Biology Reference
In-Depth Information
metabolism but also in photosynthesis, a phylogenetic footprinting is conducted to identify
conserved motifs in intergenic regions of orthologous genes from closely related genomes. Such
a study conducted by Su
et al
. (2005) on nine cyanobacterial genomes (
G
.
violaceus
PCC 7421,
Anabaena
sp. strain PCC 7120,
P
.
marinus
strains CCMP1375, MED4 and MIT9313,
S
.
elongatus
PCC
6301,
Synechococcus
sp. strain WH8102,
Synechocystis
sp. strain PCC 6803 and
T
.
elongatus
BP-1)
revealed the existence of strong NtcA promoter regions (i) for the ammonium transporters of the
amt
family in all the nine cyanobacterial genomes, and (ii) in the regulatory regions of
nirA
in all
genomes excepting in
Synechococcus
sp. strain CCMP1375 and
P
.
marinus
MED4. The clustering of
genes of nitrate/nitrite transporters of the ABC-type transporters
nrtABCD
in
Anabaena
sp. strain
PCC 7120,
G
.
violaceus
PCC 7421,
Synechocystis
sp. strain PCC 6803,
S
.
elongatus
PCC 6301 and
T
.
elongatus
BP-1 with nitrate reductase (
narB
) and nitrite reductase A (
nirA
) and regulator ntcB
upstream of transporters signifi es the regulatory control of all these genes by NtcA. A number of
transcription factors belonging to the families LuxR, LysR, AraC and TetR are encoded by the genome
of
A
.
marina
MBIC11017 (Swingley
et al
., 2008).
LexA is a transcriptional regulator that exists as a dimer and regulates transcription of genes
connected with SOS response in
E
.
coli
(Fernandez
et al
., 2000). Under normal growth conditions, LexA
prevents transcription of genes under its control by binding to their promoter regions but during
SOS response the binding of RecA to the damaged DNA strand triggers autocleavage of LexA into
monomers that no longer can bind to its binding sites. Due to this, all such genes under the regulation
of LexA are induced and expressed in a co-ordinated manner (Michel, 2005). But the type of genes
regulated by LexA in different cyanobacteria has been found to be different. Studies conducted
on
Synechocystis
sp. strain PCC 6803 point out that LexA may regulate transcription of genes of
carbon metabolism (Domain
et al
., 2004), bidirectional hydrogenase genes (
hoxEFUYH
; Gutekunst
et al
., 2005; Oliveira and Lindblad, 2005) and
crhR
gene that encodes a RNA helicase (Patterson-
Fortin
et al
., 2008). The binding of LexA to a 14 bp pseudo-palindromic sequence in
Anabaena
sp.
strain PCC 7120 has been demonstrated (Mazon
et al
., 2004). In this organism, the
hoxEFUYH
exists
as two operons, i.e.
hoxEF
and
hoxUYH
. Sjoholm
et al
. (2007) demonstrated that LexA regulates
transcription of these two operons by binding to the upstream of promoter regions of
hoxE
and
hoxU
. In
Synechocystis
also a LexA-binding region consists of a 13 bp pesudo-palindromic segment
5'-AGTAACTAGTTCG-3' upstream of the promoter of
hoxE
(Gutekunst
et al
., 2005). Li
et al
. (2010)
conducted a computational analysis of genes regulated by LexA in 33 cyanobacterial genomes. Six
of the cyanobacterial genomes (
G
.
violaceus
PCC 7421,
Synechococcus
sp. JA-3-3-A'b,
Synechococcus
sp.
JA-2-3-3B'a (2-13),
S
.
elongatus
PCC 6301,
S
.
elongatus
PCC 7942,
T
.
elongatus
BP-1 and
T
.
erythraeum
IMS101) do not possess a
lexA
gene. The SOS response in these strains is suspected to be regulated
by a transcriptional regulator other than LexA. The rest of the 27 genomes of cyanobacteria [
A
.
marina
MBIC11017,
Anabaena
sp. strain PCC 7120,
A
.
variabilis
ATCC 29413,
Cyanothece
sp. PCC 8801,
M
.
aeruginosa
NIES-843,
N
.
punctiforme
PCC 73102, 12 strains of
P
.
marinus
(AS9601, CCMP1375,
MED4, MIT9211, MIT9215, MIT9301, MIT9303, MIT9312, MIT9313, MIT9515, NATL1A, NATL2A),
8 strains of
Synechococcus
sp. (CC9311, CC9605, CC9902, PCC 7002, RCC307, WH8102, WH7803 and
WH8102) and
Synechocystis
sp. strain PCC 6803] revealed the presence of
lexA
gene. According to
Li
et al
. (2010) LexA might still serve as a transcriptional regulator for the SOS response in many of
these cyanobacterial strains as LexA-binding sites of the core SOS-responsive genes
recA
and
lexA
are the most conserved. However, the extent to which other SOS-responsive genes are regulated
is found to be different in these strains. For example,
ruvB
gene that encodes DNA helicase B has
the LexA-binding sites in the HL-adapted
P
.
marinus
strains (MIT9312, MIT9515, MIT9215, MED4
and AS9601). Of the four nucleotide excision repair genes
uvrA
,
uvrB
,
uvrC
and
uvrD
, known to be
