User talk:Nandita94/gab operon

The gab operon is responsible for the conversion of γ-aminobutyrate (GABA) to succinate. The gab operon comprises of three structural genes gabD, gabT and gabP that encode for a succinate semialdehyde dehydrogenase, GABA transaminase and a GABA permease respectively. There is a regulatory gene csiR, downstream of the operon that codes for a putative transcriptional repressor and is activated when nitrogen is limiting.

The gab operon has been characterized in Escherichia coli and significant homologies for the enzymes have been found in organisms such as Saccharomyces cerevisiae, rats and humans.

Limited nitrogen conditions activate the gab genes. The enzymes produced by these genes convert GABA to succinate which then enters the TCA cycle, to be used as a source of energy. The gab operon is also known to contribute to polyamine homeostasis during nitrogen-limited growth and maintain high internal glutamate concentrations under stress conditions.

Structure
The gab operon consists of three structural genes:
 * gabT : encodes a GABA transaminase that produces succinic semialdehyde.
 * gabD : encodes an NADP-dependent succinic semialdehyde dehydrogenase, which oxidizes succinic semialdehyde to succinate.
 * gabP : encodes a GABA-specific permease.

Physiological significance of the operon
The gabT gene encodes for GABA transaminase, an enzyme that catalyzes the conversion of GABA and 2-oxoglutarate into succinate semialdehyde and glutamate. Succinate semialdehyde is then oxidized into succinate by succinate semialdehyde dehydrogenase which is encoded by the gabP gene, thereby entering the TCA cycle as a usable source of energy. The gab operon contributes to homeostasis of polyamines such as putrescine, during nitrogen-limited growth. It is also known to maintain high internal glutamate concentrations under stress conditions.

Differential Regulation of Promoters
The expression of genes in the operon is controlled by three differentially regulated promoters, two of which are controlled by RpoS encoded sigma factor σS.
 * csiDp : is σS-dependent and is activated exclusively upon carbon starvation because cAMP-CRP acts an essential activator for σS containing RNA polymerase at the csiD promoter.
 * gabDp1: is σS -dependent and is induced by multiple stresses.
 * gabDp2: is σ70 dependent and is controlled by Nac (Nitrogen Assimilation Control) regulatory proteins expressed under nitrogen limitation.

Activation
The csiD promoter (csiDp) is essential for the expression of csiD(carbon starvation induced gene), ygaF and the gab genes. The csiDp is activated exclusively under carbon starvation conditions and stationary phase during which cAMP accumulates in high concentrations in the cell. The binding of cAMP to the cAMP receptor protein(CRP) causes CRP to bind tightly to a specific DNA site in the csiDp promoter, thus activating the transcription of genes downstream of the promoter. The gabDp1 exerts an additional control over the gabDTP region. The gabDp1 is activated by σS inducing conditions such as hyperosmotic and acidic shifts besides starvation and stationary phase. The gabDp2 promoter on the other hand, is σ70 dependent and is activated under nitrogen limitation. In nitrogen limiting conditions, the nitrogen regulator Nac binds to a site located just upstream of the promoter expressing the gab genes. The gab genes upon activation produce enzymes that degrade GABA to succinate.

Repression
The presence of nitrogen activates the csiR gene located downstream of the gabP gene. The csiR gene encodes a protein that acts as a transcriptional repressor for csiD-ygaF-gab operon hence shutting off the GABA degradation pathway.

Eukaryotic Analogue
GABA degradation pathways exists in almost all eukaryotic organisms and takes place by the action of similar enzymes. Although, GABA in E.coli is predominantly used as an alternative source of energy through GABA degradation pathways, GABA in higher eukaryotic organisms acts as an inhibitory neurotransmitter and also as regulator of muscle tone. GABA degradation pathways in eukaryotes are responsible for the inactivation of GABA.

BLAST results have predicted homology to hydrogen peroxide inducible genes in Ceratitis capitata - a Mediterranean fruit fly. Moreover, hits have been reported to several other hypothetical proteins in eukaryotes such as Oryza sativa Indica and Daphnia pulex. — Preceding unsigned comment added by Tpsanjan (talk • contribs) 17:27, 24 September 2013 (UTC)