seminar 1

Question 1

What are the basic characteristics of genomic/pathogenicity islands?

Answer 1

• 10-299 kb
• GC content lower/different -> codon usage different
• often inserted in tRNA genes
• flanked by direct repeats
• have genes involved in genomic island transfer
• carry insertion elements (transposons), implicated in mobilizing genetic nmaterial
• genes offer selective advantages (pathogenicity, symbiosis, metabolic, fitness, resistance)

Question 2

2. How are these islands usually integrated into a genome?

Answer 2

by integrases, using site specific recombination, 15-20 bp motive within 3* end of tRNA gene
integrase cutts dsdna with overhangs, foreign gene gets added, polymerase closes holes -> thereby creating direct repeats

Question 3

3. How are they transferred between bacteria

Answer 3

• transformation
• conjugation
• transduction

Question 4

4. How does HNS affect horizontally transferred DNA?

Answer 4

• silences horizontally acquired genes
• not specific

histones line nucleoid-structuring protein (HNS)
pleiotropic regulator, modulates gene expression in gram- bacteria in response to environmental stimult (temp. osmolarity)
-fuctional equivalent of hormones -> supercoiling, higher affinity for curved DNA
-role in selective silencing of horizontally acquired genes,targets sequences with high AT content, conserved binding motives foun in operons and pathogenicity islands

Question 5

5. Name some functions that are frequently encoded on genomic islands?

Answer 5

pathogenicity, symbiosis, metabolic, fitness, resistance)

Question 6

6. What problems can be caused to the bacterial cell by newly acquired DNA?

Answer 6

• problems with regulation
• loss of fitness
• high expression -> toxicity

Question 7

7. What is meant by genomic GC content (what is special about AT-rich DNA

Answer 7

varies from 20-75%
but within one genome constant -> signature of signature of the phylogenic group

it comes from a different origin