Prokaryotes First cellular life form over 3.5 billion years ago

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Prokaryotes First cellular life form over 3.5 billion years ago Slide 2 - phylogenetic tree kingdom Animalia Plantae Animalia Plantae Fungi Protists Monera Eukaryotes Prokaryotes domain Eucarya; eukaryotes Bacteria; eubacteria Archaea; archaebacteria Slide 3 Tree of life (based on rRNA sequences) Slide 4 origin vertebrate eukaryotes invertebrate dinosaurs human Prokaryotes only 40 Slide 5 1 M Fig. 18.1 Slide 6 The genetic materials E. coli chromosome: 4.6 Mb = 4.6 x 10 6 bp x 3.4 = 1.6 x 10 7 = 1.6 x 10 -3 m = 1.6 mm = 1,600m Plasmids are about 100 times smaller. 1 m Highly packed chromosomal DNA Slide 7 Prokaryotes lack nuclear membrane nucleoid Slide 8 Anatomy of a bacterial cell Slide 9 Cell envelope Slide 10 Gram-negative cell envelope Slide 11 Cell Wall Slide 12 Flagella and pili Slide 13 Slide 14 Slide 15 Photosynthetic bacteria Purple sulfur bacteria Purple nonsulfur bacteria Photosynthetic purple and green bacteria Slide 16 Cyanobacteria Extremephile habitats Ancestors of chloroplasts in plants Biochemically, cyanobacteria are very similar to the chloroplasts of red algae (Rhodophyta) Slide 17 25% 15% 60% cyanobacteria Rhizobium Slide 18 yoghurt Slide 19 Bacteria we eat Bacillus subtilis Sporulation Slide 20 black death Yersinia pestis 1347 tuberculosis Mycobacterium tuberculosis Actinomycetes Streptomyces streptomycin rifampicin Slide 21 Bacillus anthracis (Robert Koch, 1876) Koch's Postulates: microbiological standard to demonstrate that a specific microbe is the cause of a specific disease Slide 22 Slide 23 Actinomycetes Soil habitat Gram positive Differentiation: spores, substrate mycelia, aerial mycelia Linear chromosomes and linear plasmids Slide 24 Raffinose, stachyose, verbascose yoghurt Probiotics Lactobacillus competitive exclusion Slide 25 acetone Chaim Weizmann Manchester Clostridium acetobutylicus acetone 1917 Balfour Weizmann Weizmann Institute Slide 26 Bacterial insecticide Bacillus thuringiensis Toxin: spore crystal proteins Slide 27 Rickettsia prowazekii ( Ricketts Prowazek 1526 Naples 1566 1812 Slide 28 Power Unseen (Dixon, B. 1994) The outer reaches of life (Postgate 1994) Microcosmos Margulies Sagan 1995 Plagues and Peoples McNeill 1997 (Guns, Germs and Steel) Diamond 1998 Slide 29 Bacterial Genetics Slide 30 Evolution of the genomes The concept of genome The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (episomes) Plasmids Mitochondrial chromosomes and plasmids Chloroplast chromosomes and plasmids The contents of genomes change by: Mutation Recombination (broad sense) Slide 31 The first genetic exchange programs The concept of genome The whole set of genetic elements in an organism Chromosomes Extrachromosomal elements (episomes) Plasmids Mitochondrial chromosomes and plasmids Chloroplast chromosomes and plasmids Two kinds of exchanges The whole molecules (Assortments) Sequence rearrangements (Recombination) Between homologous DNA Homologous recombination Between non-homologous DNA Site-specific recombination, transposition, illegitimate recombination Slide 32 Recombination or mutation? Fig. 18.12 Frequencies of occurrences Proper controls Slide 33 1952: Lederberg Plasmid Slide 34 Fig. 18.14 Slide 35 Fig. 18.15a Conjugal transfer of plasmid Slide 36 Hfr (High frequency of recombination) 1950 Luca Cavalli-Sforza HfrC 1953 William Hayes HfrH Fig. 18.15b Slide 37 Fig. 18.15c Mobilization of Hfr chromosomes Slide 38 (interrupted mating) Slide 39 Elie Wollman & Jacob, 1955 Slide 40 Plasmids Universal presence Prokaryotic cell Bacterial Archaea Eukaryotic cell Cytoplasm Mitochondria Chloroplast Most are circular and some are linear Promoters of genetic exchanges Carriers of useful genes Drug resistance, metabolite degradation, etc. Slide 41 Bacteriophages (phages) - bacterial viruses Fig. 18.2d Slide 42 An infection cycle Fig. 18.3 Slide 43 Two kinds of phage based on cycles Lytic (virulent) phages Only lytic pathway Lysis of the host cells Lysogenic (temperate) phages Two pathways Lytic pathway Lysogenic pathway Formation of lysogens Inactive phage genomes (prophage) Usually integrated Some are freely replicating Slide 44 Fig. 18.4 Slide 45 Bacteriophage lambda Fig. 18.5 Slide 46 Virus infection is specific Host range Lock and key fit between virus and receptors on the hosts surface Some viruses have a broad host ragne, and other infect only a single species Most eukaryotic viruses attack specific tissues. Slide 47 Phage-mediated gene transfers Transduction Slide 48 Generalized vs. specialized transduction Slide 49 Three kinds of genetic exchanges between prokaryotes Three kinds Transformation Mediated by free DNA Conjugation Mediated by plasmids Transduction Mediated by phages All involving merozygote (partial diploid) All require even number of crossovers Slide 50 Transposable elements Insertion sequence Fig. 18.16 Fig. 18.18 Slide 51 A transposable element, TE (not transposon), is a piece of DNA that can move from one location to another in a cells genome. Transposon movement occurs as a type of recombination between the transposon and another DNA site, a target site. The target may be the chromosome, a plasmid, a virus, or even another TE. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings Slide 52 Some TE (not transposons) jump from one location to another (cut-and-paste transposition). However, in replicative transposition, the transposon replicates at its original site, and a copy inserts elsewhere. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings Slide 53 The simplest bacterial transposon, an insertion sequence, consists only of the DNA necessary for the act of transposition. The insertion sequence consists of the transposase gene, flanked by a pair of inverted repeat sequences. The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse along the opposite DNA strand at the other end of the transposon. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings Slide 54 The transposase enzyme recognizes the inverted repeats as the edges of the transposon. Transposase cuts the transposon from its initial site and inserts it into the target site. Gaps in the DNA strands are filled in by DNA polymerase, creating direct repeats, and then DNA ligase seals the old and new material. Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 18.17 Slide 55 Transposable elements Responsible for most spontaneous mutations fin many bacteria 60% in E. coli Natural genetic engineers Promote deletions, inversion, translocation, replicon fusion B. subtilis does not have transposable elements! Slide 56 Natural genetic engineers Create mutations Mostly bad Rarely good - become conserved Promote genome rearrangements and exchanges Same or similar TE sequences provide sustrates for homologous recombination Sometimes transposition itself causes rearrangement Slide 57 Transposable elements, plasmids, viruses They are all mobile elements They close related in evolution Some transposable elements (Tn916) are also conjugative plasmids Some prophages (N15) are like like plasmids Some phages (Mu) are transposable elements Slide 58 The newest phase in bacterial genetics The genomic approach Slide 59 Carl Woese, 1977 Archaea ribosomal RNA Slide 60 C. Venter, H. Smith, C. Fraser 1995 Haemophilus influenza 2000 6 archae 26 eubacteria 160 200 Mb 200,000 Slide 61 Genomics Slide 62 Bacterial Genomics A revolution in the practice of bacteriology Learning the life style without biochemistry Evolution studies becoming practical Contribution to our vision of the whole living world Slide 63 Metabolism with doing chemistry Primary metabolism Energy management Body building Information process Replication Transcription Translation Repair Pathogenicity Secondary metabolites What is absent is as interesting as what is present Slide 64 Physiology without biochemistry Metabolic reconstructio n from the genomes Slide 65 Genome sizes and content Sizes: 0.6 kb - 9.4 Mb, about 1.0 - 1.1 kb/gene The larger the genomes, the more complex the life styles The larger the genomes, the more paralogous genes G+C content: 25 - 75% Topology: Circular vs. linear Single or multiple chromosomes and plasmids Slide 66 Slide 67 GC skew with respect to replication Slide 68 proteome Slide 69 Studies of evolution relationship Conservation of protein families Diversity of gene repertoires and organizations Incongruities abundant in the phylogenetic tree Common and intensive horizontal gene transfers between bacteria and between bacteria and Archeae Mosaic nature of genomes Gene evolution does not equal species evolution Which set of parameters to rely on for a particular task? Slide 70 Proteobacteria Slide 71 Thermophilic ancestors? Slide 72 The third domains Archeae Originally based on rRNA sequences Carl Woese Bacteria-type morphology and yet different inside Genetic system (Replication, transcription, translation -Eukaryotic-like Metabolic system - bacterial-like Slide 73 Phylogenetic Tree Slide 74 Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings Slide 75 Virus infection by membrane fusion Fig. 18.6 Viruses equipped with an outer envelope Glycoproteins on the envelope bind to specific receptors on the hosts membrane. The envelope fuses with the hosts membrane, transporting the capsid and viral genome inside. The viral genome duplicates and directs the hosts protein synthesis machinery to synthesize its own proteins. After the capsid and viral genome self- assemble, they bud fro