Beverley R. Green

Light-harvesting antennas in photosynthesis

Editorial. Preface. Color Plates. I: Introduction to Light-Harvesting. 1. Photosynthetic Membranes and Their Light-Harvesting Antennas B.R. Green, J.M. Anderson, W.W. Parson. 2. The Pigments H. Scheer. 3. Optical Spectroscopy in Photosynthetic Antennas W.W. Parson, V. Nagarajan. 4. The Evolution of Light-Harvesting Antennas B.R. Green. II: Structure and Function in Light-Harvesting. 5. The Light-Harvesting System of Purple Bacteria B. Robert, R.J. Cogdell, R. van Grondelle. 6. Antenna Complexes from Green Photosynthetic Bacteria R.E. Blankenship, K. Matsuura. 7. Light-Harvesting in Photosystem II H. van Amerongen, J.P. Dekker. 8. Structure and Function of the Antenna System in Photsystem I P. Fromme, E. Schlodder, S. Jansson. 9. Antenna Systems and Energy Transfer in Cyanophyta and Rhodophyta M. Mimuro, H. Kikuchi. 10. Antenna Systems of Red Algae: Phycobilisomes with Photosystem II and Chlorophyll Complexes with Photosystem I E. Gantt, B. Grabowski, F.X. Cunningham Jr. 11. Light-Harvesting Systems in Chlorophyll c-Containing Algae A.N. Macpherson, R.G. Hiller. III: Biogenesis, Regulation and Adaptation. 12. Biogenesis of Green Plant Thylakoid Membranes K. Cline. 13. Pulse Amplitude Modulated Chlorophyll Fluorometry and its Application in Plant Science G.H. Krause, P. Jahns. 14. Photostasis in Plants, Green Algae and Cyanobacteria: The Role of Light-Harvesting Antenna Complexes N.P.A. Huner, G. Oquist, A. Melis. 15. Photoacclimation of Light-Harvesting Systems in EukaryoticAlgae P.G. Falkowski, Yi-Bu Chen. 16. Multi-level Regulation of Purple Bacterial Light-Harvesting Complexes C.S. Young, J.T. Beatty. 17. Environmental Regulation of Phycobilisome Biosynthesis A.R. Grossman, L.G. van Waasbergen, D. Kehoe. Index.

Single gene circles in dinoflagellate chloroplast genomes

Photosynthetic dinoflagellates are important aquatic primary producers and notorious causes of toxic ‘red tides’. Typical dinoflagellate chloroplasts differ from all other plastids in having a combination of three envelope membranes and peridinin-chlorophyll a /c light-harvesting pigments. Despite evidence of a dinoflagellete satellite DNA containing chloroplast genes, previous attempts to obtain chloroplast gene sequences have been uniformly unsuccessful. Here we show that the dinoflagellate chloroplast DNA genome structure is unique. Complete sequences of chloroplast ribosomal RNA genes and seven chloroplast protein genes from the dinoflagellate Heterocapsa triquetra reveal that each is located alone on a separate minicircular chromosome: ‘one gene–one circle’. The genes are the most divergent known from chloroplast genomes. Each circle has an unusual tripartite non-coding region (putative replicon origin), which is highly conserved among the nine circles through extensive gene conversion, but is very divergent between species. Several other dinoflagellate species have minicircular chloroplast genes, indicating that this type of genomic organization may have evolved in ancestral peridinean dinoflagellates. Phylogenetic analysis indicates that dinoflagellate chloroplasts are related to chromistan and red algal chloroplasts and supports their origin by secondary symbiogenesis,,.

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

Plastid Origins The glaucophytes, represented by the alga Cyanophora paradoxa, are the putative sister group of red and green algae and plants, which together comprise the founding group of photosynthetic eukaryotes, the Plantae. In their analysis of the genome of C. paradoxa, Price et al. (p. 843; see the Perspective by Spiegel) demonstrate a unique origin for the plastid in the ancestor of this supergroup, which retains much of the ancestral diversity in genes involved in carbohydrate metabolism and fermentation, as well as in the gene content of the mitochondrial genome. Moreover, about 3.3% of nuclear genes in C. paradoxa seem to carry a signal of cyanobacterial ancestry, and key genes involved in starch biosynthesis are derived from energy parasites such as Chlamydiae. Rapid radiation, reticulate evolution via horizontal gene transfer, high rates of gene divergence, loss, and replacement, may have diffused the evolutionary signals within this supergroup, which perhaps explains previous difficulties in resolving its evolutionary history. An ancient algal genome suggests a unique origin of the plastid in the ancestor to plants, algae, and glaucophytes. The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

A Phylogenetic Assessment of the Eukaryotic Light-Harvesting Antenna Proteins, with Implications for Plastid Evolution

Abstract. The light-harvesting complexes (LHCs) are a superfamily of chlorophyll-binding proteins present in all photosynthetic eukaryotes. The Lhc genes are nuclear-encoded, yet the pigment–protein complexes are localized to the thylakoid membrane and provide a marker to follow the evolutionary paths of plastids with different pigmentation. The LHCs are divided into the chlorophyll a/b-binding proteins of the green algae, euglenoids, and higher plants and the chlorophyll a/c-binding proteins of various algal taxa. This work examines the phylogenetic position of the LHCs from three additional taxa: the rhodophytes, the cryptophytes, and the chlorarachniophytes. Phylogenetic analysis of the LHC sequences provides strong statistical support for the clustering of the rhodophyte and cryptomonad LHC sequences within the chlorophyll a/c-binding protein lineage, which includes the fucoxanthin–chlorophyll proteins (FCP) of the heterokonts and the intrinsic peridinin–chlorophyll proteins (iPCP) of the dinoflagellates. These associations suggest that plastids from the heterokonts, haptophytes, cryptomonads, and the dinoflagellate, Amphidinium, evolved from a red algal-like ancestor. The Chlorarachnion LHC is part of the chlorophyll a/b-binding protein assemblage, consistent with pigmentation, providing further evidence that its plastid evolved from a green algal secondary endosymbiosis. The Chlorarachnion LHC sequences cluster with the green algal LHCs that are predominantly associated with photosystem II (LHCII). This suggests that the green algal endosymbiont that evolved into the Chlorarachnion plastid was acquired following the emergence of distinct LHCI and LHCII complexes.

A nomenclature for the genes encoding the chlorophylla/b-binding proteins of higher plants

We propose a nomenclature for the genes encoding the chlorophylla/b-binding proteins of the light-harvesting complexes of photosystem I and II. The genes encoding LHC I and LHC II polypeptides are namedLhca1 throughLhca4 andLhcb1 throughLhcb6, respectively. The proposal follows the general format recommended by the Commision on Plant Gene Nomenclature. We also present a table for the conversion of old gene names to the new nomenclature.

Phylogeny of Ultra-Rapidly Evolving Dinoflagellate Chloroplast Genes: A Possible Common Origin for Sporozoan and Dinoflagellate Plastids

Abstract. Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.

The chlorophyll-protein complexes of higher plant photosynthetic membranes or Just what green band is that?

Higher plant thylakoid membranes can be fractionated into a bewildering array of macrocomplexes, chlorophyll-protein complexes and chlorophyll-proteins with various deteregents and separations techniques. The chemical nature of each of these entities depends on the particular methods used to obtain them. This review summarizes the current status of the biochemical identification and characterization of individual chlorophyll-proteins and chlorophyll-protein complexes, and attempts to clarify the relationships among them.

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127–130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.

Second- and third-hand chloroplasts in dinoflagellates: Phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont

Several dinoflagellate species have plastids that more closely resemble those of an unrelated algal group, the haptophytes, suggesting these plastids have been obtained by tertiary endosymbiosis. Because both groups are photosynthetic, all of the genes for nuclear-encoded plastid proteins might be supplied by the dinoflagellate host or some of them might have been replaced by haptophyte genes. Sequences of the conserved nuclear psbO gene were obtained from the haptophyte Isochrysis galbana, the peridinin-containing dinoflagellate Heterocapsa triquetra, and the 19′hexanoyloxy-fucoxanthin-containing dinoflagellate Karenia brevis. Phylogenetic analysis of the oxygen-evolving-enhancer (PsbO) proteins confirmed that in K. brevis the original peridinin-type plastid was replaced by that of a haptophyte, an alga which had previously acquired a red algal chloroplast by secondary endosymbiosis. It showed clearly that during this tertiary symbiogenesis the original psbO gene in the dinoflagellate nucleus was replaced by a psbO gene from the haptophyte nucleus. The phylogenetic analysis also confirmed that the origin of the peridinin-type dinoflagellate plastid was indeed a red alga.