The Mosaic Nature of Genomes

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1 The Mosaic Nature of Genomes n DNA sequence is not static Mutations of single bases Large deletions Large insertions of sequence n Transferred from other species n New functions useful in particular situations Maintained via interaction with environment n Survival determined by having appropriate genes for the specific environment 2009 W. W. Norton & Company, Inc. 1

2 Horizontal Gene Transfer n Movement of genes between cells Other than through cell division n Transformation, conjugation, transduction Transposons carry genes into chromosome Plasmids carry genes between cells n Without having to become part of chromosome 2009 W. W. Norton & Company, Inc. 2

3 Gene Transfer: Transformation n Uptake of DNA directly from medium Competent cells n Translocasome takes up DNA Located in envelope n Competence induced in different species Gram + cells secrete signal Competence factor Stress induces competence n Starvation 2009 W. W. Norton & Company, Inc. 3

4 Gene Transfer: Conjugation n Bacterial sex Type IV secretion system = pilus Pilus proteins encoded on F factor Transfers DNA on F factor n Starts at orit site In recipient cell, transferred DNA forms a new F plasmid Female cells become male n Able to transfer DNA 2009 W. W. Norton & Company, Inc. 4

5 Gene Transfer: Conjugation n Fʹ factor F plasmid contains extra genes orit Fʹ lac lac genes n In addition to genes for pilus, transfer Transfers extra genes to recipient n Hfr F factor integrates on bacterial chromosome Tries to transfer entire chromosome n Requires 100 minutes for E. coli n Transfers genes in order n Can determine order of genes on chromosome F factor Bacterial chromosome 2009 W. W. Norton & Company, Inc. 5

6 Gene Transfer: Transduction n Viruses inject DNA into cell Bacteriophage n Package DNA into viral capsid Viral DNA Sometimes package bacterial DNA by mistake n Transfer DNA to new host Can bring new bacterial genes to host Recombination crossover events exchange host for donor DNA W. W. Norton & Company, Inc. 6

7 Defense against transferred DNA n Bacteria cut entering DNA to pieces Cut at specific restriction sites n Bacteria add methyl groups to DNA Prevents restriction at those sites Add as cell replicates chromosome n Entering DNA is destroyed Unless comes from a similar species n And has methyl groups protecting DNA EcoRI restriction/ modification site 2009 W. W. Norton & Company, Inc. 7

8 Recombination n Entering DNA replaces chromosomal DNA If sequence is overall very similar n DNA enters via transformation, conjugation, transduction Replaces variable-sized section of DNA Also used to repair damaged DNA Requires specific recombination proteins n RecA n RecBCD n RuvAB 2009 W. W. Norton & Company, Inc. 8

9 Mutation n Heritable change in DNA sequence n Point mutations Change in one base pair n Transition: purine purine, pyrimidine pyrimidine n Transversion: purine pyrimidine n Larger mutations Insertion of a section of DNA into chromosome Deletion of a portion of the chromosome Inversion: flipping a portion of chromosome 2009 W. W. Norton & Company, Inc. 9

10 Mutations n Most mutations are silent No effect on organism n Mutations in regions between genes n Mutations that change 3rd base of a codon n Mutations that change 1 amino acid into a similar one Protein still retains normal function n Mutations that change a protein that is not needed In current environment of organism Mutation = change in genotype Effect on organism = phenotype Normal n Study effects only if is a noticeable phenotypic change 2009 W. W. Norton & Company, Inc. 10

11 Types of Mutations n Silent n Missense mutation Change one codon to another n Nonsense mutation Change a codon to Stop n Frameshift mutation Insert or delete a single base Changes bases read by ribosome Alters all codons downstream of mutation CGA à CGA Arginine à Arginine CGA à CAA Arginine à Glutamine CGA à TGA Arginine à STOP AAA CGA CCC à AAA CTG ACC C Lysine Arginine Proline à Lysine Arginine Threonine 2009 W. W. Norton & Company, Inc. 11

12 Mutagens Cause Mutations n Electromagnetic radiation X-rays, gamma rays The Hulk UV light Don t go tanning! n Spontaneous tautomers during replication n Chemicals Analogs of bases Base-modifying chemicals n Nitrosoguanidine, nitrous acid Intercalators insert between bases n Cause frameshift mutations 2009 W. W. Norton & Company, Inc. 12

13 Measurement of Mutagens n Ames Test Uses bacterial strain auxotrophic for histidine n Has mutation in hisg gene n Cannot grow unless histidine is supplied Place on medium + chemical n Mutagen causes reversion Changes mutation to normal form Revertant Rare mutation colonies More colonies = stronger mutagen n Most mutagens are carcinogens Cancer results from multiple mutations Mutagen on paper disk 2009 W. W. Norton & Company, Inc. 13

14 DNA Repair n Mismatch repair Mispaired base cut out of strand n Strand without methyl groups is newer Assumed to be in error n Thymidine dimers Induced by UV n Cut out by UvrAB complex n Damaged bases Excised by specific enzymes n Replaced by DNA Polymerase I 2009 W. W. Norton & Company, Inc. 14

15 DNA Repair n Recombinational repair Occurs just after strand has replicated Undamaged strand is copied n Replaced damaged strand n Catalyzed by RecA recombinase n SOS repair Extensive DNA damage inactivates LexA Activation of many repair genes Rapid polymerization of DNA n Error-prone, but better than no repair 2009 W. W. Norton & Company, Inc. 15

16 Mobile Genetic Elements n Chromosomes sequence is not fixed Transposable elements insert into chromosome n Found in all species n Retroviruses (HIV) insert DNA in mammals Can jump from one site to another n Nonreplicative transposition Can copy itself to a new site n Replicative transposition 2009 W. W. Norton & Company, Inc. 16

17 Genome Evolution n Small changes in gene sequence Slow changes in a protein n Generally, no new functions created n Large changes in chromosome Insertions of new material n Via transposition Duplication of genes n Creates new functions for cell As long as copied gene maintains original function 2009 W. W. Norton & Company, Inc. 17

18 Effects of Gene Transfer n Spreads useful genes among bacteria Antibiotic-resistance genes n Spread wherever antibiotics are overused Hospitals, farms Pathogenicity islands n Encode genes for cell to act as pathogen Difference between typical E. coli in gut and pathogenic E. coli O157H7 Genes to degrade special metabolites n E.g., oil slicks 2009 W. W. Norton & Company, Inc. 18

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