Lecture 8 - Genomes.docx

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Department
Cell and Systems Biology
Course Code
CSB328H1
Professor
William Navarre

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MGY377H © Lisa | Page 13 L E C T U R E 8 : M I C R O B I A L G E N O M E S BASIC OBSERVATIONS ABOUT BACTERIAL GENOMES 1. bacterial genomes differ in size & complexity Species Siz %G Chr. Plasmid Niche e C # # 65. Burkholderia vietnamiensis 8.4 7 3 5 Soil bacterium 6.6 65. Free living water Mycobacterium marinum 2 7 1 1 bacterium Pseudomonas aeruginosa 6.3 66. 1 Soil bacterium 6 Escherichia coli O157:H7 5.5 50. 1 1 Pathogenic E. coli 9 3 5.4 35. Bacillus anthracis 7 2 1 2 Cause of anthrax, soil 50. Escherichia coli UPEC 5.2 1 Pathogenic E. coli 5 Salmonella typhimurium 4.9 52. 1 1 Intestinal pathogen 9 2 47. Yersinia pestis 4.7 7 1 1 Cause of plague 50. Escherichia coli K-12 4.6 8 1 Lab strain of E. coli Mycobacterium 65. 4.4 1 Cause of tuberculosis tuberculosis 6 Vibrio cholerae 4.1 47. 2 Cause of cholera 5 3.2 57. Mycobacterium leprae 7 8 1 Cause of leprosy 2.9 Listeria monocytogenes 4 38 1 Soil, food poisoning Staphylococcus aureus 2.9 32. 1 Human pathogen, free (MRSA) 8 living Helicobacter pylori 1.6 38. 1 Cause of gastric ulcers 7 9 1.5 28. Borrelia burgdorferi 2 2 1 21 Cause of Lyme disease 0.1 16. Candidatus Carsonella 1 Endosymbiont 6 6 2. depiction of overlapping genome size in members of the Bacteria, Archaea, Eukarya, and viruses in the size range (∼0.5-10.5 Mb) in which this overlap has been found to occur Depiction of overlapping genome size in members of the Bacteria (blue), Archaea (red), Eukarya (green), and viruses (yellow), in the size range (∼0.5-10.5 Mb) in which this overlap has been found to occur. Number of circles at a given point on the scale indicates the number of completed genomes of a specific size. Circles representing unusually small (<1 Mb) or large (>5.5 Mb) bacterial genomes are labeled with the species name. Reprinted with permission from Elsevier © 2005, from Ward and Fraser 2005. MGY377H © Lis| Page 2013 3. correlation among total number of ORFs in the genome, noncoding DNA, and genome size for prokaryotic genomes Correlation among total number of ORFs in the genome, noncoding DNA, and genome size for prokaryotic genomes. (A) The total number of ORFs in the genome vs. the genome size for 115 completed prokaryotic genomes. (B) The total amount of noncoding DNA in the genome vs. genome size. 1. we consistently observe that bacterial genomes encode ~1 ORF for every 1000 bps of DNA 2. most bacterial genomes don’t have a lot of “junk” DNA – they are very streamlined (esp when compared to animal genomes) 4. bacteria do more w less 1. bacteria will have 3000 genes in a genome of 3 million bps while humans encode ~30 000 genes (10x as many) using over 1000x as much DNA to do so 5. percentage of ORFs by fx as compared to genome size 1. smaller genomes don’t spend a lot of real estate on signal transduction or gene regulation 2. small genomes encode relatively more of the basics like ribosome subunits, DNA polymerase, etc 3. as genomes get larger, they tend to disproportionately acquire more regulatory mechanisms (signal transduction & transcription factors) 6. characteristics of bacterial genomes Siz %G Chr. Plasmid Species e C # # Niche Burkholderia 65. 8.4 3 5 Soil bacterium vietnamiensis 7 Mycobacterium 6.6 65. 1 1 Free living water marinum 2 7 bacterium Pseudomonas 66. aeruginosa 6.3 6 1 Soil bacterium 7. trends bw gene content & genome size in prokaryotic species w larger genomes 1. large genomes are disproportionately enriched in regulation & secondary metabolism genes & depleted in protein translation, DNA replication, cell division, & nucleotide metabolism genes 2. these trends suggest that larger genome-sized species may dominate in envmts where resources are scarce by diverse & where there is little penalty for slow growth (i.e. soil) 3. Konstantinos et al. PNAS 2004;101:3160-3165 MGY377H © Lisa | Page 33 8. genome size correlates strongly w envmtal niche & specific lifestyle strategy of the bacteria 1. the genome of a generalist ex. Burkholderia cepacia ~ 8,000,000 base pairs 1. lives & grows well in complex and diverse soil envmts 2. can survive on many different nutrients 2. the genome of a specialist ex. Staphylococcus aureus ~ 3,000,000 base pairs 1. hardy & can persist but not thrive in many places 2. strongly prefers association with humans (likes meat) 9. bacterial genomes display odd biases Species Siz %G Chr. Plasmid Niche e C # # Burkholderia vietnamiensis 8.4 65. 3 5 Soil bacterium 7 6.6 65. Free living water Mycobacterium marinum 2 7 1 1 bacterium 66. Pseudomonas aeruginosa 6.3 6 1 Soil bacterium Escherichia coli O157:H7 5.5 50. 1 1 Pathogenic E. coli 9 3 Bacillus anthracis 5.4 35. 1 2 Cause of anthrax, soil 7 2 50. Escherichia coli UPEC 5.2 5 1 Pathogenic E. coli 4.9 52. Salmonella typhimurium 1 1 Intestinal pathogen 9 2 Yersinia pestis 4.7 47. 1 1 Cause of plague 7 50. Escherichia coli K-12 4.6 8 1 Lab strain of E. coli Mycobacterium 65. tuberculosis 4.4 6 1 Cause of tuberculosis Vibrio cholerae 4.1 47. 2 Cause of cholera 5 Mycobacterium leprae 3.2 57. 1 Cause of leprosy 7 8 2.9 Listeria monocytogenes 4 38 1 Soil, food poisoning Staphylococcus aureus 32. Human pathogen
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