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two of them being more specifi c to cGMP ( slr2104 that encodes an element of two-component
regulatory systems and slr1575 that is responsible for cyclic nucleotide-gated cation channel) and the
rest three specifi c to cAMP (one of which sll1371 that encodes a putative transcription factor, CRP-
Syn) signifi es the presence of cGMP and cAMP signalling pathways. CRP-Syn has been identifi ed
as a global regulator since it can bind several genes (encoding enzymes involved in transport and
metabolism) upstream of crp , Cya1 and slr1575 (Ochoa de Alda et al ., 2000). P . marinus MIT9313 has
very few genes for two-component sensor kinase systems and the number of such genes was even
further reduced in P . marinus MED4 (Rocap et al ., 2003). Both these strains also lack the circadian
clock genes pex and kaiA . In the absence of regulation by two-component regulatory systems and
circadian proteins, the challenge of regulation of gene activity in this minimal photoautotroph seems
to be fulfi lled by the presence of non-coding RNAs (ncRNAs). These are functional RNA molecules
mostly without a protein-coding function. These genes are normally located in the intergenic regions.
Seven ncRNAs have been identifi ed in cyanobacteria and were fi rst described in P . marinus MED4.
These are designated as Yfr1 to Yfr7 (representing cYanobacterial functional RNA; Axmann et al .,
2005). Of these, Yfr7 is considered to be homologous to the bacterial 6S RNA that possesses global
regulatory functions. The second such molecule is Yfr1 which is required for growth of S . elongatus
PCC 6301 under multiple stress conditions (Nakamura et al. , 2007). The predicted secondary structures
of Yfr1 of Prochlorococcus strains MED4, MIT9313 and Synechococcus sp. strain WH8102 are presented
in Fig. 12. Although only three Cis-acting anti-sense RNAs (asRNAs) have been reported earlier
in cyanobacteria (Csiszar et al ., 1987; Duhring et al ., 2006; Hernandez et al ., 2006), none have been
identifi ed in Prochlorococcus genomes. The genome of S . elongatus PCC 6301 has the minimum number
of genes (37) for two-component signal transduction system noted in freshwater cyanobacteria (Sugita
et al ., 2006). Steglich et al . (2008) followed transcription of intergenic regions of P . marinus strain
MED4 cells subjected to different types of stress conditions such as light qualities and quantities,
phage infection and phosphate starvation. Analysis of microarray expression data from intergenic
regions revealed the existence of as many as 276 novel transcriptional units. Among these were 12
new ncRNAs, 24 asRNAs as well as 113 short mRNAs. With two additional ncRNAs identifi ed by
homology, the number of ncRNAs totalled up to 14. In addition fi ve of the seven ncRNAs have also
been detected (Yfr2 and Yfr4-Yfr7). The distribution of various ncRNAs, asRNAs and short mRNAs
in the genomes of various strains of Prochlorococcus (MED4, MIT9312, MIT9315, MIT9515, MIT9301,
NATL1A and NATL2A) has been compared. In view of the occurrence of considerable number of
ncRNAs equivalent to those found in bacterial cells it is suggested that these RNA regulators are
likely to play a major regulatory role in this organism. Sugita et al . (2006) identifi ed gene sequences
similar to SRP RNA, tmRNA, 6SaRNA and RNase P subunit B in S . elongatus PCC 6301.
The genome of N . punctiforme PCC 73102 revealed unusually high number of (255) combined
two-component signal transduction proteins. Majority (at least 153) of these transmitters are
unlinked to a response regulator. Single domain sensor histidine kinases comprise only about 53%
of this class of genes. Genes encoding transmitter-receivers and transmitter-receiver-transmitters
constitute 47%. The remaining 102 response regulator genes consist of 36% encoding receivers with
no apparent output domain while the remaing are helix-turn-helix DNA-binding output domains.
Meeks et al. (2001) suggested that the presence of unusually high frequency of response regulators
without output domains is indicative of the multiprotein phosphorelay signalling systems that
help in integrating multiple environmental signals. Simple chemotaxis sensor histidine kinases
and complex-chromophore-binding sensor histidine kinase proteins (complementary chromatic
adaptation, circadian rhythm and phytochrome proteins) are included here. There are 55 ORFs
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