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(3 genes including
ntcA
), ARS family (2 genes), Fur family (3 genes) and single genes for heat-shock
gene repressor
HrcA
. In addition, a complete set of genes for σ
factors for RNA polymerase (
SigA-D
,
SigF
and
SigG1
/
G2
) except SigE homologue have been identifi ed.
G
.
violaceus
PCC7421 possesses
relatively large number of transcription factors in the LuxR, LysR, PadR, TetR and MarR families.
There are 14 genes for σ
factors that include one gene for SigA, fi ve genes for group 2 σ, six genes for
extra-cytoplasmic type σ and two genes for group 3 σ factors (Nakamura
et al
., 2003). In
Synechococcus
sp. strain WH8102, in addition to the principal RNA polymerase σ factor (SigA
SYNW1783
) fi ve types
of type 2 σ factors are characteristically present as in other cyanobacteria. One homologue of type
3 σ factor is present in contrast to seven noted in other cyanobacterial genomes sequenced earlier
(
Synechocystis
sp. strain PCC 6803,
Anabaena
sp. strain PCC 7120 and
T
.
elongatus
BP-1 (Palenik
et
al
., 2003).
S
.
elongatus
PCC 6301 has 36 genes assigned for transcription factors. Of these, nine of
the encoded transcription factors belong to the response regulator OmpR family while the others
fall into LysR family (Sugita
et al
., 2006). In
M
.
aeruginosa
NIES-843, 43 genes encode transcription
factors. A global regulator for nitrogen assimilation
NtcAI,
a regulator for nirate assimilation (NtcB),
a regulator for RuBisCO (RbcR), a regulator for genes for subunits of NAD dehydrogenase (NdhR), a
cyclic AMP receptor protein for cell motility (SyCrp1), an inhibitor for genes for GroESL (HrcA) and a
regulator for zinc effl ux system (ZinR) are common with other cyanobacteria (Kaneko
et al
., 2008).
Cyclic AMP receptor protein (CRP) is an important transcriptional regulator in bacteria and the
range of genes regulated by it in cyanobacteria has come out by the studies of Xu and Su (2009),
who conducted a computational prediction of CRP-binding sites in 29 cyanobacterial genomes.
Synechocystis
sp. strain PCC 6803 genome has two genes
sll1371
and
sll1924
that encode SyCRP1
and SyCRP2, respectively. In case of
Anabaena
sp. strain PCC 7120 also there are two genes
alr0295
and
alr2325
that encode AnCRPA and AnCRPB, respectively. Orthologues of SyCRP1 one each have
been detected in ten other cyanobacterial genomes [
A
.
marina
MBIC 11017,
A
.
variabils
ATCC 29413,
strains of
P
.
marinus
MIT 9313 and MIT 9303, strains of
Synechococcus
sp. CC9311, CC9605, JA-3-3-
A'b, JA-2-3-3B'a (2-13),
T
.
elongatus
BP-1 and
T
.
erythraeum
IMS101]. The rest of the 17 cyanobacterial
strains [
G
.
violaceus
PCC 7421,
P
.
marinus
strains AS9601, MIT9211, MIT9215, MIT9301, MIT9312,
MIT9515, NATL1A, NATL2A, CCMP1375, MED4,
S
.
elongatus
PCC 6301,
S
.
elongatus
PCC 7942,
and strains of
Synechococcus
sp. strain PCC 9902, RCC307, WH7803, WH8102] do not have the
crp
gene in their genomes. There seems to be a great variation in the number and type of target genes
in the 12 cyanobacterial strains that showed the
crp
gene. Majority of the CRP-regulated genes are
distributed among fi ve cyanobacterial genomes (
Synechocystis
sp. strain PCC 6803,
Anabaena
sp.
strain PCC 7120,
A
.
variabilis
ATCC 29413,
A
.
marina
MBIC11017 and
T
.
erythraeum
IMS101) and
the number of target genes in these fi ve cyanobacteria differed from one another in the functional
domains of photosynthesis, carbon fi xation, nitrogen assimilation, transporters/porins, kinases
and transcription factors. A comparison made on the basis of total number of genes, number of
transcription units, number of CRP-regulated genes, number of CRP-regulated transcription units
and the number of CRP-regulated genes shared with
E
.
coli
revealed that
Anabaena
sp. strain PCC
7120 ranks fi rst followed by
Synechocystis
sp. strain PCC 6803 (Xu and Su, 2009).
In enteric bacteria such as
E
.
coli
and other proteobacteria, nitrogen control is mediated by
NtrB-NtrC two-component system (Reitzer, 2003). In contrast, in cyanobacteria nitrogen control
is governed by NtcA, a global transcriptional regulator that belongs to a class of CRP-family. This
helps in the repression of pathways for assimilation of nitrogen when more readily assimilable
form of nitrogen is available. The binding sites of NtcA on DNA are highly conserved and possess
a sequence of GTAN8TAC. In addition, all NtcA-activated genes also contain a 10-mer sequence
(Herrero
et al
., 2001). In view of regulation by NtcA of many genes involved not only in nitrogen
