The Experts below are selected from a list of 603 Experts worldwide ranked by ideXlab platform
Donald A Bryant - One of the best experts on this subject based on the ideXlab platform.
-
Effects of modified Phycobilin biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002.
Journal of bacteriology, 2011Co-Authors: Richard M. Alvey, Donald A BryantAbstract:The pathway for phycocyanobilin biosynthesis in Synechococcus sp. strain PCC 7002 comprises two enzymes: heme oxygenase and phycocyanobilin synthase (PcyA). The Phycobilin content of cells can be modified by overexpressing genes encoding alternative enzymes for biliverdin reduction. Overexpression of the pebAB and HY2 genes, encoding alternative ferredoxin-dependent biliverdin reductases, caused unique effects due to the overproduction of phycoerythrobilin and phytochromobilin, respectively. Colonies overexpressing pebAB became reddish brown and visually resembled strains that naturally produce phycoerythrin. This was almost exclusively due to the replacement of phycocyanobilin by phycoerythrobilin on the phycocyanin α-subunit. This phenotype was unstable, and such strains rapidly reverted to the wild-type appearance, presumably due to strong selective pressure to inactivate pebAB expression. Overproduction of phytochromobilin, synthesized by the Arabidopsis thaliana HY2 product, was tolerated much better. Cells overexpressing HY2 were only slightly less pigmented and blue-green than the wild type. Although the pcyA gene could not be inactivated in the wild type, pcyA was easily inactivated when cells expressed HY2. These results indicate that phytochromobilin can functionally substitute for phycocyanobilin in Synechococcus sp. strain PCC 7002. Although functional phycobilisomes were assembled in this strain, the overall phycobiliprotein content of cells was lower, the efficiency of energy transfer by these phycobilisomes was lower than for wild-type phycobilisomes, and the absorption cross-section of the cells was reduced relative to that of the wild type because of an increased spectral overlap of the modified phycobiliproteins with chlorophyll a. As a result, the strain producing phycobiliproteins carrying phytochromobilin grew much more slowly at low light intensity.
-
Effects of Modified Phycobilin Biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002 �
2010Co-Authors: Richard M. Alvey, Wendy M Schluchter, Avijit Biswas, Donald A BryantAbstract:Effects of modified Phycobilin biosynthesis in the cyanobacterium Synechococcus sp. strain PC
-
biogenesis of phycobiliproteins i cpcs i and cpcu mutants of the cyanobacterium synechococcus sp pcc 7002 define a heterodimeric phyococyanobilin lyase specific for β phycocyanin and allophycocyanin subunits
Journal of Biological Chemistry, 2008Co-Authors: Gaozhong Shen, Wendy M Schluchter, Donald A BryantAbstract:Abstract Phycobilin lyases covalently attach Phycobilin chromophores to apo-phycobiliproteins (PBPs). Genome analyses of the unicellular, marine cyanobacterium Synechococcus sp. PCC 7002 identified three genes, denoted cpcS-I, cpcU, and cpcV, that were possible candidates to encode phycocyanobilin (PCB) lyases. Single and double mutant strains for cpcS-I and cpcU exhibited slower growth rates, reduced PBP levels, and impaired assembly of phycobilisomes, but a cpcV mutant had no discernable phenotype. A cpcS-I cpcU cpcT triple mutant was nearly devoid of PBP. SDS-PAGE and mass spectrometry demonstrated that the cpcS-I and cpcU mutants produced an altered form of the phycocyanin (PC) β subunit, which had a mass ∼588 Da smaller than the wild-type protein. Some free PCB (mass = 588 Da) was tentatively detected in the phycobilisome fraction purified from the mutants. The modified PC from the cpcS-I, cpcU, and cpcS-I cpcU mutant strains was purified, and biochemical analyses showed that Cys-153 of CpcB carried a PCB chromophore but Cys-82 did not. These results show that both CpcS-I and CpcU are required for covalent attachment of PCB to Cys-82 of the PC β subunit in this cyanobacterium. Suggesting that CpcS-I and CpcU are also required for attachment of PCB to allophycocyanin subunits in vivo, allophycocyanin levels were significantly reduced in all but the CpcV-less strain. These conclusions have been validated by in vitro experiments described in the accompanying report (Saunee, N. A., Williams, S. R., Bryant, D. A., and Schluchter, W. M. (2008) J. Biol. Chem. 283, 7513-7522). We conclude that the maturation of PBP in vivo depends on three PCB lyases: CpcE-CpcF, CpcS-I-CpcU, and CpcT.
Samuel I Beale - One of the best experts on this subject based on the ideXlab platform.
-
Phycobilin biosynthetic reactions in extracts of cyanobacteria
Photosynthesis Research, 1997Co-Authors: Juan Cornejo, Samuel I BealeAbstract:Phycobilins are the chromophores of phycobiliproteins, the light-harvesting pigments of cyanobacteria, red algae and cryptophytes. Phycobilins are biosynthesized from heme by the action of heme oxygenase, which converts heme to biliverdin, followed by the action of other enzymes that convert biliverdin to the Phycobilins. We previously reported on the enzymes and biosynthetic intermediates of Phycobilin formation in extracts of the unicellular red alga Cyanidium caldarium. Heme oxygenase activity has now been obtained from extracts of the cyanobacterium Synechocystis sp. PCC 6701. The reaction requirements are similar to those for the C. caldarium enzyme: heme substrate, reduced ferredoxin, and a second reductant such as ascorbate or Trolox. The enzymatic nature of the reaction was verified by two criteria in addition to the requirement for cell extract: production of only the IXα isomer of the bilin product and inhibition by the substrate analog Sn-protoporphyrin IX. The enzyme was partially purified by high-speed centrifugation, 35–75% differential (NH4)2SO4 precipitation, and DEAE-cellulose anion exchange chromatography. In addition, extract capable of converting biliverdin IXα to Phycobilins has been obtained from Synechocystis sp. PCC 6701 and another cyanobacterium, Synechocystis sp. PCC 6803. Only the (3Z) isomers of the Phycobilins accumulated in the incubations containing unfractionated cell extracts, in contrast to incubations with unfractionated C. caldarium extracts which produce both the (3Z) and (3E) isomers. Phycocyanobilin and phycoerythrobilin were produced in comparable amounts by Synechocystis sp. PCC 6701 extracts, but only phycocyanobilin accumulated in Synechocystis sp. PCC 6803 extracts. This difference in in vitro product accumulation correlates with the Phycobilins that are found in vivo in these two cell types.
-
Phycobilin biosynthesis reductant requirements and product identification for heme oxygenase from cyanidium caldarium
Archives of Biochemistry and Biophysics, 1995Co-Authors: Gi-eun Rhie, Samuel I BealeAbstract:Abstract Algal heme oxygenase is a soluble enzyme from Cyanidium caldarium that catalyzes the first committed step of Phycobilin biosynthesis by converting protoheme to biliverdin IXα. Although the physiological substrate (protoheme) of algal heme oxygenase is identical to that of microsomal heme oxygenase, which catalyzes heme catabolism in animals, the two enzyme systems differ in several respects including the nature of the required reductants and solubility of the enzymes. Addition of the strong Fe 3+ ion chelators, desferrioxamine and Tiron (4,5-dihydroxy-1,3-benzenedisulfonic acid), greatly increased the yield of solvent-extracted bilin product. The effect of the Fe 3+ chelators was approximately equal whether they were added during or after the enzyme incubation. Postincubation treatment of the enzyme reaction mixture with strong acid also greatly increased the product yield. Addition of desferrioxamine to the reaction mixture after the incubation was terminated caused the appearance of an absorption spectrum, indicating an increase in the concentration of free bilin product. Acid and Fe 3+ chelators are known to cause dissociation of Fe(III)-bilin complexes. These results indicate that the in vitro enzymic reaction product of algal heme oxygenase is a nonenzyme-bound Fe(III)-biliverdin IXα complex that is poorly extracted and/or quantitated unless it is first dissociated. Algal heme oxygenase required the simultaneous presence of both reduced ferredoxin and a second reductant such as ascorbate for activity. The requirement for L-ascorbate could be substituted by Trolox (6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid) or D-ascorbate, but not by dehydroascorbate or dithiothreitol. Heme oxygenase was purified over 200-fold from C. caldarium by differential (NH 4 ) 2 SO 4 precipitation and serial column chromatography over reactive blue 2-Sepharose, DEAE - cellulose, Sephadex G-75, and ferredoxin-Sepharose.
-
regulation of heme oxygenase activity in cyanidium caldarium by light glucose and Phycobilin precursors
Journal of Biological Chemistry, 1994Co-Authors: Gi-eun Rhie, Samuel I BealeAbstract:Cyanobacteria, red algae, and cryptophytes contain phycobiliproteins which function as photosynthetic light-harvesting pigments. The chromophores of phycobiliproteins are Phycobilins, open-chain tetrapyrroles that are synthesized from protoheme. The first step of Phycobilin formation is the conversion of protoheme to biliverdin IX alpha in a reaction that is catalyzed by heme oxygenase. In the unicellular red alga, Cyanidium caldarium, light is required for the accumulation of phycobiliproteins. It has been reported previously that the synthesis of the apoprotein components of allophycocyanin and phycocyanin is induced by light in C. caldarium, that the Phycobilin precursors, delta-aminolevulinic acid (ALA), protoporphyrin IX, and protoheme can substitute for light, and that the regulation is exerted at the level of mRNA synthesis. We have determined that a key enzyme of Phycobilin formation is induced by light in C. caldarium. Extractable heme oxygenase activity is low in dark-grown cells, and it increases approximately 6-fold during the first 24 h after the cells are illuminated. After 24 h, the activity decreases to a level approximately equal to the initial activity. Heme oxygenase is induced in unilluminated cells by administration of ALA. D-Glucose, which is known to inhibit phycocyanin accumulation in C. caldarium, inhibits the induction of heme oxygenase by light or ALA. Induction of heme oxygenase by light or ALA is blocked by cycloheximide, an inhibitor of cytoplasmic protein synthesis, but not by chloramphenicol, an inhibitor of chloroplast protein synthesis. Rifampicin, an inhibitor of algal chloroplast RNA synthesis, and gabaculine, a competitive inhibitor of ALA biosynthesis, block the induction of heme oxygenase by light but not by ALA. These results indicate that heme oxygenase in C. caldarium is induced by Phycobilin precursors. The induction by light and the repression of the induction by D-glucose are probably indirect effects mediated by the effects of light and D-glucose on Phycobilin precursor formation. The results also indicate that heme oxygenase is encoded by a nuclear gene and is synthesized on cytoplasmic ribosomes.
-
Biosynthesis of Phycobilins. Ferredoxin-supported nadph-independent heme oxygenase and Phycobilin-forming activities from Cyanidium caldarium.
The Journal of biological chemistry, 1992Co-Authors: Gi-eun Rhie, Samuel I BealeAbstract:Abstract The unicellular red alga, Cyanidium caldarium, synthesizes phycocyanobilin from protoheme via biliverdin IX alpha. In vitro transformation of protoheme to biliverdin IX alpha and biliverdin IX alpha to Phycobilins were previously shown to require NADPH, ferredoxin, and ferredoxin-NADP+ reductase, as well as specific heme oxygenase and Phycobilin formation enzymes. The role of NADPH in these reactions was investigated in this study. The C. caldarium enzymatic activities that catalyze biliverdin IX alpha formation from protoheme, and Phycobilin formation from biliverdin IX alpha, were partially purified by differential (NH4)2SO4 precipitation. The enzyme fractions, when supplemented with a light-driven ferredoxin-reducing photosystem I fraction derived from spinach leaves, catalyzed light-dependent transformation of protoheme to biliverdin IX alpha and biliverdin IX alpha to Phycobilins, with or without the addition of NADPH and ferredoxin-NADP+ reductase. In the dark, neither reaction occurred unless NADPH and ferredoxin-NADP+ reductase were supplied. These results indicate that the only role of NADPH in both reactions of Phycobilin biosynthesis, in vitro, is to reduce ferredoxin via ferredoxin-NADP+ reductase and that reduced ferredoxin can directly supply the electrons needed to drive both steps in the transformation of protoheme to phycocyanobilin.
-
phytochrome assembly the structure and biological activity of 2 r 3 e phytochromobilin derived from phycobiliproteins
Journal of Biological Chemistry, 1992Co-Authors: J Cornejo, Samuel I Beale, Matthew J. Terry, J C LagariasAbstract:The unicellular rhodophyte, Porphyridium cruentum, and the filamentous cyanobacterium, Calothrix sp. PCC 7601, contain phycobiliproteins that have covalently bound Phycobilin chromophores. Overnight incubation of solvent-extracted cells at 40 degrees C with methanol liberates free Phycobilins that are derived from the protein-bound bilins by methanolytic cleavage of the thioether linkages between bilin and apoprotein. Two of the free bilins were identified as 3(E)-phycocyanobilin and 3(E)-phycoerythrombilin by comparative spectrophotometry and high pressure liquid chromatography. Methanolysis also yields a third bilin free acid whose absorption and 1H NMR spectra support the assignment of the 3(E)-phytochromobilin structure. This novel bilin is the major pigment isolated from cells that are pre-extracted with acetone-containing solvents. Since phytochrome- or phytochromobilin-containing proteins are not present in either organism, the 3(E)-phytochromobilin must arise by oxidation of Phycobilin chromophores. This pigment is not obtained by similar treatment of a cyanobacterium and a rhodophyte that lack phycoerythrin. Therefore, 3(E)-phytochromobilin appears to be derived from phycoerythrobilin-containing proteins. Comparative CD spectroscopy of 3(E)-phytochrombilin and 3(E)-phycocyanobilin suggests that the two bilins share the R stereochemistry at the 2-position in the reduced pyrrole ring. Incubation of 2(R),3(E)-phytochromobilin with recombinant oat apophytochrome yields a covalent bilin adduct that is photoactive and spectrally indistinguishable from native oat phytochrome isolated from etiolated seedlings. These results establish that the phycobiliprotein-derived 2(R),3(E)-phytochromobilin is a biologically active phytochrome chromophore precursor.
Wendy M Schluchter - One of the best experts on this subject based on the ideXlab platform.
-
CyanoLyase: a database of Phycobilin lyase sequences, motifs and functions
Nucleic Acids Research, 2012Co-Authors: Anthony Bretaudeau, Wendy M Schluchter, Laurence Garczarek, Morgane Ratin, Florian Humily, Christophe Six, François Coste, Gildas Le Corguillé, Olivier Collin, Frederic PartenskyAbstract:CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of Phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromo-phores (Phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly anno-tated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characteri-zed enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogen-etic analyses of all Phycobilin lyases families, de-scribes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliog-raphy about Phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluores-cent markers.
-
Effects of Modified Phycobilin Biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002 �
2010Co-Authors: Richard M. Alvey, Wendy M Schluchter, Avijit Biswas, Donald A BryantAbstract:Effects of modified Phycobilin biosynthesis in the cyanobacterium Synechococcus sp. strain PC
-
biogenesis of phycobiliproteins i cpcs i and cpcu mutants of the cyanobacterium synechococcus sp pcc 7002 define a heterodimeric phyococyanobilin lyase specific for β phycocyanin and allophycocyanin subunits
Journal of Biological Chemistry, 2008Co-Authors: Gaozhong Shen, Wendy M Schluchter, Donald A BryantAbstract:Abstract Phycobilin lyases covalently attach Phycobilin chromophores to apo-phycobiliproteins (PBPs). Genome analyses of the unicellular, marine cyanobacterium Synechococcus sp. PCC 7002 identified three genes, denoted cpcS-I, cpcU, and cpcV, that were possible candidates to encode phycocyanobilin (PCB) lyases. Single and double mutant strains for cpcS-I and cpcU exhibited slower growth rates, reduced PBP levels, and impaired assembly of phycobilisomes, but a cpcV mutant had no discernable phenotype. A cpcS-I cpcU cpcT triple mutant was nearly devoid of PBP. SDS-PAGE and mass spectrometry demonstrated that the cpcS-I and cpcU mutants produced an altered form of the phycocyanin (PC) β subunit, which had a mass ∼588 Da smaller than the wild-type protein. Some free PCB (mass = 588 Da) was tentatively detected in the phycobilisome fraction purified from the mutants. The modified PC from the cpcS-I, cpcU, and cpcS-I cpcU mutant strains was purified, and biochemical analyses showed that Cys-153 of CpcB carried a PCB chromophore but Cys-82 did not. These results show that both CpcS-I and CpcU are required for covalent attachment of PCB to Cys-82 of the PC β subunit in this cyanobacterium. Suggesting that CpcS-I and CpcU are also required for attachment of PCB to allophycocyanin subunits in vivo, allophycocyanin levels were significantly reduced in all but the CpcV-less strain. These conclusions have been validated by in vitro experiments described in the accompanying report (Saunee, N. A., Williams, S. R., Bryant, D. A., and Schluchter, W. M. (2008) J. Biol. Chem. 283, 7513-7522). We conclude that the maturation of PBP in vivo depends on three PCB lyases: CpcE-CpcF, CpcS-I-CpcU, and CpcT.
Richard M. Alvey - One of the best experts on this subject based on the ideXlab platform.
-
Effects of modified Phycobilin biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002.
Journal of bacteriology, 2011Co-Authors: Richard M. Alvey, Donald A BryantAbstract:The pathway for phycocyanobilin biosynthesis in Synechococcus sp. strain PCC 7002 comprises two enzymes: heme oxygenase and phycocyanobilin synthase (PcyA). The Phycobilin content of cells can be modified by overexpressing genes encoding alternative enzymes for biliverdin reduction. Overexpression of the pebAB and HY2 genes, encoding alternative ferredoxin-dependent biliverdin reductases, caused unique effects due to the overproduction of phycoerythrobilin and phytochromobilin, respectively. Colonies overexpressing pebAB became reddish brown and visually resembled strains that naturally produce phycoerythrin. This was almost exclusively due to the replacement of phycocyanobilin by phycoerythrobilin on the phycocyanin α-subunit. This phenotype was unstable, and such strains rapidly reverted to the wild-type appearance, presumably due to strong selective pressure to inactivate pebAB expression. Overproduction of phytochromobilin, synthesized by the Arabidopsis thaliana HY2 product, was tolerated much better. Cells overexpressing HY2 were only slightly less pigmented and blue-green than the wild type. Although the pcyA gene could not be inactivated in the wild type, pcyA was easily inactivated when cells expressed HY2. These results indicate that phytochromobilin can functionally substitute for phycocyanobilin in Synechococcus sp. strain PCC 7002. Although functional phycobilisomes were assembled in this strain, the overall phycobiliprotein content of cells was lower, the efficiency of energy transfer by these phycobilisomes was lower than for wild-type phycobilisomes, and the absorption cross-section of the cells was reduced relative to that of the wild type because of an increased spectral overlap of the modified phycobiliproteins with chlorophyll a. As a result, the strain producing phycobiliproteins carrying phytochromobilin grew much more slowly at low light intensity.
-
Effects of Modified Phycobilin Biosynthesis in the Cyanobacterium Synechococcus sp. Strain PCC 7002 �
2010Co-Authors: Richard M. Alvey, Wendy M Schluchter, Avijit Biswas, Donald A BryantAbstract:Effects of modified Phycobilin biosynthesis in the cyanobacterium Synechococcus sp. strain PC
Humily Florian - One of the best experts on this subject based on the ideXlab platform.
-
A Gene Island with Two Possible Configurations Is Involved in Chromatic Acclimation in Marine Synechococcus
'Public Library of Science (PLoS)', 2013Co-Authors: Humily Florian, Partensky Frédéric, Six Christophe, Farrant, Gregory K., Ratin Morgane, Marie Dominique, Garczarek LaurenceAbstract:International audienceSynechococcus, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the Phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine Synechococcus radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (fciA/b) coding for possible transcriptional regulators and one gene coding for a Phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the mpeZ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called fciC. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While mpeZ is expressed more in blue light than green light, this is the reverse for mpeW, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process
-
Etude génomique, métagénomique et physiologique de la diversité pigmentaire chez les cyanobactéries du genre synechococcus
2013Co-Authors: Humily Florian, Partensky FrédéricAbstract:Les picocyanobactéries du genre Synechococcus sont présentes dans tous les types d'environnements marins. Cette ubiquité s'explique en partie par la grande diversité pigmentaire de ces cellules, leur permettant de capturer efficacement la lumière sur une large gamme spectrale. La plupart des souches ont une composition pigmentaire fixe mais certaines sont capables d'ajuster leur pigmentation en fonction de la lumière incidente par un processus physiologique appelé acclimatation chromatique de type IV (AC4). Une approche de métagénomique ciblée originale, combinant des techniques sophistiquées, a été développée afin d'étudier la diversité et la distribution des différents types pigmentaires de Synechococcus in situ. L'intérêt de cette approche a pu être démontré après des optimisations spécifiques. La disponibilité de 25 nouveaux génomes de Synechococcus a permis de faire d'importantes avancées sur la compréhension du mécanisme d'AC4. Un cluster de 4 à 6 gènes, codant pour une Phycobiline-lyase et plusieurs régulateurs transcriptionnels, est systématiquement présent chez toutes les souches capables de cette plasticité phénotypique. Deux configurations bien distinctes de ce cluster, nommées AC4-A et AC4-B, ont été découvertes et se retrouvent dans des lignées différentes de Synechococcus. Ces deux types de clusters auraient été soumis à des processus évolutifs distincts. Par ailleurs, certaines singularités phénotypiques entre les souches possédant ces deux types de clusters génomiques ont pu être démontrées. Ce travail de thèse soulève de nouvelles hypothèses sur la régulation de cette plasticité phénotypique ainsi que sur les mécanismes biochimiques associés.Picocyanobacteria of the Synechococcus genus are present in all marine environments. This ubiquity is partly explained by the large pigment diversity found within this genus, allowing them to efficiently capture photons over a broad spectral range. Most strains have a fixed pigmentation but some of them are able to match their pigmentation with the ambient light quality by a physiological process called type IV chromatic acclimation (CA4). An original targeted metagenomics approach, combining sophisticated techniques, was developed to study the diversity and distribution of pigment types of Synechococcus in situ. The interest of our approach has been demonstrated after specific optimizations. Availability of 25 new genomes of Synechococcus has allowed us to make significant advances in the understanding of molecular mechanism of CA4. A cluster of 4 to 6 genes, encoding a Phycobilin lyase and several transcriptional regulators, is consistently present in all strains capable of this phenotypic plasticity. Two distinct configurations of this cluster, named CA4-A and CA4-B, have been discovered and were found in different Synechococcus lineages. These two types of clusters have undergone distinct evolutionary processes. In addition, some phenotypic peculiarities between strains having these two types of genomic clusters have been demonstrated. This thesis raises new hypotheses about the regulation of this phenotypic plasticity as well as the biochemical mechanisms involved.PARIS-BIUSJ-Sci.Terre recherche (751052114) / SudocROSCOFF-Observ.Océanol. (292393008) / SudocSudocFranceF
-
ÉTUDE GÉNOMIQUE, MÉTAGÉNOMIQUE ET PHYSIOLOGIQUE DE LA DIVERSITÉ PIGMENTAIRE CHEZ LES CYANOBACTÉRIES DU GENRE SYNECHOCOCCUS
HAL CCSD, 2013Co-Authors: Humily FlorianAbstract:Picocyanobacteria of the Synechococcus genus are present in all marine environments. This ubiquity is partly explained by the large pigment diversity found within this genus, allowing them to efficiently capture photons over a broad spectral range. Most strains have a fixed pigmentation but some of them are able to match their pigmentation with the ambient light quality by a physiological process called type IV chromatic acclimation (CA4). An original targeted metagenomics approach, combining sophisticated techniques, was developed to study the diversity and distribution of pigment types of Synechococcus in situ. The interest of our approach has been demonstrated after specific optimizations. Availability of 25 new genomes of Synechococcus has allowed us to make significant advances in the understanding of molecular mechanism of CA4. A cluster of 4 to 6 genes, encoding a Phycobilin lyase and several transcriptional regulators, is consistently present in all strains capable of this phenotypic plasticity. Two distinct configurations of this cluster, named CA4-A and CA4-B, have been discovered and were found in different Synechococcus lineages. These two types of clusters have undergone distinct evolutionary processes. In addition, some phenotypic peculiarities between strains having these two types of genomic clusters have been demonstrated. This thesis raises new hypotheses about the regulation of this phenotypic plasticity as well as the biochemical mechanisms involved. Keywords : Synechococcus, pigment diversity, genetic diversity, targeted metagenomics, chromatic acclimationLes picocyanobactéries du genre Synechococcus sont présentes dans tous les types d'environnements marins. Cette ubiquité s'explique en partie par la grande diversité pigmentaire de ces cellules, leur permettant de capturer efficacement la lumière sur une large gamme spectrale. La plupart des souches ont une composition pigmentaire fixe mais certaines sont capables d'ajuster leur pigmentation en fonction de la lumière incidente par un processus physiologique appelé acclimatation chromatique de type IV (AC4). Une approche de métagénomique ciblée originale, combinant des techniques sophistiquées, a été développée afin d'étudier la diversité et la distribution des différents types pigmentaires de Synechococcus in situ. L'intérêt de cette approche a pu être démontré après des optimisations spécifiques. La disponibilité de 25 nouveaux génomes de Synechococcus a permis de faire d'importantes avancées sur la compréhension du mécanisme d'AC4. Un cluster de 4 à 6 gènes, codant pour une Phycobiline-lyase et plusieurs régulateurs transcriptionnels, est systématiquement présent chez toutes les souches capables de cette plasticité phénotypique. Deux configurations bien distinctes de ce cluster, nommées AC4-A et AC4-B, ont été découvertes et se retrouvent dans des lignées différentes de Synechococcus. Ces deux types de clusters auraient été soumis à des processus évolutifs distincts. Par ailleurs, certaines singularités phénotypiques entre les souches possédant ces deux types de clusters génomiques ont pu être démontrées. Ce travail de thèse soulève de nouvelles hypothèses sur la régulation de cette plasticité phénotypique ainsi que sur les mécanismes biochimiques associés
-
CyanoLyase: a database of Phycobilin lyase sequences, motifs and functions
'Oxford University Press (OUP)', 2012Co-Authors: Bretaudeau Anthony, Garczarek Laurence, Schluchter, Wendy M, Humily Florian, Six Christophe, Ratin Morgane, Coste François, Le Corguillé Gildas, Collin Olivier, Partensky FrédéricAbstract:International audienceCyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of Phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromo-phores (Phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly anno-tated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characteri-zed enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogen-etic analyses of all Phycobilin lyases families, de-scribes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliog-raphy about Phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluores-cent markers