Biology Reference
In-Depth Information
the above heterocystous forms (excepting in
No
.
spumigena
) and probably in
Synechococcus
RF-1 also
the order of
nif
genes is
nifB
-
fdxn
-
nifS
-
nifU
-
nifH
-
nifD
-
nifK
-
Orf
-
nifE
-
nifN
-
nifX
-
Orf
-
nifW
-
hesA
-
hesB
-
fdxH
. The location and size of the excision element during heterocyst differentiation
in
N
.
punctiforme
ATCC 29133 and
Anabaena
sp. strain PCC 7120 are found to be different. In the
former the excision element is located at the 3'-end of the
nifD
gene and is of 24-kb whereas in the
latter,
nifD
gene is interrupted by a 11-kb excision element. However, the two excision elements
show a similarity in possessing a highly conserved excision gene (
xisA
) present at the beginning
of the elements. Other unique features of
N
.
punctiforme
ATCC 29133 genome are (i) the absence of
55 kb excision element in
fdxN
gene (that is present in
Anabaena
sp. strain PCC 7120), (ii) the presence
of a haemoglobin-like gene upstream of
nifH
as in
N
.
commune
, (iii) the synthesis of molybdenum-
dependent nitrogenase in the heterocysts (in contrast to the presence of an alternative vanadium-
dependent nitrogenase synthesized in the absence of molybdenum as noted in
A
.
variabilis
ATCC
29413 but not in
Anabaena
sp. strain PCC 7120), and (iv) the presence of additional copies of
nifH
(two copies),
nifE
and
nifN
(one additional copy each). The other genes governing the biosynthesis
of Mo-Fe factors (
nifB
,
fdxN
,
nifS
,
nifU
and
nifV
), Mo-Fe factor assembly (
nifE
and
nifN
), iron uptake
(
feoA
and
feoB
) and genes of unknown function too are represented in this cluster. This single
largest cluster consists of two adjacent regulons on opposite strands with
modB
gene (that encodes
molybdate ATP-binding cassette transporter permease) occurring at the end. In the heterocystous
cyanobacteria, on the other hand, the corresponding clusters are interrupted by insertion elements
(Welsh
et al
., 2008). Genes for heterocyst initiation (
ntcA
,
hetR
,
hetN
and
hetF
), pattern formation (
patA
,
patS
and
patN
) and transition to non-dividing state (
hetC
as well as
hetP
) have been recognized in
the genome of
Anabaena
sp. strain PCC 7120 on the basis of orthologues present in the related genus
N
.
punctiforme
ATCC 29133. Many of the genes (
ntcA
,
hamA
,
devA
,
hetR
,
patB
,
devR
,
devBCA
) encode
proteins which have 90% sequence similarity among the two organisms. The gene products that
share 60-70% amino acid identity between these two cyanobacteria are (i) a positive regulator for
heterocyst differentiation (
hetF
), (ii) a sensor histidine kinase of a two-component regulatory system
(
hepA
and
hepK
), (iii) pattern formation (
hglK
as well as
patA
), and (iv) a polyketide synthase (
hetM
).
Other genes of
N
.
punctiforme
ATCC 29133 that show weak similarity with
Anabaena
sp. strain PCC
7120 genes are
hepC
(required for heterocyst envelope synthesis),
hetP
and
hetC
(similar to ABC
protein exporters and required early in heterocyst differentiation). However, homologues of
hetP
have 70% similarity where as the homologues of
hetC
have 66% similarity in amino acid sequence.
The gene product of
patS
is a peptide of 13 amino acids in
N
.
punctiforme
ATCC 29133 while it may
be of 13 or 17 amino acids long in case of
Anabaena
sp. strain PCC 7120.
One gene cluster consisting
of
hglE
-(two unknown genes)-
hglD
-
hglC
-(one unknown gene)-
hetM
-
hetN
-
hetI
-
hglK
present on
the chromosome of
Anabaena
sp. strain PCC 7120 is suggested to play a role in the synthesis and
deposition of heterocyst glycolipid layer. The organization of
nif
-gene cluster in the genomes of
C.
raciborskii
CS-505,
R. brookii
D9 (Stucken
et al.,
2010) and
N. azollae
0708 (Ran
et al.,
2010) has already
been presented in the discussion on their genomes. A comprehensive account on this subject is
presented in Chapter 4.
IV. PHYLOGENOMICS
Besides the sequence-based phylogenies (single gene such as 16S rRNA gene, MLST analysis and
whole genome), the utility of concatenation of protein-encoding genes or their products and the
gene order in the construction of phylogenetic trees has been tested during recent years. Random
regrouping (concatenation) of genes or their products much depends on the genes so selected whether
