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Lecture 8

BIOC 4403 Lecture Notes - Lecture 8: Poliovirus, Mimivirus, Microorganism


Department
Biochem & Molecular Biology
Course Code
BIOC 4403
Professor
Archibald John
Lecture
8

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1. Viruses entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic
machinery, and cause the synthesis of specialized elements [virions] that can transfer the genome to other cells.
2. classification
of viruses
-nature of genome (the 'Baltimore classification');
-shape and capsid structure
-presence / absence of envelope (typically membrane / protein derived from host)
-the type of cellular organisms they parasitize
(e.g., bacteriophages infect bacteria)
3. classification
of viruses
based on
nature of
genomes
I dsDNA: Herpes virus
II ssDNA: Adenovirus
III dsRNA: Reovirus
IV (+) ssRNA: Poliovirus
V (-) ssRNA: Influenza, Ebola
VI ssRNA-RT (DNA intermediate): retroviruses, e.g., HIV
VII dsDNA-RT (RNA intermediate):
Hepatitis B
4. 'Typical'
features of
Viral
genomes
-there are no typical features! Genomes can be linear, circular, or alternate between the two (retroviruses reverse
transcribe RNA genome and incorporate DNA into host genome; becomes 'provirus').
-gene expression patterns are similarly diverse, relating to how the genomes are organized.
-gene dense is high (usually >1 gene per kbp, often with overlapping genes).
-often compositionally biased (e.g., A+T- or G+C-rich).
-Fast-evolving, divergent gene sequences, RNA viruses in particular.
-viral genomes are extremely diverse in their coding capacity (total gene number and diversity)
5. why viral
genomes
evolve fast?
-viral RNA polymerases lack proofreading capability.
-in retroviruses, process of reverse transcription is error-prone.
6. Natural
history of
viral genes
5 'types'
Genes with readily detectable homologs in cellular life forms (detectable by molecular phylogeny)
1. Genes with closely related homologs in cellular organisms (typically, the host of the given virus) and present only in a
small subset of viruses.
2. Genes that are present within a major group or several groups of viruses, and with distant related homologs in cellular
life forms.
Virus-specific genes
3. ORFans, i.e., genes without detectable homologs in any other known organism (except, possibly, in closely related
viruses). [NOTE—the term ORFan applies to all sorts of genomes, not just viral genomes]
4. Virus-specific genes that are conserved in a (relatively) broad group of viruses but have no detectable homologs in
cellular life forms.
Viral 'hallmark genes'
5. Genes shared by many (but not necessarily all) diverse groups of viruses, with only very distant homologs in cellular
organisms. (similar to 'type 2' genes above)
Examples: capsid proteins, reverse transcriptase, RNA-dependent RNA polymerase
7. Viral
'hallmark
genes'
Genes shared by many (but not necessarily all) diverse groups of viruses, with only very distant homologs in cellular
organisms. (similar to 'type 2' genes above)
Examples: capsid proteins, reverse transcriptase, RNA-dependent RNA polymerase.
a small group of viral hallmark genes that encode key proteins involved in genome replication and virion formation and
are shared by overlapping sets of diverse viruses ensures the connectivity of the evolutionary network in the virus
world. Virus hallmark genes have no obvious ancestors in cellular life forms, suggesting that virus-like elements evolved
at a pre-cellular stage of the evolution of life. <Origins and evolution of viruses of eukaryotes: The ultimate modularity>
4403 - 8 Viral Genomes
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