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Phycobilisomes linker family in cyanobacterial genomes: Divergence and evolution


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Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.
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Int. J. Biol. Sci. 2007, 3
International Journal of Biological Sciences
ISSN 1449-2288 2007 3(7):434-445
©Ivyspring International Publisher. All rights reserved
Research Paper
Phycobilisomes linker family in cyanobacterial genomes: divergence and
Xiangyu Guan
1, *
, Song Qin
2, *
, Fangqing Zhao
, Xiaowen Zhang
, Xuexi Tang
1. College of Marine Life Science, Faculty of Life Science and Technology, Ocean University of China, 266003, Qingdao, P.R.
2. Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, P.R. China
* Contributed equally to this study.
Correspondence to: Dr. Xuexi Tang, tel.: +86 532 82898500; fax: +86 532 82880645; e-mail:
Received: 2007.03.23; Accepted: 2007.11.06; Published: 2007.011.10
Cyanobacteria are the oldest life form making important contributions to global CO
fixation on the Earth.
Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability
of the whole genome database of cyanobacteria provides us a global and further view on the complex structural
PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker
polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have
been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative
linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR)
genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft
state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location,
conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker
family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A
phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in
cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were
due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental
selective pressures especially light.
Key words: phycobilisomes, cyanobacteria, linker polypeptides, evolution
1. Introduction
Cyanobacteria are prominent constituents of
marine biosphere that account for a significant
percentage of oceanic primary productivity, and are
among the oldest life forms on the Earth capable of
doing oxygenic photosynthesis about 3.5 billion years
ago, which is similar to the process found in higher
plants [1-2]. As the oldest and major light-harvesting
antennae, PBSs are highly organized complexes of
various PBPs and linker polypeptides (Fig.1.), and are
very diverse in structure and pigment composition in
cyanobacteria, red algae, and the cryptomonads [3-5].
They function in light harvesting and energy
migration toward photosystem II or I reaction centers
in thylakoid membrane, except Gloeobacter violaceus
PCC7421 (Gv) having no thylakoid membrane [6,7].
On one hand, PBSs linkers transfer energy of
PBPs to favor a unidirectional flow of excitation
energy from the peripheral rod of PBSs to the PBSs
core and then from the PBSs core to the photosynthetic
reaction center [8]. On the other, PBSs linkers function
to stabilize PBSs structure and determine positions of
the PBPs within PBSs structure. At the same time,
PBSs linkers also interact directly or indirectly with
the chromophores to cause the PBSs structure changes
that can modulate different PBPs subassemblies and
optimize absorbance characteristics [9-11]. The
structural function of PBSs linkers in PBSs has allowed
cyanobacteria to colonize environments and show a
great diversity in terms of light quantity and quality
[12,13]. Positions of highly conserved PBPs were
determined by the specific linker polypeptides, and it
is possible that linker polypeptides somehow interact
to form a scaffold-like structure within PBSs [14].
Whether or not this is the case, it is possible to
distinguish various PBPs assemblies specifically by
their state of aggregation and by their attachment to
relevant linker polypeptides [15-17]. Tandeau de
Marsac and Cohen-Bazire demonstrated for the first
time that several colorless polypeptides that take
12%–15% of the total stainable proteins of the PBS
components are accounted for linker polypeptides
from eight species of cyanobacteria by SDS-PAGE [18].
The nominated system of linker polypeptides are
according to their locations and molecular masses in
PBSs. Glazer [19] has provided a system of
abbreviations to characterize linker peptides with
respect to their locations and molecular masses in
PBSs: PBSs rod linker (L
, 27 to 35 kDa), PBSs rod-core
linker (L
, 25 to 27 kDa), PBSs core linker (L
7.7 to
7.8 kDa), and PBSs core-membrane linker (L
, 70 to
120 kDa) [16,20]. The importance of linker polypeptide
for the assembly of defined complexes and their roles
for tuning spectral characteristics of the complexes has
been well understood [21,22].
Int. J. Biol. Sci. 2007, 3
Fig. 1. Structural model of a tricylindrical hemidiscoidal phycobilisome (2, 3). The three sky blue circles represent the
tricylindrical core APC, and two bottom cylinders attach to the thylakoid membrane (grey rectangle) with L
. Six rods are arranged
by PC (blue circle), and PE (red circle), and attached FNR (grass green circle) with L
from inner to outer part. L
is the linker
between core and rod. All linkers are represented by yellow discs located in each rod.
FNR, being also considered as linker
polypeptides, transfers electrons from ferredoxin to
to generate NADPH with an average value of
1.3 FNR per PBS, [23,24]. FNR encodes a protein that
is composed of three domains: two C-termainal
domains enough to enzymatic activity of FNR and a
~9kDa N-terminal domain generally homologous to
the small phycocyanin (PC) rod-linker polypeptide
CpcD [23,25]. With the exception of CpcD, it is also
reported that there are similarity between FNR and
other PBSs linkers’ different domains [25,26]. In
contrast to other PBSs-associated linkers (cluster with
PBPs), the γ subunits serving as phycoerythrin (PE)
linker polypeptides are chromophorylated, containing
two types of covalently attached linear tetrapyrrole
chromophores, phycoerythrobilin (PEB), and
phycourobilin (PUB) [27]. Genes of L
and L
polypeptides are on the plastid genome, while genes
ending the γ subunits are present on the nuclear
genome [28,29]. Liu [27] found that no high-degree
sequences homology exists between the γ subunits
and other linker polypeptides, and suggested that
different primary structures in a range of balanced
states still perform similar physiological functions
[30,31]. In red algae, γ subunits that are also the
main chromophorylated components of PBPs and
orderly assembled into other PBPs forming a stable
complex with α and β subunits of PE [32-34].
At present, more and more cyanobacterial
genomes’ database have brought about a great
convenience in search for PBSs linkers using
bioinformatic tools. Here, a comparative genomic
analysis on all the data sequences of PBSs linkers in
the cyanobacteria is presented. Observation on PBSs
linker polypeptides was made in 25 cyanobacteria
additional to some model strain cyanobacteria with
improved method of separation of the PBSs linker
Besides, evolution of linker polypeptides in the
varieties of PBSs was analyzed and specific
connections to PBPs or other linkers were performed
for better understanding the function of PBSs in
different environments.
2. Materials and Methods
Database searching and sequence retrieving
Genomes database were searched at JGI
( Protein sequences of the
PBSs linkers previously described were used as
queries for database. Cyanobacteria species examined
included 25 cyanobacterial genomes (20 complete and
5 ongoing): Anabaena, Nostoc, Gloeobacter,
Trichodesmium, Crocosphaera, Synechocystis,
Synechococcus and Prochlorococcus. All 25 genome
sequences were accessed from IMG
( in
FASTA format. Each protein in this query dataset was
used to search potential novel sequences in all
cyanobacteria species with all available genome
sequences, by using the BLASTP and TBLASTN
programs. Sequences giving better reciprocal BLAST
hits were assumed capable of identifying homologous
counterparts in these species if they could be aligned
up with at least the BLAST-Score > 90 and the E-value
< 1E-10. The search was iterated until convergence,
examined individually, and then aligned with Clustal
X [35]. Sequence identity and similarity were
calculated using BioEdit v5.0 [36]. To elucidate the
complete genomic structure of the PBSs linkers’ genes,
all linkers onto the 20 finished cyanobacterial genomes
were mapped (Fig. 2).
Similar searches were run with the Pfam
domains of the PBSs linker proteins to avoid the
exclusion of highly diverged sequences with just
limited conserved motifs. PFAM [37] and SMART [38]
domain analyses with derived sequences that
employed as queries were then carried out to
eliminate false positives.
Int. J. Biol. Sci. 2007, 3
Fig.2. Genomic organization of PBSs linkers in 20 sequenced completely cyanobacterial genomes. Vertical bars show the
locations of PBSs linker genes, with FNR in pink and PBSs linkers except FNR in other colors. PBSs linker genes were mapped onto
the chromosome evenly. Long horizontal line indicates the chromosome. The vertical bar above horizontal line indicates the
transcriptional direction opposite to that below a horizontal line.
Phylogenetic analysis
Multiple sequences were aligned using Clustal X,
and then adjusted manually. To maximize the number
of sites available for analysis, partial sequences and
certain sequences with large deletions were excluded.
To understand the evolutionary relationships of all
PBSs linkers in these cyanobacteria genomes,
neighbor-joining method in MEGA3 [39] and
maximum parsimony method in PHYLIP [40] were
used to construct the phylogenetic tree, in which
confidence levels of each branch were determined by
analyzing 1000 bootstrap replicates.
3. Results and discussion
The PBSs linker family in cyanobacteria
From nominated linkers, PBPs-associated linker
family comprises five groups of linkers with own
locations and molecular masses in the PBSs [19]. Most
of the PBSs linkers are clustered with APC
(allophycocyanin), and PC or PE. Therefore, they are
called APC-associated linker (L
), PC- and
PE-associated linker (L
) [41,42], while L
and L
are involved in attaching peripheral rods to the APC
cores. BLASTP and TBLASTN programs analyses
show that a total of 192 linkers (159 putative
PBPs-associated linker genes, 8 γ subunits, and 25
FNR genes) were obtained and genes ApcC, CpcC,
CpcD, CpeC, CpeD, CpeE, MpeC, MpeE, PecC, CpcG,
ApcE, and PetH derived from 25 cyanobacterial
genomes in this study (Table 1). The species of 21
cyanobacterial strains, their morphologies, main
features, and habitats, as well as the abbreviations
used at the end of gene names are shown (Table 2).
The number of PBPs-associated linkers in these
cyanobacteria is from 1 to 13, and there are a
maximum number of 13 PBSs linkers in Cw and Tr. γ
subunits as special chromophoric linkers were found
in some marine Synechococcus and three low-light
adapted Prochlorococcus lineages, while other three
sequenced Prochlorococcus have only one type linker
FNR (Table 1). Although no γ subunit has been found
in low-light adapted P13 from database, it may exist
because of the same mode of light-harvesting in other
low-light adapted Prochlorococcus, and γ subunits are
difficult to be found with only
BLASTP as it is in low
sequence homology between γ subunits and other
linkers [34]. The light-harvesting structure including γ
subunit in low-light adapted Prochlorococcus can
acclimatize themselves well to same factors especially
low-light of environment.
Int. J. Biol. Sci. 2007, 3
Table 1. Cyanobacterial genes encoding PBSs linkers.
PBSs core
PBSs rod
PBSs rod-core
PBSs core-
γ subunit FNR NO
Nostoc sp. PCC 7120
(N7) (F)
ApcCN7 asr0023 CpcCN7 alr0530
CpcDN7 asr0531
PecCN7 alr0525
CpcG1N7 alr0534
CpcG2N7 alr0535
CpcG3N7 alr0536
CpcG4N7 alr0537
ApcEN7 alr0020 PetHN7 all4121 10
Anabaena variabilis
ATCC29413 (Av) (F)
Ava2620 PetHAv Ava0782 10
Nostoc punctiforme
PCC73102 (Np) (D)
NpR4843 PetHN7 NpR2751 10
Gloeobacter violaceus
PCC 7421 (Gv) (F)
ApcCGv gsr1248
CpcC1Gv glr0950,
CpcC2Gv gll3219
CpcD2Gv gsr1267
CpeCGv glr1263,
CpeDGv glr1264
CpeEGv glr1265,
glr2806, glr1262
ApcEGv glr1245
PetHGv gll2295 12
erythraeum IMS101
(Tr) (F)
Pec1Tr Tery_4106,
Pec2Tr Tery_4107
PetHTr Tery_3658 13
watsonii WH8501
(Cw) (D)
watsonii WH8501
Contig362_or6343 Contig207_or1063 PetHCw
Synechocystis sp. PCC
(S6) (F)
ApcCS6 ssr3383 CpcC1S6 sll1580
CpcC2S6 sll1579
CpcDS6 ssl3093
CpcG1S6 slr2051
CpcG2S6 sll1471
ApcES6 slr0335
PetHS6 slr1643 8
Synechococcus sp.
(S9) (F)
PetHS9 sync_1003 12
Synechococcus sp.
WH 8102
(S8) (F)
MpeES8 (II)
MpeDS8 (II)
CpeCS8 (I)
CpeES8 (I)
Int. J. Biol. Sci. 2007, 3
Synechococcus sp.
(S96) (F)
Syn_cc96050433 PetHS96
Synechococcus sp.
(S99) (F)
elongatus PCC 7942
(S79) (F)
Synechococcus sp.
PCC 6301
(S63) (F)
elongatus BP-1 (Te) (F)
ApcCTe tsl0955 CpcCTe tlr1959
CpcDTe tsr1960
CpcG1Te tlr1963
CpcG2Te tlr1964
CpcG4Te tlr1965
ApcETe tll2365 PetHTe tlr1211 8
Synechococcus sp.
WH 7805
(S78) (D)
Synechococcus sp.
WH 5701
(S57) (D)
Synechococcus sp.
(SRS) (D)
Synechococcus sp.
(SJAb) (F)
Synechococcus sp.
JA-2-3Ba (2-13) (SJBa)
marinus str. MIT 9313
(P93) (F)
marinus sp. NATL2A
(Pn) (F)
marinus str. MIT 9312
(P12) (F)
marinus subsp.
CCMP1986 (P86) (F)
str. CCMP 1375 (P75)
PetHP75 Pro1123 2
marinus MIT 9211
Number in all 19 79 40 21 8 25 192
Words in first () of species line are abbreviations; Words in second () of species line are “Genome Completion: [F]inished, [D]raft”.
Int. J. Biol. Sci. 2007, 3
Table 2. The species names of the 21 cyanobacterial strains, morphologies, main features, and habitats.
Species Morphology Genome size Linkers (%) LHC Features
Prochlorococcus marinus subsp.
Unicellular 1760 0.57 Chl a
Marine; HH
Prochlorococcus marinus str. MIT
Unicellular 1853 0.54 Chl a
Marine; HH
Prochlorococcus marinus sp.
Unicellular 1937 1.03 Chl a
Marine; LH
Prochlorococcus marinus str. CCMP
Unicellular 1926 1.04 Chl a
Marine; LH
Prochlorococcus marinus str. MIT
Unicellular 2327 0.43 Chl a
Marine; LH
Synechococcus sp. CC9311 Unicellular 2942 4.08 PBSs Marine
Synechococcus sp. WH 8102 Unicellular 2580 3.88 PBSs Marine
Synechococcus sp. CC9902 Unicellular 2358 5.09 PBSs Marine
Synechococcus sp. CC9605 Unicellular 2753 4.00 PBSs Marine
Synechococcus elongatus PCC 7942 Unicellular 2712 2.58 PBSs Freshwater
Synechococcus elongatus PCC 6301 Unicellular 2578 2.72 PBSs Freshwater
Crocosphaera watsonii WH8501 Unicellular 5996 2.17 PBSs Nitrogen-fixing
Synechocystis sp. PCC 6803 Unicellular 3618 2.21 PBSs Freshwater
Trichodesmium erythraeum IMS101 Filamentous 7750 1.68 PBSs Nitrogen-fixing
Nostoc punctiforme PCC73102 Filamentous 7672 1.30 PBSs Heterocystous
Anabaena variabilis ATCC29413 Filamentous 5760 1.74 PBSs Heterocystous
Nostoc sp. PCC 7120 Filamentous 6210 1.61 PBSs Heterocystous
Thermosynechococcus elongatus BP-1 Unicellular 2521 3.17 PBSs Thermophilic
Gloeobacter violaceus PCC 7421 Unicellular 4478 2.68 PBSs No thylakoid
Synechococcus sp. JA-3-3Ab Unicellular 2813 3.20 PBSs Thermophilic
Synechococcus sp. JA-2-3B'a(2-13) Unicellular 2913 2.75 PBSs Thermophilic
In overall, the basic architecture of PBS is widely
conserved, while PBPs, core structure, and PBSs
linkers diversified greatly across different strains of
cyanobacteria [43]. Moreover, for a single strain, it
depends upon the environmental conditions, such as
nutrient availability, temperature, light quality, and
light intensity [14]. L
coexisting with L
is a
single-gene in 19 cyanobacterial genomes except for
five sequenced Prochlorococcus, and L
and L
can be
found in different amounts in these 20 cyanobacteria.
All 25 cyanobacteria including Gv without thylakoids
have an FNR.
Multiple copies of L
were identified in
most of referred cyanobacterial species in this study.
However, only one L
was found in Cw, S79, S63,
SJAb, and SJBa (Table 1), and there is no such linker in
Gv and Prochlorococcus. The numbers of PC and
PE-associated rod linkers are also diverse among these
25 cyanobacteria. The composition of PBS in
cyanobacteria and red algae vary in response to
environmental changes in light intensity, light quality
(only cyanobacteria), and nutrient availability [43].
Differences in chromophore composition of
phycobiliproteins result in wavelength-specific
difference in light absorption among species of
cyanobacteria. The assembly of the PBS is mediated by
linker polypeptides, and each trimeric or hexameric
subassembly of PBS contains at least one specific
linker polypeptide, which determines the type,
location, and aggregation state of the PBP within the
rod and also modulates the spectroscopic properties
[34]. Light quality and quantity are among the major
factors affecting the composition of PBSs. In some
cyanobacteria, the relative proportion of PC and PE
can vary within the PBS rods in response to a change
in light climate [5,17], but such complementary
chromatic adaptation is rare among marine
Synechococcus [9,41]. Changes in photon fluxes also
have an effect on the structure of PBS. Marine
cyanobacteria can resist high light stress by decreasing
the content of PBS in cell [44,45], due to a reduction in
surface of thylakoid membranes [46]. Prochlorococcus
and Synechococcus are abundant unicellular
cyanobacteria and major participants in global carbon
cycles. Although Prochlorococcus and Synechococcus are
closely related to each other and often cohabit, they
possess very different photosynthetic light-harvesting
antennas [45,47,48,49]. Synechococcus and the majority
of cyanobacteria use PBSs having 7-12 linkers, while
Prochlorococcus uses a chlorophyll a2 /b2
light-harvesting complex. Differences in absorption
properties and cellular costs between chlorophyll
a2/b2 and PBS antennas differentiate them with own
ecological niche in the ocean [45,50]. Prochlorococcus is
a unicellular cyanobacterium that lacks PBS and
contains chlorophyll b as major accessory pigment,
which enables it to absorb blue light efficiently at
low-light intensity and blue wavelengths
characteristic in deep euphotic zone [50]. P86 and P13
are representatives of high- and low-light adapted
ecotypes. The low light-adapted strain has
significantly more genes than its high light
counterpart such as γ subunits, but neither has
PBSs-associated linkers. As transitional
light-harvesting antennae, γ subunits appeared more
recently than other PBSs-associated linkers and the
linkers (FNR and γ subunits) have some
compensatory function.
Evolution in genus Prochlorococcus would have
evolved towards genome reduction [45]. Specific
genome amplification and diversification have taken
certain place during adaptation of the latter to their
specific environments [45]. The PBSs linker genes
should be one of the reduced genes along with
Prochlorococcus genomes reduction, whereas all
Prochlorococcus strains evolved to use (divinyl-)
chlorophyll a/b-protein complexes as the major
Int. J. Biol. Sci. 2007, 3
antenna system [50]. In reverse, there are many PBSs
linkers in the genomes of Synechococcus that is also
considered as genome reduction. Whether such a
reduced genome is a derived state resulting from
progressive gene loss or is an ancestral state are
unclear. The PBSs of open-ocean Synechococcus
cyanobacteria are among the most complex ones
described so far since they possess four types of
constitutive PBPs: APC, PC, and two forms of
phycoerythrin: PEI and PEII. The PE-associated
linkers are divergent to PEI- and PEII-associated
linkers along with PE divergence. In previous studies,
the PBSs and linkers were probably co-evolved from
very early stage [51]. Some PBSs rods have one
combination of three PE-associated linkers (e.g., CpeC,
MpeD, and MpeC), while others would have another
combination (e.g., CpeE, MpeD, and MpeE) [26].
Indeed, PBSs rods are in fact more compact than we
assumed. Cyanobacteria with short PBSs rods may
have a heterogeneous linker composition, which allow
these cyanobacteria to colonize a variety of
light-quantity and light-quality environments. Ting et
al. [2] presented a scenario to explain how
Prochlorococcus antenna evolved in an ancestral
cyanobacterium in iron-limited oceans, resulting in
diversification in Prochlorococcus and marine
Synechococcus lineages from a common PBS-containing
Genomic distribution and sequence analysis of
PBSs linker genes
In many cases, the PBSs-associated linkers and
PBPs as well as enzymes that involved in biosynthesis
or binding of phycobilins are directly adjacent to each
other on chromosome and may form up an operon
that is regulated by a same activator [52,53]. From
these data, 36 gene clusters ranging from 1.5 to 13.2 kb
were found in these cyanobacterial genomes (Fig.3). In
overall, there are 15 APC-associated gene clusters, 12
PC-associated gene clusters, 4 PE with PC or
ambiguous PBPs-associated gene clusters, and 5
ambiguous PBPs-associated gene clusters (Fig.3). Most
PBSs-associated linkers and PBPs often clustered and
transcribed in the same direction, but in the reverse
direction with some enzymes’ genes. The other
linkers’ genes such as FNR are arranged randomly in
the genome. There are also many linkers contiguous to
each other in these genomes such as P99 and Cw
genomic sequences, and they do not assemble into an
operon. Although there are γ subunits in some
Prochlorococcus and Synechococcus, but they do not
form gene clusters with other PBSs linker genes.
APC-associated linker gene clusters exist universally,
and the largest putative operon makes up of PE with
PBPs and enzymes’ genes in S93. Genes encoding PC
or PEC subunits are typically followed by genes
encoding APC-associated linker polypeptides and/or
the genes for chromophore attachment to the alpha
subunit. A L
gene always follows the above operon
and forms a separate transcription unit. The apcC
gene, encoding small linker polypeptide Lc
, lies
downstream from apcB and apcE genes, and upstream
from apcA gene. apcC gene with apcA/B genes locate
together on a transcriptional unit. As one type of the
terminal acceptors of excitation energy within the
PBSs, apcC is also found in the attachment of PBSs to
the membrane.
The structure of PBSs linker gene clusters varies
among species. Almost of PBSs-associated linkers
form up gene clusters with PBPs, but the number of
CpcG and CpeC, CpeD, and CpeE that are divergent
from a same ancestor is uncertain in gene clusters. In
N7, there are a PC gene cluster constituting of four
CpcG1-4 followed by cpcB/A (C-PC β and chain),
CpcD (PC-associated rod linker), and CpcE/F
(Phycocyanobilin lyase α and β subunit), loaded in a
PE gene cluster adjacently, while in Te a gene cluster
make up of three CpcG1, 2, 4 with CpcB/A and
CpcE/F. Similarly, an obvious diversity of a
PE-cluster existed in Gv, and has three PE-associated
linkers CpeC, CpeD, and CpeE. In S63 and S79, the
duplicated PC genes arrange a tandem repeat unit
with three rod linkers’ genes between cpcB
downstream cpcB
, cpcE/F set. The occurrence of
several different gene sets in the same type of PBS
component is apparently the result of adaptation of
these organisms to different environmental
conditions, such as light quality and nutrient
availability. Some linkers have been diverged from a
common ancestor along with PBPs divergence and
may be caused by gene duplication or horizontal gene
With known morphology of PBSs linker clusters
to construct PBSs, divergence and evolution in
arrangement of PBSs cannot be excluded. For
example, some PBSs might have one combination of
APC-, PC-, and PE-associated linker clusters, while
others would have different combinations (only one or
two PBPs-associated linker clusters). It is possible that
PBSs linker clusters are in fact more compact than we
thought, with short rods having a heterogeneous
linker composition adapted well to changing
environments [46]. In another case, a model strain S81
consists of an APC core and rods that made of one
type of PC and two types of PE (I and II), and gather
into a complicated operon. PEI and PEII can bind both
PUB and PEB in different proportions to light acclimation
[46]. In some cyanobacteria, PBSs rod of only PC is
simpler since it possesses only one complete set of α
and β subunits and two PBSs rod-core linkers (CpcG1
and CpcG2), indicating probably a heterogeneous rod
linker composition [54]. Six [46] hypothesized that
PEII-associated linker would firmly anchor the
proximal PEII disk to the rest of the rod, whereas the
short C-terminus of another PEII-associated linker
makes it more susceptible to release/breakage during
photo acclimation processes.
In S81, S99, and S96, cpeR occurs downstream of
PBPs-associated linkers and genes related with PBSs.
The structure is similar to the operon structure of F.
diplosiphon, and the genes of operon are regulated by
the same activator such as CpeR. CpeR is transcribed
as a part of the cpeCDE operon on an extended
transcript, and required for expression of the cpeB/A
operon. Therefore, it is proposed that at onset of green
light, operons cpeCDESTR and cpeB/A are expressed
in series as a genetic cascade [53]. Maybe the clusters
in S81, S99, and S96 work in the same fashion to that
of the operon in F. diplosiphon. According to known
genes, ambiguous genes function in clusters of S81,
S99, and S96 can be inferred comparatively. This
method can deduce the genes’ function such as cpeS,
and cpcT [55,56], and provide information for
validation in experiment.
Int. J. Biol. Sci. 2007, 3
Fig.3. Organization of the gene clusters encoding PBSs and PBSs-associated linkers of 17 cyanobacteria. Arrows represent the
direction of translation, and the relative sizes of operon deduced from analysis of the amino acid sequence. The cyanobacteria names
are given on top of the corresponding region. Yellow arrows indicate the PBSs-associated linker; sky blue, blue, and red arrows
represent APC, PC, and PE, respectively; green arrows mean ambiguous PBPs or PBBs linkers.
Conservation domain analysis of PBSs linker
Ancestral PBPs are probably associated with
same precursor of linker polypeptides. It may be
possible that the linker polypeptides developed from
an earlier (possibly non-globin) ancestor of PBPs
[51,57]. Two additional unique β residues interact
directly with the linker polypeptides, and linker
polypeptides are conserved with β residues locating in
F' and F helices [18]. In N7, we chose a cluster
including PBSs-associated linkers, PBPs, PBPs lyase,
and FNR, which have conversion domains shown in
Fig.4. The amino acids of conversion domains are
generally hydrophobic to form β-sheet. The sequence
alignment of identified extensions from CpcG (1-4)
protein shows that these extensions have 37%-54%
identity and 59%-71% similarity, while the identity
between CpcGs and PBPs, CpcGs and PBPs lyase are
both <10%. The PC-associated linker and
PE-associated linker have also a lower identity of
about 20%. The amino acid sequences have high
sequence identity with each other ranging from 43% to
99% (Fig. 4). The CpcD-like domain of FNR is more
frequently found at the C-terminus of CpcD that
encodes the unique rod-terminating linker protein
8.9 PC
[26]. Evidenced by this domain’s presence at
the alignment between L
8.9 PC
and FNR in N7, the
identity and similarity is only 10% and 14%,
respectively. However, a CpcD-like domain is
consistent with that localization, which is at the
N-terminus of the CpcC proteins and a C-terminus
domain, which is more similar to the PC-associated
linker protein in Gv [26]. The sequence analysis shows
that the identity and similarity between N-region of
CpcA approximately 70 amino acids and CpcD are
16% and 44% in N7, respectively. Especially in
high-light-grown cells, the cpcD gene apparently did
not undergo gene duplication. Therefore, it may
assume that L
functions as rod-terminating linker
polypeptide for ending rods with PC [14]. The CpcG3
protein exhibited a strong resemblance to those of
CpcG4 at 51% in identity and 72% in similarity, for
CpcG1, a 38% identity, and a 59% similarity. CpcG1
with CpcG2 have 53% in identity and 69% in
similarity. Conversion domains massed on the
N-terminal was also observed among these series of
CpcG genes. The sequence alignment in S6 shows that
a large part of N-terminus of CpcG2 is almost identical
to that of CpcG1, while the C-terminal part is highly
diverged from each other [58]. With above values of
alignment, CpcG1 and CpcG2 came from a common
ancestor (I), and CpcG3 and CpcG4 came from
another ancestor (II) in N7. Ancestor I and II
associated with each other, and co-evolved in own
distinct roles since the very beginning.
Int. J. Biol. Sci. 2007, 3
Fig.4. Multiple amino acid sequence alignment of the PBSs linkers with PBPs in Nostoc sp. PCC 7120. (A). Sequence
alignments for an opera including pecB, pecC, pecE, pecF, cpcB, cpcA, cpcC, cpcD, cpcE, cpcF, and cpcG1-4 in N7. (B).
Sequence alignments for N-terminal domain of FNR in N7. (C). Sequence alignments for cpcG1-4 in N7. The positions of
similarity and identity are marked in gray and black, respectively.
Phylogenetic analysis
We further investigated the relationship among
these PBSs linkers of these 25 cyanobacteria by
generating an alignment of 192 identified PBSs linker
amino acid sequences followed by generation of an
MP phylogenetic tree (Supplementary Material). The
resultant tree depicts 6 phylogenetic classes of
APC-associated L
, PC, PE-associated L
, L
, L
, γ
subunit, and FNR. Linkers of APC-associated L
, L
and L
were assembled in monophyletic group
distinctly according to their sequences and functional
Int. J. Biol. Sci. 2007, 3
characteristics. Some PE-associated rod linkers are
assembled into two groups in different branches, and
others disperse throughout the rod linker cluster with
PC-associated linkers. A cluster of PE-associated core
linkers has a close relationship with γ subunits and the
other with L
. Further, APC-associated L
may share
a recent common ancestor with CpcD (L
). The
phylogenetic tree reveals that the genetic
diversification of all groups involves in a more
complex pattern in gene degeneration and
duplication. The L
(CpcG) of N7, Av, SJAb, SJBa,
and Te form another cluster, and in two branches of
that CpcG1 and CpcG2, CpcG3 and CpcG4 (except
CpcG1 of SJAb and SJBa) are in at least 91% and 98%
bootstrap values, respectively. These four copies
(CpcG1-4) most likely have evolved into a recent
duplication, whereas evolution of CpcG among these
species is more complex with horizontal gene
Some ambiguous genes can be divided into these
six classes in high bootstrap values with known PBSs
linkers by phylogenetic analysis. For example, some
innominate PBSs linkers are γ subunits
(Syn_cc96050433, Syn_cc99021895, WH5701_00450),
and they are high homologous with known MpeC
(SYNW2010) in S81. These innominate PBSs linkers
may be homological and have the same functions with
known PBSs linkers such as MpeC. The ambiguous
function genes should be validated in the future.
Although Prochlorococcus has no PBS, the vestiges
of a CpcD-like domain which sequence has diverged
and become shorter and extensively modified are still
recognizable. FNR sequence is possible to be a
potentially interesting evolutionary marker for both
ancient and recent cyanobacteria [14]. The 16s rDNA
sequences from 21 sequenced cyanobacteria were
retrieved from IMG, and FNR was the only linker in
all these cyanobacteria. Therefore, FNR as a PBSs
linker identified in 21 cyanobacteria was also used to
construct the phylogeny to discern the evolutionary
history of the PBSs linker family (Supplementary
Material graph B). Both 16s rDNA and FNR
phylogenetic trees can be divided into two major
unbalanced clades and separated into several
monophyletic clusters with strong bootstrap support.
In phylogenetic tree of FNR, clade I contains 18 FNR
proteins of these 21 cyanobacteria, while clade II
contains only 3 FNR proteins. In clade I,
Prochlorococcus and marine Synechococcus form a
cluster and share a common PBP-containing ancestor,
and may have both diversified at a similar point in
evolution [48]. FNR of S63 and S79 are identical, and
are highly homologous with the branch of FNR in Av,
Np, and N7. In clade II, SJAb sequences share a more
recent common ancestor with SJBa than with other
Synechococcus, and in a group with Gv at the bottom of
both trees except for Te that clusters together in clade
II of 16s rDNA. It is found that these groups of FNR
that correspond to their 16s rDNA phylogeny are
mostly based on the tree topology, but S79, S63, and
Te distribute in different clades from the 16s rDNA
phylogeny. Therefore, most FNR sequences are highly
conservative. The appearance of cyanobacterial FNR
might be due to the speciation, and did not diversify
under selective pressures.
4. Conclusion
The current work on the PBSs linker family
facilitates our understanding on biological functions
and complicated interactions between linker
polypeptides and the PBPs from comparative analysis
on 25 cyanobacteria genomes. 192 putative PBSs linker
genes have been identified from 25 species of
cyanobacteria using BLASTP, TBLASTN and ClustalX.
The gene clusters of 36 PBSs linkers ranging from 1.5
kb to 13.2 kb were found in these cyanobacterial
genomes. The possibilities of six classes of the linker
family were demonstrated. Gene duplication, loss,
shuffling, and/or horizontal transfer appear to have
played important roles during the evolution and
divergence of cyanobacterial PBSs linker
polypeptides. Various environmental factors
especially light acclimation were the primary selective
pressures. Future research will drive the field towards
a deeper understanding on evolutional mechanisms of
photosynthetic light-harvesting complexes in
cyanobacteria and red algae.
Supplementary Material
Unrooted MP tree for PBSs linkers in 25 cyanobacteria and
unrooted NJ trees for 16s rDNA and FNR in 21 cyanobacteria
This work was supported by the Key Project
(KZCX-2-YW-209) of Knowledge Innovation Program
of Chinese Academy of Sciences and Hi-Tech Research
and Development Program (2006AA090303) of China
Conflict of interest
The authors have declared that no conflict of
interest exists.
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Supplementary resource (1)

... Apt, Collier, and Grossman (1995) studied in depth the evolution of the PBPs by comparing PBP sequences. This study was expanded by more recent work about the evolution of linker proteins (Guan, Qin, Zhao, Zhang, & Tang, 2007;Shi, Qin, & Wang, 2011) and the PE evolution and diversification in marine Synechococcus (Everroad & Wood, 2012;Six et al., 2007;Ting, Rocap, King, & Chisholm, 2002) (see Fig. 3). ...
... The rod components seem to evolve through complex ways including gene duplication, lateral gene transfer and gene loss (see Everroad and Wood, 2012;Six et al., 2007;and references within). Rod linkers and rod-core linkers most probably co-evolved with these genes leading to modern PBS structures (Apt et al., 1995;Guan et al., 2007). The evolution from the ancestor heterodimer to the modern different PBPs brought an increased light-harvesting capacity by attaching a higher quantity and diversity of chromophores. ...
... For more extensive reviews about the evolution of phycobiliproteins, see Apt et al. (1995), Everroad and Wood (2012), Guan et al. (2007), Shi et al. (2011), Six et al. (2007, Ting et al. (2002), and Zhao and Qin (2006). ...
The light-harvesting proteins of oxygenic photosynthesis include mainly the phycobiliproteins and the light-harvesting complex (Lhc) family. Whereas the former are found in cyanobacteria, glaucophytes, red algae and cryptophytes, the latter are present in all eukaryotic organisms. Phycobiliproteins covalently bind bilins and are arranged in phycobilisomes in most organisms and form huge extramembranous protein aggregates. Only in cryptophytes they are lumenally localized. Lhc are membrane intrinsic proteins and fall in two distinct groups: the Lhca and Lhcb, serving as photosystem I (PSI) and photosystem II (PSII) antenna, respectively, are proteins of the green lineage of organisms (e.g., all green organisms from green algae to higher plants as well as chlorarachniophytes and euglenophytes). These proteins non-covalently bind Chl b, besides Chl a and carotenoids (Car). The other group consists of Lhcf, Lhcr, Lhcy, Lhcz, RedCaps and the photoprotective Lhcx. They bind a huge variety of carotenoids and often Chl c besides Chl a, depending on the taxon. These Lhc proteins are found mainly in the red lineage (red algae and all organisms derived thereof by secondary endosymbiosis, like, e.g., diatoms). Only Lhcx (also called LhcSR) is present in the green lineage as well and binds also Chl b instead of Chl c. Lhcf and Lhcr are the main light-harvesting proteins in the red lineage, whereby Lhcr often constitutes the PSI antenna. Besides these main Lhc families, another photoprotective protein, PsbS, is expressed in the green lineage that contains no pigments and consists of four helices. Only dinoflagellates contain an additional, water-soluble light-harvesting protein, the so-called peridinin-Chl protein.
... The heterologous rod linker protein CpcC (33 kDa) from T. elongatus was expressed in both TeBACD and TeBAC strains. Both CpcC and CpcC1 connect the first two PC hexamers within the rod to the APC core (David et al., 2011;Guan et al., 2007;Ughy and Ajlani, 2004). A phylogenetic comparison showed that CpcC is more closely related to CpcC1 than CpcC2 ( Supplementary Fig. S2), which may explain why CpcC was not degraded in Synechocystis. ...
Full-text available
Phycocyanin (PC) is a soluble phycobiliprotein found within the light-harvesting phycobilisome complex of cyanobacteria and red algae, and is considered a high-value product due to its brilliant blue colour and fluorescent properties. However, commercially available PC has a relatively low temperature stability. Thermophilic species produce more thermostable variants of PC, but are challenging and energetically expensive to cultivate. Here, we show that the PC operon from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (cpcBACD) is functional in the mesophile Synechocystis sp. PCC 6803. Expression of cpcBACD in an ‘Olive’ mutant strain of Synechocystis lacking endogenous PC resulted in high yields of thermostable PC (112 ± 1 mg g⁻¹ DW) comparable to that of endogenous PC in wild-type cells. Heterologous PC also improved the growth of the Olive mutant, which was further supported by evidence of a functional interaction with the endogenous allophycocyanin core of the phycobilisome complex. The thermostability properties of the heterologous PC were comparable to those of PC from T. elongatus, and could be purified from the Olive mutant using a low-cost heat treatment method. Finally, we developed a scalable model to calculate the energetic benefits of producing PC from T. elongatus in Synechocystis cultures. Our model showed that the higher yields and lower cultivation temperatures of Synechocystis resulted in a 3.5-fold increase in energy efficiency compared to T. elongatus, indicating that producing thermostable PC in non-native hosts is a cost-effective strategy for scaling to commercial production.
... Selection pressures periodically reduce genetic diversity as environmental changes select for a proportion of strains (Dvo r ak et al., 2015). Selection pressures, such as light availability, are significant drivers of ecotype diversity in co-occurring strains, as is seen in Prochlorococcus ecotypes, as well as in light specific genes across cyanobacterial species (Guan et al., 2007). The premise of genetic isolation allows us to reconcile phylogenetic and phylogenomic classification systems with traditional morphological and physiological markers, in a manner analogous to the polyphasic approach. ...
Cyanobacteria were the first oxygenic photosynthersizers, evolving ∼3.5 bya, they have since radiated into one of the most diverse and widely distributed phyla of bacteria. Cyanobacterial diversification occurs through ecological adaptation, facilitated by asexual reproduction, homologous recombination and horizontal gene transfer, and selection pressures on ecotypes leading to speciation. Delimiting cyanobacterial species is, thus, fraught with difficulties and a clear taxonomy has not yet been universally accepted. This review discusses diversity and description of cyanobacteria: covering traditional and new methods to define species boundaries and concluding with a focus on the advances made through genomics. Examples from the genera Raphidiopsis, Microcystis, and Prochlorococcus are used throughout. Genome plasticity allows cyanobacteria to rapidly adapt and be resilient to environmental changes, illustrating the means of their persistence, and is an important aspect of their biology. Genomics has revealed generalist and specialist genome strategies, intraspecific diversity, and genome evolution in response to environmental stimuli. New taxonomic definitions will need to account for intraspecific genetic variation, with a species classification that is relevant to a species concept and scientific endeavors. Capturing intraspecific diversity with comparative genomics may provide a new path to species classification. This is demonstrated with two case studies; comparison of available genomes shows differing species delineation of Raphidiopsis and Microcystis. In both genera, species boundaries occur at ∼96% average nucleotide identity (ANI), where homologous recombination is constrained, but speciation of Raphidiopsis raciborskii, R. brookii, and R. curvata has occurred through geographic isolation, whereas available data on Microcystis contain at least 15 species, reflecting, to differing extents, different ecotypes, which may co-exist. Both case studies question the relative importance of species-specific versus habitat specific gene pools as drivers of inter- and intraspecific diversity.
... Higher time requirement for extraction of A-PC than C-PC was observed in case of extraction of phycocyanins from dry biomass of A. platensis as well (Tavanandi et al. 2018a, b). A possible explanation can be given based on the structure of phycobilisomes which contain stacks of phycobiliproteins anchored to thylakoid membranes (Guan et al. 2007). Each phycobilisome consists of a core made of A-PC to which the C-PC discs are stacked on outwardly oriented rods. ...
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Spirulina maxima is reported to have the maximum protein content among different species of Cyanobacteria. In the present work, extraction of C-phycocyanin (C-PC) and Allophycocyanin (A-PC) from dry biomass of S. maxima was carried out for the first time using ultrasound-assisted extraction (UAE), enzyme-assisted extraction (EAE) and their combination. The total extractable C-PC and A-PC were estimated to be 47.89 and 39.95 mg/g dry biomass, respectively from serial extraction. UAE resulted in better yield and purity compared to EAE. At standardized conditions of UAE (1:15 solid-liquid ratio, 20% amplitude and 4 minutes ultrasonication time), the highest yield, purity and extraction efficiency achieved were 44.5 mg/g.d.b, 2.0 and 93% for C-PC and 29.93 mg/g.d.b, 0.89 and 75% for A-PC, respectively. The purity observed is the highest reported in primary extraction till date. Combination of methods did not result in significant improvement with respect to yield and purity. Considering both yield and purity, ultrasound assisted extraction alone was inferred to be the most suitable method for extraction of phycocyanins from the dry biomass of Spirulina maxima.
... Cyanobacteria are a primitive group of Gram-negative photosynthetic prokaryotes that originated around 3.5 billion years ago (Guan et al., 2007). They are ubiquitously distributed throughout the Earth surface and play a distinguished role in natural ecosystems for the production of primary biomass (Häder et al., 2015). ...
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With the rise in developmental activities, a load of pollution in the environment has increased. Most of the water bodies remain polluted due to the wastewater released by agricultural, domestic and industrial activities. Treatment of wastewater by physical, chemical and biological approaches is implied in order to cope with this problem and discharge an apparently clean effluent into natural water bodies. Recently, for the biological treatment of wastewater micro-algae have gained importance since they are able to accumulate plant nutrients, heavy metals, pesticides, organic and inorganic toxic substances and radioactive matters in their bodies. Further, the biomass left after the treatment is used for biogas generation and bio-compost. Biological wastewater treatment systems with micro-algae are now widely accepted as effective and low-cost natural treatment systems for purification of wastewater. In this chapter, we highlight the role of micro-algae in the treatment and management of wastewater.
... Cyanobacteria are a primitive group of Gram-negative photosynthetic prokaryotes that originated around 3.5 billion years ago (Guan et al., 2007). They are ubiquitously distributed throughout the Earth surface and play a distinguished role in natural ecosystems for the production of primary biomass (Häder et al., 2015). ...
Phycobiliproteins (PBPs) are brilliantly colored accessory light harvesting protein complexes around the periphery of thylakoid membrane. They can capture photonic energy over a broad region of solar spectrum which is essential for photosynthesis in cyanobacteria. Apart from photosynthesis, PBPs play an indispensable role in various biotechnological and pharmaceutical industries, and have increased demand in market worldwide. To fulfill the great demand, the utmost need is to have large-scale production of cyanobacterial biomass using cost effective technology. Several industries across the world have successfully developed cost effective strategies for large scale production of cyanobacterial biomass for the extraction of PBPs. The wide range of open and closed photobioreactor is an effective tool for large-scale production of biomass. Recently, the development of a rotating algal biofilm photobioreactor has simplified the production strategy of PBPs. Apart from quantity, quality is also extremely important for commercial for the cost effective extraction and purification of PBPs. Several physical and chemical protocols including aqueous two phase system, hydrophobic interaction/ion exchange chromatography have been developed in this context. This chapter primarily focuses to find out the gaps and current developments in the biomass production and purification technology for PBPs.
... Cyanobacteria are the oldest form of Gram-negative photosynthetic bacteria, which carry out photosynthesis similar to higher plants (Guan et al. 2007). These micro-organisms have a wide range of pigments such as carotenoids, chlorophyll a and phycobiliproteins (PBPs). ...
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Diverse phycocyanin (PC) extraction and purification methods for cyanobacteria have been reported in literature. A particular method is not applicable to all cyanobacteria and the best method seems to be genus/species specific. Here, we report PC extraction and purification method for the filamentous cyanobacterium Anabaena fertilissima, a hyperproducer of phycobiliproteins. PC was also characterised in terms of unit assembly and stability. PC was extracted by freeze-thawing in distilled water, concentrated by ammonium sulphate fractionation and purified by size exclusion chromatography. The purification process resulted in 5.85-fold increase in PC purity reaching to 3.28. SDS-PAGE of purified PC demonstrated two bands of 19 and 21 kDa. Based on analysis of non-denaturing PAGE, the native PC from this organism is suggested to be a hexamer (αβ)6 of 240 kDa. Lyophilised PC in powder form was more stable compared to PC in the solution. Half-life of dry PC is 110 days when stored at 4 °C in dark. Storage of PC in light at elevated temperature decreased its half life. When added to milk products, PC was stable up to 9 days when stored at 4 °C. Aqueous solution of PC also exhibited significant free radical scavenging activity. The PC from this organism has potential applications in food as a natural pigment and conservative due to its antioxidant properties.
... The need for stabilization functions in cyanobacteria has been reported previously (e.g. PsaE (Jeanjean et al. [20]) and PsbH (Komenda et al. [23]) in Synechocystis; CpcD in all cyanobacteria, including early studies in M. laminosus (Guan et al. [16]; Füglistaller et al. [13]; Reuter et al. [44]); and ApcD in Synechococcus (Dong et al. [10]). ...
In the Porcelana Hot Spring (Northern Patagonia), true-branching cyanobacteria are the dominant primary producers in microbial mats, and they are mainly responsible for carbon and nitrogen fixation. However, little is known about their metabolic and genomic adaptations at high temperatures. Therefore, in this study, a total of 81 Fischerella thermalis strains (also known as Mastigocladus laminosus) were isolated from mat samples in a thermal gradient between 61–46 °C. The complementary use of proteomic comparisons from these strains, and comparative genomics of F. thermalis pangenomes, suggested that at least two different ecotypes were present within these populations. MALDI-TOF MS analysis separated the strains into three clusters; two with strains obtained from mats within the upper temperature range (61 and 54 °C), and a third obtained from mats within the lower temperature range (51 and 46 °C). Both groups possessed different but synonymous nifH alleles. The main proteomic differences were associated with the abundance of photosynthesis-related proteins. Three F. thermalis metagenome assembled genomes (MAGs) were described from 66, 58 and 48 °C metagenomes. These pangenomes indicated a divergence of orthologous genes and a high abundance of exclusive genes at 66 °C. These results improved the current understanding of thermal adaptation of F. thermalis and the evolution of these thermophilic cyanobacterial species.
... phycobilisome complex is generally composed of the allophycocyanin core and the protruding rods (composed of several hexameric CpcAB discs). These chromophoric components are interconnected by specific internal linker proteins and are attached to the thylakoid membrane (78). The terminal linker CpcD is located on the apical tip of the rods, and regulates the antennae length by preventing further elongation (79). ...
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Cyanobacteria that do not fix atmospheric nitrogen gas survive prolonged periods of nitrogen starvation in a chlorotic, dormant state where cell growth and metabolism are arrested. Upon nutrient availability, these dormant cells return to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise re-installation and activation of essential cellular structures and functions. We have been investigating the transition to chlorosis and the return to vegetative growth as a simple model of a cellular developmental process and a fundamental survival strategy in biology. In the present study, we used quantitative proteomics and phosphoproteomics to describe the proteomic landscape of a dormant cyanobacterium and its dynamics during the transition to vegetative growth. We identified intriguing alterations in the set of ribosomal proteins, in RuBisCO components, in the abundance of central regulators and predicted metabolic enzymes. We found O-phosphorylation as an abundant protein modification in the chlorotic state, specifically of metabolic enzymes and proteins involved in photosynthesis. Non-degraded phycobiliproteins were hyperphosphorylated in the chlorotic state. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.
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With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
Conference Paper
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam, SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline I; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.
The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.
Phycobilisomes are specialized aggregated structures composed of phycobiliproteins, which are photosynthetic accessory pigments in red and blue-green algae. Phycobiliproteins, which can account for as much as 24% of the dry weight of blue-green algal cells and 40–60% of the total soluble protein, are the major light harvesters in these organisms. Chlorophyll a, which absorbs light primarily in the blue region and the red region of the visible spectrum, leaves a large absorption gap. This is filled in by the phycobiliproteins, which have an absorption range of 500–660 nm. These pigments work in conjunction with chlorophyll a to optimize light harvesting for photosynthesis, particularly under light limiting conditions. The only phycobiliprotein in higher plants is phytochrome, which occurs in very small amounts and serves as a photoregulatory receptor. In cryptophyte algae (flagellated unicells of indefinite taxonomic position), phycobiliproteins also serve as major photosynthetic accessory pigments, but phycobilisomes are absent. There are three major classes of phycobiliproteins—the red-colored phycoerythrins (PEs), the blue-colored phycocyanins (PCs), and allophycocyanins (APCs). This chapter focuses on the phycobilisome characteristics, their relationship to the photosystems in the thylakoid membrane, and major problems to be addressed in future investigations.