User talk:Tpsanjan/OxyR regulon

--T.P.Sanjan & Guruprasad Raghavan,Class of 2015,I.I.T-Madras (talk) 17:09, 25 September 2013

OxyR regulon which stands for “Oxidative stress Regulator”, comprises a set of operons that are triggered by stimuli such as addition of hydrogen peroxide, nitrosative stress or osmotic induction. Apart from OxyR, the SoxR coupled with SoxS plays a vital role in regulating oxidative stress. They are extremely critical for the survival of bacterial species under an oxidative stress.

The OxyR regulon is an example of a classic dual transcriptional regulator that not only efficiently controls the synthesis of mRNA (transcription) of around 40 genes involved in peroxide metabolism, redox balance and peroxide protection, but also controls translation of many other gene products through its activated protein - OxyR via OxyS RNA.

Structure of OxyR
OxyR belongs to a class of bacterial transcription factors called the "LysR family" and is 305 amino acids in length. It exists as a tetramer in solution.

It is primarily found in two major states:

Active OxyR: This is characterized by intra-molecular disulphide bond formation between Cys199 and Cys208 residues which is primarily achieved by an increase of hydrogen peroxide in the cell.

Inactive OxyR: This state is achieved through enzymatic reduction by glutaredoxin 1 (Grx1), glutathione reductase (gorA) and other thioredoxins such as trxA and trxB.

Conserved Domains in OxyR
The conserved domains present in OxyR protein (as predicted by NCBI-Conserved Domain BLAST plugin) are as follows:

1. The C-terminal substrate-binding domain of OxyR, which belongs to the superfamily of periplasmic binding proteins. This domain is responsible for OxyR to sense hydrogen peroxide and its subsequent activation.

2. DNA-binding transcriptional regulator of OxyR.

3. Bacterial regulatory helix-turn-helix protein belonging to the LysR family.

Transcriptional Regulation
Direct oxidation of OxyR protein results in a large increase in the transcription of genes encoding anti-oxidant proteins, namely:

1.	katG (hydroperoxide I)

2.	gorA (glutathione reductase)

3.	dps (a nonspecific DNA-binding protein)

4.	OxyS (a regulatory RNA)

5.     ahpCF (alkyl hydroperoxide reductase)

The katG, gorA and dps are activated at exponential phase whereas the ahpCF is activated in stationary phase [2]. OxyS non-coding RNA allows OxyR to indirectly control close to 40 other gene products by altering their mRNA stability. The genes encoding Grx1 and gorA are regulated by the activated form of OxyR, thereby exhibiting auto-regulation. This results in extremely rapid responses in vivo.

There exists an intimate relationship that tightly regulates the levels of hydrogen peroxide in the cell and the corresponding uptake of ferric ion. Reaction of iron (Fe) with hydrogen peroxide results in the formation of hydroxyl radicals through Fenton reaction which can cause extensive damage to the cell. In order to prevent the same, it has been found that OxyR activates the transcription factor, Fur which represses the genes (negatively regulated) involved in ferric ion uptake (Fur is a global repressor of genes associated with ferric ion uptake).

Along with control of production of anti-oxidant proteins, OxyR controls a diverse set of cellular functions as depicted in the adjacent mindmap.

Homologs of OxyR
The amino acid sequence similarity indicates that OxyR is homologous to LysR proteins in E.coli and NodD in Rhizobium belonging to the class of positive regulatory proteins. The former activates the gene lysA involved in lysine biosynthesis whereas the latter regulates the genes involved in node formation in leguminous species.

BLAST results have predicted homology to hydrogen peroxide inducible genes in Ceratitis capitata - a Mediterranean fruit fly. Moreover, hits have been reported to hypothetical proteins in other eukaryotes such as Oryza sativa Indica and Daphnia pulex.