Transcription and RNA Processing in DNA Viruses

Transcription and RNA Processing in DNA Viruses

Overview

This study guide covers the mechanisms and regulation of transcription and RNA processing in DNA viruses, with a focus on eukaryotic host interactions, viral strategies, and the role of noncoding RNAs. Understanding these processes is essential for grasping how viruses exploit host machinery and regulate gene expression during infection.

Viral Genomes and Transcriptional Templates

Types of Viral Genomes

• DNA Viruses: Contain double-stranded (dsDNA) or single-stranded (ssDNA) genomes. Examples: Adenovirus, Herpes simplex virus, Polyomavirus, Parvovirus.

• RNA Viruses: Contain positive-sense (+RNA), negative-sense (−RNA), or double-stranded RNA genomes. Examples: Poliovirus, Influenza virus, Retrovirus.

• Reverse Transcribing Viruses: Use reverse transcription to convert RNA to DNA (e.g., Retrovirus, Hepatitis B virus).

All viruses must produce mRNA for protein synthesis, but the pathway to mRNA varies by genome type.

Conversion to Transcriptional Templates

• Some viral DNA genomes require conversion (repair or synthesis) before transcription can occur.

• Examples:

  • Hepadnavirus: DNA repair is needed.

  • Parvovirus: DNA synthesis is required.

  • Retrovirus: Reverse transcription and integration into host genome.

Eukaryotic DNA-dependent RNA Polymerases

Types and Functions

Enzyme	Cellular RNA	Viral RNA
RNA pol I	Pre-rRNA	None known
RNA pol II	Pre-mRNA, Pri-miRNA, SnRNA, LncRNA	Pre-mRNA, Pri-miRNA, HDV genome RNA and mRNA, HHV8 PAN RNA
RNA pol III	5S rRNA, U6 snRNA	Ad-2 VA RNAs, HDV/ Boca SRI, MHV68 pri-miRNA

All initiate RNA synthesis de novo (no primer needed). Only DNA viruses replicating in the cytoplasm encode their own RNA polymerase.

Transcriptional Regulation

Promoter and Regulatory Sequences

• Promoter: DNA region where RNA polymerase binds to initiate transcription.

• Core Promoter: Contains TATA box and initiator sequence, specifies accurate start site.

• Local Regulatory Sequences: Bind transcription factors close to the promoter.

• Distant Regulatory Sequences: Enhancers and silencers, can be thousands of base pairs away.

Transcriptional Control Regions in Viruses

• Viral promoters often contain multiple regulatory elements (e.g., SV40 early, Ad2 major late).

• Regulation can be complex, involving both host and viral proteins.

Initiation of Transcription by RNA Polymerase II

• Assembly of general transcription factors (TFIID, TBP, TFIIA, TFIIB, etc.) at the promoter.

• Formation of the initiation complex, recruitment of RNA pol II.

• Enhancer-binding proteins can act at a distance to stimulate initiation.

Proteins Regulating Transcription

• Sequence-specific DNA binding proteins (host or viral origin).

• Viral co-activators: Modulate transcription without binding DNA directly.

• Chromatin modifiers: Histone methylation or acetylation alters nucleosome structure and gene accessibility.

Modular Organization of Transcriptional Activators

Domain	Features
DNA binding	Zn finger, Helix-turn-helix, Basic
Dimer formation	Leucine zipper
Nuclear localization signal (NLS)	Directs protein to nucleus
Activation	Acidic, Glutamine rich, Proline rich, Isoleucine rich

Strategies of Transcription of Viral DNA

Origin of Transcriptional Components	Virus
Host only	Retroviruses with simple genomes, Caulimoviruses, Circoviruses
Host plus one viral protein	Bacteriophages T3, T7
Viral protein transcribes late genes	Heepadnaviruses, parvoviruses, papillomaviruses, polyomaviruses, retroviruses with complex genomes
Host plus >1 viral protein that stimulate transcription	Adenoviruses, herpesviruses
Viral	Mimiviruses, Poxviruses

Regulation of Transcription by Viral Proteins

Mechanisms

• Cascade Regulation: Sequential activation of gene expression by viral proteins (e.g., E1A → E2 → IVa2/L4 in adenovirus).

• Positive/Negative Autoregulatory Loops: Viral proteins regulate their own or other gene expression.

Examples

• SV40: Early and late transcriptional phases regulated by cellular repressors and viral proteins.

• Adenovirus: E1A, E2, and IVa2 proteins govern phase transitions and transcriptional activation.

• Herpesvirus: VP16 initiates immediate-early transcription, followed by coordinated expression of early and late genes.

RNA Processing in Viral Infection

Modification of mRNA

• 5'-Cap Structure: Addition of a methylated guanosine cap to the 5' end of mRNA, essential for stability and translation.

• Cleavage and Polyadenylation: Addition of poly(A) tail at the 3' end after cleavage of pre-mRNA.

Mechanism	Enzyme	Viruses
Post-transcriptional	Cellular	Adenovirus, HBV, HDV, herpesvirus, polyomavirus, retrovirus
During mRNA synthesis	Viral	Influenza virus, VSV, poliovirus, alphavirus

Splicing of mRNA

• Constitutive Splicing: All introns are removed in a fixed manner.

• Alternative Splicing: Exons can be skipped or joined in different combinations, producing multiple mRNAs from one gene.

• Splicing marks mRNAs for nuclear export and can be regulated by viral proteins.

Noncoding RNAs in Viral Infection

Types and Functions

• miRNAs: Small RNAs (~22 nt) that regulate gene expression post-transcriptionally.

• lncRNAs: Long noncoding RNAs (>200 nt) with diverse regulatory roles.

• circRNAs: Circular RNAs produced by back-splicing, can regulate gene expression.

Viral genomes can encode noncoding RNAs that modulate host and viral gene expression.

Examples

• miR-122: Liver-specific miRNA promotes hepatitis C virus replication.

• Polyomavirus miRNA: May promote viral persistence.

• lncRNAs: Can affect virus reproduction by reshaping the metabolic environment or regulating immune responses.

Epigenetic Modifications

Reversible N6 Methylation of Adenosine

• N6-methyladenosine (m6A): A reversible modification of adenosine nucleosides in RNA, affecting RNA stability and translation.

• Enzymes involved: Writers (METTL3/14), readers, and erasers (FTO, ALKBH5).

Summary Table: Key Processes in Viral Transcription and RNA Processing

Process	Key Enzyme/Factor	Viral Example
Transcription Initiation	RNA pol II, transcription factors	Adenovirus, SV40, Herpesvirus
mRNA Capping	Capping enzyme complex	All eukaryotic viruses
Polyadenylation	Poly(A) polymerase	Adenovirus, HBV, Retrovirus
Splicing	Spliceosome	Adenovirus, Herpesvirus
Noncoding RNA Regulation	miRNA, lncRNA, circRNA	Hepatitis C virus, Polyomavirus
Epigenetic Modification	m6A methyltransferase	Hepatitis C virus

Key Concepts and Applications

• Transcriptional regulation in viruses is a complex interplay between host and viral factors, ensuring precise timing and levels of gene expression.

• RNA processing (capping, polyadenylation, splicing) is essential for mRNA stability, export, and translation.

• Noncoding RNAs and epigenetic modifications add layers of regulation, expanding coding potential and modulating host-virus interactions.

Example Application

Understanding how viral proteins regulate transcription and RNA processing can inform antiviral drug development, such as targeting viral co-activators or epigenetic modifiers.

Additional info: This guide expands on lecture slides by providing definitions, mechanisms, and examples for each process, ensuring a self-contained resource for exam preparation.