yellowstone, home of Korarchaeota

19. Crenarchaeota All cultured species are hyperthermophilic. Many inhabit “extreme environments”: hyperthermophiles- very high T loving thermoacidophiles - high T acid loving Many have short branches - evolve slowly. (should, in principle, be good models for early life on Earth) Great deal of uncultured mesophiles (moderate T loving) everywhere - 30% of biomass in the open oceans. Mesophiles have long branches - evolving more rapidly. Mesophilic lineages are peripheral. terrestrial acidic hot spring marine hydrothermal vent red cells are Archaea green are Bacteria

20. Euryarchaeota Physiologically diverse group. Inhabit many extreme environments: acidophiles- acid loving thermoacidophiles halophiles- salt loving alkaliphiles- alkaline loving hyperthermophiles Many lineages are methanogens - generate methane, are strict anaerobes (can only grow without O2) Methanogens found in diverse habitats: swamps, deep-sea hydrothermal vents, animal intestines, cow rumen, rice paddies, oil wells

21. Key Characteristics of Archaea • 1. Cell walls are different than bacteria (pseudopeptidoglycan) • 2. Lipids different from bacteria (isoprenoids with ether linkages) 3. RNA polymerase more complex than bacteria - 8 or more proteins (eukaryotes have 8-10) 4. RNA polymerase needs “help” from other proteins to begin making mRNA copies of genes (called transcription factors - are similar to eukaryotes) 5. Signature sequences also tell RNA polymerase where to start making RNA, but are unique (TATA boxes - similar to eukaryotes) 6. All proteins begin with the regular amino acid Methionine 7. The number of ribosomal proteins are different from bacteria.

22. Archaea and Bacteria Share Many Characteristics 1. Genes are often linked together in the chromosome 2. Have circular chromosomes (eukaryotes have linear chromosomes) 3. Genomes are small (eukaryote genomes are huge) 4. Both have ribosomes that are small (eukaryotes have larger ribosomes) 5. Both metabolically diverse (eukaryotes are not) 6. Lack nucleus …. many more ….

23. Eukaryotes Prokaryotes- lack nucleus/nuclei Eukaryote (“true nucleus”) are much more complex DNA containing organelles (“little organs”) nucleus mitochondrion - respiration chloroplast - photosynthesis often have multiple chromosomes (linear chromosomes) lots more genes lots of “junk DNA” in their genes } were once free-living prokaryotes

24. Eukaryotes are Typically Larger than Prokaryotes

25. Lecture 17. Why Do You Need to Construct a Tree for Prokaryotes?  Trees as Frameworks reading: none

26. Mystery of Enceladus Cassini Spacecraft found older terrains and major fractures on moon Enceladus Course crystalline ice which will degrade over time. Must be < 1000 years old! Organic compounds found in the fractures. Must be heated - required T > 100K (-173˚C) Erupting jets of water observed. Cause of eruptions not known….