The home stretch,a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1

Rhodobacter sphaeroides 2.4.1 is an α-3 purple nonsulfur eubacterium with an extensive metabolic repertoire. Under anaerobic conditions, it is able to grow by photosynthesis, respiration and fermentation. Photosynthesis may be photoheterotrophic using organic compounds as both a carbon and a reducing source, or photoautotrophic using carbon dioxide as the sole carbon source and hydrogen as the source of reducing power. In addition, R. sphaeroides can grow both chemoheterotrophically and chemoautotrophically. The structural components of this metabolically diverse organism and their modes of integrated regulation are encoded by a genome of ∼4.5 Mb in size. The genome comprises two chromosomes CI and CII (2.9 and 0.9 Mb, respectively) and five other replicons. Sequencing of the genome has been carried out by two groups, the Joint Genome Institute, which carried out shotgun-sequencing of the entire genome and The University of Texas-Houston Medical School, which carried out a targeted sequencing strategy of CII. Here we describe our current understanding of the genome when data from both of these groups are combined. Previous work had suggested that the two chromosomes are equal partners sharing responsibilities for fundamental cellular processes. This view has been reinforced by our preliminary analysis of the virtually completed genome sequence. We also have some evidence to suggest that two of the plasmids, pRS241a and pRS241b encode chromosomal type functions and their role may be more than that of accessory elements, perhaps representing replicons in a transition state. This revised version was published online in June 2006 with corrections to the Cover Date.     

The prevalence of gene duplications and their ancient origin in <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis> 2.4.1

Background  

Rhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of Proteobacteria. The present study was to identify the extent, history, and role of gene duplications in R. sphaeroides 2.4.1, an organism that possesses two chromosomes.     

History of the word photosynthesis and evolution of its definition

In 1893, Charles Barnes (1858–1910) proposed that the biological process for ‘synthesis of complex carbon compounds out of carbonic acid, in the presence of chlorophyll, under the influence of light’ should be designated as either ‘photosyntax’ or ‘photosynthesis.’ He preferred the word ‘photosyntax,’ but ‘photosynthesis’ came into common usage as the term of choice. Later discovery of anoxygenic photosynthetic bacteria and photophosphorylation necessitated redefinition of the term. This essay examines the history of changes in the meaning of photosynthesis. This revised version was published online in June 2006 with corrections to the Cover Date.     

The Laboratory of Photosynthesis and its successors at Gif-sur-Yvette,France*

This article is not a survey of all the research made during the last half century at the ‘Laboratoire de Photosynthèse’ of the ‘Centre National de la Recherche Scientifique’ (CNRS) in Gif-sur-Yvette, but rather some personal recollections, as faithful as possible. Not all people could be mentioned and the scientists named here are mainly those who, at different stages of the laboratory's evolution, created their research teams, within or outside the laboratory. The laboratory, closed now as an administrative entity, was founded in 1953 by the CNRS in Gif-sur-Yvette, near Paris. Besides the emerging research groups in Paris and at Saclay, it was then the only one in France to be entirely dedicated to photosynthesis. Initially, the focus was on metabolic biochemistry of photosynthesis in whole plants and unicellular algae. In 1959, biophysics of primary and associated processes was added and in 1966, the laboratory was enlarged to include molecular genetics and, somewhat later, structural biology. Most of the early members of the laboratory have now gone offstage, but the research goes on, in Gif and elsewhere, thanks to the numerous high-level scientists that have been trained there. Most of the basic questions have now been answered, and interest has shifted in two directions, atomic and integrated, while many other facets of research are no longer specific to photosynthesis but part of more general biological problems, a normal situation for an area that has reached its maturity. This paper is dedicated to the scientists, technicians, students and visitors who could not all be cited here, but who contributed so much to the life of the laboratory. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular cloning, sequence and regulation of expression of the recA gene of the phototrophic bacterium Rhodobacter sphaeroides

The recA gene of Rhodobacter sphaeroides 2.4.1 has been isolated by complementation of a UV-sensitive RecA^– mutant of Pseudomonas aeruginosa. Its complete nucleotide sequence consists of 1032 bp, encoding a polypeptide of 343 amino acids. The deduced amino acid sequence displayed highest identity to the RecA proteins from Rhizobium mehloti, Rhizobium phaseoli, and Agrobacterium tumefaciens. An Escherichia coli-like SOS consensus region, which functions as a binding site for the LexA repressor molecule was not present in the 215 by upstream region of the R. sphaeroides recA gene. Nevertheless, by using a recA-lacZ fusion, we have shown that expression of the recA gene of R. sphaeroides is inducible by DNA damage. A recA-defective strain of R. sphaeroides was obtained by replacement of the active recA gene by a gene copy inactived in vitro. The resulting recA mutant exhibited increased sensitivity to UV irradiation, and was impaired in its ability to perform homologous recombination as well as to trigger DNA damage-mediated expression. This is the first recA gene from a Gram-negative bacterium that lacks an E. coli-like SOS box but whose expression has been shown to be DNA damage-inducible and auto-regulated.     

An ethnobiological assessment of Rumohra adiantiformis (samambaia-preta) extractivism in Southern Brazil

The fronds of Rumohra adiantiformis, also known as ‘7-weeks-fern,’ ‘leatherleaf’ or ‘samambaia-preta,’ are used worldwide as florists’ greenery. Costa Rica and the USA cultivate and export R. adiantiformis, whereas in South Africa and Brazil this trade is based on extractivism. In Brazil, R. adiantiformis is harvested in the Atlantic Forest biome; 50% of the production comes from the slopes of the ‘Serra Geral’ (state of Rio Grande do Sul), where some 2000 families harvest and trade R. adiantiformis as their main source of revenue. However, harvesting, trading and transporting wild ornamental species is illegal in the Atlantic Forest, This study evaluates R. adiantiformis extractivism in hilly areas of Rio Grande do Sul, from an ethnobotanical/ethnoecological perspective. The study reveals that emic perceptions on the sustainability of R. adiantiformis extractivism are in agreement with relevant ecological data. The regeneration areas on the slopes of the Serra Geral have the highest plant density ever reported for R. adiantiformis; its extractivism has low environment impact and generates significant income for local communities. Further studies of these areas are important in order to support neoextractivism as a suitable form of use of the state's biodiversity.     

Effects of leguminous ground cover competition on red birch and soil nutrient status in the nursery

Legumes as ground cover are regularly planted to increase nitrogen economy of crops and to improve soil. In the present study various clover species were evaluated as vegetative ground cover in nursery field production of micropropagated red birch (Betula pubescensEhrh. f. rubraUlvinen f. nova) in two 2-year experiments. The clover species and cultivars, Trifolium pratenseL. ‘Bjursele’, T. repens L. ‘Jogeva’, T. repens L. ‘Sonja’, T. hybridum L. ‘Frida’, T. incarnatum L. ‘Opolska’, T. resupinatum L. and T. subterraneum L. were compared to grass sod Festuca rubra L. ‘Ensylva’ and to a coverless ground (control). The last one was kept weed free by hand hoeing. Birch (leaves, stems, branches and roots) and soil nutrient concentrations (N, P, K, Ca, Mg and Fe) were analysed and nutrient ratios in birch determined. The annual clovers, T. incarnatumL., T. resupinatumL. and T. subterraneumL., provided about the same nutrient status in birch as did the control. Perennial clovers and grass were strong competitors with trees. High levels of P and Mg in birch leaves relative to N concentration were typical for poorly growing seedlings. Neither annual nor perennial clovers did generally improve soil nutrient status. This revised version was published online in June 2006 with corrections to the Cover Date.     

A consensus map of rye integrating mapping data from five mapping populations

A consensus map of rye (Secale cereale L.) was constructed using JoinMap 2.0 based on mapping data from five different mapping populations, including ‘UC90’ × ‘E-line’, ‘P87’ × ‘P105’, ‘I_0.1-line’ × ‘I_0.1-line’, ‘E-line’ × ‘R-line’, and ‘Ds2’ × ‘RxL10’. The integration of the five mapping populations resulted in a 779-cM map containing 501 markers with the number of markers per chromosome ranging from 57 on 1R to 86 on 4R. The linkage sizes ranged from 71.5 cM on 2R to 148.7 cM on 4R. A comparison of the individual maps to the consensus map revealed that the linear locus order was generally in good agreement between the various populations, but the 4R orientations were not consistent among the five individual maps. The 4R short arm and long arm assignments were switched between the two population maps involving the ‘E-line’ parent and the other three individual maps. Map comparisons also indicated that marker order variations exist among the five individual maps. However, the chromosome 5R showed very little marker order variation among the five maps. The consensus map not only integrated the linkage data from different maps, but also greatly increased the map resolution, thus, facilitating molecular breeding activities involving rye and triticale.     

Which side of the π-macrocycle plane of (bacterio)chlorophylls is favored for binding of the fifth ligand?

Reported crystallographic data and calculated molecular models indicated that chlorophyll (Chl) a and bacteriochlorophyll (BChl) a tend to bind the fifth ligand on the side of the macrocycle where the C13²-(R)-methoxycarbonyl moiety protrudes (denoting the ‘back’ side). The crystal structures of 34 photosynthetic proteins possessing (B)Chl cofactors revealed that most of Chl a and BChl a (and b) are coordinated by any peptidyl residue (e.g., histydyl-imidazolyl group), peptidyl backbone or water from the ‘back’ side. Almost all the cofactors that bind a water molecule as the fifth ligand in these proteins have a ‘back’ configuration. Theoretical model calculations for methyl chlorophyllide a (MeChlid a) and methyl bacteriochlorophyllide a (MeBChlid a) bound to an imidazole molecule indicated that the ‘back’ side is energetically favored for the ligand binding. These results are consistent with the fact that ethyl chlorophyllide a (EtChlid a) dihydrate crystal consists of the ‘back’ complex. The modeling also showed that both removal and stereochemical inverse of the C13²-methoxycarbonyl group affect the relative stability between the ‘back’ and ‘face’ complexes. The effect of the C13²-moiety on the choice of the macrocycle side for the ligand binding is discussed in relation to the function of P700. This revised version was published online in June 2006 with corrections to the Cover Date.     

Development of SCAR markers linked to self-incompatibility in <Emphasis Type="Italic">Brassica napus</Emphasis> L.

‘SI1300’ is a self-incompatible Brassica napus line generated by introgressing an S haplotype from B. rapa ‘Xishuibai’ into a rapeseed cultivar ‘Huayou No. 1’. Five S-locus specific primer pairs were employed to develop cleaved amplified polymorphic sequences (CAPS) markers linked the S haplotype of ‘SI1300’. Two segregating populations (F₂ and BC₁) from the cross between ‘SI1300’ and self-compatible European spring cultivar ‘Defender’, were generated to verify the molecular markers. CAPS analysis revealed no desirable polymorphism between self-incompatible and self-compatible plants. Twenty primer pairs were designed based on the homology-based candidate gene method, and six dominant sequence characterized amplified region (SCAR) markers linked with the S-locus were developed. Of the six markers, three were derived from the SRK and SP11 alleles of class II B. rapa S haplotypes and linked with S haplotype of ‘SI1300’. The other three markers were designed from the SLG-A10 and co-segregated with S haplotype of ‘Defender’. We successfully combined two pairs of them and characterized two multiplex PCR markers which could discriminate the homozygous and heterozygous genotypes. These markers were further validated in 24 F₃ and 22 BC₁F₂ lines of ‘SI1300 × Defender’ and another two segregating populations from the cross ‘SI1300 × Yu No. 9’. Nucleotide sequences of fragments linked with S-locus of ‘SI1300’ showed 99% identity to B. rapa class II S-60 haplotype, and fragments from ‘Defender’ were 97% and 94% identical to SLG and SRK of B. rapa class I S-47 haplotype, respectively. ‘SI1300’ was considered to carry two class II S haplotypes and the S haplotype on the A-genome derived from B. rapa ‘Xishuibai’ determines the SI phenotype, while ‘Defender’ carry a class I S haplotype derived from B. rapa and a class II S haplotype from B. oleracea. SCAR markers developed in this study will be helpful for improving SI lines and accelerating marker-assisted selection process in rapeseed SI hybrid breeding program.     

Response of durum wheat cultivars to immature embryo culture,callus induction and in vitro salt stress

Response of twenty eight cultivars of durum wheat (Triticum turgidum var. durum) to immature embryo culture, callus production and in vitro salt tolerance was evaluated. For assessment of cultivars to salt tolerance, growing morphogenic calli were exposed to different concentrations of NaCl (0, 0.3, 0.6, 0.9, 1.2, 1.5, 1.8 and 2.1% w/v) added to the culture medium during two subsequent subcultures (4 weeks each). Comparison of cultivars for callus induction from immature embryo was based on callus induction frequency and fresh weight growth of callus (FWG). While, for salt tolerance, the relative fresh weight growth (RFWG) and necrosis percent of callus were used. There were significant differences among cultivars for potential of regeneration from immature embryo, and ‘Shahivandi’ a native durum wheat cultivar originating from western Iran was superior among the cultivars tested. The FWG distinguished cultivars more than callus induction frequency did for callus induction evaluation. Hence, a range of FWG from 1.23 to 14.65 g was observed in ‘Mexical-75’ and ‘Omrabi-5’ cultivars, respectively. Growing calli derived from cultivars ‘PI 40100’ and ‘Dipper-6’ showed superiority for tolerating salinity under in vitro conditions. This revised version was published online in June 2006 with corrections to the Cover Date.     

Proteins responding to drought and high-temperature stress in <Emphasis Type="Italic">Populus </Emphasis>× <Emphasis Type="Italic">euramericana</Emphasis> cv. ‘74/76’

Proteomic analysis provides a powerful method of studying plant responses to stress at the protein level. In order to study stress-responsive molecular mechanisms for Populus × euramericana cv. ‘74/76’, one of the most important forest plantation tree species in subtropical and temperate regions, we analyzed the response of 2-year-old cuttings of P. × euramericana cv. ‘74/76’ to drought and high temperature using two-dimensional gel electrophoresis. More than 1,000 reproducible leaf proteins were detected in the controls and treatments, and 26 proteins were found to change notably in abundance. We identified 13 proteins affected by drought stress and 11 proteins affected by high temperature. These proteins are mainly involved in photosynthesis such as ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and putative photosystem I reaction center subunit II precursor, and detoxification (manganese superoxide dismutase and methionine sulfoxide reductase A). Furthermore, the level of the photosynthesis proteins affected greatly by the imposed stress conditions was consistent with the observed noticeable decrease in net photosynthesis rate. These studies provides a fundamental data for future research on responses to drought and high temperature, two major factors limiting the growth of forest trees during summer under recent climatic warming.     

Analysis of volatile compounds released from embryogenic cultures and somatic embryos of sweet oranges by head space SPME

Volatile compounds released from callus and nucellar embryo tissues of ‘Valencia late’ and ‘Washington Navel’ sweet oranges (Citrus sinensis, L. Osbeck) were collected/concentrated by head space solid phase micro extraction and analysed by gas chromatography-mass spectrometry. Friable, white embryogenic cultures released a number of volatile compounds, including some essential oils. Different samples of the same embryogenic culture showed variability, possibly related to the presence of tissues undergoing differentiation. Analyses of the somatic embryos permitted the identification of several components, including limonene and methyl anthranilate. Considering the simplicity and the very small sample required (0.3 g of fresh tissue) head space solid phase micro extraction is suitable for studies and comparisons of volatile metabolites released from in vitro Citrus tissue cultures suggesting its potential in Citrus biochemical, genetic and breeding research. This revised version was published online in June 2006 with corrections to the Cover Date.     

Induced parthenogenesis in mandarin for haploid production: induction procedures and genetic analysis of plantlets

This study focused on haploid induction in mandarin through in situ gynogenesis by pollination with irradiated pollen of ‘Meyer’ lemon. Pollination was carried out for three genotypes of mandarin with four levels of gamma-ray-irradiated pollen (150, 300, 600, and 900 Gy). The resulting seeds were characterised by a small size. Embryos were rescued in vitro and the ploidy level of the plantlets was determined by flow cytometry analysis. Haploid, diploid, triploid plantlets were obtained. The haploid parthenogenetic origin was confirmed using microsatellite marker analysis and chromosome count. Diploid and triploid plants were the result of crosses between mandarin and lemon. The induction of gynogenetic haploids of ‘Fortune’ (Citrus clementina Hort ex Tan. × Citrus tangerina Hort ex Tan.) and ‘Ellendale’ (Citrus reticulata Blanco × Citrus sinensis L. Osb) is reported here for the first time.     

Characterization of ‘Schizokinen’; a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917

The Rhizobia comprise one of the most important groups of beneficial bacteria, which form nodules on the roots (rarely on the stems) of leguminous plants. They live within the nodules and reduce atmospheric nitrogen to ammonia, which is further assimilated by plants into required nitrogenous compounds. The Rhizobia in return obtain nutrition from the plant. Rhizobia are free-living soil bacteria and have to compete with other microorganisms for the limited available iron in the rhizosphere. In order to acquire iron Rhizobia have been shown to express siderophore-mediated iron transport systems. Rhizobium leguminosarum IARI 917 was investigated for its ability to produce siderophore. It was found to produce a dihydroxamate type siderophore under iron restricted conditions. The siderophore was purified and chemically characterized. The ESMS, MS/MS and NMR analysis indicate the dihydroxamate siderophore to be ‘schizokinen’, a siderophore reported to be produced by Bacillus megaterium that shares a similar structure to ‘rhizobactin 1021’ produced by Sinorhizobium meliloti 1021. This is the first report of production of schizokinen by a strain of R. leguminosarum, therefore it was carefully investigated to confirm that it is indeed ‘schizokinen’ and not a degradation product of ‘rhizobactin 1021’. Since ferric–siderophore complexes are transported across the outer membrane (OM) into the periplasm via an OM receptor protein, R. leguminosarum IARI 917 was investigated for the presence of an OM receptor for ‘ferric–schizokinen’. SDS PAGE analysis of whole cell pellet and extracted OM fractions indicate the presence of a possible iron-repressible OM receptor protein with the molecular weight (MW) of approximately 74 kDa.     

Occurrence of Polysiphonia Epiphytes in Kappaphycus Farms at Calaguas Is., Camarines Norte, Phillippines

This paper describes the occurrence of an epiphyte infestation of Kappaphycus farms in Calaguas Is. Camarines Norte, Philippines. In particular, percentage cover of ‘goose bump’-Polysiphonia and ‘ice-ice’ disease, and some environmental parameters that influence the thallus condition of Kappaphycus alvarezii in Calaguas Is. were assessed during 3 separate visits and are discussed.Commercial cultivation of Kappaphycus at Calaguas Is. began in the early 1990s. After five years of farming, the stock was destroyed by a strong typhoon. The area was re-planted the following year and production increased annually and reached its peak in 1998–1999. However, the following year, the first occurrence of a Polysiphonia epiphyte infestation occurred concurrently with an ‘ice-ice’ disease. Consequently, annual production and the number of seaweed planters declined rapidly, and this situation persists to the present time. This paper highlights the etiological factors and their consequences.Results show that farm-site selection is critical for the success of Kappaphycus production. Characteristics of water movement and light intensity in farming areas contributed to the occurrence and detrimental effect of the phenomenon described as ‘goose bumps’: a morphological distortion of the host seaweed due to the presence of a Polysiphonia sp. epiphyte. A strong inverse correlation was observed between the occurrence of Polysiphonia and water movement: areas with low water motion registered a higher % cover (65%) of Polysiphonia than those in more exposed areas (17%). Although ‘goose bump’-Polysiphonia infestation and ‘ice-ice’ disease pose a tremendous problem to the seaweed farmers, the results of this limited assessment provide a useful baseline for future work.     

Celebrating 20 years of historical papers in Photosynthesis Research

This Editorial has four goals: (1) to inform the readers of ‘Photosynthesis Research‘ about the past of the ‘Historical corner’; which began 20 years ago; (2) to encourage photosynthesis researchers and historians of science to contact me for publishing papers of historical interest; these include: (a) Obituaries and Tributes; (b) historical papers on current and past discoveries and controversies; (c) history of research in specific laboratories, or in specific countries, or at specific conferences; (d) Personal perspectives (not discussed any further); (3) to encourage researchers not to discard, but to save correspondence and data of their discoveries for the future historians by donating them to their Archives, when appropriate (not discussed any further); and (4) to reinforce to the readers that the concept of two-light reaction and two-pigment system was already there in 1959. I mention here three key papers presented at the IX^th International Botanical Congress, held at Montreal Canada (in August, 1959) prior to the famous April 9, 1960 paper by Robert Hill and Fay Bendall on the ‘Z-scheme’ of photosynthesis, that was based on thermodynamic and energetic considerations. ^★ This Historical corner Editorial is dedicated to Bessel Kok (1918–1978).     

Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.)

Woolly apple aphid (WAA; Eriosoma lanigerum Hausm.) can be a major economic problem to apple growers in most parts of the world, and resistance breeding provides a sustainable means to control this pest. We report molecular markers for three genes conferring WAA resistance and placing them on two linkage groups (LG) on the genetic map of apple. The Er1 and Er2 genes derived from ‘Northern Spy’ and ‘Robusta 5,’ respectively, are the two major genes that breeders have used to date to improve the resistance of apple rootstocks to this pest. The gene Er3, from ‘Aotea 1’ (an accession classified as Malus sieboldii), is a new major gene for WAA resistance. Genetic markers linked to the Er1 and Er3 genes were identified by screening random amplification of polymorphic deoxyribonucleic acid (DNA; RAPD) markers across DNA bulks from resistant and susceptible plants from populations segregating for these genes. The closest RAPD markers were converted into sequence-characterized amplified region markers and the genome location of these two genes was assigned to LG 08 by aligning the maps around the genes with a reference map of ‘Discovery’ using microsatellite markers. The Er2 gene was located on LG 17 of ‘Robusta 5’ using a genetic map developed in a M.9 × ‘Robusta 5’ progeny. Markers for each of the genes were validated for their usefulness for marker-assisted selection in separate populations. The potential use of the genetic markers for these genes in the breeding of apple cultivars with durable resistance to WAA is discussed.