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Virology Lecture 3: Genomes and Genetics
0:00:11 Introduction: This lecture discusses viral genomes (DNA or RNA) and their genetics, focusing on how they are studied.
0:00:38 1950s Breakthrough: Two key experiments established that viral nucleic acid is the genetic code: Hershey-Chase experiment (bacteriophage) and Fraenkel-Conrat experiment (tobacco mosaic virus).
0:01:11 Hershey-Chase Experiment: Used radioactive sulfur to label proteins and radioactive phosphorus to label DNA. The experiment showed that only the labeled DNA was passed on to new phages, proving DNA as the genetic material.
0:03:04 Fraenkel-Conrat Experiment: Separated coat protein and RNA of tobacco mosaic virus (TMV) strains. Hybrid viruses were created and used to infect tobacco leaves. The progeny virus always had coat proteins that matched the RNA, confirming RNA as the genetic material.
0:04:52 Seven Viral Genome Types: There are only seven types of viral genomes (DNA or RNA, single or double-stranded, with variations), all of which need to produce mRNA for translation by host ribosomes.
0:05:36 Baltimore Classification: David Baltimore categorized viruses based on how their genomes get to mRNA, placing mRNA at the center.
0:06:11 DNA Virus Genomes: Double-stranded DNA can be directly transcribed to mRNA. Single-stranded and gapped DNA genomes must first be converted to double-stranded DNA.
Double-stranded RNA requires an RNA polymerase to produce mRNA.
Negative-sense single-stranded RNA needs to be copied into positive-sense mRNA by a viral polymerase.
Positive-sense single-stranded RNA can be directly translated, but some must go through a negative-strand intermediate.
Retroviruses use a DNA intermediate generated from the RNA.
0:08:35 Plus vs. Minus Strand: mRNA is defined as the plus strand; same polarity as message. DNA of the same polarity is also plus strand, and complements are negative strands.
0:09:33 Baltimore System Elegance: Knowing the nature of the genome allows the prediction of the steps needed to make mRNA.
0:10:00 Structural Diversity: Viral genomes can be linear, circular, segmented, plus/minus polarity, and have proteins attached to the ends.
0:12:05 Hepatitis B Genome: Has a unique gapped, partially double-stranded DNA genome with a piece of RNA and a protein attached.
0:12:56 Functional Significance of Genome Diversity: Itβs unknown why viruses use both DNA and RNA and have so many configurations, but they are evolutionarily competitive.
0:13:12 RNA World: RNA genomes are thought to be relics of the RNA world that existed before DNA.
0:14:10 Viroids: Circular, highly base-paired RNA molecules that don't encode proteins (relics of the RNA world).
0:16:37 What is Encoded: Genomes encode gene products, regulatory signals, proteins for replication, assembly, modulation of host defenses, and spread to other cells.
0:17:40 Giant Viruses (e.g. Tupanvirus): Encode very large numbers of proteins, even including nearly all of the translation machinery except the ribosome.
0:19:07 Smallest Genomes: Satellites are very small RNA molecules packaged by helper viruses, hepatitis Delta also has a very small RNA.
0:20:05 Genome Size Span: Enormous range from 2.4 million base pairs (Pandora virus) to about 220 base pairs (satellite RNAs).
0:20:53 RNA Genomes: Nidoviruses are largest RNA genomes (~40 kb), most are ~10-12 kb.
0:24:29 What is Encoded?: Viral genomes always encode the enzymes needed for replication, but never a full protein translation machinery (except the largest viruses).
0:25:19 Viral DNA Genomes: Most bacterial viruses are dsDNA, and many eukaryotic ones as well, generally emulating the host. But viral genomes lack chromatin, unlike cell chromosomes.
0:26:29 DNA Genome Types: Double-stranded DNA genomes can be circular (e.g., polyoma) or linear (e.g. adenovirus, herpes, pox)
0:29:14 Hepatitis B Genome: Has a gapped, partially double stranded genome with a piece of RNA that must be repaired by the host into a double-stranded genome for transcription.
0:30:59 Single-Stranded DNA Genomes: Must be repaired by the cell into a double-stranded form.
0:32:38 RNA Viruses and Polymerases: Mammalian cells have no RNA dependent RNA polymerase and therefore RNA viruses must encode their own to replicate in host cells.
0:34:36 Double-Stranded RNA Viruses: (e.g. Rotavirus) need an RNA polymerase to copy mRNA since ribosomes cannot access the double stranded RNA directly.
0:35:42 Plus-Stranded RNA Viruses: (e.g., coronavirus, flavivirus, picornavirus) Have genomes that can immediately translate into proteins.
0:37:31 Retroviruses: RNA genome but use a DNA intermediate for replication.
0:38:36 Negative-Sense RNA Viruses: Must carry a polymerase within the virus to copy the genome to an mRNA.
0:41:28 Segmented Genomes: (e.g. Influenza) Allow for reassortment, which creates genetic diversity.
0:42:55 Ambisense Genomes: Some RNA viruses (e.g., Lassa) have a mix of plus and minus strand polarity segments.
0:43:39 RNA Structure: RNA molecules are not just simple lines but rather complicated structures due to base pairing.
0:46:23 Genetics Manipulations: Old methods like plaque assays were used, but today, genetic manipulation is done via DNA clones.
0:46:58 Definitions: Mutation is a change in RNA or DNA.
0:47:22 Infectious DNA Clones: Viral genomes are cloned into bacterial plasmids for manipulation. Plasmids are transfected into cells to make new viruses.
0:48:01 Viral Vectors: Can be made with these techniques to try to cure disease or make vaccines.
0:48:44 RNA Introduction: RNA can be introduced into cells to replicate and make viral proteins. (e.g. MRNA vaccines)
0:49:40 1918 Influenza: Reconstructed by taking RNA from autopsies and using cloned plasmids.
0:51:14 Horsepox Reconstitution: An extinct virus was recovered from its DNA sequence.
0:52:00 Biosecurity: These experiments raise dual use concerns (good and bad uses) that are handled by government committees.
0:52:41 Gain-of-Function Research: Modifying viruses can give them new traits, which is both powerful for study and can raise safety issues.
0:53:13 Examples of Gain of Function: Poliovirus passaged to infect rodents. Coronavirus bat spike proteins substituted to increase infectivity.
0:55:37 Political Controversy: Debate over risky gain-of-function research is highly contentious.
0:56:13 Next Time: Discussion will shift to viral building.