Unit 3--Lecture 18 (Viral Genomics) Flashcards
Mobilome
Mobilome: the total of all mobile genetic elements in a cell’s genome
1) Self-splicing RNA
–enzymatic genetic elements
2) Transposons
–mobile genetic elements
3) Plasmids
–autonomous genetic elements
4) Viruses
–infectious genetic elements
Group II Introns
Large ribosomes
Self-splicing
Transposable Elements
DNA transposons:
–insertion sequences
–transposons
–conjugative transposons
Retrotransposons:
–retrons (msNDA)
–SINE (short interspersed elements)
–LINE (long interspersed elements)
–LTR (long terminal repeat)
IS Elements
Inverted terminal repeats
Transposase
Replicative or non-replicative transposition
Transposons
Composite: capture an intervening gene
–one on each end
Complex: gene within the element
Genomic Islands
Provide evidence for horizontal gene transfer
Altered %G+C
These include:
–pathogenicity islands
–symbiosis islands
–fitness islands
Retrons
msDNA: satellite DNA in prokaryotes
Widely distributed in bacteria and archaea
Made by reverse transcriptase
Both ssDNA and ssRNA
SINE
SINE: Short Interspersed Elements
1,500,000 in human genome (11%)
RNA polymerase III genes
Alu sequences
Composite SINEs
LINE
LINE: Long Interspersed Elements
500,000 in human genome (17%)
RNA polymerase II genes
LTR
LTR: Long Terminal Repeats
Around 500,000 in human genome (8%)
Similar to retroviruses
Lack envelope proteins
Plasmids
Retroplasmid: rare, found in some fungal mitochondria
Episomes
Conjugation
Addiction Modules
Toxin-antitoxin set on plasmid
Antitoxin is unstable
If plasmid is lost:
–protease destroys antitoxin
–toxin activated
–cell dies
Plasmid ensures that the cell doesn’t lose it
Bacteriophage
Circular chromosomes
Rolling circle replication
Lytic phage
Temperate phage
Can mobilize host genes
Herpes Virus (Class I)
Rolling circle replication
Exocytosis
*Parvovirus (Class II)
ssDNA
Use host DNA polymerase
Rolling hairpin mechanism to deal with ends
