Genomes and Genetics Flashcards
Universal functions of viral genomes are to produce proteins, and reproduce DNA/ RNA
Production of proteins uses host ribosomes. This requires mRNA.
All viruses have different methods to produce mRNA
What is unique about RNA viruses?
DNA viruses utilised human host cell machinery directly
+ssRNA mRNA used directly as mRNA
+ssRNA retroviruses need to convert to DNA. Virus must provide its own RT as humans do not have this enzyme
-ssRNA needs converted to +ssRNA. Virus must provide its own RNA-dependent RNA polymerase as humans do not have this enzyme
Viral genome encodes encodes all proteins for replication, expression of genome, assembly of virus, and modulation of host defences
What does it not encode?
• genes encoding a complete protein synthesis machinery (e.g., no ribosomal RNA and no ribosomal or translation proteins);
note: the genomes of some large DNA viruses contain genes for transfer RNAs (tRNAs), aminoacyl-tRNA synthetases, and
enzymes that participate in sugar and lipid metabolism
• genes encoding proteins of energy metabolism or membrane biosynthesis
• telomeres (to maintain genomes) or centromeres (to ensure
segregation of genomes)
mRNA is defined as the positive (+) strand, because it can be translated into a protein.
A strand of DNA of the equivalent polarity is also designated as a (+) strand; i.e., if it were mRNA, it would be translated into protein.
The RNA or DNA complement of the (+) strand is called the (-) strand.
The (-) strand cannot be translated; it must first be copied to make the (+) strand.
What polarity does ambisense RNA have?
Ambisense RNA contains both (+) and (-) sequences. e.g Arenavirida (Lassa) and Bunyaviridae
Ambisense RNA contains both (+) and (-) sequences. e.g Lassa
The ambisense RNA viruses and the minus-sense viruses are closely related. One family, the Bunyaviridae, even contains both types of viruses as members. The ambisense strategy is, in fact, a simple modification of the minus-sense strategy, and these viruses are generally lumped together as “negative-strand” or “minus-strand” RNA viruses
What are the benefits of an ambisense strategy?
(+) RNA can be directly translated to proteins, after virus enters cells
(-) RNA needs converted to (+) RNA
Thus, ambisense viruses modify the minus-sense strategy by synthesizing mRNA from both the genome and the antigenome. Neither the genome nor the antigenome serves as mRNA.
The benefit is to delay the synthesis of mRNAs that are made from the (-) RNA and thus to introduce a timing mechanism into the virus life cycle. Results in proteins being produced at most useful time for viral life cycle.
Gapped DNA genome is an incomplete template for transcription - e.g HBV
What must occur before transcription of gapped dsDNA?
HBV has gapped, circular, dsDNA
host RNA polymerase can only transcribe fully complete circular dsDNA
HBV reverse transcriptase coverts into complete circular dsDNA. Which then acts as template for transcription
ssDNA genome
How is RNA produced?
RNA can only be made from a dsDNA template, whatever the sense of ssDNA
therefore some DNA synthesis must occur, to produce dsDNA prior to mRNA production
cellular DNA polymerases are used for this
Human cells are unable to work with RNA as a template
Cells have no RNA-dependent RNA polymerases that can replicate genomes of RNA viruses, or make mRNA from RNA templates
How do RNA viruses overcome this?
1 - One solution to this problem is that RNA virus genomes encode RNA-dependent RNA polymerases that produce RNA from RNA templates.
2 - The other solution, exemplified by retrovirus genomes, is reverse transcription of the genome to dsDNA, which can be transcribed by host RNA polymerase.
dsRNA includes viruses such as Reoviridae
The (+) sense strand of dsRNA cannot be translated to viral proteins
What steps are required first?
While dsRNA contains a ( + ) strand, it cannot be translated as part of a duplex to synthesize viral proteins.
The ( - ) strand of the genomic dsRNA is first copied into mRNAs by a viral RNA-dependent RNA polymerase.
Newly synthesized mRNAs are encapsidated and then copied to produce dsRNAs.
+ssRNA are the most plentiful of viruses on planet
+ssRNA can be translated directly into protein by host ribosomes
How is the genome copied?
The genome is replicated in two steps.
1 - the ( + ) strand genome is first copied into a full-length ( - ) strand
2 - the ( - ) strand is then copied into full-length ( + ) strand genomes.
In some cases, a subgenomic mRNA is produced
+ssRNA with DNA intermedoate viruses (retroviruses) have a unique mechanism of replication
What are the steps?
In contrast to other ( + ) strand RNA viruses, the ( + ) strand RNA genome of retroviruses is converted to a dsDNA intermediate
by viral RNA-dependent DNA polymerase (reverse transcriptase).
This DNA then serves as the template for viral mRNA and genome RNA synthesis by cellular enzymes. T
here are three families of ( + ) strand RNA viruses with a DNA intermediate; members of the Retroviridae infect vertebrates.
-ssRNA viruses cannot be translated directly into protein
What steps occur for protein production?
-ssRNA acts as template for +mRNA, which can be used for translation
no enzymes in cell that can make RNA from -ssRNA
viruses encode RNA-dependent RNA polymerases to enable conversion
For -ssRNA replication, +ssRNA template produced, which acts as a template for creation of -ssRNA
What does 5’ and 3’ mean in relation to single strand of DNA or RNA
5’ - 3’ direction refers to the orientation of nucleotides of a single strand of DNA or RNA.
The 5’ and 3’ specifically refer to the 5th and 3rd carbon atoms in the deoxyribose/ribose sugar ring.
The phosphate group attached to the 5’ end of one nucleotide and the hydroxyl group at the 3’ end of another nucleotide have the potential to form phospodiester bonds, and hence link adjacent nucleotides.
This linkage provides the sugar-phosphate backbone that gives DNA its structural rigidity. Any single strand of DNA/RNA will always have an unbound 5’ phosphate at one end and an unbound 3’ hydroxyl group at the opposite end.
DNA is always read in the 5’ to 3’ direction, and hence you would start reading from the free phosphate and finish at the free hydroxyl group.
Previously thought that one gene, coded for one mRNA.
However compact viral genomes can produce many mRNAs, all encoding different proteins
What techniques to viruses use?
Extraordinary tactics for information retrieval, such as:
- the production of multiple subgenomic mRNAs, mRNA splicing, RNA editing, and nested transcription
units (Fig. 3.10), allow the production of multiple proteins from a single viral genome. - Further expansion of the coding capacity of the viral genome is achieved by posttranscriptional mechanisms, such as polyprotein synthesis, leaky scanning, suppression of termination, and ribosomal frameshifting. In general, the smaller the genome, the greater the compression of genetic information
Size of genome does not correlate to number of proteins that can be produced
RNA virus genomes are sometimes segmented
What does this mean?
RNA viruses can contain a single (unsegmented) or multiple (segmented) genomic molecules. However, the evolutionary connection between these two fundamentally different forms of genome organization is unclear.
Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle.
These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA
Arenaviridae, Birnaviridae, Bunyavirales, Orthomyxoviridae, Picobirnaviridae, and Reoviridae
RNA genomes are very susceptible to mutation
why is this?
RNA less stable - 1 mis-incorporation in 10 4 or 10 5 nucleotides polymerized. So for every copy produced, would expect 1 mutation
This therefore limits the length of RNA, as long RNA will invariably have a lethal mutation
Very few RNA exonucleases exist. Coronavirus has an exonuclease which can proof read and eliminate errors in RNA
DNA has proof reading to reduce errors
