Microbial Genetics and Genomics

Question 1

Traits of asexual gene transfer

Answer 1

• near identical genetic material copy
• can occur between distantly related species influencing their phenotypes
  -diversity is attained through horizontal gene transfer and mutation

Question 2

transformation

Answer 2

• naked DNA taken up from the environment
• important for acquisition of genetic material for virulence factors and antibiotic resistance
• not very efficient as introducing diversity (not that much DNA in the environment)
• Recombinant DNA once incorporated can change the phenotype and stuff

Question 3

horizontal gene transfer

Answer 3

• introduction of genetic material from one organism to another IN THE SAME GENERATION
• distantly related species can share genes, influencing their phenotypes
  transformation, transduction, conjugation

Question 4

Sexual reproduction

Answer 4

slower to produce offsprings
generates diversity
- material from 2 parents
- crossover
- independent assortment of chromosomes during meiosis
-chromosomal segregation not always correct

Question 5

Asexual reproduction

Answer 5

generates offspring more quickly
generates less diversity
- identical genome passed down
- mutations could give rise to a selective advantage
- mutations are random and rare (ash)

Question 6

Vertical Gene Transfer

Answer 6

Between mother and daughter cells, different generations

Question 7

Competent Cells

Answer 7

can bind DNA in the environment, transport across the plasma membrane and make it single stranded, most bacteria are naturally competent

Question 8

Why does the bacterial cell make the environmental DNA into a single stranded form

Answer 8

endo and exonuclease would normally digest dsDNA but are mostly ineffective against ssDNA

Question 9

RecA

Answer 9

recombination protein A implicated in DNA repair, implicated in transformation mediates homologous recombination

Question 10

Transduction

Answer 10

• Genes are transferred between cells by a virus
• Major contributor to genetic hyper-mobility and both bacterial and phage evolution
• host acquires new properties through lysogenic conversion or phage conversion

Question 11

Clinical Consequences of transduction

Answer 11

pathogenic strains of V.cholerae result from horizontal gene transfer by specialized transduction, bacteria can become virulent

Question 12

Cholera Toxin

Answer 12

gene carried by phage and incorporated into the bacterial chromosome through infection
- when it enters the cell through vesicle mediated transport it disrupts cAMP a second messenger which triggers the releases of Cl- ions out of the cell and the water follows causing watery diarrhea characteristic of cholera

Question 13

Mechanism of Transformation

Answer 13

Mechanism:
1. DNA is bound by the bacterial cell and transformed from the donor cell, DNA-binding protein holds DNA, nucleases cleave it
2. Uptake of ssDNA by the cell, DNA enters the cell and ssDNA binding proteins bind the donor DNA as it enters
3. Rec-A mediated homologous recombination
4. Donor DNA is added to bacteria chromosome

Question 14

Mechanism of Transduction

Answer 14

Phage conversion: host phenotype is altered by lysogenization
contribution to diversity: once prophage is integrated the bacteria can become immune to further infection by same phage or phages of the same time
transducer cells may acquire new phenotypic abilities like virulence

Question 15

lysogenization

Answer 15

integration of phage DNA into host chromosome

Question 16

generalized transduction

Answer 16

chromosomal DNA is transferred by accident from one infected cell to another because it was accidentally packed into the capsid when visions are assembling

Question 17

specialized transduction

Answer 17

a specific piece of DNA is lifted from the infected cell from either side of where the lysogenic phage had integrated into the host cells, these sequences are then encapsulated and transported to other cells and will integrate in the newly infected cells at the viral integration site.

Question 18

Conjugation

Answer 18

DNA transferred through hollow conjugation pills to transfer genes bwt cells
Transfer through cell contact so transfer can be to closely or even distantly related cells
conjugation pilus = F pilus
capacity to form pilus encoded on plasmid
archaea have these too
Diversity: transfer for even distantly related cells, can transfer new operons
starts with F+ and F- and ends with 2 F+

Question 19

F+ cells

Answer 19

have plasmid and can make a pilus, DONOR cells

Question 20

F- cells

Answer 20

don’t have plasmid, RECIPIENT

Question 21

Mechanism of conjugation of the F plasmid

Answer 21

• pilus of F+ attaches to F- and contracts drawing cells together to make contact
• one strand of the F plasmid transfers from donor to recipient -> rolling circle replication
• Cells synthesize complementary strands to complete their plasmids

Question 22

Hfr strains

Answer 22

Cells possessing an integrated F plasmid (f plasmid episome integrates into host chromosome)
Hfr -> high frequency of recombination: high recombinant rate between genes on the Hfr donor and F- recipient chromosomes

Question 23

Conjugation of F’ and Hfr cells

Answer 23

Imprecise excision of the F plasmid from the Hfr chromosome leads to formation of F’ chromosome which carries extra DNA adjacent to the integration site which can then be transferred to an F- cell

Question 24

Conjugation of Hfr Cells

Answer 24

• bacteria attempts to transfer the whole chromosome
  genes closet to F plasmid integration site transferred first
• rarely happens since contact bwt cells is transient and short-lived: but sufficient to transfer on or several operons and whole new biochemical pathways

Question 25

Plasmids

Answer 25

• extrachromosomal DNA with autonomous replication
  donut in all kingdom microbes
  usually circular and negatively supercoiled
  nonessential genes but critical in some situations like antibiotic resistance

Question 26

Plasmid tricks

Answer 26

• by having beneficiary functions like abs resistance
• high copy numbers: so many of them in the cell so the chance of daughter cell getting one is high
• low copy numbers use partitioning system filaments connect 2 plasmids, plasmid keeps going towards cell pole which triggers filament depolymerization, stable filaments polymerize pushing plasmids towards opposite poles

Question 27

Transposition

Answer 27

• transposons are genetically mobile elements
• transferred vertically
• exist in both pro and eukaryotic cells
• shuffle sequences around the genome, create new sequences and disrupt functional genetic units

Question 28

Mechanism of Transposition

Answer 28

Transposon encodes transposes surround by inverted repeat sequences, transposes facilitates recombination between inverted repates, and the transposon is cut and inserted in a new location

Question 29

Chromosomal Islands

Answer 29

also known as genomic islands
clusters of genes for specialized functions nonessential to survival
creates diversity within a species cause some strains of species have them others don’t

Question 30

Why are chromosomal islands hypothesized to be of foreign origin?

Answer 30

1. extra genes are surrounded by inverted repeats indicating they may have been inserted by transposition
2. Base composition and codon bias of the differ from rest of genome sometimes
3. Chromosomal island are found in certain strains in the species suggesting they aren’t a product of evolution or vertical transmission

Question 31

core genome

Answer 31

shared by all strains of the same species

Question 32

pan genome

Answer 32

core genome plus the ones shared by all strain in a species

Question 33

How have microbial genomes evolved and fostered diversity?

Answer 33

• microbial genomes are dynamic and continue to evolve through the gain and loss go genes through
  1. horizontal gene transfer: pathogenicity, symbiosis and fitness islands
  2. genome reduction: large scale loss of genes through evolution
  3. duplication leading to functionaL divergence through mutation: