Unique Origin and Lateral Transfer of Prokaryotic Chlorophyll-b and Chlorophyll-d Light-Harvesting Systems

Min Chen*, Roger G. Hiller{dagger}, Christopher J. Howe{ddagger} and Anthony W. D. Larkum*

* School of Biological Sciences, University of Sydney, Australia and Sydney University Biological Informatics and Technology Centre (SUBIT), University of Sydney, NSW, Australia; {dagger} Department of Biology, Macquarie University, NSW, Australia; and {ddagger} Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

Correspondence: E-mail: alark{at}mail.usyd.edu.au.


    Abstract
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
pcb genes, encoding proteins binding light-harvesting chlorophylls, were cloned and sequenced from the Chl d–containing cyanobacterium, Acaryochloris marina, and the Chl b–containing cyanobacterium, Prochloron didemni. Both organisms contained two tandem pcb genes. Peptide fingerprinting confirmed the expression of one of the A. marina pcb genes. Phylogenetic tree reconstruction using distance-matrix and maximum-likelihood methods indicated a single origin of the pcb gene family, whether occurring in Chl b–containing or Chl d–containing organisms. This may indicate widespread lateral transfer of the Pcb protein–based light-harvesting system.

Key Words: prochlorophyte chlorophyll a/b protein • Acaryochloris marina • Prochloron didemni • lateral genes transfer • chlorophyll-d • light-harvesting protein complexes


    Introduction
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
Although the majority of species of oxygenic photosynthetic bacteria utilize phycobilisomes as light-harvesting pigments, a number of important species use different systems. These include the prochlorophytes, Prochlorococcus, Prochlorothrix, and Prochloron, which are characterized by having Chl b as a light-harvesting pigment, as do green algal protists and eukaryotic plants. All three prochlorophyte genera have been shown to have light-harvesting Chl a/b–binding (Pcb [prochlorophyte chlorophyll–binding]) proteins that are homologous to the iron stress-induced proteins (IsiA) of cyanobacteria, rather than to the light-harvesting Chl a/b–binding (Lhc) proteins of plants (La Roche et al. 1996). More recently, an oxygenic photosynthetic prokaryote, Acaryochloris marina was discovered that uses Chl d as a light-harvesting pigment rather than phycobilisomes or Chl b (Miyashita et al. 1996). Like the prochlorophytes, A. marina possesses Pcb protein as its major light-harvesting complex, but it binds predominantly Chl d, rather than Chl a/b as in the prochlorophytes (Chen, Quinnell, and Larkum 2002a). Although A. marina also contains functional phycobiliproteins, they do not form phycobilisomes (Hu et al. 1998; Marquardt et al. 1997; Marquardt et al. 2000).

The origin and phylogenetic position of Pcb light-harvesting protein complexes relative to other members of the six-helix Chl–binding protein family (e.g., IsiA, and CP43 and CP47 of photosystem II) is of considerable interest. Prochlorothrix and Prochlorococcus have been shown to have multiple pcb genes (van der Staay, Yurkova, and Green 1998; Garczarek et al. 2000), and the products of individual genes have been shown to be associated specifically with either photosystem I or photosystem II in Prochlorococcus sp. MIT9313 (Bibby et al. 2003a). We have characterized multiple pcb genes from A. marina and Prochloron didemni and demonstrate a single origin of pcb genes for Chl b–containing and Chl d–containing organisms, together with an ancient duplication of the genes. Given the positions of these organisms in 16S rRNA trees, this strongly suggests a widespread lateral transfer of the genes for these light-harvesting systems.

The Acaryochloris marina and Prochloron didemni pcb sequences reported here have GenBank accession numbers AY552463and AY 552464, respectively.


    Materials and Methods
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
A. marina Cell Culture and DNA Isolation
Acaryochloris marina cells were grown in 2 L culture as described previously (Chen, Quinnell, and Larkum 2002a) and harvested by centrifugation. The cells were washed once in 5 mM EDTA (pH 8.0) in seawater, then resuspended in 50 mM Tris-HCl, 10 mM EDTA, 2% w/v SDS, pH 7.5. Proteinase K was added to the cell suspension to a final concentration of 0.15 mg·mL–1, and the mixture was incubated at 55°C for 90 min. The cell suspension was then extracted with buffer-saturated phenol, followed by phenol-chloroform (1:1) and finally with chloroform. DNA was precipitated by addition of 0.1 vol. sodium acetate pH 6.0, 2.5 vol. ethanol and incubation at –20°C for at least 30 min. The resultant DNA pellets were collected and resuspended in 2 ml of water and stored at –20°C. RNase was used to degrade RNA in DNA preparations if needed.

A. marina pcb Probes and Gene Sequences
The general degenerate primers for pcb genes 5'-ATGCARACNTAYGGNAAYCC-3' (primer 3144) and 5'-ATRTGCCADATNCCNCC-3' (primer 3145) (La Roche et al. 1996) were used for amplification by the polymerase chain reaction (PCR) by 35 cycles of 94°C, 1 min; 52°C, 1 min; and 72°C, 3 min for extension. A 516-bp PCR product was obtained from genomic DNA of A. marina, which was shown by BlastX sequence analysis to contain part of a pcb gene. This fragment, designated A12, was labeled with fluorescein using the Renaissance Random Primer Fluorescein labeling kit New England Nuclear, Boston, Mass. according to the manufacturer's instructions and used to screen a Sau3A genomic library of A. marina established in bacteriophage EMBL3 (Promega). Several independent hybridizing clones were isolated. Inserts from three of them were subcloned into plasmid pGEM-3Z (Promega) and sequenced. Two of these clones contained the same insert. A 4,700-bp sequence was obtained from the two different clones, which both contained an identical overlapping region of 600 bp.

The fluorescein-labeled 516-bp fragment (A12) was also used to probe Southern blots of genomic DNA of A. marina digested with a range of restriction enzymes to determine the number of copies of pcb genes. The resultant DNA digests were electrophoresed in 0.7% (w/v) agarose gels in TAE buffer (40 mM Tris-acetate, 1 mM EDTA, pH 8.0) containing 0.3 mg·mL–1 ethidium bromide and then transferred to Immobilon-Ny+ membrane (Millipore, Australia) by capillary action in 20xSSC buffer overnight. DNA was fixed onto the membrane by UV cross-linking. Hybridization used 10 mL of A12 probe and was carried out overnight at 58°C to 60°C. Hybridization, stringency wash procedures, and chemiluminescence detection were performed using the Renaissance Random Primer Fluorescein Labeling Kit following the manufacturer's instructions.

Prochloron didemni DNA Isolation, Library Construction, and Sequence Determination
Prochloron didemni cells were expelled by gently squeezing Lissoclinum patella colonies, which had been slashed with a razor blade. Cells were filtered through Miracloth into 1M Tris-HCl pH 8.0 then washed once in buffer and DNA extracted as described above for A. marina. The DNA was further purified by centrifugation through a CsCl gradient. Fifty milligrams of purified DNA was subjected to a brief exposure to BglII and, after phenol-chloroform and chloroform purification, was ligated into EMBL3 DNA cut with BamHI (Promega). Plaques from the resulting Prochloron didemni library were screened with a 984-bp PCR product generated from the cloned sequence reported previously (La Roche et al. 1996) using primers 3144 and 3321 (5'-GGNYYTNTGGCAYGC-3'). DNA from a library clone hybridizing to the probe was digested with SalI and showed the insert to be approximately 13 kbp. After digestion with SalI/HindIII, fragments were cloned in pUC18. Colonies containing recombinant plasmids were screened as before, and a single colony giving a positive signal was picked and sequenced. Additional sequence data were obtained by sequencing of a PCR product generated using a forward primer based on the sequence already obtained (5'-AAAGGATCCGGTATTGCGGATGGCGGC-3') and a reverse primer (5'-AAAGGATCCGCDCGRGTWGCRTGCCAHACRTGDCC-3' based on the conserved motif GHVWHATRA of Prochlorothrix hollandica pcb sequences.

Identification of A. marina pcb Gene Products Using Mass Spectral Analysis
Chl d–binding protein complexes were isolated by nondenaturing electrophoresis followed by denaturing SDS-PAGE to obtain approximately 34-kDa Pcb-type polypeptides (Chen, Quinnell, and Larkum 2002a, 2002b), which were excised from the stained gel matrix (Wang, Sun, and Chitnis 2000) and analyzed by mass spectral analysis at the Department of Chemistry and Biochemistry, Arizona State University. The Pcb-type protein sequences predicted from DNA sequence data were analyzed for their trypsin cleavage sites using the program Peptide Cutter (http://kr.expasy.org/tools/peptidecutter/), which predicts the mass weight map of cut fragments (Barrett, Rawlings, and Woessner 1998).

Phylogenetic Analysis
Phylogenetic analysis was performed on protein sequences aligned using ClustalW (Thompson, Higgins, and Gibson 1994), followed by manual refinement. MEGA version 2 (Kumar, Tamura, and Nei 1994) was used to construct Neighbor-Joining (distance) and maximum-parsimony trees and bootstrapped 1,000 times. ProML, SeqBoot, and Consense from the PHYLIP program (Felsenstein 1989) were used to infer and assemble bootstrapped maximum-likelihood trees (256 replicates), using the JTT model of amino acid substitution and also incorporating the best-tree estimated by minimum ln-likelihood. The sequences of isiA, pcb and psbC genes used in the analyses were obtained from GenBank and http://www.jgi.doe.gov/JGI_microbial/html/ and are listed in table 1.


View this table:
[in this window]
[in a new window]
 
Table 1 Sequences Used for Phylogenetic Analysis in This Paper

 

    Results
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
A. marina pcb Sequences
Two pcb genes were identified in tandem in genomic DNA of Acaryochloris marina, separated by a noncoding region of approximately 269 bp, depending on the actual site of initiation. They are designated pcbA and pcbC, as discussed below. No open reading frame (ORF) of significant size was found in the 522 bp of sequence determined upstream. Approximately 1,800 bp were sequenced downstream of the pcb cluster. This region contained an ORF of approximately 730 bp in the same orientation as the pcb genes, encoding a putative 2-phosphosulfolactate phosphatase gene (fig. 1A). When Southern blots of A. marina genomic DNA were probed for the pcb genes, single bands were seen with DNA digested singly with the enzymes BamHI, BglII, EcoRV, HindIII, PstI, and SalI, indicating that there are no other closely similar pcb genes in the A. marina genome (data not shown).



View larger version (9K):
[in this window]
[in a new window]
 
FIG. 1.— Schematic diagram to show the arrangement of the genes for the Pcb proteins of Acaryochloris marina (A), Prochloron didemni (B), and Prochlorothrix hollandica (C). The figure incorporates the results of van der Staay, Yurkova, and Green (1998). Bar A12 indicates the sequence used to construct the probe for the Southern blot.

 
Putative Pcb polypeptides were isolated as Chl d–binding protein complexes (Chen, Quinnell, and Larkum 2002a, 2002b) and analyzed using mass spectral fingerprinting of tryptic peptides as shown in table 2. The experimental mass spectral peaks with relatively strong intensity agree well with the tryptic peptide masses predicted from the pcbA gene (table 2). There are 14 predicted peptide fragments from tryptic digestion with molecular mass greater than 800 Da, five of which (excluding N-terminal and C-terminal peptide fragments) fall in the region 800 to 2,300 Da. Experimentally, nine peptides were observed by mass spectrometry, and six of them were a good match with the predicted peptide masses, as shown in table 2. Computer predictions also indicated a few larger mass fragments that could not be matched with experimental results. Also, experimental mass determination included many peaks with relatively weak intensity, which were considered to be part of the background noise and omitted. A general problem with peptide-mass fingerprinting is that a failure to ionize can result in low coverage of detected peptides, but three to five fragments with matches to the predicted masses can be used to identify proteins on two-dimensional gels (Henzel et al. 1993). Our results provide good evidence that the pcbA gene is expressed as a Chl d–binding protein of approximately 34 kDa. The pcbC gene is expressed at higher levels under iron-stress culture conditions (Chen et al. unpublished data) and may not be abundant in the cultures grown under iron-replete conditions.


View this table:
[in this window]
[in a new window]
 
Table 2 Assigned Peptide Masses for A. marina for the Major Light-Harvesting pcb Gene Product

 
Prochloron didemni pcb Sequences
A total of 3,513 bp of genomic DNA sequence was determined and found to contain two pcb genes in tandem, as with A. marina (fig. 1B). These are likewise designated pcbA (1,050 bp) and pcbC (sequence incomplete) as discussed below. The pcbA gene corresponds to the pcb sequence reported previously from Prochloron with 99% identities (La Roche et al. 1996). There is a noncoding region of 143 bp between pcbA and pcbC, which is a similar gene arrangement to A. marina (pcbA/pcbC). Upstream of pcbA/C there is an ORF potentially encoding a polypeptide with sequence similarity to the Sll1063 peptidase of Synechocystis sp. PCC6803. Because the pcbC sequence is incomplete, it is not known whether there are additional pcb genes downstream. The amino acid sequence data of La Roche et al. (1996) indicate that the pcbA gene is expressed under normal conditions. Minor N-terminal differences between determined and predicted amino acid sequences suggest that there may be at least one additional pcb gene in the Prochloron genome closely similar to the pcbA gene, or else there is polymorphism within the population.

Phylogenetic Tree Reconstruction
The sequence alignment is provided as Supplementary Material online. The phylogenetic analyses were performed using the region of 308 residues with excluded the gaps; that is, the loop between helix 5 and helix 6 of CP43. The relatedness of the Pcb proteins to each other, and to cyanobacterial IsiA proteins and to a variety of CP43 proteins was studied by phylogenetic tree reconstruction from the aligned amino acid sequences using maximum-likelihood (fig. 2), parsimony and distance-matrix methods (fig. 3). The bootstrap supports for the branches on these trees is shown in the figures and generally show good support for the tree topology. The phylogenetic tree in figure 2 shows the unrooted relationship among 35 proteins. The PcbA/C of A. marina group with the other Pcb proteins with reliable bootstrap support, although with extended edge lengths (fig. 2).



View larger version (33K):
[in this window]
[in a new window]
 
FIG. 2.— Maximum-likelihood tree for the selected sequences of Pcb, IsiA, and CP43 proteins of Acaryochloris marina, prochlorophytes, and classical cyanobacteria. The tree was the best tree chosen by ProML with minimum ln-likelihood from 257 trees. The numbers on the node represent the bootstrap support percentages with 256 bootstrap replicates. isiA A represents isiA of Anabaena; isiA F represents isiA of Fischerella. For other abbreviations see table 1.

 


View larger version (23K):
[in this window]
[in a new window]
 
FIG. 3.— Phylogenetic tree of different Pcbs in prochlorophytes and Acaryochloris marina inferred by the Neighbor-Joining method with pairwise distances between the sequences calculated on the basis of Kimura's (1983) method to correct for multiple substitution at he same site; CP43 of Prochlorothrix hollandica was used as the outgroup. Numbers on the internal branches show the bootstrap values for 1,000 replicate trees obtained with both maximum-parsimony and Neighbor-Joining methods. (Full sequence alignment details are given as Supplementary Material online.)

 

    Discussion
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
Chl Types and Binding
A central focus of this work is the unique Chl, Chl d, which predominates in Acaryochloris marina (>95% in our cultures). This Chl must be the major light-harvesting Chl, but it also forms the special pair in the reaction center of photosystem I (Hu et al. 1998) and may be present in the reaction center of photosystem II (Itoh et al. 2001). Clearly this Chl has replaced the functions of Chl a and Chl b in other oxygenic photosynthetic organisms. It may not be surprising, therefore, that the fraction of Chl d involved in light harvesting in A. marina is bound to a similar protein to those found in prochlorophytes, the Pcb proteins, where, in the latter, they bind Chl a and Chl b. Nevertheless, this new finding is clearly important in piecing together the evolutionary history of these types of cyanobacteria. Furthermore, the new evidence that Prochloron didemni has two similar genes for binding, in this case, Chl a, Chl b, and a chlorophyll c–type pigment provides further important evidence on which to base proposals of the evolution of these organisms. Despite the fact that prochlorophytes have been placed on distinctly different branches of the cyanobacterial tree and that A. marina lies on yet another branch (Miyashita et al. 2003), their light-harvesting antennae are clearly related. A satisfactory explanation of how these cyanobacteria and their light-harvesting systems evolved is clearly an important challenge.

The Evolution of pcb Genes
There is a strong similarity in the arrangement of pcb genes in A. marina and Prochloron didemni, with duplicated genes in tandem in both organisms. This is also similar to the arrangement in Prochlorothrix hollandica, although the latter contains three pcb genes (fig. 1C), pcbA/B/C, with the pcbC gene strongly divergent from the other two pcb genes (van der Staay, Yurkova, and Green 1998). The Acaryochloris pcbA and pcbC genes are most similar to the pcbA/B and pcbC genes, respectively, of Prochlorothrix, and the same is true for the Prochloron genes. All three pcbC genes share a 24 amino acid deletion compared with the others between amino acids 296 and 297 in the numbering of van der Staay Yurkova, and Green (1998). This would suggest that the pcb genes of all these organisms are derived from a series of duplications, as originally suggested for Prochlorothrix hollandica (van der Staay, Yurkova, and Green 1998) (fig. 1C). A range of pcb gene organization is seen in Prochlorococcus isolates, with a single gene in an isolate adapted to high light intensity, two genes in an isolate adapted to moderate light, and multiple genes in a strain adapted to low light (Garczarek et al. 2001).

The relatedness of the Pcb proteins to each other, to cyanobacterial IsiA proteins, and to a variety of CP43 proteins is shown in figure 2 using maximum-likelihood and in figure 3 using parismony and distance-matrix methods. It is particularly noteworthy that all the PcbA/B sequences group together to the exclusion of IsiA and CP43 (psbC) sequences in contrast to other suggestions (Rüdiger 2002). The same is true for the PcbC sequences. This indicates a single origin of the pcbA/B genes and of the pcbC genes, whether binding Chl b or Chl d, rather than multiple origins (from IsiA or CP43 sequences). Rooting the trees using CP43 (which seems justified, given the integral role of this protein in photosystem II), suggests an evolution of the pcb genes as shown in figure 4. An ancestral gene for a Chl-binding protein (probably derived by duplication of a gene for CP43) was duplicated to give a pcbC gene and a second gene that became specialized as an isiA gene in some lineages and in others as a single pcbA/B gene. (The latter may have duplicated again to generate tandem pcbA/B genes.) In many of the pcbC-isiA lineages, the pcbC gene was lost, but this was not the case with all of them. We propose that the Pcb proteins were (and remain) able to bind a range of different Chls, according to what was available. It is not clear whether IsiA proteins can do likewise. This scheme could also account for the unexpected existence of pcbC homologs adjacent to isiA as seen in cyanobacteria such as Fischerella muscicola PCC73103 (Geiss et al. 2001). In some lineages, the pcbA/B genes proliferated further, to allow organisms to exploit niches with different light levels, as seen with Prochlorococcus strains today (Garczarek et al. 2001). If the inferred order of divergence of the gene families were incorrect, one could postulate a simple divergence of a Chl-binding protein into IsiA or Pcb families, followed by duplication and divergence within the Pcb family.



View larger version (39K):
[in this window]
[in a new window]
 
FIG. 4.— A schematic representation of the evolution of pcb and isiA genes. Horizontal arrows indicate gene orientation, and vertical arrows indicate sequential events in the evolution of the genes. The groupings shown in the figure indicate where the extant organisms lie. Group 1 includes Acaryochloris marina, Prochloron didemni, and Prochlorothrix hollandica; group 2 includes Fischerella and Anabeana; group 3 includes Prochlorococcus spp; and group 4 includes classic cyanobacteria.

 
Bibby et al. (2003a) showed that different proteins belonging to the PcbA/B family are targeted to specific photosystems in Prochlorococcus sp. MIT9313. It is tempting to suggest, in the light of the present work on A. marina indicating that the PcbA protein, as identified by peptide fingerprinting, is targeted to photosystem II (Chen et al., unpublished data.), that the PcbA protein in Prochlorothrix and Prochloron is also targeted to photosystem II (Bibby et al. 2003b) and that the product of the pcbC gene in all three organisms is targeted to photosystem I.

The prochlorophytes are widely separated from each other and scattered among the phycobilisome-containing and IsiA-containing cyanobacteria in phylogenetic trees based on 16S rRNA sequences (Urbach, Roberson, and Chishholm 1992). The prochlorophytes are also widely separated from A. marina in 16S rRNA trees (Miyashita et al. 2003). This appears to conflict with the inference of a single origin of pcbA/B and pcbC sequences. The simplest way to account for this observation is to invoke lateral gene transfer of pcb genes into isiA-containing lineages, generally (but perhaps not invariably) replacing the need for phycobilisomes. This model would also readily explain the apparent existence of an isiA gene in the pcb-containing Prochloron didemni (La Roche et al. 1996) and the existence of phycobiliprotein genes in some prochlorophytes, if these genes were not completely lost. Lateral gene transfer among prokaryotes is well documented (Nesbo, Boucher, and Doolittle 2001). In addition, the existence of a phycoerythrin-containing cyanobacterium Synechocystis trididemni in didemnid ascidians (also the host organisms for Prochloron didemni) that groups very closely with Prochloron didemni in 16S and rbcL trees (Shimada et al. 2003) adds support to the proposal of lateral transfer. It is interesting that prochlorophytes contain a homologous Chl a–oxygenase sequence (Tomitani et al. 1999), suggesting that this too may have been transferred laterally. It is not clear at what stage the ability to produce Chl d was developed, but it is clear that oxygenic photosynthetic bacteria are relatively flexible in the use of different chlorophyll types for light harvesting (Satoh et al. 2001). Noting that some prochlorophytes also contain a Chl c–like pigment (Larkum et al. 1994), we suggest that the use of a particular light-harvesting Chl by an organism is merely a consequence of which Chl(s) they are able to synthesize. In this regard, it is worth noting that a wide variety of light-harvesting proteins can be reconstituted in vitro with chlorophylls, which are not present in the native complexes (Grabowski, Cunningham, and Gantt 2002; Scheer 2003). In addition, reconstitutions of plant light-harvesting complex (LHCII) demonstrate that some chlorophyll-binding sites can accept either chlorophyll a or b (Bassi et al. 1999), and it is probable that this also occurs in vivo. Of particular relevance to the flexibility and opportunism (Green 2001) for binding exotic chlorophylls that may become available, is the demonstration that engineering chlorophyll a oxygenase together with an LHCII gene into Synechocystis PC6803 results in significant chlorophyll b incorporation into CP43 and CP47 (Xu, Vavilin, and Vermaas 2001).

It is possible to propose a different model in which the ancestor to all oxygenic photosynthetic bacteria contained both PcbA/B/C and IsiA/phycobilisome systems. (This arrangement is not shown in figure 4 but could be derived by duplication of the chlorophyll-binding protein gene to generate both a pcbA/B and an isiA gene.) Although this avoids the need to propose lateral transfer, it would require the development of a mixture of light-harvesting systems followed by the elimination of one or other independently in a large number of lineages, which seems less plausible.

These results, therefore, show that the Pcb system used by Chl b-containing and Chl d-containing prokaryotes evolved once and that the distribution of different light-harvesting systems in 16S rRNA trees can most easily be explained by lateral gene transfer. This model can also account for the fact that the two forms of Prochlorococccus, the deep water form (Dufresne et al. 2003) and the shallow water forms (Dufresne et al. 2003; Rocap et al. 2003), whose genomes have been sequenced, have little in common apart from the presence of pcb genes. It also explains other unexpected observations such as the existence of pcb genes in some cyanobacteria (Geiss et al. 2001).


    Acknowledgements
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 
This work was supported by an Australian Research Council grant to A.W.D.L. and R.G.H. and a Macquarie University Research Fellowship to C.J.H. Part of this work was presented as a PhD thesis by Dr. Min Chen at the University of Sydney in 2003. We are grateful to Adrian Barbrook and Peter Lockhart for helpful discussions. We thank Professor Blankenship and Dr. Brune of Arizona State University for mass spectral analysis. This is research report #008 from SUBIT.


    Footnotes
 
Geoffrey McFadden, Associate Editor


    References
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 References
 

    Barrett, A., N. D. Rawlings, and J. F. Woessner. 1998. Handbook of proteolytic enzymes. Academic Press, San Diego, Calif.

    Bassi, R., R. Croce, D. Cugini, and D. Sandona. 1999. Mutational analysis of a higher plant antenna protein provides identification of chromophores bound into multiple sites. Proc. Natl. Acad. Sci. USA 96:10056–10061.[Abstract/Free Full Text]

    Bibby, T. S., I. Mary, J. Nield, F. Partensky, and J. Barber. 2003a. Low-light-adapted Prochlorococcus species possess specific antennae for each photosystem. Nature 424:1051–1054.[CrossRef][ISI][Medline]

    Bibby, T. S., J. Nield, M. Chen, A. W. D. Larkum, and J. Barber. 2003b. Structure of a photosystem II supercomplex isolated from Prochloron didemni retaining its chlorophyll a/b light-harvesting system. Proc. Natl. Acad. Sci. USA 100:9050–9054.[Abstract/Free Full Text]

    Chen, M., R. G. Quinnell, and A. W. D. Larkum. 2002a. The major light-harvesting pigment protein of Acaryochloris marina. FEBS Lett. 514:149–151.[CrossRef][ISI][Medline]

    ———. 2002b. Chlorophyll d as the major photopigment in Acaryochloris marina. J. Porphyrins Phthalocyanines 6:763–773.[ISI]

    Dufresne, A., M. Salanoubat, F. Partensky et al. (21 co-authors). 2003. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl. Acad. Sci. USA 100:10020–10025.[Abstract/Free Full Text]

    Felsenstein, J. 1989. PHYLIP (phylogeny inference package). Version 3.2. Cladistics 5:164–166.

    Garczarek, L., W. R. Hess, J. Holtzendorf, G. W. M. van der Staay, and F. Partensky. 2000. Multiplication of antenna genes as a major adaptation to low light in a marine prokaryote. Proc. Natl. Acad. Sci. USA 97:4098–4101.[Abstract/Free Full Text]

    Garczarek, L., G. W. M. van der Staay, W. R. Hess, F. Le Gall, and F. Partensky. 2001. Expression and phylogeny of the multiple antenna genes of the low-light-adapted strain Prochlorococcus marinus SS120 (Oxyphotobacteria). Plant Mol. Biol. 46:683–693.[CrossRef][ISI][Medline]

    Geiss, U., J. Vinnemeier, A. Schoor, and M. Hagemann. 2001. The iron-regulated isiA gene of Fischerella muscicola strain PCC 73103 is linked to a likewise regulated gene encoding a Pcb-like chlorophyll-binding protein. FEMS Microbiol. Lett. 197:123–129.[CrossRef][ISI][Medline]

    Grabowski, B., F. X. Cunningham Jr, and E. Gantt. 2002. Chlorophyll and carotenoid binding in a simple red algal light-harvesting complex crosses phylogenetic lines. Proc. Natl. Acad. Sci. USA 98:2911–2916.[CrossRef][ISI]

    Green, B. R. 2001. Was "molecular opportunism" a factor in the evolution of different photosynthetic light-harvesting pigment systems. Proc. Natl. Acad. Sci. USA 98:2119–2121.[Free Full Text]

    Henzel, W. J., T. M. Billeci, J. T. Stult, S. C. Wong, C. Grimley, and C. Watanabe. 1993. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90:5011–5015.[Abstract]

    Hu, Q., H. Miyashita, I. Iwasaki, N. Kurano, S. Miyachi, M. Iwaki, and S. Itoh. 1998. A photosystem I reaction center driven by chlorophyll d in oxygenic photosynthesis. Proc. Natl. Acad. Sci. USA 95:13319–13323.[Abstract/Free Full Text]

    Itoh, S., M. Iwaki, T. Noguti, A. Kawamori, and H. Mino. 2001. Photosystem I and II reaction centre based on chlorophyll d in a cyanobacteria-like organism Acaryochloris marina. Proceedings of the 12th International Congress on Photosynthesis. CSIRO Publishing, Melbourne, Australia.

    Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.

    Kumar, S., K. Tamura, and M. Nei. 1994. MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput. Appl. Biosci. 10:189–191.[Abstract]

    Larkum, A. W. D., C. Scaramuzzi, R. G. Hiller, G. C. Cox, and A. C. Turner. 1994. Light-harvesting chlorophyll c-like pigment in Prochloron. Proc. Natl. Acad. Sci. USA 91:679–683.[Abstract]

    La Roche, J., G. W. M. van der Staay, F. Partensky et al. (11 co-authors). 1996. Independent evolution of the prochlorophyte and green chlorophyll a/b light-harvesting proteins. Proc. Natl. Acad. Sci. USA 93:15244–15248.[Abstract/Free Full Text]

    Marquardt, J., H. Senger, H. Miyashita, S. Miyachi, and E. Morschel. 1997. Isolation and characterization of biliprotein aggregates from Acaryochloris marina, a Prochloron-like prokaryote containing mainly chlorophyll d.. FEBS Lett. 410:428–432.[CrossRef][ISI][Medline]

    Marquardt, J., E. Morschel, E. Rhiel, and M. Westermann. 2000. Ultrastructure of Acaryochloris marina, an oxyphotobacterium containing mainly chlorophyll d.. Arch. Microbiol. 174:181–188.[CrossRef][ISI][Medline]

    Miyashita, H., H. Ikemoto, N. Kurano, K. Adachi, M. Chilara, and S. Miyachi. 1996. Chlorophyll d as a major pigment. Nature 383:402.[CrossRef][ISI]

    Miyashita, H., H. Ikemoto, N. Kurano, S. Miyachi, and M. Chihara. 2003. Acaryochloris marina gen. et sp. nov. (Cyanobacteria), an oxygenic photosynthetic prokaryote containing Chl d as a major pigment. J. Phycol. 39:1247–1253.[CrossRef][ISI]

    Nesbo, C. L., Y. Boucher, and W. F. Doolittle. 2001. Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J. Mol. Evol. 53:340–350.[CrossRef][ISI][Medline]

    Rocap, G., F. W. Larimer, J. Lamerdin et al. (24 co-authors). 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042–1047.[CrossRef][ISI][Medline]

    Rüdiger, W. 2002. Biosynthesis of chlorophyll b and the chlorophyll cycle. Photosynthesis Res. 74:187–193.[CrossRef][ISI]

    Satoh, S., M. Ikeuchi, M. Mimuro, and A. Tanaka. 2001. Chlorophyll b expressed in cyanobacteria functions as a light-harvesting antenna in photosystem I through flexibility of the proteins. J. Biol. Chem. 276:4293–4297.[Abstract/Free Full Text]

    Scheer, H. 2003. The pigments in light-harvesting antennas in photosynthesis. Pp. 29–81 in B. R. Green and W. W. Parsons, eds. Advances in photosynthesis. Vol. 13. Kluwer Academic Publishers, Dordrecht, the Netherlands.

    Shimada, A., N. Yano, S. Kanai, R. A. Lewin, and T. Maruyama. 2003. Molecular phylogenetic relationship between two symbiotic photo-oxygenic prokaryotes, Prochloron sp. and Synechocystis trididemni. Phycologia 42:193–197.[ISI]

    Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.[Abstract]

    Tomitani, A., K. Okada, H. Miyashita, H. C. P. Matthijs, T. Ohno, and A. Tanaka. 1999. Chlorophyll b and phycobilins in the common anacestor of cyanobacteria and chloroplasts. Nature 400:159–162.[CrossRef][ISI][Medline]

    Urbach, E., D. L. Robertson, and S. W. Chishholm. 1992. Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355:267–270.[CrossRef][ISI][Medline]

    van der Staay, G. W. M., N. Yurkova, and B. R. Green. 1998. The 38 kDa chlorophyll a/b protein of the prokaryote Prochlorothrix hollandica is encoded by a divergent pcb gene. Plant Mol. Biol. 36:709–716.[CrossRef][ISI][Medline]

    Wang, Y. C., J. Sun, and P. R. Chitnis. 2000. Proteomic study of the peripheral proteins from thylakoid membranes of the cyanobacterium Synechocystis sp. PCC 6803. Electrophoresis 21:1746–1754.[CrossRef][ISI][Medline]

    Xu, H., D. Vavilin, and W. Vermaas. 2001. Chlorophyll b can serve as the major pigment in functional photosystem II complexes of cyanobacteria. Proc. Natl. Acad. Sci. USA 98:14168–14173.[Abstract/Free Full Text]

Accepted for publication August 30, 2004.





This Article
Abstract
FREE Full Text (PDF)
Supplementary Material
All Versions of this Article:
22/1/21    most recent
msh250v1
Alert me when this article is cited
Alert me if a correction is posted
Services
Email this article to a friend
Similar articles in this journal
Similar articles in ISI Web of Science
Similar articles in PubMed
Alert me to new issues of the journal
Add to My Personal Archive
Download to citation manager
Search for citing articles in:
ISI Web of Science (7)
Request Permissions
Google Scholar
Articles by Chen, M.
Articles by Larkum, A. W. D.
PubMed
PubMed Citation
Articles by Chen, M.
Articles by Larkum, A. W. D.