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The increasing role of structural proteomics in cyanobacteria. Essays Biochem 2022; 67:269-282. [PMID: 36503929 PMCID: PMC10070481 DOI: 10.1042/ebc20220095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Abstract
Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.
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Soulier N, Laremore TN, Bryant DA. Characterization of cyanobacterial allophycocyanins absorbing far-red light. PHOTOSYNTHESIS RESEARCH 2020; 145:189-207. [PMID: 32710194 DOI: 10.1007/s11120-020-00775-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Phycobiliproteins (PBPs) are pigment proteins that comprise phycobilisomes (PBS), major light-harvesting antenna complexes of cyanobacteria and red algae. PBS core substructures are made up of allophycocyanins (APs), a subfamily of PBPs. Five paralogous AP subunits are encoded by the Far-Red Light Photoacclimation (FaRLiP) gene cluster, which is transcriptionally activated in cells grown in far-red light (FRL; λ = 700 to 800 nm). FaRLiP gene expression enables some terrestrial cyanobacteria to remodel their PBS and photosystems and perform oxygenic photosynthesis in far-red light (FRL). Paralogous AP genes encoding a putative, FRL-absorbing AP (FRL-AP) are also found in an operon associated with improved low-light growth (LL; < 50 μmol photons m-2 s-1) in some thermophilic Synechococcus spp., a phenomenon termed low-light photoacclimation (LoLiP). In this study, apc genes from FaRLiP and LoLiP gene clusters were heterologously expressed individually and in combinations in Escherichia coli. The resulting novel FRL-APs were characterized and identified as major contributors to the FRL absorbance observed in whole cells after FaRLiP and potentially LoLiP. Post-translational modifications of native FRL-APs from FaRLiP cyanobacterium, Leptolyngbya sp. strain JSC-1, were analyzed by mass spectrometry. The PBP complexes made in two FaRLiP organisms were compared, revealing strain-specific diversity in the FaRLiP responses of cyanobacteria. Through analyses of native and recombinant proteins, we improved our understanding of how different cyanobacterial strains utilize specialized APs to acclimate to FRL and LL. We discuss some insights into structural changes that may allow these APs to absorb longer light wavelengths than their visible-light-absorbing paralogs.
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Affiliation(s)
- Nathan Soulier
- S-002 Frear Laboratory, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tatiana N Laremore
- Proteomics and Mass Spectrometry Core Facility, Huck Institute for the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Donald A Bryant
- S-002 Frear Laboratory, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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3
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Sonani RR, Roszak AW, Liu H, Gross ML, Blankenship RE, Madamwar D, Cogdell RJ. Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin. PHOTOSYNTHESIS RESEARCH 2020; 144:349-360. [PMID: 32303893 PMCID: PMC7491960 DOI: 10.1007/s11120-020-00746-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
The crystal structure of phycocyanin (pr-PC) isolated from Phormidium rubidum A09DM (P. rubidum) is described at a resolution of 1.17 Å. Electron density maps derived from crystallographic data showed many clear differences in amino acid sequences when compared with the previously obtained gene-derived sequences. The differences were found in 57 positions (30 in α-subunit and 27 in β-subunit of pr-PC), in which all residues except one (β145Arg) are not interacting with the three phycocyanobilin chromophores. Highly purified pr-PC was then sequenced by mass spectrometry (MS) using LC-MS/MS. The MS data were analyzed using two independent proteomic search engines. As a result of this analysis, complete agreement between the polypeptide sequences and the electron density maps was obtained. We attribute the difference to multiple genes in the bacterium encoding the phycocyanin apoproteins and that the gene sequencing sequenced the wrong ones. We are not implying that protein sequencing by mass spectrometry is more accurate than that of gene sequencing. The final 1.17 Å structure of pr-PC allows the chromophore interactions with the protein to be described with high accuracy.
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Affiliation(s)
- Ravi R Sonani
- Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India
- Małopolska Centre of Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Aleksander W Roszak
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Haijun Liu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, Sardar Patel University, Bakrol, Anand, Gujarat, 388 315, India.
| | - Richard J Cogdell
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK.
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Bar-Zvi S, Lahav A, Harris D, Niedzwiedzki DM, Blankenship RE, Adir N. Structural heterogeneity leads to functional homogeneity in A. marina phycocyanin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:544-553. [DOI: 10.1016/j.bbabio.2018.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
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5
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Franke B, Colgrave ML, Mylne JS, Rosengren KJ. Mature forms of the major seed storage albumins in sunflower: A mass spectrometric approach. J Proteomics 2016; 147:177-186. [DOI: 10.1016/j.jprot.2016.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/15/2016] [Accepted: 05/06/2016] [Indexed: 11/27/2022]
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6
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Marx A, David L, Adir N. Piecing Together the Phycobilisome. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet 2013; 9:e1003210. [PMID: 23349634 PMCID: PMC3547847 DOI: 10.1371/journal.pgen.1003210] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 11/14/2012] [Indexed: 01/01/2023] Open
Abstract
Methylation is a post-translational modification that can affect numerous features of proteins, notably cellular localization, turnover, activity, and molecular interactions. Recent genome-wide analyses have considerably extended the list of human genes encoding putative methyltransferases. Studies on protein methyltransferases have revealed that the regulatory function of methylation is not limited to epigenetics, with many non-histone substrates now being discovered. We present here our findings on a novel family of distantly related putative methyltransferases. Affinity purification coupled to mass spectrometry shows a marked preference for these proteins to associate with various chaperones. Based on the spectral data, we were able to identify methylation sites in substrates, notably trimethylation of K135 of KIN/Kin17, K561 of HSPA8/Hsc70 as well as corresponding lysine residues in other Hsp70 isoforms, and K315 of VCP/p97. All modification sites were subsequently confirmed in vitro. In the case of VCP, methylation by METTL21D was stimulated by the addition of the UBX cofactor ASPSCR1, which we show directly interacts with the methyltransferase. This stimulatory effect was lost when we used VCP mutants (R155H, R159G, and R191Q) known to cause Inclusion Body Myopathy with Paget's disease of bone and Fronto-temporal Dementia (IBMPFD) and/or familial Amyotrophic Lateral Sclerosis (ALS). Lysine 315 falls in proximity to the Walker B motif of VCP's first ATPase/D1 domain. Our results indicate that methylation of this site negatively impacts its ATPase activity. Overall, this report uncovers a new role for protein methylation as a regulatory pathway for molecular chaperones and defines a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of degenerative neuromuscular diseases. Methylation, or transfer of a single or multiple methyl groups (CH3), is one of many post-translational modifications that occur on proteins. Such modifications can, in turn, affect numerous aspects of a protein, notably cellular localization, turnover, activity, and molecular interactions. In addition to post-translational modifications, the structural organization of a protein or protein complex can also have a significant impact on its function and stability. A group of factors known as “molecular chaperones” aid newly synthesized proteins in reaching their native conformation or alternating between physiologically relevant states. We present here a new family of factors that promote methylation of chaperones and show that, at least in one case, this modification translates into a modulation in the activity of the substrate chaperone. Our results not only characterize the function of previously unknown gene products, uncover a new role for protein methylation as a regulatory pathway for chaperones, and define a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of neuromuscular diseases, but also suggest the existence of a post-translational modification code that regulates molecular chaperones. Further decrypting this “chaperone code” will help understanding how the functional organization of the proteome is orchestrated.
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Mathieu Lavallée-Adam
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
- Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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8
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Marx A, Adir N. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [PMID: 23201474 DOI: 10.1016/j.bbabio.2012.11.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.
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Affiliation(s)
- Ailie Marx
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
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Camara-Artigas A, Bacarizo J, Andujar-Sanchez M, Ortiz-Salmeron E, Mesa-Valle C, Cuadri C, Martin-Garcia JM, Martinez-Rodriguez S, Mazzuca-Sobczuk T, Ibañez MJ, Allen JP. pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum. FEBS J 2012; 279:3680-3691. [PMID: 22863205 DOI: 10.1111/j.1742-4658.2012.08730.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/22/2012] [Accepted: 07/25/2012] [Indexed: 11/26/2022]
Abstract
B-phycoerythrin from the red alga Porphyridium cruentum was crystallized using the technique of capillary counter-diffusion. Crystals belonging to the space group R3 with almost identical unit cell constants and diffracting to 1.85 and 1.70 Å were obtained at pH values of 5 and 8, respectively. The most important difference between structures is the presence of the residue His88α in two different conformations at pH 8. This residue is placed next to the chromophore phycoerythrobilin PEB82α and the new conformation results in the relocation of the hydrogen-bond network and hydration around PEB82α, which probably contributes to the observed pH dependence of the optical spectrum associated with this chromophore. Comparison with the structures of B-phycoerythrin from other red algae shows differences in the conformation of the A-ring of the chromophore PEB139α. This conformational difference in B-phycoerythrin from P. cruentum enables the formation of several hydrogen bonds that connect PEB139α with the chromophore PEB158β at the (αβ)(3) hexamer association interface. The possible influence of these structural differences on the optical spectrum and the ability of the protein to perform energy transfer are discussed, with the two pH-dependent conformations of His88α and PEB82α being proposed as representing critical structural features that are correlated with the pH dependence of the optical spectrum and transient optical states during energy transfer.
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Affiliation(s)
- Ana Camara-Artigas
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Julio Bacarizo
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Montserrat Andujar-Sanchez
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Emilia Ortiz-Salmeron
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Concepcion Mesa-Valle
- Department of Applied Biology, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Celia Cuadri
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Jose M Martin-Garcia
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain.,Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA
| | - Sergio Martinez-Rodriguez
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Tania Mazzuca-Sobczuk
- Department of Chemical Engineering, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - Maria J Ibañez
- Department of Chemical Engineering, Agrifood Campus of International Excellence (CeiA3), University of Almería, Spain
| | - James P Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA
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10
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Biswas A, Vasquez YM, Dragomani TM, Kronfel ML, Williams SR, Alvey RM, Bryant DA, Schluchter WM. Biosynthesis of cyanobacterial phycobiliproteins in Escherichia coli: chromophorylation efficiency and specificity of all bilin lyases from Synechococcus sp. strain PCC 7002. Appl Environ Microbiol 2010; 76:2729-39. [PMID: 20228104 PMCID: PMC2863458 DOI: 10.1128/aem.03100-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/01/2010] [Indexed: 11/20/2022] Open
Abstract
Phycobiliproteins are water-soluble, light-harvesting proteins that are highly fluorescent due to linear tetrapyrrole chromophores, which makes them valuable as probes. Enzymes called bilin lyases usually attach these bilin chromophores to specific cysteine residues within the alpha and beta subunits via thioether linkages. A multiplasmid coexpression system was used to recreate the biosynthetic pathway for phycobiliproteins from the cyanobacterium Synechococcus sp. strain PCC 7002 in Escherichia coli. This system efficiently produced chromophorylated allophycocyanin (ApcA/ApcB) and alpha-phycocyanin with holoprotein yields ranging from 3 to 12 mg liter(-1) of culture. This heterologous expression system was used to demonstrate that the CpcS-I and CpcU proteins are both required to attach phycocyanobilin (PCB) to allophycocyanin subunits ApcD (alpha(AP-B)) and ApcF (beta(18)). The N-terminal, allophycocyanin-like domain of ApcE (L(CM)(99)) was produced in soluble form and was shown to have intrinsic bilin lyase activity. Lastly, this in vivo system was used to evaluate the efficiency of the bilin lyases for production of beta-phycocyanin.
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Affiliation(s)
- Avijit Biswas
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yasmin M. Vasquez
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tierna M. Dragomani
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Monica L. Kronfel
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Shervonda R. Williams
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Richard M. Alvey
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Donald A. Bryant
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wendy M. Schluchter
- Department of Biological Science, University of New Orleans, New Orleans, Louisiana 70148, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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Schluchter WM, Shen G, Alvey RM, Biswas A, Saunée NA, Williams SR, Mille CA, Bryant DA. Phycobiliprotein biosynthesis in cyanobacteria: structure and function of enzymes involved in post-translational modification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 675:211-28. [PMID: 20532743 DOI: 10.1007/978-1-4419-1528-3_12] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyanobacterial phycobiliproteins are brilliantly colored due to the presence of covalently attached chromophores called bilins, linear tetrapyrroles derived from heme. For most phycobiliproteins, these post-translational modifications are catalyzed by enzymes called bilin lyases; these enzymes ensure that the appropriate bilins are attached to the correct cysteine residues with the proper stereochemistry on each phycobiliprotein subunit. Phycobiliproteins also contain a unique, post-translational modification, the methylation of a conserved asparagine (Asn) present at beta-72, which occurs on the beta-subunits of all phycobiliproteins. We have identified and characterized several new families of bilin lyases, which are responsible for attaching PCB to phycobiliproteins as well as the Asn methyl transferase for beta-subunits in Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. All of the enzymes responsible for synthesis of holo-phycobiliproteins are now known for this cyanobacterium, and a brief discussion of each enzyme family and its role in the biosynthesis of phycobiliproteins is presented here. In addition, the first structure of a bilin lyase has recently been solved (PDB ID: 3BDR). This structure shows that the bilin lyases are most similar to the lipocalin protein structural family, which also includes the bilin-binding protein found in some butterflies.
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Affiliation(s)
- Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA.
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12
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Miller CA, Leonard HS, Pinsky IG, Turner BM, Williams SR, Harrison L, Fletcher AF, Shen G, Bryant DA, Schluchter WM. Biogenesis of phycobiliproteins. III. CpcM is the asparagine methyltransferase for phycobiliprotein beta-subunits in cyanobacteria. J Biol Chem 2008; 283:19293-300. [PMID: 18482977 DOI: 10.1074/jbc.m802734200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All phycobiliproteins contain a conserved, post-translational modification on asparagine 72 of their beta-subunits. Methylation of this Asn to produce gamma-N-methylasparagine has been shown to increase energy transfer efficiency within the phycobilisome and to prevent photoinhibition. We report here the biochemical characterization of the product of sll0487, which we have named cpcM, from the cyanobacterium Synechocystis sp. PCC 6803. Recombinant apo-phycocyanin and apo-allophycocyanin subunits were used as the substrates for assays with [methyl-3H]S-adenosylmethionine and recombinant CpcM. CpcM methylated the beta-subunits of phycobiliproteins (CpcB, ApcB, and ApcF) and did not methylate the corresponding alpha-subunits (CpcA, ApcA, and ApcD), although they are similar in primary and tertiary structure. CpcM preferentially methylated its CpcB substrate after chromophorylation had occurred at Cys82. CpcM exhibited lower activity on trimeric phycocyanin after complete chromophorylation and oligomerization had occurred. Based upon these in vitro studies, we conclude that this post-translational modification probably occurs after chromophorylation but before trimer assembly in vivo.
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Affiliation(s)
- Crystal A Miller
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70148, USA
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13
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CpcM posttranslationally methylates asparagine-71/72 of phycobiliprotein beta subunits in Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803. J Bacteriol 2008; 190:4808-17. [PMID: 18469097 DOI: 10.1128/jb.00436-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved gamma-N-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted cpcM, that (i) encodes a protein with sequence similarity to other S-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding phycobiliproteins in cyanobacterial genomes. The cpcM genes of Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the cpcM mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the cpcM mutant of Synechocystis sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the cpcM mutants and suggested that energy transfer from phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of phycobiliproteins are discussed.
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14
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Shen G, Schluchter WM, Bryant DA. Biogenesis of phycobiliproteins: I. cpcS-I and cpcU mutants of the cyanobacterium Synechococcus sp. PCC 7002 define a heterodimeric phyococyanobilin lyase specific for beta-phycocyanin and allophycocyanin subunits. J Biol Chem 2008; 283:7503-12. [PMID: 18199754 DOI: 10.1074/jbc.m708164200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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) beta subunit, which had a mass approximately 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 beta 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 (Saunée, 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.
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Affiliation(s)
- Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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15
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Klotz AV. 15 Modification of phycobiliproteins at asparagine residues. Enzymes 2007; 24:455-463. [PMID: 26718049 DOI: 10.1016/s1874-6047(06)80017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Side-chain amide methylation of asparagine was described in a special complement of photosynthesis accessory pigment-protein complexes called phycobiliproteins nearly 20 years ago. Since that report, several investigations have assigned this posttranslational modification a functional role in tuning the spectroscopic properties of the phycobiliprotein chromophores. Asparagine methylation has not been reported in other systems and is restricted to the broader phycobiliprotein family. The methyltransferase responsible for this modification has been partially characterized but the structural gene has not been identified.
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Affiliation(s)
- Alan V Klotz
- Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis, IN 46285, USA
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16
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Krishna RG, Wold F. Post-translational modification of proteins. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:265-98. [PMID: 8322616 DOI: 10.1002/9780470123133.ch3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R G Krishna
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston
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17
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Adir N, Dines M, Klartag M, McGregor A, Melamed-Frank M. Assembly and Disassembly of Phycobilisomes. MICROBIOLOGY MONOGRAPHS 2006. [DOI: 10.1007/7171_020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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18
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Adir N, Lerner N. The crystal structure of a novel unmethylated form of C-phycocyanin, a possible connector between cores and rods in pycobilisomes. J Biol Chem 2003; 278:25926-32. [PMID: 12709431 DOI: 10.1074/jbc.m302838200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel fraction of c-phycocyanin from the thermophilic cyanobacterium Thermosynechcoccus vulcanus, with an absorption maxima blue-shifted to 612 nm (PC612), has been purified from allophycocyanin and crystallized. The crystals belong to the P63 space group with cell dimensions of 153 A x 153 A x 59 A with a single (alphabeta) monomer in the asymmetric unit, resulting in a solvent content of 65%, and diffract to 2.7 A. The PC612 crystal structure has been determined by molecular replacement and refined to a crystallographic R-factor of 20.9% (Rfree = 27.8%). The crystal packing in this form shows that the PC612 form of phycocyanin does not associate into hexamers and that its association with adjacent trimers in the unit cell is very different from that found in a previously determined structure of the normal form of T. vulcanus phycocyanin, which absorbs at 620 nm. Analysis of the PC612 structure shows that the alpha subunits, which typically form the interface between two trimers within a hexamer, have a high degree of flexibility, as indicated by elevated B-factors in portions of helices B, E, and G. Examination of calculated electron density omit maps shows that unlike all other structures of phycobiliproteins determined so far, the Asnbeta72 residue is not methylated, explaining the blue-shift in its absorption spectra. On the basis of the results presented here, we suggest that this new form of trimeric phycocyanin may constitute a special minor component of the phycobilisome and may form the contact between the phycocyanin rods and the allophycocyanin core.
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Affiliation(s)
- Noam Adir
- Department of Chemistry and Institute of Catalysis, Science and Technology, Technion, Israel Institute of Technology, Technion City, Haifa 32000, Israel
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19
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Affiliation(s)
- Steven Clarke
- Department of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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20
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Rümbeli R, Suter F, Wirth M, Sidler W, Zuber H. γ-N-Methylasparagine in phycobiliproteins from the cyanobacteriaMastigocladus laminosusandCalothrix. FEBS Lett 2001. [DOI: 10.1016/0014-5793(87)80341-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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The structure of γ-N-methylasparagine in C-phycocyanin fromMastigocladus laminosusandAgmenellum quadruplicatum. FEBS Lett 2001. [DOI: 10.1016/0014-5793(88)80308-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Metzler DE, Metzler CM, Sauke DJ. An Introduction to Metabolism. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Wilk KE, Harrop SJ, Jankova L, Edler D, Keenan G, Sharples F, Hiller RG, Curmi PM. Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution. Proc Natl Acad Sci U S A 1999; 96:8901-6. [PMID: 10430868 PMCID: PMC17705 DOI: 10.1073/pnas.96.16.8901] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels. The crystal structure of the heterodimeric alpha(1)alpha(2)betabeta PE 545 from the marine cryptophyte Rhodomonas CS24 has been determined at 1.63-A resolution. Although the beta-chain structure is similar to the alpha and beta chains of other known phycobiliproteins, the overall structure of PE 545 is novel with the alpha chains forming a simple extended fold with an antiparallel beta-ribbon followed by an alpha-helix. The two doubly linked beta50/beta61 chromophores (one on each beta subunit) are in van der Waals contact, suggesting that exciton-coupling mechanisms may alter their spectral properties. Each alpha subunit carries a covalently linked 15,16-dihydrobiliverdin chromophore that is likely to be the final energy acceptor. The architecture of the heterodimer suggests that PE 545 may dock to an acceptor protein via a deep cleft and that energy may be transferred via this intermediary protein to the reaction center.
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Affiliation(s)
- K E Wilk
- Initiative in Biomolecular Structure, School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
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24
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Stec B, Troxler RF, Teeter MM. Crystal structure of C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly. Biophys J 1999; 76:2912-21. [PMID: 10354419 PMCID: PMC1300263 DOI: 10.1016/s0006-3495(99)77446-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The crystal structure of the light-harvesting protein phycocyanin from the cyanobacterium Cyanidium caldarium with novel crystal packing has been solved at 1.65-A resolution. The structure has been refined to an R value of 18.3% with excellent backbone and side-chain stereochemical parameters. In crystals of phycocyanin used in this study, the hexamers are offset rather than aligned as in other phycocyanins that have been crystallized to date. Analysis of this crystal's unique packing leads to a proposal for phycobilisome assembly in vivo and for a more prominent role for chromophore beta-155. This new role assigned to chromophore beta-155 in phycocyanin sheds light on the numerical relationships among and function of external chromophores found in phycoerythrins and phycoerythrocyanins.
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Affiliation(s)
- B Stec
- Department of Chemistry, Merkert Chemistry Building, Boston College, Chestnut Hill, Massachusetts 02167, USA.
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25
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Ducret A, Sidler W, Frank G, Zuber H. The complete amino acid sequence of R-phycocyanin-I alpha and beta subunits from the red alga Porphyridium cruentum. Structural and phylogenetic relationships of the phycocyanins within the phycobiliprotein families. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:563-80. [PMID: 8168545 DOI: 10.1111/j.1432-1033.1994.tb18769.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present here the complete primary structure of R-phycocyanin-I alpha and beta subunits from the red alga Porphyridium cruentum. The alpha chain is composed of 162 amino acid residues (18049 Da, calculated from sequence, including chromophore) and carries a phycocyanobilin pigment covalently linked to Cys84. The beta chain contains 172 amino acids (19344Da, calculated from sequence, including chromophores) and carries a phycocyanobilin pigment covalently linked at Cys82 and a phycoerythrobilin pigment at Cys153. A gamma-N-methyl asparagine residue was also characterised at position beta 72 similar to other phycobiliprotein beta subunits. R-phycocyanin-I from Porphyridium cruentum shares high sequence identity with C-phycocyanins (69-83%), R-phycocyanins (66-70%) and in a less extent with phycoerythrocyanins (57-65%) from various sources. The presented phylogenetic trees are based on a comparison of all phycobiliprotein amino acid sequences known so far and confirm the clear affiliation of the R-phycocyanins in the phycocyanin family. In spite of their particular phycobilin pattern, they do not represent intermediate forms between the phycocyanin and the phycoerythrin family. Phycoerythrocyanin, a phycocyanin-related phycobiliprotein adapted to green light harvesting, is also shown to belong to the phycocyanin family. However, the phycoerythrocyanins diverge from phycocyanins in their different function and it is suggested that they should be assigned to a separate group within the phycocyanin family.
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Affiliation(s)
- A Ducret
- Institute for Molecular Biology and Biophysics, Federal Institute of Technology, Zürich, Switzerland
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26
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Adaptive Variations in Phycobilisome Structure. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s1569-2558(08)60396-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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27
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Han KK, Martinage A. Post-translational chemical modifications of proteins--III. Current developments in analytical procedures of identification and quantitation of post-translational chemically modified amino acid(s) and its derivatives. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1993; 25:957-70. [PMID: 8365549 DOI: 10.1016/0020-711x(93)90108-q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
1. The Chemical modifications of amino acids and their derivatives are mainly due to different post-translational enzymatic reactions. 2. The enzymatic reactions resulting in amino acids such as acetylation-, formylation, methylation-phosphorylation-, sulfation-, hydroxylation, ADP ribosylation-, carboxylation-, amidation-, adenylylation-, glycosylation-, ubiquitination-, prenylation and acylation are listed and analytical methods are reported and extensively reviewed. 3. The post-translationally modified cross-linking molecules after maturations such as desmosines, allo-desmosine, hydroxy-, lysylpyridinoline, 3-hydroxypyridinium derivatives, cyclopentenosine recently found in matured elastin, and in collagen, and pulcherosine a novel tyrosine-derived found in fertilization envelope of Sea Urchin embryo, di-tyrosine in resilin, gamma-glutamyl-lysine isopeptide cross-linking molecule etc. are listed and both physico-chemical and analytical methods are extensively reviewed and discussed. 4. Other consequences of post-translational modifications encountered in the analytical procedure such as N-terminal step-wise Edman degradation of glycosylated site(s), phosphorylated-site(s) and or sulfated-site(s) were also reported by us.
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Affiliation(s)
- K K Han
- Unité INSERM No. 16, Lille, France
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28
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Post-translational methylation of phycobilisomes and oxygen evolution efficiency in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1993. [DOI: 10.1016/0005-2728(93)90222-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Reuter W, Nickel-Reuter C. Molecular assembly of the phycobilisomes from the cyanobacterium Mastigocladus laminosus. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1993. [DOI: 10.1016/1011-1344(93)80040-g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Ching WM, Carl M, Dasch GA. Mapping of monoclonal antibody binding sites on CNBr fragments of the S-layer protein antigens of Rickettsia typhi and Rickettsia prowazekii. Mol Immunol 1992; 29:95-105. [PMID: 1370573 DOI: 10.1016/0161-5890(92)90161-p] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The 120 kDa surface protein antigens (SPAs) of typhus rickettsiae lie external to the outer membrane in regular arrays and chemically resemble the S-layer proteins of other bacteria. These proteins elicit protective immune responses against the rickettsiae. In order to study the immunochemistry of these proteins, purified SPAs from Rickettsia typhi and Rickettsia prowazekii were fragmented with CNBr. The fragments were separated by SDS-PAGE and were recovered on PVDF membrane following electroblotting. The origin of eight major fragments from R. prowazekii and seven major fragments from R. typhi was determined by automated N-terminal amino acid sequencing and by comparison with the DNA sequence encoding R. prowazekii SPA. The cleavage patterns and protein sequences of the two proteins differed significantly. CNBr fragments corresponding to the C-terminus (amino acid 1372-1612 of the deduced sequence from encoding gene spaP) were not present in both SPAs. This suggests that the corresponding C-terminal region was not synthesized or was removed during SPA translocation to the cell surface. Modified amino acids were detected in each protein. Eighteen monoclonal antibodies selected for varied reactivity with both native and denatured SPA proteins could be classified into eight different types based on western blot analysis of the CNBr fragments. Six of the monoclonal antibody types reacted predominantly with a single region of the SPAs. Two types of antibodies bound to several CNBr fragments which contained both limited sequence similarity and modified amino acids either of which might account for the multisite binding of these antibodies.
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Affiliation(s)
- W M Ching
- Infectious Diseases Department, Naval Medical Research Institute, Bethesda, MD 20889-5055
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31
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Han KK, Martinage A. Post-translational chemical modification(s) of proteins. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1992; 24:19-28. [PMID: 1582530 DOI: 10.1016/0020-711x(92)90225-p] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1. The role played by the modification of protein in determining its fate is reported by us. 2. Post-translational modifications such as acetylation, phosphorylation, sulfation, methylation, hydroxylation, ADP-ribosylation, maturation, amidation, carboxylation, adenylylation, glycosylation, ubiquitination, and prenylation are extensively reviewed. 3. Each post-translational modification's significance and its role played in biological function(s) is summarized in the general discussion and the conclusion's remark is directed at the problems left to solve (e.g. post-translational modification reactions in recombinant protein in modern genetic engineering).
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Affiliation(s)
- K K Han
- Unité INSERM No. 16, Lille, France
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32
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Wilbanks S, de Lorimier R, Glazer A. Phycoerythrins of marine unicellular cyanobacteria. III. Sequence of a class II phycoerythrin. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92853-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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33
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Swanson RV, Glazer AN. Phycobiliprotein methylation. Effect of the gamma-N-methylasparagine residue on energy transfer in phycocyanin and the phycobilisome. J Mol Biol 1990; 214:787-96. [PMID: 2117667 DOI: 10.1016/0022-2836(90)90293-u] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The phycobiliproteins contain a conserved unique modified residue, gamma-N-methylasparagine at beta-72. This study examines the consequences of this methylation for the structure and function of phycocyanin and of phycobilisomes. An assay for the protein asparagine methylase activity was developed using [methyl-3H]S-adenosylmethionine and apophycocyanin purified from Escherichia coli containing the genes for the alpha and beta subunits of phycocyanin from Synechococcus sp. PCC 7002 as substrates. This assay permitted the partial purification, from Synechococcus sp. PCC 6301, of the activity that methylates phycocyanin and allophycocyanin completely at residue beta-72. Using the methylase assay, two independent nitrosoguanidine-induced mutants of Synechococcus sp. PCC 7942 were isolated that do not exhibit detectable phycobiliprotein methylase activity. These mutants, designated pcm 1 and pcm 2, produce phycocyanin and allophycocyanin unmethylated at beta-72. The phycobiliproteins in these mutants are assembled into phycobilisomes and can be methylated in vitro by the partially purified methylase from Synechococcus sp. PCC 6301. The mutants produce phycobiliproteins in amounts comparable to those of wild-type and the mutant and wild-type phycocyanins are equivalent with respect to thermal stability profiles. Monomeric phycocyanins purified from these strains show small spectral shifts that correlate with the level of methylation. Phycobilisomes from the mutant strains exhibit defects in energy transfer, both in vivo and in vitro, that are also correlated with deficiencies in methylation. Unmethylated or undermethylated phycobilisomes show greater emission from phycocyanin and allophycocyanin and lower fluorescence emission quantum yields than do fully methylated particles. The results support the conclusion that the site-specific methylation of phycobiliproteins contributes significantly to the efficiency of directional energy transfer in the phycobilisome.
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Affiliation(s)
- R V Swanson
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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Sidler W, Nutt H, Kumpf B, Frank G, Suter F, Brenzel A, Wehrmeyer W, Zuber H. The complete amino-acid sequence and the phylogenetic origin of phycocyanin-645 from the cryptophytan alga Chroomonas sp. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1990; 371:537-47. [PMID: 2222853 DOI: 10.1515/bchm3.1990.371.2.537] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The first complete amino-acid sequence of the cryptomonad phycobiliprotein phycocyanin-645 from Chroomonas sp. is presented. The alpha 1-subunit contains 70 amino-acid residues and the alpha 2-subunit 80 residues. In each of the alpha-subunits a green, 697-nm absorbing chromophore is covalently bound to Cys18. Both alpha-subunits contain a high number of charged residues. The phycocyanin-645 beta-subunit consists of 177 amino-acid residues. Two phycocyanobilin chromophores are singly bound to Cys beta 82 and Cys beta 158. A purple cryptoviolin-like chromophore is doubly bound to Cys beta 50 and Cys beta 61. Sequence comparisons revealed that the phycocyanin-645 beta-subunit is closely related to red algal phycoerythrin (73% identical amino-acid residues) and not so close to C-phycocyanin (55% identical amino-acid residues). The phycocyanin-645 alpha-subunits represent a special type of phycobiliprotein and a direct relationship to other phycobiliproteins or any light-harvesting polypeptide-pigment complexes could not be derived by sequence comparisons.
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Affiliation(s)
- W Sidler
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule, Zürich
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Klotz AV, Thomas BA, Glazer AN, Blacher RW. Detection of methylated asparagine and glutamine residues in polypeptides. Anal Biochem 1990; 186:95-100. [PMID: 2356973 DOI: 10.1016/0003-2697(90)90579-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A residue of gamma-N-methylasparagine (gamma-NMA) is found at position beta-72 of many phycobiliproteins. delta-N-Methylglutamine is present in some bacterial ribosomal proteins. gamma-NMA was synthesized by reacting the omega-methyl ester of aspartate with methylamine and delta-N-methylglutamine by reaction of pyroglutamate with methylamine. These derivatives and the omega-methyl esters of aspartate and glutamate were characterized by melting point, by thin-layer chromatography, by amino acid analysis, by NMR spectroscopy, and after conversion to the phenylthiohydantoin (PTH) derivative. The gamma-NMA residues in peptides from allophycocyanin, C-phycocyanin, and B-phycoerythrin were stable under the conditions of automated sequential gas-liquid phase Edman degradation. On HPLC, PTH-gamma-NMA co-eluted with PTH-serine and was accompanied by a minor component eluting just prior to dimethylphenylthiourea. Similar results were obtained on manual derivatization of synthetic gamma-NMA to prepare the PTH derivative. The PTH-delta-N-methylglutamine standard eluted near the position of dimethylphenylthiourea under the usual conditions employed for the identification of PTH-amino acid derivatives in automated protein sequencing.
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Affiliation(s)
- A V Klotz
- Department of Biochemistry, Louisiana State University, Baton Rouge 70803
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Sidler W, Kumpf B, Suter F, Klotz AV, Glazer AN, Zuber H. The complete amino-acid sequence of the alpha and beta subunits of B-phycoerythrin from the rhodophytan alga Porphyridium cruentum. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1989; 370:115-24. [PMID: 2495805 DOI: 10.1515/bchm3.1989.370.1.115] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Determination of the complete amino-acid sequence of the subunits of B-phycoerythrin from Porphyridium cruentum has shown that the alpha subunit contains 164 amino-acid residues and the beta subunit contains 177 residues. When the sequences of B- and C-phycoerythrins are aligned with those of other phycobiliproteins, it is obvious that B-phycoerythrin lacks a deletion at beta-21-22 present in C-phycoerythrin. However, relative to C-phycoerythrin from Fremyella diplosiphon (Calothrix) (Sidler, W., Kumpf, B., Rüdiger, W. and Zuber, H. (1986) Biol. Chem. Hoppe-Seyler 367, 627-642), B-phycoerythrin has deletions at beta-141k-o, beta-142, beta-143, beta-147 and beta-148. The four singly-linked phycoerythrobilins at positions alpha-84, alpha-143a, beta-84 and beta-155, and the doubly-linked phycoerythrobilin at position beta-50/61 are at sites homologous to the attachment sites in C-phycoerythrin. The aspartyl residues (alpha-87, beta-87, and beta-39), that interact with the bilins at alpha-84, beta-84, and beta-155 in C-phycocyanin, are found in the homologous positions in B-phycoerythrin. B-Phycoerythrin, in common with other phycobiliproteins, contains a N gamma-methylasparagine residue at position beta-72.
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Affiliation(s)
- W Sidler
- Institut für Molekularbiologie und Biophysik, Eidgenössiche Technische Hochschule, Zürich
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De Marsac NT, Mazel D, Damerval T, Guglielmi G, Capuano V, Houmard J. Photoregulation of gene expression in the filamentous cyanobacterium Calothrix sp. PCC 7601: light-harvesting complexes and cell differentiation. PHOTOSYNTHESIS RESEARCH 1988; 18:99-132. [PMID: 24425162 DOI: 10.1007/bf00042981] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/1987] [Accepted: 12/23/1987] [Indexed: 06/03/2023]
Abstract
Light plays a major role in many physiological processes in cyanobacteria. In Calothrix sp. PCC 7601, these include the biosynthesis of the components of the light-harvesting antenna (phycobilisomes) and the differentiation of the vegetative trichomes into hormogonia (short chains of smaller cells). In order to study the molecular basis for the photoregulation of gene expression, physiological studies have been coupled with the characterization of genes involved either in the formation of phycobilisomes or in the synthesis of gas vesicles, which are only present at the hormogonial stage.In each system, a number of genes have been isolated and sequenced. This demonstrated the existence of multigene families, as well as of gene products which have not yet been identified biochemically. Further studies have also established the occurrence of both transcriptional and post-transcriptional regulation. The transcription of genes encoding components of the phycobilisome rods is light-wavelength dependent, while translation of the phycocyanin genes may require the synthesis of another gene product irrespective of the light regime. In this report, we propose two hypothetical models which might be part of the complex regulatory mechanisms involved in the formation of functional phycobilisomes. On the other hand, transcription of genes involved in the gas vesicles formation (gvp genes) is turned on during hormogonia differentiation, while that of phycobiliprotein genes is simultaneously turned off. In addition, and antisense RNA which might modulate the translation of the gvp mRNAs is synthezised.
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Affiliation(s)
- N T De Marsac
- Unité de Physiologie Microbienne (C.N.R.S., U.A. 1129), Département de Biochimie et Génétique Moléculaire, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
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Mazel D, Houmard J, de Marsac NT. A multigene family in Calothrix sp. PCC 7601 encodes phycocyanin, the major component of the cyanobacterial light-harvesting antenna. ACTA ACUST UNITED AC 1988; 211:296-304. [DOI: 10.1007/bf00330607] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/1987] [Indexed: 11/27/2022]
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Alix JH. Post-translational methylations of ribosomal proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1988; 231:371-85. [PMID: 3046249 DOI: 10.1007/978-1-4684-9042-8_30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- J H Alix
- Institut de Biologie Physico-Chimique, Paris, France
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Rümbeli R, Suter F, Wirth M, Sidler W, Zuber H. Isolation and localization of N4-methylasparagine in phycobiliproteins from the cyanobacterium Mastigocladus laminosus. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1987; 368:1401-6. [PMID: 3122783 DOI: 10.1515/bchm3.1987.368.2.1401] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The occurrence of post-translationally methylated asparagine residues in beta AP from Anabaena variabilis, Synechococcus PCC 6301 and Porphyridium cruentum has recently been reported (Klotz, A.V., Leary, J.A. & Glazer, A.N. (1986) J. Biol. Chem. 261, 15891-15894). We reinvestigated the amino-acid compositions of all phycobiliproteins from Mastigocladus laminosus. During total hydrolysis of beta AP, beta 16.2 and beta PC one mol methylamine per mol protein was released. These proteins were chemically and enzymatically fragmented and the sequences of the fragments containing the modified asparagine residue were determined by automated Edman degradation. Residues beta AP72, beta 16.2 72 and beta PC 72 were identified as N4-methylasparagine. This derivative of asparagine was also found at a homologous position in beta PE of Calothrix. In the x-ray structure model of C-phycocyanin (PC) the residue beta PC 72 points towards the chromophore beta 84, presumably having an effect on the spectroscopic characteristics of this light harvesting pigment protein complex.
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Affiliation(s)
- R Rümbeli
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule, Zürich
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