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The Plant Journal : For Cell and... Nov 2020The photosynthetic bacterial phycobiliprotein lyases, also called CpcT lyases, catalyze the biogenesis of phycobilisome, a light-harvesting antenna complex, through the...
The photosynthetic bacterial phycobiliprotein lyases, also called CpcT lyases, catalyze the biogenesis of phycobilisome, a light-harvesting antenna complex, through the covalent attachment of chromophores to the antenna proteins. The Arabidopsis CRUMPLED LEAF (CRL) protein is a homolog of the cyanobacterial CpcT lyase. Loss of CRL leads to multiple lesions, including localized foliar cell death, constitutive expression of stress-related nuclear genes, abnormal cell cycle, and impaired plastid division. Notwithstanding the apparent phenotypes, the function of CRL still remains elusive. To gain insight into the function of CRL, we examined whether CRL still retains the capacity to bind with the bacterial chromophore phycocyanobilin (PCB) and its plant analog phytochromobilin (PΦB). The revealed structure of the CpcT domain of CRL is comparable to that of the CpcT lyase, despite the low sequence identity. The subsequent in vitro biochemical assays found, as shown for the CpcT lyase, that PCB/PΦB binds to the CRL dimer. However, some mutant forms of CRL, substantially compromised in their bilin-binding ability, still restore the crl-induced multiple lesions. These results suggest that although CRL retains the bilin-binding pocket, it seems not functionally associated with the crl-induced multiple lesions.
Topics: Arabidopsis; Arabidopsis Proteins; Bile Pigments; Cell Division; Cyanobacteria; Lyases; Mutation; Phenotype; Phycobilins; Phycobiliproteins; Phycobilisomes; Phycocyanin; Plastids; Protein Binding
PubMed: 32860438
DOI: 10.1111/tpj.14974 -
Journal of Applied Phycology 2016The optical properties, i.e., absorption and scattering spectra of ten strains of cyanobacteria from the Baltic Sea and Pomeranian lakes ( KAC 15, CCNP 1101, sp. CCNP...
The optical properties, i.e., absorption and scattering spectra of ten strains of cyanobacteria from the Baltic Sea and Pomeranian lakes ( KAC 15, CCNP 1101, sp. CCNP 1406, CCNP 1104, sp. CCNP 1317, CCNP 1401, sp. CCNP 1108, sp. CCNP 1411, sp. CCNP 1105, CCNP 1312) grown under low light conditions were investigated. Moreover, the chlorophylls, carotenoids, and phycobilin composition as well as the size structure of chosen cyanobacteria were measured. Studied species revealed high diversity both in optical properties with the absorption spectra similarity index ranging from 0.67 to 0.94 and the pigment composition. The chlorophyll-specific absorption coefficient at 440 nm *(440) varied between 0.017 and 0.065 m mg. The influence of the package effect was only observed in the case of large filamentous cyanobacteria like or sp. Interestingly, the package effect factor *(675) for large-celled sp. was 0.92. Besides chlorophyll , only echinenone, -carotene, and phycocyanin were present in all analyzed cyanobacteria strains. Zeaxanthin, which is widely used as a marker pigment for cyanobacteria, was absent in the toxic and sp., which are the species that occur in the Baltic Sea most frequently causing summer cyanobacterial blooms. The investigation also showed that the sample preservation technique can introduce some major errors within the absorption band affected by the phycocyanin absorption.
PubMed: 27471342
DOI: 10.1007/s10811-015-0774-3 -
Photosynthesis Research Mar 2018Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel...
Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active αβ·αβ-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.
Topics: Acclimatization; Amino Acid Sequence; Cells, Cultured; Cryptophyta; Light; Light-Harvesting Protein Complexes; Models, Genetic; Models, Molecular; Photosynthesis; Phycobiliproteins; Plant Proteins; Protein Subunits; Proteomics; Spectrometry, Fluorescence; Temperature
PubMed: 28540588
DOI: 10.1007/s11120-017-0400-0 -
BMC Genomics Jun 2016Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of...
BACKGROUND
Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture.
RESULTS
The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90.
CONCLUSION
Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and function.
Topics: Anabaena; Computational Biology; Cyanobacteria Toxins; Energy Metabolism; Genome, Bacterial; Genomics; High-Throughput Nucleotide Sequencing; Metabolic Networks and Pathways; Metabolome; Metabolomics; Molecular Sequence Annotation; Phylogeny; Promoter Regions, Genetic; Synteny; Tandem Repeat Sequences; Tropanes
PubMed: 27296936
DOI: 10.1186/s12864-016-2738-7 -
Proceedings. Biological Sciences May 2019Evolutionary biologists have long sought to identify phenotypic traits whose evolution enhances an organism's performance in its environment. Diversification of traits...
Evolutionary biologists have long sought to identify phenotypic traits whose evolution enhances an organism's performance in its environment. Diversification of traits related to resource acquisition can occur owing to spatial or temporal resource heterogeneity. We examined the ability to capture light in the Cryptophyta, a phylum of single-celled eukaryotic algae with diverse photosynthetic pigments, to better understand how acquisition of an abiotic resource may be associated with diversification. Cryptophytes originated through secondary endosymbiosis between an unknown eukaryotic host and a red algal symbiont. This merger resulted in distinctive pigment-protein complexes, the cryptophyte phycobiliproteins, which are the products of genes from both ancestors. These novel complexes may have facilitated diversification across environments where the spectrum of light available for photosynthesis varies widely. We measured light capture and pigments under controlled conditions in a phenotypically and phylogenetically diverse collection of cryptophytes. Using phylogenetic comparative methods, we found that phycobiliprotein characteristics were evolutionarily associated with diversification of light capture in cryptophytes, while non-phycobiliprotein pigments were not. Furthermore, phycobiliproteins were evolutionarily labile with repeated transitions and reversals. Thus, the endosymbiotic origin of cryptophyte phycobiliproteins provided an evolutionary spark that drove diversification of light capture, the resource that is the foundation of photosynthesis.
Topics: Biological Evolution; Cryptophyta; Photosynthesis; Phycobiliproteins; Symbiosis
PubMed: 31088271
DOI: 10.1098/rspb.2019.0655 -
Molecules (Basel, Switzerland) Nov 2020We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR)...
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.
Topics: Carbon; Carbon Isotopes; Color; Magnetic Resonance Spectroscopy; Models, Theoretical; Molecular Conformation; Molecular Dynamics Simulation; Phycobilins; Phycocyanin
PubMed: 33255423
DOI: 10.3390/molecules25235505 -
Frontiers in Microbiology 2017Marine has successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant group of...
Marine has successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant group of microorganisms worldwide. Populations of that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromophore phycourobilin (PUB) in their light harvesting complexes (phycobilisomes). Here, we show that all strains adapted to blue light possess a gene called . MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of caused a reduction in PUB content, impaired phycobilisome assembly and reduced growth rate more strongly in blue than green light. When was reintroduced in the mutant background, the less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mutant cells and purified phycobilisomes revealed red-shifted phycoerythrin emission peaks, likely indicating a defect in chromophore ligation to phycoerythrin-I (PE-I) or phycoerythrin-II (PE-II). Our results suggest that MpeU is a lyase-isomerase that attaches a phycoerythrobilin to a PEI or PEII subunit and isomerizes it to PUB. MpeU is therefore an important determinant in adaptation of spp. to capture photons in blue light environments throughout the world's oceans.
PubMed: 28270800
DOI: 10.3389/fmicb.2017.00243 -
Bioengineered Jan 2018The fusion protein (SLA) of streptavidin and allophycocyanin α subunit (holo-ApcA) was biosynthesized in Escherichia coli by a dual plasmid system. The recombinant SLA,...
The fusion protein (SLA) of streptavidin and allophycocyanin α subunit (holo-ApcA) was biosynthesized in Escherichia coli by a dual plasmid system. The recombinant SLA, purified by affinity chromatography, showed spectral properties similar to natural allophycocyanin α subunit (ApcA). Spectral and Zinc staining analysis indicated that the recombinant SLA covalently bound phycocyanobilin (PCB). To improve chromophorylation rate of recombinant SLA, an in vitro chromophore attachment reaction system was established, which contained partially chromophylated SLA, PCB and lyase CpcS. Spectral analysis showed that PCB bound to the recombinant SLA rapidly during the reaction. The chromophorylation rate of SLA was improved from 21.1% to 86.5%. Immunofluorescence assay showed that SLA with high chromophorylation rate had higher detection signal. Thus, in vitro chromophore attachment is an effective way to improve the chromophorylation rate of recombinant phycobiliprotein.
Topics: Cloning, Molecular; Escherichia coli; Fluorescent Antibody Technique, Direct; Gene Expression; Genetic Vectors; Hydrogen-Ion Concentration; Phycobilins; Phycocyanin; Protein Subunits; Recombinant Fusion Proteins; Streptavidin; Temperature
PubMed: 28448741
DOI: 10.1080/21655979.2017.1321282 -
The Journal of General and Applied... Jul 2016Two-component signal transduction systems (TCS) are involved in widespread cellular responses to diverse signals from bacteria to plants. Cyanobacteria have evolved...
Two-component signal transduction systems (TCS) are involved in widespread cellular responses to diverse signals from bacteria to plants. Cyanobacteria have evolved photoperception systems for efficient photosynthesis, and some histidine kinases are known to function as photosensors. In this study, we attempt to reconstruct the photoperception system in Escherichia coli to make an easily controllable ON/OFF switch for gene expressions. For this purpose, a CcaS-CcaR two-component system from Nostoc punctiforme was expressed with phycocyanobilin (PCB) producing enzymes in E. coli which carries a G-box-controlled reporter gene. We succeeded to endow E. coli with a gene activation switch that is regulated in a light-color dependent manner. The possibility of such a switch for the development of synthetic biology is pointed out.
Topics: Bacterial Proteins; Escherichia coli; Gene Expression Regulation, Bacterial; Genetic Engineering; Light; Light Signal Transduction; Nostoc; Photoreceptors, Microbial; Photosynthesis; Phycobilins; Phycocyanin; Synthetic Biology
PubMed: 27246537
DOI: 10.2323/jgam.2016.01.006 -
Biophysical Journal Nov 2014Cyanobacteriochromes are members of the phytochrome superfamily of photoreceptors and are of central importance in biological light-activated signaling mechanisms. These...
Cyanobacteriochromes are members of the phytochrome superfamily of photoreceptors and are of central importance in biological light-activated signaling mechanisms. These photoreceptors are known to reversibly convert between two states in a photoinitiated process that involves a basic E/Z isomerization of the bilin chromophore and, in certain cases, the breakage of a thioether linkage to a conserved cysteine residue in the bulk protein structure. The exact details and timescales of the reactions involved in these photoconversions have not been conclusively shown. The cyanobacteriochrome Tlr0924 contains phycocyanobilin and phycoviolobilin chromophores, both of which photoconvert between two species: blue-absorbing and green-absorbing, and blue-absorbing and red-absorbing, respectively. Here, we followed the complete green-to-blue photoconversion process of the phycoviolobilin chromophore in the full-length form of Tlr0924 over timescales ranging from femtoseconds to seconds. Using a combination of time-resolved visible and mid-infrared transient absorption spectroscopy and cryotrapping techniques, we showed that after photoisomerization, which occurs with a lifetime of 3.6 ps, the phycoviolobilin twists or distorts slightly with a lifetime of 5.3 ?s. The final step, the formation of the thioether linkage with the protein, occurs with a lifetime of 23.6 ms.
Topics: Cyanobacteria; Light; Molecular Structure; Photochemical Processes; Photoreceptors, Microbial; Phycobilins; Phycocyanin; Protein Conformation; Spectrum Analysis
PubMed: 25418104
DOI: 10.1016/j.bpj.2014.09.020