Question

Question – Discuss sigma factor, it’s structure and the function of the different parts/domains.

Question – Discuss the structure of promoter for RNA Polymerase II

Question – Discuss what events occur at the promotor after binding of the basal transcription factors and before elongation can completely begin

Question – discuss the structure of histones in the nucleosome. Why is it important to have part of the histone proteins accessible

Answer 1

Hey there, as per my guidelines, I would like to answer your first question.

Sigma factor-

Sigma factor is a protein needed for initiation of transcription in bacteria so that it allows specific binding of RNA polymerase to a promoter. It is similar to archaeal transcription factor B and to eukaryotic factor TFIIB. The type and number of sigma factors varies within species and the sigma factor together with RNA polymerase is called RNA polymerase holoenzyme.

Example of sigma factors in E.coli, each with varying functions-

σ70(RpoD)- It is responsible for the transcription of all essential genes.

σ19 (FecI)- It is responsible for transcription of fec gene required for iron transport and metabolism.

σ24 (RpoE)- It works during the heat stress response.

σ28 (RpoF/FliA)- It transcribes genes for flagellar synthesis or chemotaxis signaling.  

σ32 (RpoH)- It transcribes the genes for treating heat shock when the bacteria are exposed to heat.

σ38 (RpoS)- It works under the stationary phase.

σ54 (RpoN)- nitrogen limitation sigma factor.

The structure of the sigma factor is somewhat like this,

 N-terminus --------------------- C-terminus 1.1 2 3 4

It has conserved domains, each of them having a certain function.

Domain 1.1 ensures the binding of the sigma factor to the promoter only when it is complexed with an RNA polymerase.

The rest of the domains interact with specific promoter regions.

Domain 2 is subdivided into a domain 1.2 and 2.1 through 2.4, Domain 2.4 recognizes and binds to the promoter −10 element, whereas Domain 4.2 recognizes and binds to the promoter −35 element.