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Characterization of Molecular Diversity and Organization of Phycobilisomes in Thermophilic Cyanobacteria. Int J Mol Sci 2023; 24:ijms24065632. [PMID: 36982707 PMCID: PMC10053587 DOI: 10.3390/ijms24065632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Thermophilic cyanobacteria are cosmopolitan and abundant in the thermal environment. Their light-harvesting complexes, phycobilisomes (PBS), are highly important in photosynthesis. To date, there is limited information on the PBS composition of thermophilic cyanobacteria whose habitats are challenging for survival. Herein, genome-based methods were used to investigate the molecular components of PBS in 19 well-described thermophilic cyanobacteria. These cyanobacteria are from the genera Leptolyngbya, Leptothermofonsia, Ocullathermofonsia, Thermoleptolyngbya, Trichothermofonsia, Synechococcus, Thermostichus, and Thermosynechococcus. According to the phycobiliprotein (PBP) composition of the rods, two pigment types are observed in these thermophiles. The amino acid sequence analysis of different PBP subunits suggests several highly conserved cysteine residues in these thermophiles. Certain amino acid contents in the PBP of thermophiles are significantly higher than their mesophilic counterparts, highlighting the potential roles of specific substitutions of amino acid in the adaptive thermostability of light-harvesting complexes in thermophilic cyanobacteria. Genes encoding PBS linker polypeptides vary among the thermophiles. Intriguingly, motifs in linker apcE indicate a photoacclimation of a far-red light by Leptolyngbya JSC-1, Leptothermofonsia E412, and Ocullathermofonsia A174. The composition pattern of phycobilin lyases is consistent among the thermophiles, except for Thermostichus strains that have extra homologs of cpcE, cpcF, and cpcT. In addition, phylogenetic analyses of genes coding for PBPs, linkers, and lyases suggest extensive genetic diversity among these thermophiles, which is further discussed with the domain analyses. Moreover, comparative genomic analysis suggests different genomic distributions of PBS-related genes among the thermophiles, indicating probably various regulations of expression. In summary, the comparative analysis elucidates distinct molecular components and organization of PBS in thermophilic cyanobacteria. These results provide insights into the PBS components of thermophilic cyanobacteria and fundamental knowledge for future research regarding structures, functions, and photosynthetic improvement.
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Carrigee LA, Frick JP, Liu X, Karty JA, Trinidad JC, Tom IP, Yang X, Dufour L, Partensky F, Schluchter WM. The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate. Front Microbiol 2022; 13:1011189. [PMID: 36458192 PMCID: PMC9705338 DOI: 10.3389/fmicb.2022.1011189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains.
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Affiliation(s)
- Lyndsay A. Carrigee
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
- Environmental Laboratory, Engineering and Research Development Center, US Army Corps of Engineers, Vicksburg, MS, United States
| | - Jacob P. Frick
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Xindi Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Jonathan A. Karty
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | | | - Irin P. Tom
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, United States
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, United States
| | - Louison Dufour
- Ecology of Marine Plankton Team, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique, Sorbonne Université, CNRS, Roscoff, France
| | - Frédéric Partensky
- Ecology of Marine Plankton Team, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique, Sorbonne Université, CNRS, Roscoff, France
| | - Wendy M. Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
- *Correspondence: Wendy M. Schluchter,
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Otsu T, Eki T, Hirose Y. A hybrid type of chromatic acclimation regulated by the dual green/red photosensory systems in cyanobacteria. PLANT PHYSIOLOGY 2022; 190:779-793. [PMID: 35751608 PMCID: PMC9434153 DOI: 10.1093/plphys/kiac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria are phototrophic bacteria that perform oxygenic photosynthesis. They use a supermolecular light-harvesting antenna complex, the phycobilisome (PBS), to capture and transfer light energy to photosynthetic reaction centers. Certain cyanobacteria alter the absorption maxima and/or overall structure of their PBSs in response to the ambient light wavelength-a process called chromatic acclimation (CA). One of the most well-known CA types is the response to green and red light, which is controlled by either the RcaEFC or CcaSR photosensory system. Here, we characterized a hybrid type of CA in the cyanobacterium Pleurocapsa sp. Pasteur Culture Collection (PCC) 7319 that uses both RcaEFC and CcaSR systems. In vivo spectroscopy suggested that strain PCC 7319 alters the relative composition of green-absorbing phycoerythrin and red-absorbing phycocyanin in the PBS. RNA sequencing and promoter motif analyses suggested that the RcaEFC system induces a gene operon for phycocyanin under red light, whereas the CcaSR system induces a rod-membrane linker gene under green light. Induction of the phycoerythrin genes under green light may be regulated through a yet unidentified photosensory system called the Cgi system. Spectroscopy analyses of the isolated PBSs suggested that hemidiscoidal and rod-shaped PBSs enriched with phycoerythrin were produced under green light, whereas only hemidiscoidal PBSs enriched with phycocyanin were produced under red light. PCC 7319 uses the RcaEFC and CcaSR systems to regulate absorption of green or red light (CA3) and the amount of rod-shaped PBSs (CA1), respectively. Cyanobacteria can thus flexibly combine diverse CA types to acclimate to different light environments.
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Affiliation(s)
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
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Chen H, Qi H, Xiong P. Phycobiliproteins-A Family of Algae-Derived Biliproteins: Productions, Characterization and Pharmaceutical Potentials. Mar Drugs 2022; 20:md20070450. [PMID: 35877743 PMCID: PMC9318637 DOI: 10.3390/md20070450] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Phycobiliproteins (PBPs) are colored and water-soluble biliproteins found in cyanobacteria, rhodophytes, cryptomonads and cyanelles. They are divided into three main types: allophycocyanin, phycocyanin and phycoerythrin, according to their spectral properties. There are two methods for PBPs preparation. One is the extraction and purification of native PBPs from Cyanobacteria, Cryptophyta and Rhodophyta, and the other way is the production of recombinant PBPs by heterologous hosts. Apart from their function as light-harvesting antenna in photosynthesis, PBPs can be used as food colorants, nutraceuticals and fluorescent probes in immunofluorescence analysis. An increasing number of reports have revealed their pharmaceutical potentials such as antioxidant, anti-tumor, anti-inflammatory and antidiabetic effects. The advances in PBP biogenesis make it feasible to construct novel PBPs with various activities and produce recombinant PBPs by heterologous hosts at low cost. In this review, we present a critical overview on the productions, characterization and pharmaceutical potentials of PBPs, and discuss the key issues and future perspectives on the exploration of these valuable proteins.
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Affiliation(s)
- Huaxin Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China;
- Correspondence:
| | - Hongtao Qi
- School of Life Sciences, Qingdao University, Qingdao 266000, China;
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China;
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Kumarapperuma I, Joseph KL, Wang C, Biju LM, Tom IP, Weaver KD, Grébert T, Partensky F, Schluchter WM, Yang X. Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase. Structure 2022; 30:564-574.e3. [PMID: 35148828 PMCID: PMC8995348 DOI: 10.1016/j.str.2022.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 12/19/2022]
Abstract
Chromophore attachment of the light-harvesting apparatus represents one of the most important post-translational modifications in photosynthetic cyanobacteria. Extensive pigment diversity of cyanobacteria critically depends on bilin lyases that covalently attach chemically distinct chromophores to phycobiliproteins. However, how bilin lyases catalyze bilin ligation reactions and how some lyases acquire additional isomerase abilities remain elusive at the molecular level. Here, we report the crystal structure of a representative bilin lyase-isomerase MpeQ. This structure has revealed a "question-mark" protein architecture that unambiguously establishes the active site conserved among the E/F-type bilin lyases. Based on structural, mutational, and modeling data, we demonstrate that stereoselectivity of the active site plays a critical role in conferring the isomerase activity of MpeQ. We further advance a tyrosine-mediated reaction scheme unifying different types of bilin lyases. These results suggest that lyases and isomerase actions of bilin lyases arise from two coupled molecular events of distinct origin.
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Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria. Proc Natl Acad Sci U S A 2021; 118:2019715118. [PMID: 33627406 DOI: 10.1073/pnas.2019715118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Marine Synechococcus cyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, in Synechococcus sp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.
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Carrigee LA, Frick JP, Karty JA, Garczarek L, Partensky F, Schluchter WM. MpeV is a lyase isomerase that ligates a doubly linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus. J Biol Chem 2021; 296:100031. [PMID: 33154169 PMCID: PMC7948978 DOI: 10.1074/jbc.ra120.015289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
Synechococcus cyanobacteria are widespread in the marine environment, as the extensive pigment diversity within their light-harvesting phycobilisomes enables them to utilize various wavelengths of light for photosynthesis. The phycobilisomes of Synechococcus sp. RS9916 contain two forms of the protein phycoerythrin (PEI and PEII), each binding two chromophores, green-light absorbing phycoerythrobilin and blue-light absorbing phycourobilin. These chromophores are ligated to specific cysteines via bilin lyases, and some of these enzymes, called lyase isomerases, attach phycoerythrobilin and simultaneously isomerize it to phycourobilin. MpeV is a putative lyase isomerase whose role in PEI and PEII biosynthesis is not clear. We examined MpeV in RS9916 using recombinant protein expression, absorbance spectroscopy, and tandem mass spectrometry. Our results show that MpeV is the lyase isomerase that covalently attaches a doubly linked phycourobilin to two cysteine residues (C50, C61) on the β-subunit of both PEI (CpeB) and PEII (MpeB). MpeV activity requires that CpeB or MpeB is first chromophorylated by the lyase CpeS (which adds phycoerythrobilin to C82). Its activity is further enhanced by CpeZ (a homolog of a chaperone-like protein first characterized in Fremyella diplosiphon). MpeV showed no detectable activity on the α-subunits of PEI or PEII. The mechanism by which MpeV links the A and D rings of phycourobilin to C50 and C61 of CpeB was also explored using site-directed mutants, revealing that linkage at the A ring to C50 is a critical step in chromophore attachment, isomerization, and stability. These data provide novel insights into β-PE biosynthesis and advance our understanding of the mechanisms guiding lyase isomerases.
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Affiliation(s)
- Lyndsay A Carrigee
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA
| | - Jacob P Frick
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Laurence Garczarek
- Ecology of Marine Plankton (ECOMAP) Team, Station Biologique, Sorbonne Université & CNRS, UMR 7144, Roscoff, France
| | - Frédéric Partensky
- Ecology of Marine Plankton (ECOMAP) Team, Station Biologique, Sorbonne Université & CNRS, UMR 7144, Roscoff, France
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA.
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Nguyen AA, Joseph KL, Bussell AN, Pokhrel S, Karty JA, Kronfel CM, Kehoe DM, Schluchter WM. CpeT is the phycoerythrobilin lyase for Cys-165 on β-phycoerythrin from Fremyella diplosiphon and the chaperone-like protein CpeZ greatly improves its activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148284. [PMID: 32777305 DOI: 10.1016/j.bbabio.2020.148284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
Bilin lyases are enzymes which ligate linear tetrapyrrole chromophores to specific cysteine residues on light harvesting proteins present in cyanobacteria and red algae. The lyases responsible for chromophorylating the light harvesting protein phycoerythrin (PE) have not been fully characterized. In this study, we explore the role of CpeT, a putative bilin lyase, in the biosynthesis of PE in the cyanobacterium Fremyella diplosiphon. Recombinant protein studies show that CpeT alone can bind phycoerythrobilin (PEB), but CpeZ, a chaperone-like protein, is needed in order to correctly and efficiently attach PEB to the β-subunit of PE. MS analyses of the recombinant β-subunit of PE coexpressed with CpeT and CpeZ show that PEB is attached at Cys-165. Purified phycobilisomes from a cpeT knockout mutant and wild type (WT) samples from F. diplosiphon were analyzed and compared. The cpeT mutant contained much less PE and more phycocyanin than WT cells grown under green light, conditions which should maximize the production of PE. In addition, Northern blot analyses showed that the cpeCDESTR operon mRNAs were upregulated while the cpeBcpeA mRNAs were downregulated in the cpeT mutant strain when compared with WT, suggesting that CpeT may also play a direct or indirect regulatory role in transcription of these operons or their mRNA stability, in addition to its role as a PEB lyase for Cys-165 on β-PE.
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Affiliation(s)
- Adam A Nguyen
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Kes Lynn Joseph
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Adam N Bussell
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Suman Pokhrel
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Christina M Kronfel
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA.
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9
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Carrigee LA, Mahmoud RM, Sanfilippo JE, Frick JP, Strnat JA, Karty JA, Chen B, Kehoe DM, Schluchter WM. CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I α-subunit in marine Synechococcus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148215. [PMID: 32360311 DOI: 10.1016/j.bbabio.2020.148215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 11/15/2022]
Abstract
Marine Synechococcus are widespread in part because they are efficient at harvesting available light using their complex antenna, or phycobilisome, composed of multiple phycobiliproteins and bilin chromophores. Over 40% of Synechococcus strains are predicted to perform a type of chromatic acclimation that alters the ratio of two chromophores, green-light-absorbing phycoerythrobilin and blue-light-absorbing phycourobilin, to optimize light capture by phycoerythrin in the phycobilisome. Lyases are enzymes which catalyze the addition of bilin chromophores to specific cysteine residues on phycobiliproteins and are involved in chromatic acclimation. CpeY, a candidate lyase in the model strain Synechococcus sp. RS9916, added phycoerythrobilin to cysteine 82 of only the α subunit of phycoerythrin I (CpeA) in the presence or absence of the chaperone-like protein CpeZ in a recombinant protein expression system. These studies demonstrated that recombinant CpeY attaches phycoerythrobilin to as much as 72% of CpeA, making it one of the most efficient phycoerythrin lyases characterized to date. Phycobilisomes from a cpeY- mutant showed a near native bilin composition in all light conditions except for a slight replacement of phycoerythrobilin by phycourobilin at CpeA cysteine 82. This demonstrates that CpeY is not involved in any chromatic acclimation-driven chromophore changes and suggests that the chromophore attached at cysteine 82 of CpeA in the cpeY- mutant is ligated by an alternative phycoerythrobilin lyase. Although loss of CpeY does not greatly inhibit native phycobilisome assembly in vivo, the highly active recombinant CpeY can be used to generate large amounts of fluorescent CpeA for biotechnological uses.
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Affiliation(s)
- Lyndsay A Carrigee
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Rania M Mahmoud
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; Department of Botany, Faculty of Science, University of Fayoum, Fayoum, Egypt
| | | | - Jacob P Frick
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Johann A Strnat
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Bo Chen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA.
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10
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Song JY, Lee HY, Yang HW, Song JJ, Lagarias JC, Park YI. Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes. J Biol Chem 2020; 295:6754-6766. [PMID: 32184354 DOI: 10.1074/jbc.ra120.012950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/13/2020] [Indexed: 11/06/2022] Open
Abstract
The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, here we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue-absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical "second" cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.
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Affiliation(s)
- Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ha Yong Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Joon Song
- Department of Biological Science and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
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11
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Kronfel CM, Biswas A, Frick JP, Gutu A, Blensdorf T, Karty JA, Kehoe DM, Schluchter WM. The roles of the chaperone-like protein CpeZ and the phycoerythrobilin lyase CpeY in phycoerythrin biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:549-561. [PMID: 31173730 DOI: 10.1016/j.bbabio.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/26/2019] [Accepted: 06/02/2019] [Indexed: 02/08/2023]
Abstract
Phycoerythrin (PE) present in the distal ends of light-harvesting phycobilisome rods in Fremyella diplosiphon (Tolypothrix sp. PCC 7601) contains five phycoerythrobilin (PEB) chromophores attached to six cysteine residues for efficient green light capture for photosynthesis. Chromophore ligation on PE subunits occurs through bilin lyase catalyzed reactions, but the characterization of the roles of all bilin lyases for phycoerythrin is not yet complete. To gain a more complete understanding about the individual functions of CpeZ and CpeY in PE biogenesis in cyanobacteria, we examined PE and phycobilisomes purified from wild type F. diplosiphon, cpeZ and cpeY knockout mutants. We find that the cpeZ and cpeY mutants accumulate less PE than wild type cells. We show that in the cpeZ mutant, chromophorylation of both PE subunits is affected, especially the Cys-80 and Cys-48/Cys-59 sites of CpeB, the beta-subunit of PE. The cpeY mutant showed reduced chromophorylation at Cys-82 of CpeA. We also show that, in vitro, CpeZ stabilizes PE subunits and assists in refolding of CpeB after denaturation. Taken together, we conclude that CpeZ acts as a chaperone-like protein, assisting in the folding/stability of PE subunits, allowing bilin lyases such as CpeY and CpeS to attach PEB to their PE subunit.
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Affiliation(s)
- Christina M Kronfel
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Avijit Biswas
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| | - Jacob P Frick
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Andrian Gutu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Tyler Blensdorf
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - 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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Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus. Proc Natl Acad Sci U S A 2019; 116:6457-6462. [PMID: 30846551 DOI: 10.1073/pnas.1810491116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine Synechococcus, a globally important group of cyanobacteria, thrives in various light niches in part due to its varied photosynthetic light-harvesting pigments. Many Synechococcus strains use a process known as chromatic acclimation to optimize the ratio of two chromophores, green-light-absorbing phycoerythrobilin (PEB) and blue-light-absorbing phycourobilin (PUB), within their light-harvesting complexes. A full mechanistic understanding of how Synechococcus cells tune their PEB to PUB ratio during chromatic acclimation has not yet been obtained. Here, we show that interplay between two enzymes named MpeY and MpeZ controls differential PEB and PUB covalent attachment to the same cysteine residue. MpeY attaches PEB to the light-harvesting protein MpeA in green light, while MpeZ attaches PUB to MpeA in blue light. We demonstrate that the ratio of mpeY to mpeZ mRNA determines if PEB or PUB is attached. Additionally, strains encoding only MpeY or MpeZ do not acclimate. Examination of strains of Synechococcus isolated from across the globe indicates that the interplay between MpeY and MpeZ uncovered here is a critical feature of chromatic acclimation for marine Synechococcus worldwide.
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13
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Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes ( mpeBA and cpeBA). Front Microbiol 2019; 10:45. [PMID: 30761097 PMCID: PMC6363710 DOI: 10.3389/fmicb.2019.00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.
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Affiliation(s)
| | - Giorgio Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrea Di Cesare
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
- Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Cristiana Callieri
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
| | - Nathan A. M. Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
- The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
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14
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Kronfel CM, Hernandez CV, Frick JP, Hernandez LS, Gutu A, Karty JA, Boutaghou MN, Kehoe DM, Cole RB, Schluchter WM. CpeF is the bilin lyase that ligates the doubly linked phycoerythrobilin on β-phycoerythrin in the cyanobacterium Fremyella diplosiphon. J Biol Chem 2019; 294:3987-3999. [PMID: 30670589 DOI: 10.1074/jbc.ra118.007221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Phycoerythrin (PE) is a green light-absorbing protein present in the light-harvesting complex of cyanobacteria and red algae. The spectral characteristics of PE are due to its prosthetic groups, or phycoerythrobilins (PEBs), that are covalently attached to the protein chain by specific bilin lyases. Only two PE lyases have been identified and characterized so far, and the other bilin lyases are unknown. Here, using in silico analyses, markerless deletion, biochemical assays with purified and recombinant proteins, and site-directed mutagenesis, we examined the role of a putative lyase-encoding gene, cpeF, in the cyanobacterium Fremyella diplosiphon. Analyzing the phenotype of the cpeF deletion, we found that cpeF is required for proper PE biogenesis, specifically for ligation of the doubly linked PEB to Cys-48/Cys-59 residues of the CpeB subunit of PE. We also show that in a heterologous host, CpeF can attach PEB to Cys-48/Cys-59 of CpeB, but only in the presence of the chaperone-like protein CpeZ. Additionally, we report that CpeF likely ligates the A ring of PEB to Cys-48 prior to the attachment of the D ring to Cys-59. We conclude that CpeF is the bilin lyase responsible for attachment of the doubly ligated PEB to Cys-48/Cys-59 of CpeB and together with other specific bilin lyases contributes to the post-translational modification and assembly of PE into mature light-harvesting complexes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Richard B Cole
- Chemistry, University of New Orleans, New Orleans, Louisiana 70148.,Sorbonne Universités-Paris 06, 75252 Paris, France
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15
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Xu Y, Zhang R, Wang N, Cai L, Tong Y, Sun Q, Chen F, Jiao N. Novel phage-host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment. Environ Microbiol 2018; 20:2974-2989. [DOI: 10.1111/1462-2920.14326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/09/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- School of Life Science; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
| | - Rui Zhang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Nannan Wang
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Lanlan Cai
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity; Beijing Institute of Microbiology and Epidemiology; Beijing China
| | - Feng Chen
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine and Environmental Technology; University of Maryland Center for Environmental Science; Baltimore MD USA
| | - Nianzhi Jiao
- Institute of Marine Science and Technology; Shandong University; Qingdao China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Marine Environmental Sciences, College of Ocean & Earth Sciences; Xiamen University; Xiamen China
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16
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Mahmoud RM, Sanfilippo JE, Nguyen AA, Strnat JA, Partensky F, Garczarek L, Abo El Kassem N, Kehoe DM, Schluchter WM. Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases. Front Microbiol 2017; 8:243. [PMID: 28270800 PMCID: PMC5318389 DOI: 10.3389/fmicb.2017.00243] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/03/2017] [Indexed: 11/25/2022] Open
Abstract
Marine Synechococcus 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 Synechococcus 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 Synechococcus strains adapted to blue light possess a gene called mpeU. MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of mpeU caused a reduction in PUB content, impaired phycobilisome assembly and reduced growth rate more strongly in blue than green light. When mpeU was reintroduced in the mpeU mutant background, the mpeU-less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mpeU 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 Synechococcus spp. to capture photons in blue light environments throughout the world’s oceans.
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Affiliation(s)
- Rania M Mahmoud
- Department of Biology, Indiana University, BloomingtonIN, USA; Department of Botany, Faculty of Science, University of FayoumFayoum, Egypt
| | | | - Adam A Nguyen
- Department of Biological Sciences, University of New Orleans, New OrleansLA, USA; Department of Chemistry, University of New Orleans, New OrleansLA, USA
| | - Johann A Strnat
- Department of Biology, Indiana University, Bloomington IN, USA
| | - Frédéric Partensky
- CNRS, Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, UMR 7144 Roscoff, France
| | - Laurence Garczarek
- CNRS, Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, UMR 7144 Roscoff, France
| | - Nabil Abo El Kassem
- Department of Botany, Faculty of Science, University of Fayoum Fayoum, Egypt
| | - David M Kehoe
- Department of Biology, Indiana University, BloomingtonIN, USA; Indiana Molecular Biology Institute, Indiana University, BloomingtonIN, USA
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New OrleansLA, USA; Department of Chemistry, University of New Orleans, New OrleansLA, USA
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17
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Sanfilippo JE, Nguyen AA, Karty JA, Shukla A, Schluchter WM, Garczarek L, Partensky F, Kehoe DM. Self-regulating genomic island encoding tandem regulators confers chromatic acclimation to marine Synechococcus. Proc Natl Acad Sci U S A 2016; 113:6077-82. [PMID: 27152022 PMCID: PMC4889380 DOI: 10.1073/pnas.1600625113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary success of marine Synechococcus, the second-most abundant phototrophic group in the marine environment, is partly attributable to this group's ability to use the entire visible spectrum of light for photosynthesis. This group possesses a remarkable diversity of light-harvesting pigments, and most of the group's members are orange and pink because of their use of phycourobilin and phycoerythrobilin chromophores, which are attached to antennae proteins called phycoerythrins. Many strains can alter phycoerythrin chromophore ratios to optimize photon capture in changing blue-green environments using type IV chromatic acclimation (CA4). Although CA4 is common in most marine Synechococcus lineages, the regulation of this process remains unexplored. Here, we show that a widely distributed genomic island encoding tandem master regulators named FciA (for type four chromatic acclimation island) and FciB plays a central role in controlling CA4. FciA and FciB have diametric effects on CA4. Interruption of fciA causes a constitutive green light phenotype, and interruption of fciB causes a constitutive blue light phenotype. These proteins regulate all of the molecular responses occurring during CA4, and the proteins' activity is apparently regulated posttranscriptionally, although their cellular ratio appears to be critical for establishing the set point for the blue-green switch in ecologically relevant light environments. Surprisingly, FciA and FciB coregulate only three genes within the Synechococcus genome, all located within the same genomic island as fciA and fciB These findings, along with the widespread distribution of strains possessing this island, suggest that horizontal transfer of a small, self-regulating DNA region has conferred CA4 capability to marine Synechococcus throughout many oceanic areas.
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Affiliation(s)
| | - Adam A Nguyen
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148; Department of Chemistry, University of New Orleans, New Orleans, LA 70148
| | - Jonathan A Karty
- Mass Spectrometry Facility, Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Animesh Shukla
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148; Department of Chemistry, University of New Orleans, New Orleans, LA 70148
| | - Laurence Garczarek
- Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, CNRS, UMR 7144, Station Biologique, Plankton Group, 29688 Roscoff, France
| | - Frédéric Partensky
- Sorbonne Universités, Université Pierre et Marie Curie University Paris 06, CNRS, UMR 7144, Station Biologique, Plankton Group, 29688 Roscoff, France
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN 47405; Indiana Molecular Biology Institute, Indiana University, Bloomington, IN 47405
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18
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Busch AWU, Montgomery BL. The Tryptophan-Rich Sensory Protein (TSPO) is Involved in Stress-Related and Light-Dependent Processes in the Cyanobacterium Fremyella diplosiphon. Front Microbiol 2015; 6:1393. [PMID: 26696996 PMCID: PMC4677103 DOI: 10.3389/fmicb.2015.01393] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/23/2015] [Indexed: 11/20/2022] Open
Abstract
The tryptophan-rich sensory protein (TSPO) is a membrane protein, which is a member of the 18 kDa translocator protein/peripheral-type benzodiazepine receptor (MBR) family of proteins that is present in most organisms and is also referred to as Translocator protein 18 kDa. Although TSPO is associated with stress- and disease-related processes in organisms from bacteria to mammals, full elucidation of the functional role of the TSPO protein is lacking for most organisms in which it is found. In this study, we describe the regulation and function of a TSPO homolog in the cyanobacterium Fremyella diplosiphon, designated FdTSPO. Accumulation of the FdTSPO transcript is upregulated by green light and in response to nutrient deficiency and stress. A F. diplosiphon TSPO deletion mutant (i.e., ΔFdTSPO) showed altered responses compared to the wild type (WT) strain under stress conditions, including salt treatment, osmotic stress, and induced oxidative stress. Under salt stress, the FdTSPO transcript is upregulated and a ΔFdTSPO mutant accumulates lower levels of reactive oxygen species (ROS) and displays increased growth compared to WT. In response to osmotic stress, FdTSPO transcript levels are upregulated and ΔFdTSPO mutant cells exhibit impaired growth compared to the WT. By comparison, methyl viologen-induced oxidative stress results in higher ROS levels in the ΔFdTSPO mutant compared to the WT strain. Taken together, our results provide support for the involvement of membrane-localized FdTSPO in mediating cellular responses to stress in F. diplosiphon and represent detailed functional analysis of a cyanobacterial TSPO. This study advances our understanding of the functional roles of TSPO homologs in vivo.
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Affiliation(s)
- Andrea W. U. Busch
- Department of Energy – Plant Research Laboratory, Michigan State University, East LansingMI, USA
| | - Beronda L. Montgomery
- Department of Energy – Plant Research Laboratory, Michigan State University, East LansingMI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East LansingMI, USA
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19
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Liu B, Chen S, Zhang L. Functional studies of the gene slr2049 from Synechocystis sp. PCC6803 and its site-directed mutation. Gene 2015; 563:196-202. [PMID: 25791490 DOI: 10.1016/j.gene.2015.03.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 10/23/2022]
Abstract
Phycobiliprotein is a homologous family of light-harvesting chromoproteins existing in cyanobacteria, red algae and cryptophytes. Phycobiliprotein is made up of phycobilin and its corresponding apophycobiliprotein, and they are covalently linked by the thioether bond with the bilin lyase. Using the software BLAST, we have found gene slr2049 in Synechocystis sp. PCC6803 homologous to the biliprotein lyase gene cpeS. This paper investigates the protein expressed by gene slr2049 to find the enzymatic activity characteristics. We cloned slr2049 and its related genes cpcB, ho1, and pcyA which are linked with the synthesis of phycocyanin. Special amino acid mutagenesis was performed on slr2049 to construct eight mutants slr2049 (H21S), slr2049 (L23S), slr2049 (A24S), slr2049 (F25S), slr2049 (W72L), slr2049 (G84S), slr2049 (R107S) and slr2049 (Y124S). These mutants were ligated with vectors pEDFDuet-1 and pET-23a to construct pCDF-cpcB-slr2049 wild-type, pCDF-cpcB-slr2049 mutants and pET-ho1-pcyA, for the purpose of protein expression and analysis. The results showed that the wild-type and mutants slr2049 (H21S), slr2049 (L23S), slr2049 (F25S), slr2049 (W72L), slr2049 (G84S), and slr2049 (Y124S) can catalyze CpcB to couple on PCB correctly and the products have unique spectral characteristics. However mutants slr2049 (A24S) and slr2049 (R107S) have no spectral characteristics. Thus, it is suggested that alanine at position 24 and arginine at position 107 are the active sites.
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Affiliation(s)
- Bingjun Liu
- College of Life Science, South-central University for Nationalities, Wuhan 430074, China
| | - Sili Chen
- College of Life Science, South-central University for Nationalities, Wuhan 430074, China.
| | - Lei Zhang
- College of Life Science, South-central University for Nationalities, Wuhan 430074, China
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20
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Zhou W, Ding WL, Zeng XL, Dong LL, Zhao B, Zhou M, Scheer H, Zhao KH, Yang X. Structure and mechanism of the phycobiliprotein lyase CpcT. J Biol Chem 2014; 289:26677-26689. [PMID: 25074932 PMCID: PMC4175310 DOI: 10.1074/jbc.m114.586743] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/24/2014] [Indexed: 12/15/2022] Open
Abstract
Pigmentation of light-harvesting phycobiliproteins of cyanobacteria requires covalent attachment of open-chain tetrapyrroles, bilins, to the apoproteins. Thioether formation via addition of a cysteine residue to the 3-ethylidene substituent of bilins is mediated by lyases. T-type lyases are responsible for attachment to Cys-155 of phycobiliprotein β-subunits. We present crystal structures of CpcT (All5339) from Nostoc (Anabaena) sp. PCC 7120 and its complex with phycocyanobilin at 1.95 and 2.50 Å resolution, respectively. CpcT forms a dimer and adopts a calyx-shaped β-barrel fold. Although the overall structure of CpcT is largely retained upon chromophore binding, arginine residues at the opening of the binding pocket undergo major rotameric rearrangements anchoring the propionate groups of phycocyanobilin. Based on the structure and mutational analysis, a reaction mechanism is proposed that accounts for chromophore stabilization and regio- and stereospecificity of the addition reaction. At the dimer interface, a loop extending from one subunit partially shields the opening of the phycocyanobilin binding pocket in the other subunit. Deletion of the loop or disruptions of the dimer interface significantly reduce CpcT lyase activity, suggesting functional relevance of the dimer. Dimerization is further enhanced by chromophore binding. The chromophore is largely buried in the dimer, but in the monomer, the 3-ethylidene group is accessible for the apophycobiliprotein, preferentially from the chromophore α-side. Asp-163 and Tyr-65 at the β- and α-face near the E-configured ethylidene group, respectively, support the acid-catalyzed nucleophilic Michael addition of cysteine 155 of the apoprotein to an N-acylimmonium intermediate proposed by Grubmayr and Wagner (Grubmayr, K., and Wagner, U. G. (1988) Monatsh. Chem. 119, 965-983).
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Affiliation(s)
- Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Long Ding
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Li Zeng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang-Liang Dong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hugo Scheer
- Department of Biologie I, Universität München, Menzinger Str. 67, D-80638 München, Germany
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China,.
| | - Xiaojing Yang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, and; Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607.
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21
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Overkamp KE, Gasper R, Kock K, Herrmann C, Hofmann E, Frankenberg-Dinkel N. Insights into the biosynthesis and assembly of cryptophycean phycobiliproteins. J Biol Chem 2014; 289:26691-26707. [PMID: 25096577 DOI: 10.1074/jbc.m114.591131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phycobiliproteins are employed by cyanobacteria, red algae, glaucophytes, and cryptophytes for light-harvesting and consist of apoproteins covalently associated with open-chain tetrapyrrole chromophores. Although the majority of organisms assemble the individual phycobiliproteins into larger aggregates called phycobilisomes, members of the cryptophytes use a single type of phycobiliprotein that is localized in the thylakoid lumen. The cryptophyte Guillardia theta (Gt) uses phycoerythrin PE545 utilizing the uncommon chromophore 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB). Both the biosynthesis and the attachment of chromophores to the apophycobiliprotein have not yet been investigated for cryptophytes. In this study, we identified and characterized enzymes involved in PEB biosynthesis. In addition, we present the first in-depth biochemical characterization of a eukaryotic phycobiliprotein lyase (GtCPES). Plastid-encoded HO (GtHo) was shown to convert heme into biliverdin IXα providing the substrate with a putative nucleus-encoded DHBV:ferredoxin oxidoreductase (GtPEBA). A PEB:ferredoxin oxidoreductase (GtPEBB) was found to convert DHBV to PEB, which is the substrate for the phycobiliprotein lyase GtCPES. The x-ray structure of GtCPES was solved at 2.0 Å revealing a 10-stranded β-barrel with a modified lipocalin fold. GtCPES is an S-type lyase specific for binding of phycobilins with reduced C15=C16 double bonds (DHBV and PEB). Site-directed mutagenesis identified residues Glu-136 and Arg-146 involved in phycobilin binding. Based on the crystal structure, a model for the interaction of GtCPES with the apophycobiliprotein CpeB is proposed and discussed.
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Affiliation(s)
- Kristina E Overkamp
- Physiology of Microorganisms, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Raphael Gasper
- Protein Crystallography, Faculty for Biology and Biotechnology, and Ruhr University Bochum, 44780 Bochum, Germany
| | - Klaus Kock
- Physical Chemistry I, Protein Interactions, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Christian Herrmann
- Physical Chemistry I, Protein Interactions, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty for Biology and Biotechnology, and Ruhr University Bochum, 44780 Bochum, Germany
| | - Nicole Frankenberg-Dinkel
- Physiology of Microorganisms, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.
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22
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Humily F, Partensky F, Six C, Farrant GK, Ratin M, Marie D, Garczarek L. A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus. PLoS One 2013; 8:e84459. [PMID: 24391958 PMCID: PMC3877281 DOI: 10.1371/journal.pone.0084459] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/21/2013] [Indexed: 12/31/2022] Open
Abstract
Synechococcus, 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.
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Affiliation(s)
- Florian Humily
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Frédéric Partensky
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Christophe Six
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Gregory K. Farrant
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Morgane Ratin
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Dominique Marie
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
| | - Laurence Garczarek
- Université Pierre et Marie Curie (Paris VI), Station Biologique, Roscoff, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7144, Oceanic Plankton group, Marine Phototrophic Prokaryotes team, Roscoff, France
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23
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Kronfel CM, Kuzin AP, Forouhar F, Biswas A, Su M, Lew S, Seetharaman J, Xiao R, Everett JK, Ma LC, Acton TB, Montelione GT, Hunt JF, Paul CEC, Dragomani TM, Boutaghou MN, Cole RB, Riml C, Alvey RM, Bryant DA, Schluchter WM. Structural and biochemical characterization of the bilin lyase CpcS from Thermosynechococcus elongatus. Biochemistry 2013; 52:8663-76. [PMID: 24215428 DOI: 10.1021/bi401192z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacterial phycobiliproteins have evolved to capture light energy over most of the visible spectrum due to their bilin chromophores, which are linear tetrapyrroles that have been covalently attached by enzymes called bilin lyases. We report here the crystal structure of a bilin lyase of the CpcS family from Thermosynechococcus elongatus (TeCpcS-III). TeCpcS-III is a 10-stranded β barrel with two alpha helices and belongs to the lipocalin structural family. TeCpcS-III catalyzes both cognate as well as noncognate bilin attachment to a variety of phycobiliprotein subunits. TeCpcS-III ligates phycocyanobilin, phycoerythrobilin, and phytochromobilin to the alpha and beta subunits of allophycocyanin and to the beta subunit of phycocyanin at the Cys82-equivalent position in all cases. The active form of TeCpcS-III is a dimer, which is consistent with the structure observed in the crystal. With the use of the UnaG protein and its association with bilirubin as a guide, a model for the association between the native substrate, phycocyanobilin, and TeCpcS was produced.
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Affiliation(s)
- Christina M Kronfel
- Department of Biological Sciences, University of New Orleans , New Orleans, LA 70148, United States
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24
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Boutaghou MN, Kronfel CM, Hernandez LS, Biswas A, Schluchter WM, Cole RB. Direct differentiation of A-ring single attachment versus A- and D-ring double attachment of phycoerythrobilin chromophores to phycobiliproteins using MALDI mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:187-192. [PMID: 23378091 DOI: 10.1002/jms.3146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 06/01/2023]
Abstract
Bilin chromophore attachment to phycobiliproteins is an enzyme-catalyzed post-translational modification process. Bilin-lyases attach a bilin chromophore to their cognate protein through a thioether bond between the chromophore and a cysteine moiety. Bilin chromophores are attached to their phycobiliproteins through the 3(1) carbon of the bilin. Double attachment may also occur, and in this case, carbons 3(1) and 18(1) of the bilin are both forming covalent linkages to cysteine moieties. There is a mass spectrometric limitation when examining tryptic peptides containing two (or more) cysteines if one seeks to ascertain whether chromopeptides are singly or doubly attached. The problem is that singly and doubly attached chromopeptides appear at the same m/z value; thus, up until the present, only NMR analysis has been successful at determining whether the chromophore is singly or doubly attached. We report in this work a new, fast and accurate method for discriminating singly from doubly attached chromophores using MALDI-TOF mass spectrometry. This method was developed from mass spectral analysis of chromopeptides that had undergone in vitro or in vivo attachment of bilin chromophores to phycobiliproteins. Distinction is based on a characteristic neutral loss that appears in the MALDI-TOF mass spectrum only when the bilin is singly attached.
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Affiliation(s)
- M Nazim Boutaghou
- Department of Chemistry, University of New Orleans, 2000 Lakeshore Dr., New Orleans, LA 70148, USA
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25
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Wu XJ, Chang K, Luo J, Zhou M, Scheer H, Zhao KH. Modular generation of fluorescent phycobiliproteins. Photochem Photobiol Sci 2013; 12:1036-40. [DOI: 10.1039/c3pp25383j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Phycoerythrin-specific bilin lyase-isomerase controls blue-green chromatic acclimation in marine Synechococcus. Proc Natl Acad Sci U S A 2012; 109:20136-41. [PMID: 23161909 DOI: 10.1073/pnas.1211777109] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The marine cyanobacterium Synechococcus is the second most abundant phytoplanktonic organism in the world's oceans. The ubiquity of this genus is in large part due to its use of a diverse set of photosynthetic light-harvesting pigments called phycobiliproteins, which allow it to efficiently exploit a wide range of light colors. Here we uncover a pivotal molecular mechanism underpinning a widespread response among marine Synechococcus cells known as "type IV chromatic acclimation" (CA4). During this process, the pigmentation of the two main phycobiliproteins of this organism, phycoerythrins I and II, is reversibly modified to match changes in the ambient light color so as to maximize photon capture for photosynthesis. CA4 involves the replacement of three molecules of the green light-absorbing chromophore phycoerythrobilin with an equivalent number of the blue light-absorbing chromophore phycourobilin when cells are shifted from green to blue light, and the reverse after a shift from blue to green light. We have identified and characterized MpeZ, an enzyme critical for CA4 in marine Synechococcus. MpeZ attaches phycoerythrobilin to cysteine-83 of the α-subunit of phycoerythrin II and isomerizes it to phycourobilin. mpeZ RNA is six times more abundant in blue light, suggesting that its proper regulation is critical for CA4. Furthermore, mpeZ mutants fail to normally acclimate in blue light. These findings provide insights into the molecular mechanisms controlling an ecologically important photosynthetic process and identify a unique class of phycoerythrin lyase/isomerases, which will further expand the already widespread use of phycoerythrin in biotechnology and cell biology applications.
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