Transcription strategies of viruses

1
Transcription strategies of viruses
Majority of DNA viruses depend on cellular RNA
polymerase II, including Parvovirus (AAV),
Papovavirus (SV40), Hepadnavirus (Hapatitis B),
Adenovirus (human adenovirus), Herpesvirus
(herpes simplex virus) Retroviruses also use
cellular RNA polymerase II The mechanisms of
transcription and the signals are similar between
viral and cellular genes Poxviruses are
transcribed by viral DNA-dependent RNA polymerase
and accessory viral proteins that control
recognition of viral promoters In cells
infected with DNA viruses, viral genes are
expressed in a strictly defined reproducible
order -viral enzymes and regulatory proteins
are made first -structural proteins are
synthesized only after viral DNA synthesis
begins -transcription of viral genes is
activated during specific periods in the
infection cycle.
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Several of the 12-16 subunits of these enzymes
are identical -they can bind to rNTP substrates,
template DNA and product RNA -they can catalyze
phosphodiester bond formation
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The transcription cycle

• Initiation- The transcriptional machinery binds
  to the promoter and induces local unwinding of
  the double-stranded DNA template
• Elongation- The transcribing complex
  progressively unwinds the template as it reads
  the DNA sequence and adds nucleotides to the 3
  end of the nascent RNA chain
• Termination- Transcription ceases when the
  termination signal is encountered and both the
  RNA transcript and the transcriptional machinery
  are released from the DNA template

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The transcription cycle
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(No Transcript)
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RNA polymerase II transcriptional control elements
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Mechanisms of enhancer action

• DNA looping model postulates that proteins
  bound to a distant enhancer interact directly
  with components of the transcription initiation
  complex, by looping out the DNA
• An enhancer noncovalently linked to a promoter
  via a protein bridge is functional
• Enhancer function requires close proximity to
  the promoter
• Enhancers do not serve as entry sites for RNA
  polymerase II

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Initiation of transcription by RNA polymerase II
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Modular organization of transcriptional activators
Composed of different domains -DNA binding
domain -Activation domain Bind to DNA as
dimers
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Structure of a basic leucine zipper domain bound
to DNA
Nf-kb
Leucine zipper forms a a-helical coiled coil
DNA binding region is also a-helical, but in
solution it is disordered DNA binding induces a
major conformational change Proteins of this
class bind to DNA as dimers
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Transcriptional control region of avian leukosis
virus
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General mechanisms of stimulation of
transcription by viral proteins
Protein A stimulates transcription of the same
transcription unit (A) or a different
transcription unit (B)
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Regulation of transcription by the Tat protein of
HIV-1
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Regulation of HIV-1 transcription by the Tat
protein

• Stimulation of HIV-1 transcription by Tat
  requires an LTR sequence, termed the
  trans-activation response (TAR) sequence
• TAR element is recognized as RNA
• Tat protein binds specifically to a
  trinucleotide bulge in the stem of the TAR RNA
  stem loop structure
• Binding of Tat to this region of TAR induces
  local conformational rearrangement in the RNA,
  resulting in formation of a more compact
  structure
• Binding of Tat to TAR stimulates production of
  viral RNA as much as 100-fold
• Tat protein has little effect on initiation,
  it greatly improves elongation

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Stimulation of transcription by HIV-1 Tat protein
Before Tat is made proviral transcripts are
terminated within 60 bp of the initiation site
Production of the Tat protein allows
transcription complexes to synthesize full length
RNA Binding of Tat to TAR together with the
cyclin T subunit of Tak leads to stimulation of
phosphorylation of the largest subunit of RNA
polymerase II The transcriptional complexes
become competent to carry out transcription
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Transcriptional strategies of DNA viruses

• Viral genes are transcribed in a reproducible and
  precise order.
• During immediate-early and early phases viral
  proteins necessary for viral DNA synthesis are
  produced.
• Transcription of the late genes, most of which
  encode viral structural proteins, requires viral
  DNA synthesis.
• This property ensures coordinated production of
  the DNA genomes and structural proteins from
  which virus particles are assembled.
• Viral proteins and replication of viral DNA
  control the transition from one transcriptional
  stage to the next.
• Many transcription activating proteins (SV40 T
  antigen, HSV ICP4 protein) can repress
  transcription of their own genes.

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Transcription of different DNA viruses
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• SV40
• SV 40 contains only two transcription units,
  early and late
• Early domain is transcribed from one strand and
  late domain is transcribed from another strand
• An origin serves for transcription by RNA PolII
  and for DNA replication
• Expression of early transcription unit leads to
  synthesis of large T antigen (LT)

• Expression of T antigen in the absence of viral
  infection leads to cell transformation and
  formation of tumors in animals
• LT binds to ori, regulates its own production
  also DNA replication
• Binding unwinds the DNA allows DNA polymerase
  and the initiation factors to bind to form an
  initiation complex
• Host specific association with a-primase occurs
  during initiation
• LT also activates transcription of late mRNAs

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Adenovirus

• Eight transcription units encoding more than 40
  viral proteins
• Transcribed in the nucleus by RNA Pol II to
  produce a set of early RNAs
• Upon entry of viral genome into the nucleus,
  E1A is transcribed.
• E1A and E1B products are oncogenes that
  stimulate cellular replication and induce an
  environment for viral DNA replication
• E1A is necessary for transcription of all viral
  early transcription units
• Proteins from E2 region are involved in
  replicating viral DNA
• Multiple splicing events that occur during
  processing of the adenoviral late mRNA led to the
  discovery of RNA splicing by Phil Sharp (1993
  Nobel Prize)
• VA genes are transcribed by RNA Pol III, short
  RNAs are not translated

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Herpes simplex virus

• More that 80 genes are expressed as individual
  transcription units
• A viral activating protein is imported into
  cells infected by HSV.
• This virion structural protein, VP16, is
  necessary for efficient transcription of viral
  immediate-early genes.
• VP16 resembles adenoviral E1A in performing
  regulatory functions
• ICP4 protein is the major transcriptional
  activator.
• ICP4 stimulates transcription of both early and
  late genes, also acts as a repressor of
  immediate-early gene transcription.