User talk:Aravindabharathi/Alpha operon

The α operon in Escherichia coli contains genes coding for 4 ribosomal proteins (r-proteins) and also the rpoA gene, which codes for the α subunit of RNA polymerase. From a regulatory standpoint, the α operon is quite unique since control is mainly through translational repression by one of the gene products. However, the influence of this repression on the expression of rpoA is quite weak, and differential expression of the r-proteins and the α subunit can occur. Even though the expression of rpoA is differentially regulated to a very large extent, it is considered a part of the same operon since it is transcribed along with the other genes. It is the translation of the genes where the regulation occurs. Although the genes which code for r-proteins are divided into many different operons, all these genes are coordinately regulated, and all r-proteins are synthesised at the same rate.

Structure of the α operon
The α operon contains 5 structural genes, in the order listed :
 * rpsM, encoding the S13 r-protein
 * rpsK, encoding the S11 r-protein
 * rpsD, encoding the S4 r-protein
 * rpoA, which codes for the α subunit of RNA polymerase
 * rplQ, encoding the L17 r-protein

Ribosomal proteins

 * S13 is one of the proteins which make up the 30S subunit of the bacterial ribosome. Along with the r-protein S12, it is thought to be responsible for controlling the movement of the mRNA:tRNA complex through the ribosome during protein synthesis.
 * S11 is found on the 30S ribosomal subunit and is vital for the selection of the correct tRNA corresponding to a codon during protein synthesis.
 * S4 is another protein on the 30S subunit. Apart from its functions on the ribosome, it functions as a tranlational repressor, preventing the translation of the mRNA sequence of the α operon when not associated into a ribosome. Also, it is an antitermination factor, and slows down termination during the transcription process. It can act as an antitermination factor since it is capable of binding to RNA polymerase.
 * L17 is found on the 50S subunit of the bacterial ribosome. Along with another r-protein L2, it can form a complex consisting of itself, L2, and a tRNA molecule which has a site for another tRNA molecule to bind to. In this way, it is vital for maintaining continuity during protein synthesis in the ribosome.

α subunit of RNA polymerase
RNA polymerase, also known as RNAP, is one of the most pivotal enzymes in the process of transcription. It is responsible for the de novo synthesis of the polynucleotide RNA molecule from a template DNA strand. RNA polymerase is a complex made up of five proteins, denoted as the α, β, β', ω, and σ subunits.

Two copies of the α subunit are present in one RNAP molecule, and are denoted as αI and αII. The α subunit is imperative for the assembly of RNAP from its constitutent proteins, which are present in different regions of the genome. The assembly reaction proceeds as follows:

2α → α2 → α2β → α2ββ' → α2ββ'σ

RNAP subunit α is also capable of directly binding to DNA. Some "strong" promoter have a supplementary promoter element upstream of the normal promoter site, in addition to the promoter itself. By recognising and binding to these promoters, RNAP subunit α enhances the stability of the binding of RNAP to the DNA, which results in an improvement in the efficiency of transcription initiation.

Regulation
The α operon mRNA has a pseudoknot structure which stimulates the binding of the 30S subunit of the ribosome. It is, however, inactive at low temperatures and prevents the binding of the methionine-carrying tRNA, the first step in translation. It gets activated at higher temperatures, and translation can occur.

Translational repression of r-protein expression
In general, the regulation of r-protein synthesis occurs by post-translational feedback inhibition by "free" r-proteins which are not part of a ribosome. The repressive ability of the r-protein is removed when they are assembled together into a ribosome. This ensures that all r-proteins are synthesised at the same rate. In the α operon, the feedback inhibitor is the S4 protein, encoded by the gene rpsD.

The S4 protein is capable of binding to a single site on the mRNA synthesised from the α operon. By changing the shape of the mRNA, the binding of S4 prevents the formation of the mRNA-ribosome complex required for translation. Since the binding site of S4 is distinct from the Shine-Dalgarno sequence of the mRNA, this is a form of allosteric regulation.

Regulation of rpoA expression
Translational repression of the synthesis of the r-proteins occurs due to a change in the mRNA conformation caused by the binding of S4. However, the new conformation still permits the the translation of the mRNA from the rpoA gene, which codes for the α subunit of RNAP. This allows the differential expression of the rpoA gene with respect to its neighbours on the operon. Small changes to the rate of α subunit synthesis are observed in response to repression by S4, but this is attributed to a decrease in the stability of the mRNA caused by the binding of S4 to it. It is also predicted that the synthesis of the α subunit takes place from separate mRNA strands, which are independent of the α operon transcripts, and comprise solely of transcripts of the rpoA gene.

Eukaryotic analogues
Studies of the α subunit have shown that the amino acid sequence of the subunit in prokaryotes matches closely the sequence of the α subunit found in plant chloroplasts. This is one of the many supporting evidences for the endosymbiotic theory of the origin of organelles.

The α-subunit contains an amino-terminal domain (denoted αNTD) and a carboxy-terminal domain (denoted αCTD), which are independently folded. Large sequences of the αNTD have been found to be conserved across eukaryotic RNAP I, II and III. Primarily due to this, the role of the αNTD sequence in the assembly of the RNAP complex is believed to be conserved in eukaryotes and archaea also. However, the αCTD sequence from prokaryotes is not seen in archaea or eukaryotes, and so the promoter recognition functions of the α subunit are absent in those organisms.