Lecture 2&3 - Topic 2 - Genome Organization I AND II Lecture notes, lecture 2&3 PDF

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Lecture II – Genome Organization 1&2 Each Species has a Characteristic Set of Chromosomes

Bacterial Genetic Material 

Prokaryotic genomes generally contain one large circular piece of DNA referred to a bacterial "chromosome" (not a true chromosome in the eukaryotic sense).

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Some bacteria have linear "chromosomes". Chromosomes sizes vary between 0.6 and 10 Mbp. DNA must be compacted: chromosome has an ~ 1.6 mm circumference and E. coli dimensions are: ~1.0 x 2.0 mm.

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Many bacteria have small circular DNA structures called “plasmids” which can be exchanged across bacterial species.

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Plasmids: A. introduced by the molecular biologist J. Lederberg (1952). B. are separate from, and can replicate independently of, the chromosomal DNA. C. Plasmid size varies from 1 to over 1,000 (kbp).

D. Not considered as part of the bacterial genome Bacterial Genome Sequence - Sequence Analysis: 1. Coding DNA accounts for ~90% of the total genome and ~10% is noncoding DNA. a. For humans it’s the opposite situation, only 1.2% coding. 2. Genes have no introns with few exceptions. 3. Genes are smaller than their eukaryotic counterparts: average length of a bacterial gene ~ 2/3 that of a eukaryotic gene. 4. Space between genes is very small compared to eukaryotes and varies between 1. 0 and a few nts. 5. Genes are often organized in operon structures; encode proteins are involved in the same biochemical pathway.  3 genes in same metabolic pathway will turn on automatically if one trigger is present.

6. Low frequency of repetitive sequences in prokaryotes; 1. none in Campilobacter jejuni 2. Neisseria meningitis has over 3700 copies of repeat sequence (11% of the 2.2 Mb genome) Sequence Analysis - Phylogenic analysis  Phylogeny: For two different strains of the same species, genome differences: o E. coli K12: 4.64 Mb genome (non pathologic) o E. coli O157:H7: 5.53 Mb genome (pathologic) o 1387 genes not present in E. coli K12.  Strain-specific genes: 26% E. coli O157:H7 and 12% E. coli K12.  Conclusion: substantial variation in genome content and species concept can’t be applied to prokaryotes as for higher organisms. o Different criteria applied to eukaryotes

Genome Structure of Prokaryotes: Mobile Genetic Elements  Analysis of the large number of available genomic and metagenomics sequences in the public databases.  Prokaryotic genomes are highly mosaic; composed of DNA segments acquired both by vertical descent and by lateral transfer.  Mobile genetic elements: “a nucleotide region of varying length with either intragenome, intergenome or intercellular mobility, and which often carries the information necessary for transfer and for recombination with the host genome.”  Possible role: the emergence of antibiotic resistance in bacterial populations?  Three major biological processes ensure lateral gene transfer: transformation, conjugative transfer and viral infection and the release of viral particles.

Plasmid: mobile genetic element  Can be integrated into genome

Rare to find bacteria with non plasmid DNA. Comparison of Prokaryote Genomes: Evidence for Red = seq laterally transferred = plasmid DNA  Some don’t have any plasmid DNA.  Does not allow incorporated DNA into genome  Separate DNA based on size.  Can be in bacteria but not in genome 

Eukaryote Genetic Material: Human (nucleus) 

Eukaryotic genomes generally contain many large linear piece of DNA referred to as a "chromosome" (human have 46 chromosomes).

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Large variation in sizes of eukaryote chromosomes: 2.9 (Chr 21) to 4000 Mbp (Chr 1): human chromosomes are not of equal sizes.

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Each chr consists in a piece of linear DNA associated to proteins involved in folding and compacting to form chromatin.

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Genetic material is also stored in mitochondria: ~16.6 kb.

Aligned by centromeres, done by size except 21...