RNA polymerases: The other DNA binding protein.....
RNA polymerases catalyze the polymerization
of all types of RNAs:
Types of Eukaryotic RNA polymerases:
(in Europe, RNA polymerase are A,B,C
not I, II, III)
THE DEATH CAP MUSHROOM, Amantia phalloides
(Death Cap mushrooms link)
Structure of a-Amantin
and other transcription inhibitors:
Rifampicin inhibits prokaryotic RNA polymerases, a-Amantin
eukaryotic RNA pol II.
Cordycepin inhibits because of lack of 3'-OH, and Actinomycin
D binds DNA
Composition of Eukaryotic RNA polymerases:
C-terminal domain (CTD) is critical for
transcriptional initiation, and is phosphorylated during transcription in vivo
(evidence from antibody staining on polytene chromosome)
Large numbers of parallel strands of DNA
produce large bands on polytene chromosomes.
Antibody staining of polytene chromosome: red - phosphorylated RNA pol II CTD,
green - unphosphorylated RNA pol II CTD. Red is at "puffs" where
transcription is active.
Transcription Initiation by general
factors (required
in every transcription initiation regardless of specifics of control region:
(I've provided several views of same process)
TATA binding protein (TBP)
c-terminal domain:
TFIIB-TBP-DNA complex:
Another view of the RNA polymerase initiation complex with
TBP and some TAF's
Transcriptional Regulation:
1. Heterochromatin modification / Gene Silencing
Silencing at yeast telomeres through Rap1
and three Sir (silent information regulator) genes via protein-protein
interactions.
Hypoacetylation - no acetylation.
Due to specific residues (K) at N-terminal tails
Gene control through histone acetylation /
deacetylation by histone acetylases / deacetylases. Specific
for DNA at TATA box sequences.
2. Promoter-proximal and enhancer (enhancesomes):
ENHANCESOME
HMGI: (High
Mobility
Group
- 1)
binds DNA minor groove and
induces bend in DNA
(architectural protein).
All of the other proteins are transcription factors
Example: the TTR control region
(promoter):
tissue-specific activators:
expressed only in one tissue (e.g. HNF1, HNF3.
(HNF: hepatocyte nuclear factor))
general activators: expressed
in many tissues (e.g. C/EBP, AP1(Fos/Jun))
co-activators: mediate
protein-protein interactions between activators
general transcription factors: required
in all cases for RNA polymerase II activation
Signal transduction through phosphorylation
of transcription factors (JAK/STAT):
RNA polymerase I and II control
regions:
Eukaryotic ribosomal gene structure (tandem
repeats):
RNA polymerase III control elements are
downstream from transcription initiation site:
The "Tree of Life". Three
divisions of all organisms - Bacteria, Archaea, Eucarya.
Note - Mitochondria and Chloroplast genomes group them
within bacteria. People are closer to Archaea than Bacteria, and this is
reflected in Archaea RNA polymerase structure.
