CIRCADIAN RHYTHMS - Cyanobacteria - page 314

et al . (2004). These observations signify that the circadian feedback loop in cyanobacteria does not
require negative feed back of clock proteins upon specifi c clock promoters. The expression of an
appropriate level of Kai proteins suffi ces the purpose for the oscillation of the circadian clock. Mori
and Johnson (2001a) suggested that KaiC might mediate both its negative feedback regulation and
global regulation of the cyanobacterial genome by bringing oscillations in the condensation and/
or supercoiling status of the entire cyanobacterial chromosome. Subsequent observations of Xu et
al . (2003), Min et al . (2004) and Nakahira et al . (2004) added support to the observations of Mori
and Johnson (2001a) that the cyanobacterial genome becomes an “oscillating nucleoid” or in other
words an “oscilloid”. This oscilloid model proposes that the global regulation of gene expression is
in other words dependent on the rhythmic changes of chromosome topology (Woelfl e and Johnson,
2006). They also emphasized the role of ' cis ' elements that not only globally mediate rhythmic
gene expression governed by the chromosomal status but also on a promoter-by-promoter basis
by specifi c ' trans ' acting factors. Woelfl e et al . (2007) put this model to test by assaying changes in
the topology of a non-essential cryptic plasmid (pANS) in S . elongatus PCC 7942. This plasmid was
chosen as a reporter to identify the superhelical state of DNA in cyanobacteria that can change in a
circadian fashion in vivo . They found that the plasmid topology changed in a circadian manner with
rhythmic KaiC phosphorylation. When other cyanobacterial promoters were removed from their
native chromosomal surroundings and introduced into this plasmid these also exhibited rhythmicity
in expression that were dependent on KaiC and were repressed by kaiC overexpression. There is a
possibility that KaiC-containing protein complexes either directly or indirectly modulate chromosome
structure leading to global regulation of promoter activities in cyanobacteria.
Kucho et al . (2004a) demonstrated that DNA microarrays with unmodifi ed oligonucleotide probes
have been helpful in the detection of gene transcripts with greater sensitivity and specifi city. With
the application of such probes, they conducted a global analysis of circadian expression of genes in
T . elongatus BP-1 and identifi ed 2397 genes that accounted for 95% of genes in this organism. A
comparison of the gene expression profi les at two different circadian times, i.e. LL2 (early subjective
day) and LL14 (early subjective night) revealed that (i) the expression levels of 143 genes were
signifi cantly different at the two circadian times; (ii) the expression of 69 genes was enhanced at
LL14 that were responsible for NADH dehydrogenase complex and other respiratory genes had
peak expressions, and (iii) the expression of the remaining 74 genes was enhanced in the early
subjective day corresponding to photosynthesis related genes (light-harvesting phycobilisome
complex, chlorophyll synthesis, ferredoxin, chaperonin DnaK). The expression levels of genes
involved in transcription and translation encoding elongation factor (EF-G) and eight ribosomal
proteins were highest in between LL2 and LL14 (Kucho et al ., 2004b). In order to understand cellular
physiology and the mechanism of clock-controlled genes, Kucho et al . (2005) used DNA microarrays
to identify the cycling genes that are under circadian control. The expression of most of the genes
peaked around the time of transition from day to night so as to enable the organism to adjust to the
night condition. These genes related to a wide variety of metabolic pathways, membrane transport
and signal transduction. Genes involved in respiration and poly-3-hydroxyalkonoate synthesis
showed coordinated circadian expression suggesting that the regulation is important for the supply
of energy and carbon source in the night. Genes involved in transcription and translation also
followed a circadian cycling. Stoeckel et al . (2008) identifi ed genes encoding different enzymes of
central metabolic pathways such as glycolysis, oxidative pentose phosphate pathway and glycogen
metabolism that showed oscillating transcript levels during diurnal cycles in Cyanothece sp. ATCC
51142. Since in this organism photosynthesis and nitrogen fi xation are temporally separated, increased
transcriptional activity at night coincided with the demands of nitrogen fi xation.