User talk:Tolkappiyan/Cyanobacterial circadian rhythm/

Introduction
Circadian biological clocks are found throughout the eukaryotes, where they help to keep track of the daily cycle. One group of prokaryotes, the eubacterial cyanobacteria, are also circadian timekeepers. The fundamental properties of circadian clocks in eukaryotes and in cyanobacteria are the same: surprisingly precise self-sustained oscillations with an approximately 24 h period that are temperature compensated and entrainable by environmental cycles. While it does not seem very intuitive that prokaryotes would have a 24 hr circadian cycle(which in a lot of cases might even be greater than their lifetime),it has been found in the prokaryotic cyanobacterium Synechococcus elongatus PCC 7942 that essentially all promoters are rhythmically regulated by the circadian clock.(Liu et al., 1995) A cluster of three genes in S.elongatus, named kaiA, kaiB and kaiC, encodes essential circadian clock components.

Gene Arrangement of the Clock Proteins
The genome construct consists of KaiA which follows KaiAp promoter giving rise to a monocistronic mRNA;a KaiBCp promoter giving rise to a dicistronic mRNA KaiBC. This is in the model organism Synechococcus elongatus PCC 7942 ..

The Circadian Clock At Molecular Level
KaiC is the protein responsible for the time period and properties of the circadian clock of cyanobacteria. The active-phosphorylated protein concentration plays an important role in phase reset while the concentration of both P-KaiC and non P-KaiC determines the time period of the clock ..

KaiA gives positive feedback on KaiBCp(Xu et all 2000). The KaiC gets auto phosphorylated in vivo and Kai A and KaiB are involved in the phosphorylation of the KaiC. KaiA is expressed constituently and rhythmically. KaiA prevents the dephosphorylation of the KaiC which otherwise is very unstable. KaiB which is expressed along with the KaiC acts as an antagonist to KaiA which means in the absence of KaiA, Kai B doesn’t affect the clock work in any manner. So KaiA whose concentration is in rhythm extends the half life of the P-KaiC and KaiB intervenes with KaiA maintaining P-KaiC: nonP-KaiC ratio as a function of different physiological states. KaiC in higher concentration does feedback inhibition on KaiBCp. But it was also observed that KaiBCp is not necessary for the rhythm of KaiC, and KaiC follows rhythm flawlessly under any heterogenous promoter .. KaiC is phosphorylated in rhythms can bind DNA thereby can control the genetic expression. KaiC concentration is less during the night and it is regulated by light.

KaiC can go several cycles of circadian rhythm without an external input.Many other transcription factors are involved in light based induction and control of KaiC concentration.Cyano bacteria use cyclic redox loops and few of factors don’t sense light directly.Few of those factors that regulates the circadian clocks are as follows; CikA a redox sensor(doesn’t sense light) involved in reset of the clock. It also plays an important role in cell division.CikA binds bacteriophytochrome which serves as violet light sensor[8]. This light sensor is believed to provide input to the clock. There is one SasA- a KaiC interacting sensor kinase required for sustained robust oscillations. sasA- and/or rpaA-  lower levels of gene expression and decreased amplitude. There is no cell division defect; Metabolism continues unabated. SasA/RpaA comprise a two-component sensor kinase/response regulator for energy transfer from phycobilisomes to photosystems.

It mediates circadian timing. Together, they mediate global transcriptional rhythms in response to cycles of KaiC phosphorylation. (Takai et al., 2006). Another protein, LabA (phenotype of a knockout: low amplitude and bright) is required for negative feedback regulation of KaiBC expression. It acts in parallel with SasA, upstream of RpaA (Taniguchi et al., 2007). However a cikA- sasA- double mutant has normal cell division.

Relationship between Circadian Clock and cell processes
Cell division is regulated by the clock. Division occurs only in the light phase. Though division is dependent on the clock, the clock is not dependent on cell division. Sigma factors work as a consortium to convey circadian information to “downstream” genes. Nitrogen fixation occurs in the absence of oxygen expiration which is regulated by circadian rhythm.

Circadian Homologue in other Prokaryotes and Eukaryotes
Unlike Cyanobacteria, in eukaryotes about 5-10% of the genes are under circadian clockwork. In eukaryotes circadian rhythm is controlled through feed back loops involving the respective cis promoters unlike in cyanobacteria which involves redox loops, KaiBCp is not necessary (promoter in cis of KaiC). Even though there is no sequence similarity among kai cluster and eukaryotic clock protiens, kai clusters functionally are similar to eukaryotic circadian protiens(PER and FRQ). Proofs for existence of circadian rhythms in other bacteria which are non-photosynthetic was also found.Many nitrogen fixing bacteria uses circadian rhythms for fixing nitrogen when they aren’t breathing out oxygen. Circadian rhythm was also observed in many other heterotrophic bacteria too.