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Virology Lectures 2025: Transcription and RNA Processing
0:08 Introduction: The lecture focuses on transcription (making RNA from a DNA template) and RNA processing in DNA viruses.
0:34 Baltimore Scheme: mRNA is central, and today's focus is on DNA viruses that transcribe their genomes to make mRNA. Transcription always occurs from a double-stranded DNA template.
1:11 DNA Template Preparation: Some viral DNA genomes (single-stranded or gapped) need to be converted to fully double-stranded DNA before transcription can occur. The cell's DNA repair mechanisms often assist in this process.
1:45 Key Concept: For DNA viruses, at least one, sometimes many, viral protein(s) must be produced before DNA replication, necessitating transcription.
4:55 Ready Templates: Some viruses, like adenoviruses, herpesviruses, polyomaviruses, and papillomaviruses, have double-stranded DNA genomes ready for transcription upon entry into the nucleus.
5:46 Enzymes: DNA-dependent RNA polymerases are cellular enzymes used by most DNA viruses for transcription. There are three main types (Pol I, Pol II, Pol III), with Pol II being responsible for mRNA synthesis.
7:05 Viral Polymerases: Some viruses, particularly those replicating in the cytoplasm (e.g., poxviruses, giant viruses), encode their own DNA-dependent RNA polymerases because the cellular enzymes are located in the nucleus.
8:05 Transcription Process: Overview of transcription initiation at promoters, 5' capping, pre-mRNA synthesis, intron removal (splicing), polyadenylation, and mRNA export to the cytoplasm for translation.
9:35 Splicing Importance Splicing is required for the nuclear export of mRNAs.
9:46 Transcriptional Regulation: Transcription is highly regulated, involving a transcriptional control region with an initiator sequence, core promoter, and upstream regulatory sequences.
11:12 Viral Genome Examples: Different viral genomes (adenovirus, SV40) have distinct transcriptional control regions.
12:35 Transcription Initiation: Description of the complex process of transcription initiation, involving the assembly of multiple proteins (including RNA polymerase II) at the promoter.
14:11 Polymerase Action: The RNA polymerase denatures the double-stranded DNA, transcribes the template strand, and produces mRNA.
15:42 Enhancers: Long-distance regulatory sequences (enhancers) can enhance transcription by binding proteins that interact with the initiation complex.
16:36 Regulatory Proteins: Both host and viral proteins can regulate transcription. They are sequence-specific DNA-binding proteins or co-activating molecules that modulate nucleosome structure (histone modification).
18:18 Protein Structure: Sequence-specific transcriptional regulatory proteins have a modular organization, including a nuclear localization signal, dimerization domain, DNA-binding domain, and activation domain.
20:36 Transcriptional Strategies:
* Viruses using only the host transcriptional system.
* Viruses using the host system plus one viral protein.
* Viruses using the host system plus multiple viral protein.
* Viruses with entirely viral transcriptional systems (cytoplasmic replication).
22:48 Regulatory Strategies: Cascade regulation (one gene's product activates another) and positive/negative auto-regulatory loops (a gene's product regulates its own transcription).
25:16 SV40 Example: SV40 has early and late promoters. The early promoter produces T antigen, which stimulates DNA replication. DNA replication, in turn, activates the late promoter, leading to structural protein production. A cellular repressor (IBP) initially blocks the late promoter.
31:37 Adenovirus Example: Adenovirus has a more complex system with immediate early, early, and late genes. The E1A protein (immediate early) is crucial for activating early genes by freeing up the E2F transcription factor (which is normally bound by the retinoblastoma protein, RB).
37:25 Herpesvirus Example: Herpesviruses also have immediate early, early, and late genes. The immediate early promoter requires a viral protein (VP16, carried in the virion) for activation.
41:43 mRNA Processing: Mature mRNA has a 5' cap (a GTP linked by a 5'-5' triphosphate linkage) and a 3' poly(A) tail.
42:58 Capping: Capping is co-transcriptional (occurs during transcription) and is important for mRNA stability and export.
43:41 Polyadenylation: Polyadenylation occurs in the nucleus after cleavage of the pre-mRNA at a polyadenylation signal (AAUAAA).
44:42 Poly(A) Mechanisms: Different viruses use different mechanisms for polyadenylation.
45:42 Splicing: Splicing removes introns from pre-mRNA. It was discovered in adenovirus-infected cells.
47:35 Splicing Mechanism: Involves conserved sequences at intron-exon junctions and an RNA-driven reaction (ribozyme) within a complex called the spliceosome.
49:58 Splicing Function: Splicing allows for the production of multiple mRNAs (and thus proteins) from a single gene through alternative splicing.
53:40 Splicing and Export: Splicing marks mRNAs for nuclear export. Splicing proteins remain bound to the spliced mRNA and are recognized by the nuclear export machinery.
55:31 Unspliced RNA Export: Some viral RNAs (e.g., retroviral genomes) need to be exported unspliced. They achieve this through specific RNA elements (e.g., constitutive transport element, CTE, in retroviruses, or the Rev responsive element, RRE, in HIV) that interact with the export machinery.
58:56 RNA Editing: Non-templated RNA synthesis, such as RNA editing in hepatitis delta virus, where a termination codon is changed, leading to a longer protein.
1:00:31 Other RNAs: Cells encode many other non-coding RNAs (short and long), including microRNAs, long non-coding RNAs, and circular RNAs, with various regulatory functions.
1:01:04 MicroRNAs: MicroRNAs regulate gene expression by binding to mRNAs and causing translational suppression or mRNA degradation.
1:02:11 Mir-122 Example: Mir-122, a liver-specific microRNA, is essential for hepatitis C virus replication.
1:03:29 Circular RNAs: Circular RNAs, formed by back-splicing, can act as sponges for microRNAs and RNA-binding proteins.
1:04:09 RNA Methylation: RNA methylation, particularly N6-methylation of adenosines, can regulate gene expression. Writers, readers, and erasers control the methylation process. An example is seen with hepatitis C virus, where methylation of the viral RNA can impact packaging into particles.