Viral DNA Transcription and Replication

Flashcards covering key terms and concepts related to viral DNA transcription and replication, including mechanisms, control strategies, and fidelity.

Baltimore Scheme

A classification system for viruses that emphasizes their need to transcribe mRNAs for the translation of viral proteins and the various routes taken to accomplish this.

RNA Polymerase I

A eukaryotic enzyme responsible for transcribing ribosomal RNAs (rRNA), specifically 18S, 28S, and 5.8S ribosomal RNAs.

RNA Polymerase II

A eukaryotic enzyme that transcribes messenger RNAs (mRNAs), enabling the translation of both cellular and viral proteins. It is also involved in transcribing pri-miRNA, snRNAs, and Lnc RNAs.

RNA Polymerase III

A eukaryotic enzyme that transcribes shorter RNAs, including transfer RNAs (tRNAs), 5S RNA, and other small RNAs like U6 snRNA.

Transcription Initiation

The first step of RNA synthesis where RNA Polymerase finds the proper DNA sequence to begin transcription, without requiring a primer.

Transcription Elongation

The process where RNA Polymerase moves down the DNA template, adding ribonucleotides in a 5' to 3' direction to synthesize the RNA transcript, involving local unwinding of the DNA.

Transcription Termination

The final step of RNA synthesis, involving cleavage of the growing RNA, addition of a 'poly(A) tail' at the 3' end, and potentially a cap structure at the 5' end and splicing.

Promoter

A region of DNA containing short sequences that control where RNA polymerase will bind and initiate transcription for a gene.

Core Promoter

A region within about 35 base pairs upstream of the transcription start site where RNA polymerase directly binds, often recognized initially by general transcription factors.

General Transcription Factors (TFII)

Proteins (e.g., TFIID) that operate at virtually all promoters, recognizing the core promoter and facilitating the binding of RNA Polymerase II, DNA unwinding, and modifying the polymerase.

Cis-regulatory regions

Short DNA sequences that act as binding sites for additional proteins (transcriptional activators or repressors) that regulate gene transcription, located locally or distantly from the transcriptional start site.

Mediator (Coactivator)

A large protein complex that orchestrates the assembly of numerous factors involved in transcriptional initiation, promoting interactions between transcription factors and upstream regulatory elements.

SV40 Enhancer

A cis-regulatory element located approximately 200 bp upstream of a transcriptional start site on the Simian Virus 40 genome, serving as a binding site for cellular transcriptional activator proteins to increase transcription.

Proviral DNA

The integrated DNA copy of a retroviral RNA genome into the host cell's genomic DNA, which serves as a template for viral gene transcription.

Long Terminal Repeat (LTR)

A duplicated sequence found at both ends of proviral DNA that serves as a promoter for the transcription of viral RNA in retroviruses.

Promoter Occlusion

A phenomenon where transcription initiated at an upstream promoter (e.g., 5' LTR) blocks the binding of transcription factors to a downstream promoter (e.g., 3' LTR).

Autoregulatory Loops (Viral)

A viral transcriptional strategy where a basal level of expression of a viral transcription factor activates and increases its own expression, often in conjunction with cellular factors.

Transcriptional Cascades (Viral)

A viral transcriptional strategy that controls the rate and timing of transcription of different viral genes by triggering a sequence of events, leading to the sequential expression of viral gene products (e.g., immediate-early, early, late).

Tat Protein (HIV-1)

A viral transcriptional activator protein unique to HIV-1 that binds to the TAR element in newly initiated viral RNAs, enhancing transcription elongation to produce full-length transcripts.

TAR (transactivation response element)

A structured stem-loop region of RNA found at the 5' end of all HIV-1 viral transcripts, serving as the binding site for the Tat protein.

P-TEFb (Positive Transcription Elongation Factor b)

A cellular protein complex (Cyclin T and CDK9) recruited by the HIV-1 Tat protein to newly initiated viral RNAs, which phosphorylates RNA Polymerase II to increase its processivity.

Immediate-early Genes

Viral genes expressed immediately upon infection, often encoding proteins that regulate viral gene expression, establish a favorable cellular environment, or counter host defenses.

Early Genes

Viral genes expressed after immediate-early genes, often encoding proteins necessary for viral DNA genome synthesis and further regulation of viral gene expression.

Late Genes

Viral genes expressed after viral DNA synthesis has begun, typically encoding viral structural proteins and other proteins necessary for the assembly and egress of viral particles.

Large T-antigen (SV40)

An early gene product of SV40 that represses early gene expression, activates viral DNA synthesis, and activates transcription of the late gene region.

E1A Protein (Adenovirus)

An immediate-early gene product of human adenovirus that acts as a transcriptional activator, influencing cellular and viral gene expression to create an environment favorable for viral replication (e.g., inducing S-phase, inhibiting apoptosis).

E2F (Transcription Factor)

A cellular transcription factor whose activity is regulated by the retinoblastoma (Rb) protein; E1A binding to Rb releases E2F, allowing it to activate genes involved in cell proliferation and viral DNA synthesis.

VP16 (Herpesvirus)

A viral protein packaged within herpesvirus virions that is delivered to the infected cell upon entry and acts as a transcriptional activator of immediate-early genes.

Poxviridae Transcriptional Strategy

A unique viral transcriptional strategy where, due to their cytoplasmic replication, these viruses supply their own complete transcription machinery and processing components, including a DNA-dependent RNA polymerase.

Semi-conservative Replication

The mechanism of DNA synthesis where each new double-stranded DNA molecule contains one original parental strand and one newly synthesized daughter strand.

Origins of Replication (ori)

Specific sites along a DNA molecule where DNA synthesis initiates, serving as binding sites for proteins that unwind DNA and start synthesis.

Leading Strand

The DNA daughter strand synthesized continuously in the 5' to 3' direction during DNA replication, starting from the origin of replication.

Lagging Strand

The DNA daughter strand synthesized discontinuously in short fragments (Okazaki fragments) in a 5' to 3' direction during DNA replication, requiring multiple RNA primers.

Okazaki Fragments

Short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.

Strand Displacement Replication

A viral DNA replication mechanism where only one template strand is initially copied, displacing the complementary strand, which is then copied later; this mechanism often uses DNA or protein primers instead of RNA primers.

Inverted Terminal Repeats (ITR)

Palindromic sequences found at the ends of parvovirus (e.g., AAV) genomes that fold to create T-shaped secondary structures, providing 3'-hydroxyl ends for self-priming of DNA synthesis.

Preterminal Protein (pTP) (Adenovirus)

A viral protein that acts as a primer for adenoviral DNA synthesis by having a dCMP residue attached to a serine hydroxyl group, which then initiates DNA elongation.

Rolling Circle Mechanism

A model proposed for the second stage of herpesvirus DNA replication where replication continues around a circular template, extruding new double-stranded product from a single replication fork.

DNA Proof-reading Activity

An inherent function of DNA polymerases (cellular and viral) involving an exonuclease activity (typically 3' to 5') that removes mismatched or incorrectly incorporated nucleotides, significantly increasing replication fidelity.

Mismatch Repair

A cellular DNA repair mechanism that detects, excises, and replaces sequences containing DNA defects that escaped proof-reading or were caused by other damage.

Latency (Viral)

A state of viral infection where viral gene expression is very limited, and the infection is maintained by the presence of extrachromosomal (non-integrated) viral genomes in limited numbers, without active virus replication.