Microbial Genomics and Chromosome Organization

Transcription

1 Microbial Genomics and Chromosome Organization Microbial Chromosome Organization Generation of full genome sequences Genomic Structure & Functional Genomics Genome size vs. No. of orfs Minimal genome concept Lessons from full genomes Metagenomes

2 Microbial Genetic Exchange & Plasmids Microbial Genetic Exchange is unidirectional! Transformation Transduction Conjugation Each requires Homologous Recombination Types of plasmids

3 Microbial Genetic Exchange

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5 Transformation by a Gram + competent cell

6 Demonstration of transformation Streptococcust pneumoniae Frederick Griffith, 1928

7 Demonstration of transformation Frederick Griffith, 1928

8 Figure 15.8 (Part 3) Demonstration of transformation

9 Generalized transduction

10 Generalized transduction (cont.)

11 Specialized transduction

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13 Bacterial Conjugation Donor Recipient

14 Bacterial Conjugation

15 Hfr cells Hfr = High Frequency Recombination

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17 F cells

18 Homologous Recombination

19 Homologous Recombination strand invasion

20 Homologous Recombination

21 Types of homologous recombination in bacteria

22 Types of homologous recombination in bacteria

23 Plasmids Genomic DNA Bacterial Cell Plasmids

24 F plasmid

25 R plasmids of pathogenic bacteria

26 Ti plasmid Brock, 13 th ed. 2012, page 729

27 Chromosomal & nonchromosomal genetic elements

28 Whole-genome shotgun sequencing Depends on sequencing method

29 Sanger Sequencing

30 Next-Generation Sequencing (NGS) Illumina Platform

31 Next-Generation Sequencing (NGS) 454 Platform

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33 Sequencing & Annotation General outline 1. Find Sample 2. Make Library-Depends on sequencing technology 3. Assemble & Annotate Sanger vs. NGS Sanger is expensive NGS is computationally demanding for assembly Other methods for DNA sequencing include Ion Torrent, PacBio, SOLiD

34 Genes in a portion of bacterial genome

35 Genome Organization Origin Terminus Dehalobacter 12DCB1 Forward Strand Reverse Strand rdh genes CPR/FNR regulator GC Skew an asymmetry between the nucleotide compositions of the leading lagging strand

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39 Genome size vs. ORFs

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41 265 to 350 genes are the minimum i necessary genome

42 Science, 2008 Science, 2010

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44 Totals:

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46 Lessons from full genomes Size range 600Kb to 12Mb Vast number of putative genes with no known function Pathogenicity can be conferred by Pathogenicity Islands 44.5Kb in Bacillus anthracis Symbiotic Island of >600Kb in Sinorhizobium loti including genes for nodulation and N-fixation Adaptive gene losses in parasitic bacteria Rickettsia and Chlamidia are ATP thieves using the same alien ADP/ATP translocase Relative proportions of functional genes

47 Metagenomics Genomic analysis of pooled DNA from an environmental sample containing organisms that have not been isolated Describes the functional capacities of the community

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49 Figure 4: The cell cartoons are shown within a biofilm that is attached to the surface of an acid mine drainage stream (viewed in crosssection). Tight coupling between ferrous iron oxidation, pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5- bisphosphate carboxylase oxygenase. THF, tetrahydrofolate. Tyson et al 2004 Nature

50 Human Microbiome Project To demonstrate hypothesized correlations between the microbiome and human health and disease. These projects will leverage advances made by the HMP's large scale sequencing efforts to examine the relationship between changes in the human microbiome and diseases of interest.

51 Human Microbiome 1600 Implicated din Obesity Mental Illnesses Bacterial Vaginosis Various Cancers 800 Inflammatory Bowel 600 Disease 400 Autism Arthritis 200 Psoriasis 0 Asthma Pubmed: Human Microbiome Literature Search