Download Origin and Spread of Photosynthesis Based upon Conserved

Origin and Spread of Photosynthesis Based upon
Conserved Sequence Features in Key Bacteriochlorophyll
Biosynthesis Proteins
Radhey S. Gupta*
Department of Biochemistry, McMaster University, Hamilton, ON, Canada
*Corresponding author: E-mail: [email protected].
Associate editor: Neelima Sinha
Abstract
Key words: origin of photosynthesis, conserved signature indels, BchL, BchX, NifH, BchN, BchB, Clade C cyanobacteria,
phylogenetic trees, Chloroflexi, Chlorobi, Heliobacteriaceae, Proteobacteria, lateral gene transfers.
Introduction
The origin of photosynthesis, which sustains most life on
earth, and its spread to various bacterial groups remain
important unresolved problems in the evolutionary history
of life (Blankenship 1992; Blankenship and Hartman 1998;
Hartman 1998; Dismukes et al. 2001; Raymond and Segre
2006; Hohmann-Marriott and Blankenship 2011). With
the exception of plants and algae that are secondarily
photosynthetic due to endosymbiotic acquisition of cyanobacteria (Morden et al. 1992; Margulis 1993), the (bacterio)chlorophyll [Bchl]-based photosynthesis is found in five discontinuous phyla of cultured bacteria viz. Cyanobacteria
(Cyano), Chloroflexi, Bacteroidetes/Chlorobi, Firmicutes
(Heliobacteriaceae), and Proteobacteria (Proteo) (Gest and
Favinger 1983; Olson and Pierson 1987; Blankenship 1992;
Bryant and Frigaard 2006; Hohmann-Marriott and
Blankenship 2011). Additionally, an uncultured bacterium
belonging to the phylum Acidobacteria is also inferred to be
photosynthetic (Bryant et al. 2007; Raymond 2008). The similarities in the photosynthetic pigments and overall charge
transfer mechanisms in the reaction centers (RCs) of various
phototrophs suggest that photosynthesis has evolved only
once (Nitschke and Rutherford 1991; Golbeck 1993;
Blankenship 1994; Schubert et al. 1998; Olson and
Blankenship 2004; Nelson and Ben Shem 2005; Sadekar
et al. 2006). However, it has proven difficult to determine
in which of these bacterial groups photosynthesis first originated and how other groups acquired this ability (Raymond
et al. 2002; Xiong and Bauer 2002; Raymond et al. 2003;
Raymond 2009). Different approaches used to investigate
this problem have given discordant results indicating the
origin of photosynthesis in Proteobacteria (Xiong et al. 2000;
Xiong and Bauer 2002), Firmicutes (Vermaas 1994; Gupta
et al. 1999; Gupta 2003), Chloroflexi (Pierson 1994;
ß The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please
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Mol. Biol. Evol. 29(11):3397–3412 doi:10.1093/molbev/mss145 Advance Access publication May 24, 2012
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Research article
The origin of photosynthesis and how this capability has spread to other bacterial phyla remain important unresolved questions.
I describe here a number of conserved signature indels (CSIs) in key proteins involved in bacteriochlorophyll (Bchl) biosynthesis
that provide important insights in these regards. The proteins BchL and BchX, which are essential for Bchl biosynthesis, are
derived by gene duplication in a common ancestor of all phototrophs. More ancient gene duplication gave rise to the BchX–BchL
proteins and the NifH protein of the nitrogenase complex. The sequence alignment of NifH–BchX–BchL proteins contain two
CSIs that are uniquely shared by all NifH and BchX homologs, but not by any BchL homologs. These CSIs and phylogenetic
analysis of NifH–BchX–BchL protein sequences strongly suggest that the BchX homologs are ancestral to BchL and that the
Bchl-based anoxygenic photosynthesis originated prior to the chlorophyll (Chl)-based photosynthesis in cyanobacteria. Another
CSI in the BchX–BchL sequence alignment that is uniquely shared by all BchX homologs and the BchL sequences from
Heliobacteriaceae, but absent in all other BchL homologs, suggests that the BchL homologs from Heliobacteriaceae are primitive
in comparison to all other photosynthetic lineages. Several other identified CSIs in the BchN homologs are commonly shared by
all proteobacterial homologs and a clade consisting of the marine unicellular Cyanobacteria (Clade C). These CSIs in conjunction
with the results of phylogenetic analyses and pair-wise sequence similarity on the BchL, BchN, and BchB proteins, where the
homologs from Clade C Cyanobacteria and Proteobacteria exhibited close relationship, provide strong evidence that these two
groups have incurred lateral gene transfers. Additionally, phylogenetic analyses and several CSIs in the BchL-N-B proteins that are
uniquely shared by all Chlorobi and Chloroflexi homologs provide evidence that the genes for these proteins have also been
laterally transferred between these groups. Other results and observations reported here indicate that the genes for the BchL-N-B
proteins in Proteobacteria are derived from the Clade C Cyanobacteria, whereas those in Chlorobi were acquired from
Chloroflexus or related bacteria by means of LGTs. Some implications of these observations regarding the origin and spread
of photosynthesis are discussed.
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Gupta . doi:10.1093/molbev/mss145
Dismukes et al. 2001), and in anoxygenic ancestors of
Cyanobacteria (Mulkidjanian et al. 2006).
The origin of photosynthesis has proven difficult to resolve
because photosynthesis-related genes, which are clustered in
genomes (Xiong et al. 1998; Choudhary and Kaplan 2000) are
prone to lateral gene transfers (LGTs) (Raymond et al. 2002;
Raymond et al. 2003; Zhaxybayeva et al. 2006; Raymond
2009). This makes it difficult to interpret the results of phylogenetic analyses based on such genes/proteins (Xiong et al.
1998; Xiong et al. 2000; Green and Gantt 2000). The analyses
based on other genes and proteins that are less prone to
LGTs, although they provide useful insights regarding the
branching orders of these bacterial phyla (Olsen et al. 1994;
Gupta et al. 1999; Gupta 2000; Gupta 2003; Ciccarelli et al.
2006), they do not necessarily indicate that photosynthesis
evolved in this manner. Thus, an understanding of this important problem can only emerge from some novel characteristics of the photosynthesis-related genes/proteins, which
despite the widespread occurrence of LGTs can provide useful
insights to resolve this problem. Recent analyses of genome
sequences have revealed that only nine proteins related to
photosynthesis, all of which are involved in the biosynthesis of
Bchl, are shared by all phototrophs (Raymond et al. 2002;
Mulkidjanian et al. 2006). Of these nine proteins, only three
proteins viz. BchL, BchN, and BchB, are uniquely found in all
phototrophic lineages indicating their central importance in
the origin of photosynthesis (Raymond et al. 2002;
Mulkidjanian et al. 2006).
The proteins BchL, BchN, and BchB (referred to as
BchL-N-B), which are unique to all phototrophs, are part of
an enzyme complex viz. light-independent (or darkoperative) protochlorophyllide oxidoreductase (DPOR) that
plays a key role in the biosynthesis of Bchl by converting
protochlorophyllide to chlorophyllide a (chlorin) (Burke
et al. 1993; Beale 1999; Raymond et al. 2004; Chew and
Bryant 2007). A second enzyme complex, chlorin reductase,
consisting of the proteins BchX, BchY, and BchZ (referred to
as BchX-Y-Z), found in various phototrophic bacteria except
cyanobacteria, further reduces chlorin to bacteriochlorin that
serves as the direct precursor for the Bchls (Beale 1999; Chew
and Bryant 2007). Importantly, the three proteins BchL-N-B
from the DPOR complex exhibit significant sequence similarity to the three subunits (viz. BchX–Y–Z) of chlorin reductase,
indicating that these two sets of proteins have evolved from
an ancient gene duplication in a common ancestor of all
phototrophs (Burke et al. 1993; Xiong and Bauer 2002;
Raymond et al. 2004; Chew and Bryant 2007). Additionally,
these two sets of proteins also exhibit significant sequence
and structural similarity to the three subunits viz. NifH, NifD,
and NifK, of the nitrogenase complex (Sarma et al. 2008;
Muraki et al. 2010), which plays a central role in nitrogen
fixation and is sporadically distributed in prokaryotes
(Haselkorn 1986; Burke et al. 1993; Xiong et al. 2000;
Raymond et al. 2004). Of these proteins, the homologs of
BchL, BchX, and NifH show maximal sequence conservation
making them particularly useful for understanding the origin
of photosynthesis (Burke et al. 1993; Xiong et al. 2000;
Raymond et al. 2004).
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In recent years, genome sequences for large numbers of
photosynthetic prokaryotes representing different bacterial
phyla have become available (Raymond and Swingley 2008;
NCBI 2011). They provide valuable resource for using different
approaches to gain insights into the origin of photosynthesis.
For understanding of ancient evolutionary relationships, one
approach that has proven very useful consists of identifying
conserved indels (i.e., inserts or deletions) in protein sequences that are uniquely shared by particular groups of organisms (Rivera and Lake 1992; Gupta and Golding 1993;
Baldauf and Palmer 1993; Delwiche et al. 1995; Gupta 1998;
Gupta 2011). Because conserved indels in protein sequences
(even a 1 amino acid indel) are the results of rare and highly
specific genetic changes, their presence or absence in gene/
protein sequences is generally not affected by factors such as
differences in evolutionary rates at different sites or among
different species that greatly influence the branching patterns
of species in phylogenetic trees (Felsenstein 1988; Gupta 1998;
Moreira and Philippe 2000; Felsenstein 2004). Hence, the
shared presence of such markers in different group(s) of species provides powerful means to establish ancestral evolutionary relationships as well as to identify cases of LGTs among
unrelated taxa. Further, depending upon the presence or absence of these characters (viz. indels) in outgroup species, it is
possible to infer which of the two character states of the
protein (i.e., indel-containing or indel-lacking) is ancestral
(Baldauf and Palmer 1993; Gupta 1998; Gupta 2003; Gupta
2010).
In this work, I describe a number of conserved signature
indels in the NifH, BchX, BchL, BchN, and BchB proteins,
which together with the results of phylogenetic analyses provide valuable information regarding the origin of photosynthesis and its spread among bacterial phyla. Based upon the
novel CSIs that are reported here and other sequence characteristics of these proteins, the proteobacterial homologs of
the BchL-N-B proteins are specifically related to a clade consisting of the marine unicellular cyanobacteria (Clade C
Cyano), whereas those from Chlorobi are closely related to
the Chloroflexi. Phylogenetic analyses and other CSIs reported
here further indicate that the BchX homologs originated prior
to the BchL and that the BchL homologs in Heliobacteriaceae
(Firmicutes phylum) are primitive in comparison to those
found in other photosynthetic lineages.
Materials and Methods
Using Blastp searches on the BchL, BchN, and BchB proteins
(Altschul et al. 1997), homologs of these proteins from different photosynthetic bacteria were retrieved and their multiple
sequence alignments were created using the ClustalX 1.83
program (Jeanmougin et al. 1998). These alignments were
visually inspected to identify all indels that were flanked on
both sides by at least 4–5 identical/conserved residues in the
neighboring 30–40 amino acids. The indels that were not
flanked by conserved regions were not considered as they
do not provide reliable markers for evolutionary studies
(Gupta 1998). The species distribution patterns of all potentially useful indels were further evaluated by detailed Blastp
searches on short sequence segments (generally between
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60–100 amino acids depending upon the lengths of the
indels) containing the indels and their flanking conserved
regions (Gupta 2009; Gupta and Mathews 2010). The sequence information for various conserved indels from different phototrophic bacteria was compiled into signature files.
Sequence information for only representative species from
larger photosynthetic phyla is provided in the figures that
are shown here. However, all of the indels reported are
highly specific for the indicated groups. It should be clarified
that the term Chloroflexi in this work refers only to the filamentous anoxygenic phototrophs (FAP)(Bryant and Frigaard
2006; Hanada and Pierson 2006; Tang et al. 2011), as other
Chloroflexi that are not photosynthetic, do not contain homologs of these proteins.
The sequences for BchX and NifH homologs from various
photosynthetic organisms as well as other lineages (for NifH)
were also retrieved and multiple sequence alignments of
these proteins together with the BchL sequences were created. These alignments were also inspected for the presence
of conserved indels and their specificities were evaluated as
described above. Phylogenetic trees based on sequence
alignments of the BchL, BchX, and NifH homologs were constructed using both neighbour joining (NJ) and maximumlikelihood (ML) algorithms. Bootstrapped NJ trees based on
these sequences were constructed using the Kimura model
(Kimura 1983) employing the TREECON 1.3b program (Van
de Peer and De Wachter 1994). ML analysis based on these
sequences was carried out using the WAG + F model with
gamma distribution of evolutionary rates with four categories
and 10,000 puzzling steps employing the TREE-PUZZLE program (Schmidt et al. 2002). The pair-wise identity and similarity between different homologs for the BchL, BchN, and
BchB proteins were determined using the EMBOSS molecular
biology program package with default parameters (Rice et al.
2000).
Results
Identification of a Conserved Indel in the BchL
Protein Suggesting the Primitive Nature of the BchL
Homolog from Heliobacteriaceae
In the sequence alignments of BchL homologs from various
phototrophs two different CSIs were identified (fig. 1A). Both
these CSIs are of defined lengths and they are flanked on both
sides by a number of conserved residues, indicating that they
provide useful molecular markers for evolutionary studies. Of
these two CSIs, the first consisting of a 1 aa indel (CSI ¶) is
specifically present in the two Heliobacteriaceae species
(fig. 1A). The absence of this indel in the BchL homologs
from all other phyla of bacteria indicates that it is a specific
characteristic of the Heliobacteriaceae BchL. The second CSI
(CSI •), which is present in an adjoining region, is comprised
of a 5 amino acid indel that is uniquely found in different
Chlorobi and Chloroflexi homologs, but absent in all other
bacteria. These CSIs could represent either inserts in the
genes from these particular taxa or alternatively they could
result from deletion(s) in the BchL homologs from other
phototrophic lineages. To gain insights in these regards, a
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multiple sequence alignment of diverse BchL and BchX homologs was created. The sequence region where these CSIs
are present is sufficiently conserved between the BchL and
BchX homologs so that their sequences can be reliably
aligned. Figure 1B shows the sequence alignment of the
BchX homologs to the corresponding region of the BchL proteins where these CSIs are found. From the sequence alignments of these two proteins, it is clear that the 1 aa CSI that is
uniquely found in the BchL homologs of Heliobacteriaceae is a
shared characteristic of all BchX homologs from different lineages. Because, BchX and BchL homologs are derived by gene
duplication in a common ancestor of all phototrophs (Burke
et al. 1993; Xiong et al. 2000), the presence of this CSI in all
BchX homologs as well as the BchL homolog from
Heliobacteriaceae suggests that the BchL homologs from
Heliobacteriaceae containing this CSI are primitive in comparison to those from other phototrophic lineages. The most
parsimonious explanation to account for the absence of
this CSI in the BchL homologs from other phototrophs is
that a deletion occurred in the ancestral form of the protein,
before it spread to other lineages. However, other possibilities
cannot be entirely excluded, In contrast to the CSI ¶, the CSI
• that is specifically present in the in BchL homologs of
Chlorobi and Chloroflexi was absent in all of the BchX homologs indicating that the absence of this indel was the ancestral
character state of the BchX–BchL protein. Therefore, this CSI
likely represents an insert in the BchL homologs of Chlorobi
and Chloroflexi and its shared presence in these two phylogenetically distinct lineages could be due to LGTs. Other observations supporting this inference will be described later.
Conserved Indels in the NifH, BchX, and BchL
Proteins Provide Evidence that BchX Homologs
Originated Prior to the BchL Homologs
The BchL and BchX proteins are distantly related to the
dinitrogenase reductase (NifH) protein of the nitrogenase
complex (Burke et al. 1993; Xiong et al. 2000; Raymond
et al. 2004). The nitrogenases are present in a number of
bacterial phyla as well as in methanogenic archaea and they
perform similar function as the DPOR and chlorin reductase
complexes by coupling ATP hydrolysis-driven electron transfer to enable substrate (nitrogen) reduction (Haselkorn 1986;
Burke et al. 1993; Xiong et al. 2000; Raymond et al. 2004). The
observed sequence, structural and functional similarities between these proteins complexes indicate that they have
evolved from an ancestral protein complex (Burke et al.
1993; Xiong et al. 2000; Raymond et al. 2004; Sarma et al.
2008; Muraki et al. 2010). Hence, a multiple sequence alignment of the BchL, BchX, and NifH proteins was also created to
determine if it contains any informative CSIs. The sequence
alignments of these three proteins have led to identification
of two CSIs that are of much interest. A partial sequence
alignment of representative NifH, BchX, and BchL homologs
from different phototrophic lineages showing these two CSIs
(‚ and „) is presented in fig. 2. As seen from this sequence
alignment, all of the NifH and BchX homologs commonly
contained two CSIs (boxed) that are not found in any of
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FIG. 1. (A) Excerpts from the sequence alignment of BchL protein showing two conserved signature indels (CSIs, boxed) that are specific for particular
lineages of phototrophic bacteria. The CSI ¶ is specific for the Heliobacteriaceae, whereas CSI • is commonly shared by different Chlorobi and
Chloroflexi (FAP) homologs. Although sequence information is shown for only representative species, all available sequences from these groups behaved
as shown here with regard to the presence or absence of these CSIs. The dashes (-) in these as well as other sequence alignments indicate identity with
the amino acid on the top line. The numbers on the top indicate the position of the sequence in the species on the top line. (B) A sequence alignment
of the BchX homologs from different phototrophic lineages for the same region as shown in (A) for the BchL protein sequences.
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FIG. 2. Partial sequence alignments of the NifH, BchX, and BchL homologs showing two CSIs in different region of these proteins that are commonly
shared by the NifH and BchX homologs. The roman numerals in the names of the NifH sequences refer to different clusters of the NifH family of
proteins (Raymond et al. 2004). The numbers below the group or phyla names indicate the presence or absence of these CSIs in all available NifH, BchX,
and BchL homologs. The dashes (-) indicate identity with the amino acid on the top line. The abbreviations in the species names are as follows: Az. vin.,
Azotobacter vinelandii; Cb. pha., Chlorobium phaeobacteroides; Cb. tep., Chlorobium tepidum; Cf. aur., Chloroflexus aurantiacus; Cf. agg., Chloroflexus
aggregans; Ch.tha., Chloroherpeton thalassium; Cl. ace., Clostridium acetobutylicum; De. haf., Desulfitobacterium hafniense; Ha. hal., Halorhodospira
halophila; He. mob., Heliobacterium mobilis; He. mod., Heliobacterium modesticaldum; He. chl., He. chlorum; Me. bar., Methanosarcina barkeri; Me.
ace, Methanosarcina acetivorans; Me. ext., Methylobacterium extorquens; No. pun., Nostoc punctiforme; Pmar9303, Prochlorococcus marinus MIT9303; Pr.
vib., Prosthecochloris vibrioformis; Ro. cas., Roseiflexus castenholzii; Ro. RS-1, Ro. sp. RS-1; Rh. pal., Rhodopseudomonas palustris; Rh. rub., Rhodospirillum
rubrum; Rh. sph., Rhodobacter sphaeroides; Ru. gel., Rubrivivax gelatinosus; Si. mel., Sinorhizobium meliloti; Syn6803, Synechocystis sp. PCC6803; SynRC307,
Synechococcus sp. RC307; Tr. ery., Trichodesmium erythraeum.
the BchL homologs. Because the split between the nitrogenases (viz. NifH) and the Bchl biosynthesis proteins (viz. BchX
and BchL) occurred before the gene duplication event that
led to the formation of the DPOR (viz. BchL) and chlorin
reductase (viz. BchX) complexes, the unique shared presence of these two CSIs by all NifH and BchX homologs, but
not by any BchL homologs, provides strong evidence that the
BchX homologs are ancestral in comparison to the BchL
homologs.
Phylogenetic trees were also constructed based upon NifH,
BchX, and BchL sequences from representative prokaryotic
taxa, omitting the indels in these sequence alignments. These
trees were made using both maximum-likelihood (ML) and
neighbor-joining (NJ) methods and their results are presented
in figure 3 and supplementary figure 1, Supplementary
Material online. In both these trees, the NifH, BchX, and
BchL homologs formed distinct clades that were strongly
supported by the bootstrap and puzzling scores. The distinct
clustering of homologs from these three families provides
evidence that these proteins carry out distinct functions
and no LGTs have occurred between them. In these trees,
the clade consisting of the BchX protein was more closely
related to the NifH proteins than that seen for the BchL family
of proteins. This result provides further evidence that the
BchX homologs are primitive in comparison to the BchL proteins. Similar results based upon phylogenetic analyses of
these proteins have been obtained in earlier studies (Burke
et al. 1993; Xiong and Bauer 2002). Within the BchL clade, the
branching of different phototrophs showed a number of interesting relationships. The most surprising of these was that
the BchL homologs from Cyanobacteria did not form a
monophyletic grouping, but they were split into two distinct
clades. One of these clades (referred to as Clade C) (Gupta
2009; Gupta and Mathews 2010) consisting of various marine
unicellular cyanobacteria grouped 100% of the time with the
homologs from different proteobacteria and it was separated
from all other cyanobacteria by a long branch. The remainder
of the cyanobacteria branched with or in close proximity of
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FIG. 3. Phylogenetic tree based on NifH, BchX, and BchL sequences. The tree shown is a ML distance tree and numbers on the nodes indicate
percentage of puzzling score and bootstrap scores for the nodes in the ML and NJ trees. Only values >50% are shown. A NJ tree based upon these
sequences is shown in supplementary figure 1, Supplementary Material online.
Heliobacteriaceae, but neither ML nor NJ method supported a
specific relationship between these two groups. In the ML
tree (shown in fig. 3), the homolog from Heliobacteriaceae
branched in the midst of other cyanobacteria with a long
branch, whereas in the NJ tree it formed an outgroup of
the clade consisting of the remainder of the cyanobacteria
(supplementary fig. 1, Supplementary Material online). Both
these trees additionally showed that the BchL homologs from
Chlorobi and Chloroflexi were closely related and formed
strongly supported clusters. A close relationship between
these two groups was also reported in earlier studies
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(Raymond et al. 2002; Xiong and Bauer 2002) and its significance will be discussed later.
Identification of Conserved Indels in the BchN and
BchB Proteins Showing a Specific Relationship of
the Proteobacterial Homologs to the Clade C
Cyanobacteria and the Chlorobi Homologs to
the Chloroflexi
In phylogenetic trees based upon different data sets of protein
sequences, the sequenced cyanobacterial species/strains form
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a number of distinct clades (Swingley et al. 2008; Shi and
Falkowski 2008; Gupta 2009; Blank and Sanchez-Baracaldo
2010; Gupta and Mathews 2010). One of the major clades
observed in these trees, referred to as Clade C in our work
(Gupta 2009; Gupta and Mathews 2010), is mainly comprised
of the marine unicellular Prochlorococcus and Synechococcus
species and strains. These bacteria are the dominant photosynthetic organisms in oceans and they also contain the
smallest genomes of any photosynthetic organisms
(Dufresne et al. 2003; Zhaxybayeva et al. 2009). The species/
strains belonging to this clade are also clearly distinguished
from all other cyanobacteria by large numbers of CSIs in
widely distributed proteins (Gupta 2009) as well as by numerous signature proteins that are uniquely found in all of the
species/strains from this clade of cyanobacteria (Gupta and
Mathews 2010). In the present work, in the sequence alignments of BchN homologs, I have identified three CSIs (viz. ›,
fi, and ) that distinguish the Clade C cyanobacteria from
other cyanobacteria. Excerpts from the sequence alignment
of BchN homologs where these CSIs are found are shown in
figure 4. These signature indels include 4, 2, and 1 amino acid
inserts in the BchN protein that are commonly shared by all
Clade C cyanobacteria (fig. 4), but which are lacking in all
other cyanobacteria. At the same time, this protein also contains an 8 amino acid conserved insert (CSI –) that is commonly shared by all other cyanobacteria, except the Clade C
cyanobacteria (fig. 5A). The mutually exclusive presence of
these CSIs in either the Clade C cyanobacteria or all other
cyanobacteria provides further evidence that these two
groups/clades of cyanobacteria are distinct. Importantly, all
three of the CSIs that are specific for the Clade C cyanobacteria (CSIs ›, fi, and ) are also present in all of the BchN
homologs from different classes of Proteobacteria. The shared
presence of these CSIs by all Clade C cyanobacteria and the
proteobacterial homologs strongly suggests that the BchN
gene has been laterally transferred between these two
groups. Further, similar to the phylogenetic tree for BchL homologs (fig. 3), in a phylogenetic tree based upon BchN sequences (fig. 6), the clade C cyanobacteria exhibited a strong
and specific association with the proteobacterial homologs.
Additionally, a specific grouping of the Clade C cyanobacteria
with the proteobacteria is also observed in the phylogenetic
tree based upon BchB sequences (supplementary fig. 2,
Supplementary Material online).
As shown above, the CSI • in BchL homologs is uniquely
present in all sequenced Chlorobi and Chloroflexi species
(fig. 1). In the sequence alignments of BchN and BchB proteins, four other CSIs were also identified that are specifically
present in species from these two phyla. Sequence information for these CSIs is presented in figures 4 and 5. The BchN
protein contains three CSIs (marked ‹, fl, and ‡), all three
consisting of 1 amino acid deletions, that are specific for
Chlorobi and Chloroflexi (figs. 4A, 4C, and 5A). Similarly, the
BchB protein also contains a 1 amino acid conserved deletion
that is restricted to these two phototrophic lineages (CSI ” in
fig. 5B). It is important to note that all four of these CSIs are
uniquely present in all available Chlorobi and Chloroflexi (FAP)
homologs, but they are not found in the homologs from any
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other phototrophic lineages. Based upon our analysis of the
CSI • in the BchL protein sequences (see previous section),
where it was shown to be an insert in these lineages, it is likely
that the genetic changes leading to these CSIs occurred in the
BchN and BchB genes within these lineages. The unique
shared presence of these CSIs by these two phylogenetically
distinct lineages in all three subunits of the DPOR complex
suggests that the genetic changes responsible for them initially occurred in these genes in one of these two lineages (or
in an extinct lineage), followed by lateral transfer of these
genes to the other group(s).
In addition to the phylogenetic studies and the shared CSIs
in the BchL, BchB, and BchN proteins, I have also examined
pair-wise sequence identity/similarity for these protein sequences. The results of these analyses, which are presented
in table 1, show that the Chlorobi homologs for all three
proteins were most similar to those from Chloroflexi and
the pair-wise identity/similarity values for them were at
least 15% higher than those seen for any other phototrophic
lineage. Both these lineages also contain the unique
Bchl-containing light-harvesting complexes “chlorosomes,”
which are not found in other lineages (Olson and Pierson
1987; Olson and Blankenship 2004; Bryant and Frigaard
2006; Hohmann-Marriott and Blankenship 2007). Another
observation that stands out from table 1 is that for all three
of these proteins the Clade C cyanobacterial homologs exhibited maximal sequence similarity (58–68% identity) to the
proteobacterial homologs in comparison to those from other
cyanobacteria or any other phototrophic lineage (32–36%
identity). All of these observations strongly indicate that the
genes for these proteins have been laterally transferred between Chloroflexi and Chlorobi on one hand and the Clade C
cyanobacteria and proteobacteria on the other hand.
Discussion
The results presented in this manuscript provide important
insights into a number of different aspects of evolution of
photosynthesis and its spread to other bacterial phyla. One
important question is of the two forms of photosynthesis, i.e.,
oxygenic photosynthesis carried out cyanobacteria and the
anoxygenic photosynthesis carried out by other bacterial
phyla, which form originated first (Blankenship 1992; Burke
et al. 1993; Olson and Blankenship 2004; Mulkidjanian et al.
2006; Blankenship 2010; Hohmann-Marriott and Blankenship
2011). According to the Granick hypothesis (Granick 1965), in
a given biochemical pathway the enzymes/proteins that carry
out an earlier biochemical step have likely evolved earlier than
those carrying out later steps. In photosynthesis, a key biochemical process/pathway is the synthesis of bacteriochlorophyll and chlorophyll (Beale 1999; Chew and Bryant 2007). In
the pathway leading to the biosynthesis of Bchl/Chl, the
enzyme complex protochlorophyllide oxidoreductase
(BchL-N-B), responsible for the production of chlorin (a precursor to Chl), precedes the complex chlorin reductase
(BchX–Y–Z) that reduces chlorin to bacteriochlorin, which
is a direct precursor for Bchl (Burke et al. 1993; Beale 1999;
Chew and Bryant 2007). Thus, based upon this hypothesis, the
oxygenic photosynthesis based on Chl should have evolved
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FIG. 4. Excerpts from the sequence alignment for BchN homologs showing a number of CSIs that are specific for different groups of phototrophs.
The dashes in the alignments show identity with the amino acid on the top line. All of these CSIs are highly specific for the indicated groups and the
numbers below the group names indicate their presence or absence in the available sequences from these groups.
3404
Evolutionary Origin and Spread of Photosynthesis . doi:10.1093/molbev/mss145
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FIG. 5. Partial sequence alignments of (A) the BchN protein and (B) BchB protein showing some CSIs that are specific for different groups of
phototrophs. Other details are same as in figures 1 and 4.
prior to the anoxygenic photosynthesis requiring Bchl and
some models for the evolution of photosynthesis based
upon this have been proposed (Mauzerall 1978; Olson and
Pierson 1987; Olson and Blankenship 2004). However, earlier
phylogenetic studies based on NifH, BchX, and BchL proteins
indicated that the BchX homologs originated prior to the
BchL homologs, suggesting that anoxygenic photosynthesis
requiring BchX homologs preceded the oxygenic photosynthesis that requires BchL (Burke et al. 1993; Xiong et al. 2000;
Raymond et al. 2003). The phylogenetic studies based upon
these protein sequences reported here also strongly support
the results of earlier studies. However, because construction
of phylogenetic trees and inferences derived from them are
influenced by large numbers of variables and assumptions
(Felsenstein 1988; Moreira and Philippe 2000), it is important
to confirm this inference by other means.
In this context, the two CSIs (‚ and „) in the sequence
alignments of NifH, BchX, and BchL sequences that have been
identified in the present work, which are uniquely shared by
all NifH and BchX homologs but not found in any BchL
homologs, are highly significant. Because of the earlier divergence of the NifH protein from the BchX and BchL proteins,
the NifH sequences can be used to determine whether any
conserved characteristic that is present in the BchX or BchL
protein is ancestral or derived. Based upon this simple premise, the unique shared presence of the CSIs ‚ and „ by all
NifH and BchX homologs, but not by any of the BchL homologs, strongly indicates that the BchX homologs containing
these CSIs are ancestral and that the genetic changes leading
to deletion of sequences corresponding to these CSIs occurred in the ancestral BchL gene after its divergence from
BchX by gene duplication. It should be emphasized that the
interpretation of these shared CSIs is straightforward and it
only assumes that these shared genetic characteristics (synapomorphies) have a common evolutionary origin, which is
the most parsimonious explanation to account for them. Due
to the presence of these CSIs in conserved regions and their
presence in all NifH and BchX homologs, but none of the
BchL homologs, it is difficult to explain these results by any
other means except by inferring that the NifH and the BchX
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Table 1. Pair-wise Sequence Identity/Similarity Values for the BChL, BChN, and BChlB Homologs.
ChlB
Pm9303
Syn9902
Amax
Sc6803
Gvio
Rpal
Rrub
Caur
Rcas
Paes
Ctep
Hmod
BChN
Pm9303
Syn9902
Amax
Sc6803
Gvio
Rpal
Rrub
Caur
Rcas
Paes
Ctep
Hmod
BchB
Pm9303
Syn9902
Amax
Sc6803
Gvio
Rpal
Rrub
Caur
Rcas
Paes
Ctep
Hmod
Pm9303
Sy9902
Amax
Sc6803
Gvio
Rpal
Rrub
Caur
Rcas
Paes
Ctep
Hmod
–
86.7
49.5
51.4
51.0
72.8
73.0
50.5
49.2
50.9
50.8
50.0
77.2
–
50.7
51.2
48.7
72.5
72.6
51.3
49.2
50.8
51.1
51.8
33.6
32.7
–
92.5
86.6
50.0
47.8
58.7
54.7
56.7
56.3
56.6
33.8
33.5
83.5
–
84.8
49.6
47.3
58.0
54.5
57.2
55.4
57.0
33.9
33.0
74.6
73.4
–
50.7
48.9
57.1
55.8
56.0
56.4
56.7
61.8
60.9
32.7
32.0
33.3
–
81.8
51.0
50.8
50.9
51.3
50.7
60.1
59.9
31.6
30.6
32.9
71.2
–
50.6
51.2
51.2
52.1
49.6
34.8
34.2
39.7
39.5
39.8
37.3
36.5
–
76.3
72.6
72.6
55.8
34.1
32.9
36.4
36.2
36.7
34.9
34.7
66.5
–
71.1
71.8
54.8
33.6
33.4
36.8
37.0
35.9
34.6
35.3
57.1
56.0
–
84.0
58.3
32.7
33.3
35.6
36.0
36.2
35.8
36.4
58.7
56.7
73.0
–
59.3
32.1
35.1
40.6
40.2
40.9
33.3
33.0
39.7
37.2
39.7
40.5
–
–
84.8
51.5
50.6
52.7
74.9
69.3
52.9
56.7
52.5
52.7
54.1
76.5
–
51.0
52.3
50.4
74.0
71.7
53.9
56.7
51.9
54.9
55.6
33.5
32.8
–
91.3
83.2
47.9
47.4
54.3
53.2
53.9
53.9
56.7
32.2
33.5
85.2
–
82.3
50.0
49.3
54.4
56.8
52.8
53.4
55.9
33.7
33.5
73.1
70.7
–
47.7
46.7
52.8
53.3
52.8
52.7
56.0
61.8
61.2
32.9
33.7
32.0
–
79.3
49.8
53.5
51.7
51.2
51.3
57.8
60.5
33.1
33.2
32.3
68.2
–
48.5
50.3
49.2
51.1
50.4
33.7
35.6
35.5
36.2
33.3
33.0
34.7
–
81.5
73.7
75.8
55.1
37.5
38.0
35.7
38.3
35.0
36.1
35.7
71.1
–
77.7
78.4
56.6
34.0
34.1
35.2
36.2
35.4
33.3
33.9
60.8
64.8
–
90.5
55.7
34.7
35.5
33.6
34.3
33.3
33.8
35.6
61.3
64.4
81.4
–
56.4
34.9
36.8
41.0
39.2
39.5
34.8
36.5
39.4
40.1
38.4
40.1
–
–
92.6
61.6
65.5
62.3
78.3
82.5
63.2
62.3
62.4
63.4
59.5
88.8
–
60.4
63.6
62.1
78.7
82.6
61.8
60.8
64.1
62.9
58.9
43.1
44.2
–
64.4
89.6
58.8
59.5
66.1
67.5
65.9
67.9
69.1
46.5
47.0
47.9
–
81.4
61.3
62.1
62.7
63.9
62.8
64.4
63.0
46.4
46.0
81.2
73.6
–
59.9
61.0
70.2
69.1
68.5
68.6
70.0
66.2
68.2
44.2
44.6
45.3
–
83.7
60.1
58.8
59.9
60.8
57.4
71.4
71.9
45.8
48.3
47.1
72.4
–
61.8
60.8
61.9
62.7
58.9
46.4
46.6
50.2
47.5
52.1
46.2
47.5
–
91.6
89.5
87.3
67.0
47.7
47.1
49.8
46.8
50.0
46.5
49.5
85.7
–
88.0
87.3
67.7
44.6
44.8
49.0
46.7
51.0
43.6
45.7
75.6
73.8
–
94.2
68.5
45.2
46.3
51.0
47.9
50.2
44.8
46.5
71.7
73.2
85.9
–
67.8
41.8
41.4
51.3
46.0
50.9
39.3
41.8
48.3
48.6
48.1
45.1
–
NOTE—The abbreviations for the species are: Pm 9303, Pro. marinus MIT9303; Syn9902, Synechochoccus sp. PCC9902: Amax, Arthrospira maxima, Sc8803, Synechocystis sp.
PCC6803; Gvio., Gloebacter violaceus; Rpal, Rhodopseud. palustris; Rrub, Rhodospirillum rubrum; Caur., Chloroflexus aurantiacus; Rcas, Roseiflexus castenholzii; Paes, Prostheco.
aestuarii; Ctep. Chlorobium tepidum; Hmod., Heliobacterium modesticaldum.
homologs shared a common ancestor exclusive of the BchL
homologs. The earlier origin of the BchX homologs in comparison to the BchL homologs as strongly suggested by these
CSIs provides strong and independent evidence that the
anoxygenic photosynthesis supported by BchX homologs
originated before the oxygenic photosynthesis requiring
BchL homologs. The lack of support of Granick hypothesis
by these results can be explained (Burke et al. 1993) if the
ancestral BchX–Y–Z enzyme complex carried out the functions of both the DPOR (BchL-N-B) and chlorin reductase
(BchX–Y–Z) complexes, and these complexes became more
specialized after the gene duplication event. However, other
3406
explanations to account for this anomaly are also possible
(Xiong et al. 2000; Olson and Blankenship 2004).
Another important unresolved question concerning the
evolution of photosynthesis is to determine in which bacterial
group or phyla this process first evolved. The results presented here again provide important insights in this regard.
One of the CSIs in the BchL protein identified here (CSI ¶ in
fig. 1) is specifically present in the BchL homologs from
Heliobacteriaceae, but it is absent in all other BchL homologs.
Importantly, based upon the presence of this CSI in different
BchX homologs it is possible to infer that the presence of this
CSI represents the ancestral character state of the BchL–BchX
Evolutionary Origin and Spread of Photosynthesis . doi:10.1093/molbev/mss145
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FIG. 6. Phylogenetic tree based on BchN sequences showing the relationships among different photosynthetic taxa. The tree shown is a ML distance
tree, which was arbitrarily rooted using H. modesticaldum sequence. The numbers on the nodes indicate percentage of puzzling quartets or bootstrap
scores (>50%) supporting these nodes.
protein and that the BchL homologs from Heliobacteriaceae
are ancestral in comparison to those from other lineages. In
view of the absence of this indel in all other BchL homologs
and the distinct branching of the BchX and BchL homologs,
the possibility of chance occurrence of this indel in the
Heliobacteriaceae BchL homologs, or their acquisition of a
gene containing this CSI by means of LGT from other sources
is considered unlikely, but they cannot be entirely excluded.
Because the Firmicutes phylum, of which Heliobacteriaceae
are part of, represents the earliest branching phylum within
the Bacteria (Gupta 2001, 2003, 2011; Ciccarelli et al. 2006), it
suggests that photosynthesis evolved very early in the evolutionary history of life.
It should be noted that earlier phylogenetic studies based
on BchL, BchN, and BchB proteins have led to the inference
that Proteobacteria were the earliest photosynthetic lineage
that evolved (Xiong et al. 2000; Xiong and Bauer 2002).
However, the data set employed in these studies lacked any
Clade C cyanobacteria to which the proteobacterial homologs
are most closely related. Because of the highly divergent
nature of the proteobacterial homologs and the lack of any
close relatives to them (viz. Clade C cyanobacteria) in the
datasets that were employed, the deep branching of proteobacterial homologs in earlier studies was very likely a result of
long branch length effect (Green and Gantt 2000).
Although photosynthesis-related genes are known to have
undergone extensive LGTs, it has proven difficult to determine the directions of LGTs or how photosynthetic ability
was acquired by various phyla (Raymond et al. 2002; Xiong
and Bauer 2002; Raymond et al. 2003; Raymond 2009;
Hohmann-Marriott and Blankenship 2011). In the present
work, we have identified several CSIs in the BchL, BchB, and
BchN protein sequences that are commonly shared by either
Chlorobi and Chloroflexi, or by Clade C Cyanobacteria and
Proteobacteria, providing further evidence that these genes
have incurred LGTs. Importantly, based upon a number of
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FIG. 7. Partial sequence alignments of the BchB protein showing two CSIs that are present in the same position, which are specific for either species
from the genus Roxiflexus or for all of the Chlorobi. A 2 amino acid insert in this position is also present in O. trichoides. Other details are the same as in
figures 1 and 4.
observations made in this work and our earlier work, it is
possible to infer for the above genes the directions of LGTs.
In the protein BchB, which contains CSI ” that is commonly
shared by various Chlorobi and Chloroflexi, two other CSIs
have also been identified (fig. 7). One of these CSIs consisting
of a 9 amino acid insert (») is uniquely found in the two
Roseiflexus species, whereas the other CSI consisting of 1
amino acid insert (…) is specific for various Chlorobi homologs (fig. 7). The genetic changes responsible for these CSIs
likely occurred in the common ancestors of these particular
taxa. Based upon these CSIs, for the BchB gene, if the gene
transfer had taken place from Chlorobi to Chloroflexi than it
was expected that the CSI … that is specific for various
Chlorobi should also be found in the Chloroflexi homologs.
However, the absence of the CSI … in the Chloroflexi homologs indicates that the gene transfer has not occurred in this
direction, but it has likely occurred from Chloroflexi (FAP) to
Chlorobi followed by the introduction of the genetic change
leading to the CSI … in the common ancestor of Chlorobi.
Furthermore, the absence of the large Roseiflexus-specific
CSI » in the Chlorobi homologs indicates that this genus
3408
was not the source of LGT and suggests that the ancestral
Chloroflexi from which this gene transfer occurred was either
a Chloroflexus or some related filamentous anoxygenic phototroph (FAP) that lacked this indel. The presence of a 2 amino
acid insert in this position in Oscillochloris also makes it less
likely as the source of LGT. Based upon these observations
and the fact that BchL-N-B proteins are part of the same
enzyme complex (DPOR), it is likely that the genes for the
BchN and BchL proteins that also contain CSIs that are commonly shared by Chloroflexi and Chlorobi were also laterally
transferred from Chloroflexus or a related FAP to the Chlorobi.
Our results also provide compelling evidence that the homologs of the BchL-N-B proteins from Proteobacteria are
closely related to those from Clade C cyanobacteria. This inference is based upon several CSIs that are uniquely shared by
these two groups (viz. ›, fi, and ), by phylogenetic analyses
based on these protein sequences, and the pair-wise sequence
identity/similarity scores for these proteins. Of the different
phyla of photosynthetic bacteria, Cyanobacteria are made up
entirely of photosynthetic organisms (Castenholz and Phylum
2001; Mulkidjanian et al. 2006; Gupta 2010; Blank and
Evolutionary Origin and Spread of Photosynthesis . doi:10.1093/molbev/mss145
Sanchez-Baracaldo 2010) and their monophyletic nature is
supported by different lines of evidence (Castenholz and
Phylum 2001; Wilmotte and Herdman 2001; Ciccarelli et al.
2006) including large numbers of CSIs and signature proteins
that are uniquely present in all Cyanobacteria (Gupta 2009;
Gupta and Mathews 2010). Further, our recent work on
Cyanobacteria provides evidence that the Clade C is a derived
clade and several other cyanobacterial species/strains, particularly those belonging to Clade A, constitute the deepest
branching lineage within this phylum (Gupta 2009; Gupta
and Mathews 2010). In contrast to Cyanobacteria, photosynthetic ability within Proteobacteria is sporadically distributed
in a limited number of species belonging to the Alpha-, Beta-,
and Gamma-classes of proteobacteria (Yurkov and Beatty
1998; Imhoff 2001; Gupta and Mok 2007; Gupta 2010). In
view of these observations, it is more likely that the various
CSIs (viz. ›, fi, and ) and other genetic changes in the
BchL-N-B proteins that distinguish the Clade C cyanobacteria
from other cyanobacteria initially occurred in a common ancestor of the Clade C cyanobacteria and then these genes
were laterally acquired by Proteobacteria. The alternate possibility that these genetic changes first occurred in a proteobacterial ancestor and their subsequent transfer to the Clade
C cyanobacteria would require numerous gene losses, gene
transfers as well as gene replacement events and it is considered highly unlikely. The transfer of these genes from Clade C
cyanobacteria to proteobacteria, both of which are major
components of the marine microbial community, could
have occurred in oceanic environments (Partensky et al.
1999; Kolber et al. 2001; Dufresne et al. 2003; Oda et al.
2008) and their further dissemination within the proteobacteria may have been facilitated by the gene transfer agent that
are present in many alpha proteobacteria (Lang and Beatty
2007). Presently, no unique aspects of photosynthesis are
known that are commonly shared by Proteobacteria and
the Clade C Cyanobacteria. In view of the close similarities
seen for the components of the DPOR complex between
these two groups, studies aimed at identifying common
and unique aspects of photosynthesis between them
should be of much interest. It should also be mentioned
that in contrast to the Cyanobacteria, which contain both
reaction centers I and II, the Proteobacteria possess only the
RC II and carry out anoxygenic photosynthesis. Therefore, if
the genes for other photosynthesis related proteins were also
transferred from Clade C cyanobacteria to proteobacteria,
then this gene transfer was likely accompanied/followed by
loss of genes for many photosynthesis-related proteins.
The results of pair-wise sequence similarities on the
BchL-N-B proteins (table 1) indicate that for all three of
these proteins, the homologs from Heliobacteriaceae exhibited higher similarity to those from cyanobacteria
(except Clade C) and Chloroflexi/Chlorobi. Our earlier work
based on many other CSIs in universally distributed proteins
indicates that the phylum Chloroflexi branched after the
Firmicutes but prior to Cyanobacteria (Gupta 2001, 2003;
Ciccarelli et al. 2006). These observations suggest that either
Chloroflexi or Cyanobacteria were the earliest recipients of
these genes from Heliobacteriaceae. It should be noted that
MBE
FIG. 8. Structure of the A chain of the BchL protein from Rhodobacter
sphaeroides showing the location of the two identified CSIs (¶ and •)
in this protein. The structure of the BchL protein from R. sphaeroides
was obtained from the Protein Data Bank (Sarma et al. 2008; Muraki
et al. 2010) and the image was constructed using the PyMol program.
The protein contains a bound MgADP and a [4Fe-4S] cluster that are
shown in dull yellow and red colors, respectively. The positions of the
two CSIs that are specific for Heliobacteriaceae and Chlorobi-Chloroflexi,
respectively, in this structure are marked with arrows and they were
inferred based upon sequence alignment (fig. 1).
the Heliobacteriaceae species, which our results indicate contain a primitive form of the BchL protein (i.e., DPOR complex),
they also possess a primitive photosynthetic reaction center
(RC), where both antenna and RC complexes are part of a
single protein (Trost and Blankenship 1989; Blankenship 1992;
Vermaas 1994; Vassiliev et al. 2001; Heinnickel and Golbeck
2007; Sattley et al. 2008). Further, unlike other photosynthetic
prokaryotes, no photo-autotrophic growth thus far has been
observed for any Heliobacteriaceae species (Gest and Favinger
1983; Bryant and Frigaard 2006; Madigan 2006; Sattley and
Blankenship 2010). It should also be noted that photosynthetic ability or genes within the phylum Firmicutes have only
been found within the Heliobacteriaceae family (Gest and
Favinger 1983; Sattley and Blankenship 2010). It is possible
that due to the primitive nature of the photosynthetic apparatus within the Firmicutes and its inability to support photoautotrophic growth, in an environment that is now
predominantly oxygenic, photosynthesis related genes have
been lost from other extant Firmicutes. These observations
raise the possibility that although the genes for some of the
key photosynthesis proteins (viz. DPOR complex) and a primitive photosynthetic RC first evolved in the Heliobacteriaceae,
functional photosynthetic ability was not developed until the
later diverging phototrophic lineages such as Chloroflexi and/
or Cyanobacteria. This possibility can also account for the
geological and fossil evidence that the earliest phototrophic
microbial communities existing as early as 3.4 Ga ago, and
which used Calvin cycle for CO2 fixation, were comprised of
filamentous anoxygenic bacteria (Dismukes et al. 2001; Tice
and Lowe 2004, 2006). In contrast, oxygenic photosynthesis
3409
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Gupta . doi:10.1093/molbev/mss145
attributable to Cyanobacteria is indicated to have evolved
2.2–2.6 Ga ago (Kazmierczak and Altermann 2002; Olson
and Blankenship 2004; Olson 2006; Blank and
Sanchez-Baracaldo 2010). Because Chloroflexi have filamentous morphology and they are capable of carrying out anoxygenic photosynthesis by a variety of mechanisms including
the Calvin cycle (Hanada and Pierson 2006), they could account for the earliest phototrophic microbial communities
(Tice and Lowe 2006; Olson 2006).
It should be acknowledged that the inferences drawn in
this study concerning the origin of photosynthesis and its
spread to other bacteria phyla are made almost solely on
the basis of the proteins (viz. BchL, BchN, BchB, BchX, Nifh)
that were studied in this work. Although these proteins (all
except NifH) are unique and central components of the photosynthesis pathway, the process of photosynthesis overall is
very complex and it involves varied sets of genes in different
lineages that have been acquired by different means including
gene gains and losses and LGTs (Raymond et al. 2002; Xiong
and Bauer 2002; Olson and Blankenship 2004; Mulkidjanian
et al. 2006; Raymond 2009; Hohmann-Marriott and
Blankenship 2011). Therefore, it is likely and may in fact be
expected that not all components of this complex process
will exhibit similar evolutionary histories. Nonetheless, unlike
other photosynthesis components, the genes/proteins that
were studied in this work are unique characteristics of all
photosynthetic organisms and they play pivotal roles in the
photosynthesis process. Hence, the evolutionary histories of
these genes/proteins are of central importance in understanding the origin and spread of photosynthesis.
Lastly, this work has identified large numbers of CSIs in key
photosynthesis proteins that are specific for different groups
of photosynthetic prokaryotes. Hence, it is of much interest to
understand the functional significance of these evolutionary
conserved genetic changes. Recent work on several CSIs in
other important proteins has shown that such CSIs, which are
generally located in the surface loops of proteins (Akiva et al.
2008; Gupta 2010), are essential for the groups of species
where they are found (Singh and Gupta 2009). Two of the
important CSIs (¶ and •) in the BchL protein that were
identified in the present work (fig. 1), are also located in
the surface loops in the structure of this protein (fig. 8)
(Sarma et al. 2008; Muraki et al. 2010). The surface loops in
protein sequences play important roles in mediating protein–
protein interactions (Akiva et al. 2008; Singh and Gupta 2009;
Hormozdiari et al. 2009). Hence, it is likely that the identified
CSIs in the BchL, BchN, and BchB proteins are also involved in
mediating protein–protein interaction that are specific and
essential for different groups of phototrophs. Therefore, further studies on understanding the functional significance of
these CSIs could reveal novel aspects of these important proteins that are specific for different lineages of photosynthetic
bacteria.
Supplementary Material
Supplementary figures 1 and 2 are available at
Molecular Biology and Evolution online (http://www.mbe.
oxfordjournals.org/).
3410
Acknowledgments
This work was supported by a research grant from the Natural
Science and Engineering Research Council of Canada. I acknowledge the assistance of Sanjan George in Blast searches
and in the creation of signature files.
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