DNA/Horizontal Gene Transfer

Question 1

What is the name for the fragments of DNA made on the lagging strand started by primers and joined by DNA ligase?

Answer 1

Okazaki fragments

Question 2

What is the name of the enzyme that performs supercoiling?

Answer 2

topoisomerases
mostly negative supercoils
stabilised by proteins

Question 3

What is the definition of a species?

Answer 3

a monophyletic and genomically coherent cluster of individuals that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property
monophyletic = recent common ancestor

Question 4

What is the difference between core genes and accessory genes?

Answer 4

core genes: genes present in all individuals
accessory genes: dispensable genes (strain specific)
PAN genome = core + accessory

Question 5

What are the conditions for two bacteria to be genetically similar?

Answer 5

via 16S rRNA sequencing:
Average Nucleotide Identity (ANI): >95%
DNA-DNA Hybridization (DDH): 70%

Question 6

What are the 3 main mechanisms of horizontal gene transfer?

Answer 6

1. transformation
2. transduction
3. conjugation

Question 7

What genetic elements make up the mobilome?

Answer 7

• plasmids
• prophages
• integrons
• insertion sequences
• transposons

Question 8

What are the characteristics of a genome that has undergone horizontal gene transfer?

Answer 8

1. the presence of genes that encode proteins typically found in distantly related species
2. the presence of a stretch of DNA whose G:C content differs greatly from the rest of the genome

Question 9

What are transposons?

Answer 9

mobile genetic elements that move between different host DNA molecules by activity of transposase which are encoded on their DNA sequences
may pick up and horizontally transfer genes encoding various characteristics

Question 10

What are insertion sequences?

Answer 10

simple transposable elements whose genes only encode for transposases

Question 11

What bacteria would contain relatively large numbers of mobile elements?

Answer 11

those that are undergoing rapid evolutionary change, usually due to stressful conditions

Question 12

What are the consequences of transposition by mobile elements?

Answer 12

generates chromosomal rearrangements such as inversions, deletions or translocations which provide a source of genetic diversity
these arrangements are often flanked by repeats or insertion sequences

Question 13

What is transformation?

Answer 13

genetic transfer process by which free DNA is incorporated into a competent recipient cell
occurs in both gram+ and gram- bacteria
competence is regulated by proteins

Question 14

What is electroporation?

Answer 14

shocking bacterial cells with high voltage electric pulses which makes their cell envelope permeable to DNA
forces bacteria to be competent

Question 15

Why is transformation of a plasmid often less effective than that of chromosomal DNA?

Answer 15

plasmid DNA must stay double-stranded and circular to replicate

Question 16

How is DNA taken up during transformation?

Answer 16

DNA is bound at cell surface by a DNA binding proteins which pulls the DNA into the periplasm of gram- or through thick wall f gram+
either whole double strand is taken up or one strand is degraded by a nuclease
a competence-specific protein binds the donor DNA which protects the DNA from further nuclease attack
DNA is then integrated into the genome via recombination

Question 17

What is generalised transduction?

Answer 17

a bacteriophage transfers DNA from one cell to another

DNA from any portion of the host genome is packaged inside the mature virion in place of the virus genome forming a transductant

happens during lytic cycle of bacteriophages
the resulting transducting particle DNA cannot replicate inside another bacteria it may integrate into the genome
frequency and specificity is low

Question 18

What is specialised transduction?

Answer 18

a bacteriophage transfers DNA from one cell to another

DNA from a specific region of the host genome chromosome is integrated directly into the virus genome

occurs when phage DNA has been inserted into host genome is replicated to produce new virions but genes adjacent to the prophage have been picked up as well
high frequency, efficiency, and specificity

Question 19

What is conjugation?

Answer 19

plasmid encoded mechanism that involves transfer of plasmids and other mobilised genetic material via the pili

uses rolling circle replication for DNA synthesis instead of the usual normal bidirectional replication

one strand is transferred to the recipient bacteria
as this transfer occurs, the rolling circle mechanism replaces the transferred strand in the donor while a complementary strand is made in the recipient