1
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Hoshino H, Miyake K, Fushimi K, Narikawa R. Red/green cyanobacteriochromes acquire isomerization from phycocyanobilin to phycoviolobilin. Protein Sci 2024; 33:e5132. [PMID: 39072823 DOI: 10.1002/pro.5132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/01/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
Cyanobacteriochromes (CBCRs) are unique cyanobacteria-specific photoreceptors that share a distant relation with phytochromes. Most CBCRs contain conserved cysteine residues known as canonical Cys, while some CBCRs have additional cysteine residues called second Cys within the DXCF motif, leading to their classification as DXCF CBCRs. They typically undergo a process where they incorporate phycocyanobilin (PCB) and subsequently isomerize it to phycoviolobilin (PVB). Conversely, CBCRs with conserved Trp residues and without the second Cys are called extended red/green (XRG) CBCRs. Typical XRG CBCRs bind PCB without undergoing PCB-to-PVB isomerization, displaying red/green reversible photoconversion, and there are also atypical CBCRs that exhibit diverse photoconversions. We discovered novel XRG CBCRs with Cys residue instead of the conserved Trp residue. These novel XRG CBCRs exhibited the ability to isomerize PCB to PVB, displaying green/teal reversible photoconversion. Through sequence- and structure-based comparisons coupled with mutagenesis experiments, we identified three amino acid residues, including the Cys residue, crucial for facilitating PCB-to-PVB isomerization. This research expands our understanding of the diversity of XRG CBCRs, highlighting the remarkable molecular plasticity of CBCRs.
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Affiliation(s)
- Hiroki Hoshino
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Keita Miyake
- Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo, Japan
| | - Keiji Fushimi
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Rei Narikawa
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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2
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Jensen GC, Janis MK, Jara J, Abbasi N, Zastrow ML. Zinc-Induced Fluorescence Turn-On in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins. Biochemistry 2023; 62:2828-2840. [PMID: 37699411 PMCID: PMC11057272 DOI: 10.1021/acs.biochem.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to the near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 (All1280g2) from Nostoc sp. PCC7120 is a DXCF motif-containing protein that exhibits blue-light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. All1280g2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent All1280g2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here, we show that All1280g2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with a blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF from Synechocystis sp. PCC6803 (Slr1393g3). Zn2+ significantly enhances All1280g2-PEB fluorescence across a biologically relevant pH range from 6.0 to 9.0, with pH-dependent dissociation constants from 1 μM to ∼20-80 nM. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement. Mutation of the cysteine residue within the DXCF motif to alanine abolishes the zinc-induced fluorescence enhancement. Collectively, these results support the presence of a unique fluorescence-enhancing Zn2+ binding site in All1280g2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Jazzmin Jara
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Nasir Abbasi
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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3
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Suzuki T, Yoshimura M, Hoshino H, Fushimi K, Arai M, Narikawa R. Introduction of reversible cysteine ligation ability to the biliverdin-binding cyanobacteriochrome photoreceptor. FEBS J 2023; 290:4999-5015. [PMID: 37488966 DOI: 10.1111/febs.16911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Cyanobacteriochrome (CBCR) photoreceptors are distantly related to the canonical red/far-red reversible phytochrome photoreceptors. In the case of the CBCRs, only the GAF domain is required for chromophore incorporation and photoconversion. The GAF domains of CBCR are highly diversified into many lineages to sense various colors of light. These CBCR GAF domains are divided into two types: those possessing only the canonical Cys residue and those with both canonical and second Cys residues. The canonical Cys residue stably ligates to the chromophore in both cases. The second Cys residue mostly shows reversible adduct formation with the chromophore during photoconversion for spectral tuning. In this study, we focused on the CBCR GAF domain AnPixJg2_BV4, which possesses only the canonical Cys residue. AnPixJg2_BV4 covalently ligates to the biliverdin (BV) chromophore and shows far-red/orange reversible photoconversion. Because BV is a mammalian intrinsic chromophore, BV-binding molecules are advantageous for in vivo optogenetic and bioimaging tool development. To obtain a better developmental platform molecule, we performed site-saturation random mutagenesis and serendipitously obtained a unique variant molecule that showed far-red/blue reversible photoconversion, in which the Cys residue was introduced near the chromophore. This introduced Cys residue functioned as the second Cys residue that reversibly ligated with the chromophore. Because the position of the introduced Cys residue is distinct from the known second Cys residues, the variant molecule obtained in this study would expand our knowledge about the spectral tuning mechanism of CBCRs and contribute to tool development.
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Affiliation(s)
- Takahisa Suzuki
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Masataka Yoshimura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
| | - Hiroki Hoshino
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Keiji Fushimi
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Japan
| | - Rei Narikawa
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
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4
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Church JR, Olsen JMH, Schapiro I. Induction effects on the absorption maxima of photoreceptor proteins. Biophys Physicobiol 2023; 20:e201007. [PMID: 38362325 PMCID: PMC10865876 DOI: 10.2142/biophysico.bppb-v20.s007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50% and 71% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results.
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Affiliation(s)
- Jonathan R. Church
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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5
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Hoshino H, Narikawa R. Novel cyanobacteriochrome photoreceptor with the second Cys residue showing atypical orange/blue reversible photoconversion. Photochem Photobiol Sci 2023; 22:251-261. [PMID: 36156209 DOI: 10.1007/s43630-022-00310-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial linear tetrapyrrole-binding photoreceptors distantly related to phytochromes. Only the GAF domain is needed for chromophore incorporation and proper photoconversion of the CBCRs. Most CBCR GAF domains possess the canonical Cys residue stably ligating to the chromophore. DXCF-type CBCR GAF domains also possess a second Cys residue within the DXCF motif. This second Cys residue reversibly ligates to the C10 of the chromophore. The Cys adduct formation is mostly observed for the dark-adapted state but not for the photoproduct state. In this study, we discovered novel CBCR GAF domains with a DXCI motif instead of the DXCF motif. Since these CBCR GAF domains are categorized into two subfamilies (DXCI-1 and DXCI-2), the GAF domains from each subfamily were analyzed. Although the CBCR GAF domain belonging to the DXCI-2 subfamily showed orange/green reversible photoconversion without transient Cys ligation, the CBCR GAF domain belonging to the DXCI-1 subfamily showed reversible photoconversion between an orange-absorbing dark-adapted state and a blue-absorbing photoproduct state. This indicates that the second Cys residue is covalently bound to the C10 of the chromophore in the photoproduct state but not in the dark-adapted state. Since the covalent bond formation in the photoproduct state is atypical, site-directed mutagenesis was conducted to understand the molecular mechanism of this GAF domain. The Ile residue within the DXCI motif may be key for covalent bond formation in the photoproduct state.
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Affiliation(s)
- Hiroki Hoshino
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Rei Narikawa
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan.
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6
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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)
- Takuto Otsu
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi 441-8580, Japan
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7
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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8
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Unusual ring D fixation by three crucial residues promotes phycoviolobilin formation in the DXCF-type cyanobacteriochrome without the second Cys. Biochem J 2021; 478:1043-1059. [PMID: 33559683 DOI: 10.1042/bcj20210013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/17/2022]
Abstract
Cyanobacteriochromes are linear tetrapyrrole-binding photoreceptors produced by cyanobacteria. Their chromophore-binding GAF domains are categorized into many lineages. Among them, dual Cys-type cyanobacteriochrome GAF domains possessing not only a highly conserved 'first Cys' but also a 'second Cys' are found from multiple lineages. The first Cys stably attaches to C31 of the A-ring, while the second Cys mostly shows reversible ligation to the C10 of the chromophore. Notably, the position of the second Cys in the primary sequence is diversified, and the most abundant dual Cys-type GAF domains have a 'second Cys' within the DXCF motif, which are called DXCF GAF domains. It has been long known that the second Cys in the DXCF GAF domains not only shows the reversible ligation but also is involved in isomerization activity (reduction in C4=C5 double bond) from the initially incorporated phycocyanobilin to phycoviolobilin. However, comprehensive site-directed mutagenesis on the DXCF GAF domains, AM1_6305g1 and AM1_1499g1, revealed that the second Cys is dispensable for isomerization activity, in which three residues participate by fixing the C- and D-rings. Fixation of the chromophore on both sides of the C5 bridge is necessary, even though one side of the fixation site is far from this bridge, with the other side at C31 fixed by the first Cys.
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9
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Jiang SD, sheng Y, Wu XJ, Zhu YL, Li PP. Chromophorylation of a Novel Cyanobacteriochrome GAF Domain from Spirulina and Its Response to Copper Ions. J Microbiol Biotechnol 2021; 31:233-239. [PMID: 33203817 PMCID: PMC9705869 DOI: 10.4014/jmb.2009.09048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photoreceptor proteins in cyanobacteria and cover a wide spectral range from ultraviolet to far-red. A single GAF domain that they contain can bind bilin(s) autocatalytically via heterologous recombination and then fluoresce, with potential applications as biomarkers and biosensors. Here, we report that a novel red/green CBCR GAF domain, SPI1085g2 from Spirulina subsalsa, covalently binds both phycocyanobilin (PCB) and phycoerythrobilin (PEB). The PCB-binding GAF domain exhibited canonical red/green photoconversion with weak fluorescence emission. However, the PEB-binding GAF domain, SPI1085g2-PEB, exhibited an intense orange fluorescence (λabs.max = 520 nm, λfluor.max = 555 nm), with a fluorescence quantum yield close to 1.0. The fluorescence of SPI1085g2-PEB was selectively and instantaneously quenched by copper ions in a concentration-dependent manner and exhibited reversibility upon treatment with the metal chelator EDTA. This study identified a novel PEB-binding cyanobacteriochrome-based fluorescent protein with the highest quantum yield reported to date and suggests its potential as a biosensor for the rapid detection of copper ions.
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Affiliation(s)
- Su-Dan Jiang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China
| | - Yi sheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China
| | - Xian-Jun Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China,Corresponding authors X. Wu Phone: +86-158-5052-0507 E-mail:
| | - Yong-Li Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China
| | - Ping-Ping Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China,P. Li Phone: +86-25-8542-7210 E-mail:
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10
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Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
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Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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11
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Phytochromes and Cyanobacteriochromes: Photoreceptor Molecules Incorporating a Linear Tetrapyrrole Chromophore. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:167-187. [PMID: 33398813 DOI: 10.1007/978-981-15-8763-4_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this chapter, we summarize the molecular mechanisms of the linear tetrapyrrole-binding photoreceptors, phytochromes, and cyanobacteriochromes. We especially focus on the color-tuning mechanisms and conformational changes during the photoconversion process. Furthermore, we introduce current status of development of the optogenetic tools based on these molecules. Huge repertoire of these photoreceptors with diverse spectral properties would contribute to development of multiplex optogenetic regulation. Among them, the photoreceptors incorporating the biliverdin IXα chromophore is advantageous for in vivo optogenetics because this is intrinsic in the mammalian cells, and absorbs far-red light penetrating into deep mammalian tissues.
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12
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Jähnigen S, Sebastiani D. Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ. Molecules 2020; 25:E5505. [PMID: 33255423 PMCID: PMC7727823 DOI: 10.3390/molecules25235505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics-statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.
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Affiliation(s)
| | - Daniel Sebastiani
- Institut für Chemie, Naturwissenschaftliche Fakultät II, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany;
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13
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Fushimi K, Matsunaga T, Narikawa R. A photoproduct of DXCF cyanobacteriochromes without reversible Cys ligation is destabilized by rotating ring twist of the chromophore. Photochem Photobiol Sci 2020; 19:1289-1299. [PMID: 32789394 DOI: 10.1039/d0pp00208a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyanobacteriochrome photoreceptors (CBCRs) ligate linear tetrapyrrole chromophores via their first (canonical) Cys residue and show reversible photoconversion triggered by light-dependent Z/E isomerization of the chromophore. Among the huge repertoire of CBCRs, DXCF CBCRs contain a second Cys residue within the highly conserved Asp-Xaa-Cys-Phe (DXCF) motif. In the typical receptors, the second Cys covalently attaches to the 15Z-chromophore in the dark state and detaches from the 15E-chromophore in the photoproduct state, whereas atypical ones that lack reversible ligation activity show red-shifted absorption in the dark state due to a more extended π-conjugated system. Moreover, some DXCF CBCRs show blue-shifted absorption in the photoproduct state due to the twisted geometry of the rotating ring. During the process of rational color tuning of a certain DXCF CBCR, we unexpectedly found that twisted photoproducts of some variant molecules showed dark reversion to the dark state, which prompted us to hypothesize that the photoproduct is destabilized by the twisted geometry of the rotating ring. In this study, we comprehensively examined the photoproduct stability of the twisted and relaxed molecules derived from the same CBCR scaffolds under dark conditions. In the DXCF CBCRs lacking reversible ligation activity, the twisted photoproducts showed faster dark reversion than the relaxed ones, supporting our hypothesis. By contrast, in the DXCF CBCRs exhibiting reversible ligation activity, the twisted photoproducts showed no detectable photoconversion. Reversible Cys adduct formation thus results in drastic rearrangement of the protein-chromophore interaction in the photoproduct state, which would contribute to the previously unknown photoproduct stability.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan. and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takumi Matsunaga
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Rei Narikawa
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan. and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan and Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan
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14
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Abstract
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Due
to the recent advances in X-ray free electron laser techniques,
bilin-containing cyanobacteriochrome photoreceptors have become prime
targets for the ever-expanding field of time-resolved structural biology.
However, to facilitate these challenging studies, it is essential
that the time scales of any structural changes during the photocycles
of cyanobacteriochromes be established. Here, we have used visible
and infrared transient absorption spectroscopy to probe the photocycle
of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple
orders of magnitude from picoseconds to seconds. Localized changes
in the bilin binding pocket occur in picoseconds to nanoseconds, followed
by more large-scale changes in protein structure, including formation
and breakage of a second thioether linkage, in microseconds to milliseconds.
The characterization of the entire photocycle will provide a vital
frame of reference for future time-resolved structural studies of
this model photoreceptor.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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15
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Enomoto G, Kamiya A, Okuda Y, Narikawa R, Ikeuchi M. Tlr0485 is a cAMP-activated c-di-GMP phosphodiesterase in a cyanobacterium Thermosynechococcus. J GEN APPL MICROBIOL 2020; 66:147-152. [PMID: 32224605 DOI: 10.2323/jgam.2020.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Second messenger molecules are crucial components of environmental signaling systems to integrate multiple inputs and elicit physiological responses. Among various kinds of second messengers, cyclic nucleotides cAMP and cyclic di-GMP (c-di-GMP) play pivotal roles in bacterial environmental responses. However, how these signaling systems are interconnected for a concerted regulation of cellular physiology remains elusive. In a thermophilic cyanobacterium Thermosynechococcus vulcanus strain RKN, incident light color is sensed by cyanobacteriochrome photoreceptors to transduce the light information to the levels of c-di-GMP, which induces cellular aggregation probably via cellulose synthase activation. Herein, we identified that Tlr0485, which is composed of a cGMP-specific phosphodiesterases, adenylate cyclases, and FhlA (GAF) domain and an HD-GYP domain, is a cAMP-activated c-di-GMP phosphodiesterase. We also show biochemical evidence that the two class-III nucleotide cyclases, Cya1 and Cya2, are both adenylate cyclases to produce cAMP in T. vulcanus. The prevalence of cAMP-activated c-di-GMP phosphodiesterase genes in cyanobacterial genomes suggests that the direct crosstalk between cAMP and c-di-GMP signaling systems may be crucial for cyanobacterial environmental responses.
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Affiliation(s)
- Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo.,Institute for Biology III, Faculty of Biology, University of Freiburg
| | - Ayako Kamiya
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo
| | - Yukiko Okuda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo
| | - Rei Narikawa
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency.,Department of Biological Science, Faculty of Science, Shizuoka University
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency.,Faculty of Education and Integrated Arts and Sciences, Waseda University
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16
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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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17
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Blue-/Green-Light-Responsive Cyanobacteriochromes Are Cell Shade Sensors in Red-Light Replete Niches. iScience 2020; 23:100936. [PMID: 32146329 PMCID: PMC7063230 DOI: 10.1016/j.isci.2020.100936] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/31/2020] [Accepted: 02/20/2020] [Indexed: 11/23/2022] Open
Abstract
Cyanobacteriochrome (CBCRs) photoreceptors show various photochemical properties, but their ecophysiological functions remain elusive. Here, we report that the blue/green CBCRs SesA/B/C can serve as physiological sensors of cell density. Because cyanobacterial cells show lower transmittance of blue light than green light, higher cell density gives more green-light-enriched irradiance to cells. The cell-density-dependent suppression of cell aggregation under blue-/green-mixed light and white light conditions support this idea. Such a sensing mechanism may provide information about the cell position in cyanobacterial mats in hot springs, the natural habitat of Thermosynechococcus. This cell-position-dependent SesA/B/C-mediated regulation of cellular sessility (aggregation) might be ecophysiologically essential for the reorganization and growth of phototrophic mats. We also report that the green-light-induced dispersion of cell aggregates requires red-light-driven photosynthesis. Blue/green CBCRs might work as shade detectors in a different niche than red/far-red phytochromes, which may be why CBCRs have evolved in cyanobacteria. Blue- and green-light-sensing cyanobacteriochromes can be sensors of cell density They may provide information about the cell position in microbial mats Green-light-induced dispersion of aggregates needs red-light-driven photosynthesis Cyanobacteriochromes might work in a different niche than red/far-red phytochromes
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18
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Sato T, Kikukawa T, Miyoshi R, Kajimoto K, Yonekawa C, Fujisawa T, Unno M, Eki T, Hirose Y. Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome. J Biol Chem 2019; 294:18909-18922. [PMID: 31649035 DOI: 10.1074/jbc.ra119.010384] [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: 07/26/2019] [Revised: 10/23/2019] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( 15Z Pb) and orange-absorbing 15E state ( 15E Po). pH titration analysis revealed that 15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, 15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( 15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in 15Z Pb and bilin protonation in 15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated 15Z Pg and protonated 15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed 15Z Pg formation as an intermediate in the 15E Pr-to- 15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.
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Affiliation(s)
- Teppei Sato
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Takashi Kikukawa
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Kousuke Kajimoto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Chinatsu Yonekawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
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19
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Fushimi K, Narikawa R. Cyanobacteriochromes: photoreceptors covering the entire UV-to-visible spectrum. Curr Opin Struct Biol 2019; 57:39-46. [DOI: 10.1016/j.sbi.2019.01.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/08/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
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20
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Protein Engineering of Dual-Cys Cyanobacteriochrome AM1_1186g2 for Biliverdin Incorporation and Far-Red/Blue Reversible Photoconversion. Int J Mol Sci 2019; 20:ijms20122935. [PMID: 31208089 PMCID: PMC6628166 DOI: 10.3390/ijms20122935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 01/14/2023] Open
Abstract
Cyanobacteria have cyanobacteriochromes (CBCRs), which are photoreceptors that bind to a linear tetrapyrrole chromophore and sense UV-to-visible light. A recent study revealed that the dual-Cys CBCR AM1_1186g2 covalently attaches to phycocyanobilin and exhibits unique photoconversion between a Pr form (red-absorbing dark state, λmax = 641 nm) and Pb form (blue-absorbing photoproduct, λmax = 416 nm). This wavelength separation is larger than those of the other CBCRs, which is advantageous for optical tools. Nowadays, bioimaging and optogenetics technologies are powerful tools for biological research. In particular, the utilization of far-red and near-infrared light sources is required for noninvasive applications to mammals because of their high potential to penetrate into deep tissues. Biliverdin (BV) is an intrinsic chromophore and absorbs the longest wavelength among natural linear tetrapyrrole chromophores. Although the BV-binding photoreceptors are promising platforms for developing optical tools, AM1_1186g2 cannot efficiently attach BV. Herein, by rationally introducing several replacements, we developed a BV-binding AM1_1186g2 variant, KCAP_QV, that exhibited reversible photoconversion between a Pfr form (far-red-absorbing dark state, λmax = 691 nm) and Pb form (λmax = 398 nm). This wavelength separation reached 293 nm, which is the largest among the known phytochrome and CBCR photoreceptors. In conclusion, the KCAP_QV molecule developed in this study can offer an alternative platform for the development of unique optical tools.
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21
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Kirpich JS, Gottlieb SM, Chang CW, Kim PW, Martin SS, Lagarias JC, Larsen DS. Reverse Photodynamics of the Noncanonical Red/Green NpR3784 Cyanobacteriochrome from Nostoc punctiforme. Biochemistry 2019; 58:2307-2317. [PMID: 30977638 DOI: 10.1021/acs.biochem.8b01275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the companion paper (10.1021/acs.biochem.8b01274), we examined the forward Pr photodynamics of NpR3784 (UniProtKB B2J457 ), a representative member of a noncanonical red/green (R/G) cyanobacteriochrome (CBCR) subfamily. Here the reverse Pg → Pr photodynamics of NpR3784 was studied by broadband transient absorption pump-probe spectroscopy. Primary (100 fs to 10 ns) and secondary (10 ns to 1 ms) photodynamics were characterized over nine decades of time, which also were complemented with temperature-jump cryokinetics measurements. In contrast with canonical R/G CBCRs, the NpR3784 reverse photoconversion yielded two spectrally distinct primary photoproducts, Lumi-Go and Lumi-Gr, which decay on different time scales. The two primary photoproducts of NpR3784 equilibrate on the 40 ns time scale and subsequently propagate as a single intermediate population into Pr. Such heterogeneity could arise from differences in the direction of D-ring rotation, in chromophore protonation or hydrogen bonding, or in the mobility of protein residues or of solvent water nearby the chromophore or some combination therein. We conclude that the atypical photodynamics of NpR3784 reflects chromophore-protein interactions that differ from those present in the canonical R/G CBCR family.
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Affiliation(s)
- Julia S Kirpich
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Sean M Gottlieb
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Che-Wei Chang
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Peter W Kim
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Shelley S Martin
- Department of Molecular and Cell Biology , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - J Clark Lagarias
- Department of Molecular and Cell Biology , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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22
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Wiebeler C, Rao AG, Gärtner W, Schapiro I. Die effektive Konjugationslänge ist für die spektrale Verschiebung im rot/grün schaltenden Cyanobakteriochrom Slr1393g3 verantwortlich. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Aditya G. Rao
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Wolfgang Gärtner
- Institut für Analytische Chemie; Fakultät für Chemie und Mineralogie; Universität Leipzig; 04103 Leipzig Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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23
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Wiebeler C, Rao AG, Gärtner W, Schapiro I. The Effective Conjugation Length Is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3. Angew Chem Int Ed Engl 2019; 58:1934-1938. [PMID: 30508317 DOI: 10.1002/anie.201810266] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 01/19/2023]
Abstract
The origin of the spectral shift from a red- to a green-absorbing form in a cyanobacteriochrome, Slr1393g3, was identified by combined quantum mechanics/molecular mechanics simulations. This protein, related to classical phytochromes, carries the open-chain tetrapyrrole chromophore phycocyanobilin. Our calculations reveal that the effective conjugation length in the chromophore becomes shorter upon conversion from the red to the green form. This is related to the planarity of the entire chromophore. A large distortion was found for the terminal pyrrole rings A and D; however, the D ring contributes more strongly to the photoproduct tuning, despite a larger change in the twist of the A ring. Our findings implicate that the D ring twist can be exploited to regulate the absorption of the photoproduct. Hence, mutations that affect the D ring twist can lead to rational tuning of the photoproduct absorption, allowing the tailoring of cyanobacteriochromes for biotechnological applications such as optogenetics and bioimaging.
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Affiliation(s)
- Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, 04103, Leipzig, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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24
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Fushimi K, Ikeuchi M, Narikawa R. The Expanded Red/Green Cyanobacteriochrome Lineage: An Evolutionary Hot Spot. Photochem Photobiol 2018; 93:903-906. [PMID: 28500709 DOI: 10.1111/php.12764] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/16/2017] [Indexed: 01/03/2023]
Abstract
This article highlights the paper by Rockwell et al. in the current issue of Photochemistry and Photobiology. Rockwell et al. describe the discovery of novel two-Cys photocycles within the "expanded red/green" (XRG) cyanobacteriochrome (CBCR) lineage. Comprehensive phylogenetic analysis revealed that several XRG CBCRs possess a second Cys residue in the DXCF (Asp-Xaa-Cys-Phe) motif conserved among the DXCF CBCR lineage. Spectral studies identified that these CBCRs showed green/blue or ultraviolet/blue reversible photoconversion abilities. The green/blue reversible photocycle had not been reported previously among the XRG CBCR lineage. Based on these findings, Rockwell et al. replaced three amino acid residues in a red/green reversible CBCR, NpR6012g4, and succeeded in constructing a violet/green reversible photocycle. These findings, together with previous studies, provide a good explanation for the evolutionary flexibility of the XRG CBCRs.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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25
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Fushimi K, Enomoto G, Ikeuchi M, Narikawa R. Distinctive Properties of Dark Reversion Kinetics between Two Red/Green-Type Cyanobacteriochromes and their Application in the Photoregulation of cAMP Synthesis. Photochem Photobiol 2018; 93:681-691. [PMID: 28500699 DOI: 10.1111/php.12732] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/07/2016] [Indexed: 12/13/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors that bind to a linear tetrapyrrole within a conserved cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domain and exhibit reversible photoconversion. Red/green-type CBCR GAF domains that photoconvert between red- (Pr) and green-absorbing (Pg) forms occur widely in various cyanobacteria. A putative phototaxis regulator, AnPixJ, contains multiple red/green-type CBCR GAF domains. We previously reported that AnPixJ's second domain (AnPixJg2) but not its fourth domain (AnPixJg4) shows red/green reversible photoconversion. Herein, we found that AnPixJg4 showed Pr-to-Pg photoconversion and rapid Pg-to-Pr dark reversion, whereas AnPixJg2 showed a barely detectable dark reversion. Site-directed mutagenesis revealed the involvement of six residues in Pg stability. Replacement at the Leu294/Ile660 positions of AnPixJg2/AnPixJg4 showed the highest influence on dark reversion kinetics. AnPixJg2_DR6, wherein the six residues of AnPixJg2 were entirely replaced with those of AnPixJg4, showed a 300-fold faster dark reversion than that of the wild type. We constructed chimeric proteins by fusing the GAF domains with adenylate cyclase catalytic regions, such as AnPixJg2-AC, AnPixJg4-AC and AnPixJg2_DR6-AC. We detected successful enzymatic activation under red light for both AnPixJg2-AC and AnPixJg2_DR6-AC, and repression under green light for AnPixJg2-AC and under dark incubation for AnPixJg2_DR6-AC. These results provide platforms to develop cAMP synthetic optogenetic tools.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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26
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Wu XJ, Yang H, Sheng Y, Zhu YL, Li PP. Fluorescence Properties of a Novel Cyanobacteriochrome GAF Domain from Spirulina that Exhibits Moderate Dark Reversion. Int J Mol Sci 2018; 19:ijms19082253. [PMID: 30071622 PMCID: PMC6121604 DOI: 10.3390/ijms19082253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/11/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are biliproteins for photoreception that are present in cyanobacteria. These proteins possess one or more unique cGMP-specific phosphodiesterase/adenylate cyclase/FhlA (GAF) domains that can covalently bind the linear tetrapyrrole (bilin). Light absorption triggers the photoisomerization of bilin between the 15Z and 15E photostates. The 15E photoproduct of some CBCR GAF domains can revert to the stable 15Z state in the absence of light. In some cases, this property makes these domains function as sensors of light intensity or as red/dark optogenetic switches. However, there have been few reports regarding the applicability of these fluorescent properties. Here, we report a red/green cyanobacteriochrome GAF domain from Spirulina subsalsa, designated SPI1085g3, which exhibited photoconversion from the red-absorbing dark state (Pr, λmax = 642 nm) to the orange-absorbing photoproduct state (Po, λmax = 590 nm), and exhibited moderate dark reversion (t1/2 = 3.3 min) from the Po state to the Pr state. The SPI1085g3 Pr state exhibited intense red fluorescence (λmax = 662 nm), with a quantum yield of 0.14. The fluorescence was switched off by red light irradiation and increased in the dark. Replacement of Cys448 of SPI1085g3 with Ser resulted in a slightly improved fluorescence quantum yield and nearly 13-fold faster dark reversion (t1/2 = 15.2 s) than that of the wild type. This novel red/dark-switchable fluorescent biliprotein expands the present repertoire and diversity of photoswitchable fluorescent protein candidates.
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Affiliation(s)
- Xian-Jun Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
| | - Hong Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Yi Sheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Yong-Li Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
| | - Ping-Ping Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
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27
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Tlr1612 is the major repressor of cell aggregation in the light-color-dependent c-di-GMP signaling network of Thermosynechococcus vulcanus. Sci Rep 2018; 8:5338. [PMID: 29593349 PMCID: PMC5871770 DOI: 10.1038/s41598-018-23628-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/16/2018] [Indexed: 11/08/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is a bacterial second messenger involved in sessile/motile lifestyle transitions. We previously reported that c-di-GMP is a crucial inducer of cell aggregation of the cyanobacterium Thermosynechococcus vulcanus. The three cooperating cyanobacteriochrome photoreceptors (SesA/B/C) regulate cell aggregation in a light color-dependent manner by synthesizing/degrading c-di-GMP. Although a variety of c-di-GMP signaling proteins are encoded in cyanobacterial genomes, how c-di-GMP signaling networks are organized remains elusive. Here we experimentally demonstrate that the cellulose synthase Tll0007, which is essential for cell aggregation, binds c-di-GMP although the affinity is low (Kd = 63.9 ± 5.1 µM). We also show that SesA-the main trigger of cell aggregation-is subject to strict product feedback inhibition (IC50 = 1.07 ± 0.13 µM). These results suggest that SesA-produced c-di-GMP may not directly bind to Tll0007. We therefore systematically analyzed all 10 of the genes encoding proteins containing a c-di-GMP synthesis/degradation domain. We identified Tlr1612, harboring both domains, as the major repressor of cell aggregation under the repressing teal-green light irradiation. tlr1612 acts downstream of sesA and is not regulated transcriptionally by light color, suggesting that Tlr1612 may be involved in c-di-GMP amplification in the signaling cascade. Post-transcriptional control is likely crucial for the light-regulated c-di-GMP signaling.
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Hasegawa M, Fushimi K, Miyake K, Nakajima T, Oikawa Y, Enomoto G, Sato M, Ikeuchi M, Narikawa R. Molecular characterization of D XCF cyanobacteriochromes from the cyanobacterium Acaryochloris marina identifies a blue-light power sensor. J Biol Chem 2017; 293:1713-1727. [PMID: 29229775 DOI: 10.1074/jbc.m117.816553] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/07/2017] [Indexed: 12/25/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole-binding photoreceptors that sense a wide range of wavelengths from ultraviolet to far-red. The primary photoreaction in these reactions is a Z/E isomerization of the double bond between rings C and D. After this isomerization, various color-tuning events establish distinct spectral properties of the CBCRs. Among the various CBCRs, the DXCF CBCR lineage is widely distributed among cyanobacteria. Because the DXCF CBCRs from the cyanobacterium Acaryochloris marina vary widely in sequence, we focused on these CBCRs in this study. We identified seven DXCF CBCRs in A. marina and analyzed them after isolation from Escherichia coli that produces phycocyanobilin, a main chromophore for the CBCRs. We found that six of these CBCRs covalently bound a chromophore and exhibited variable properties, including blue/green, blue/teal, green/teal, and blue/orange reversible photoconversions. Notably, one CBCR, AM1_1870g4, displayed unidirectional photoconversion in response to blue-light illumination, with a rapid dark reversion that was temperature-dependent. Furthermore, the photoconversion took place without Z/E isomerization. This observation indicated that AM1_1870g4 likely functions as a blue-light power sensor, whereas typical CBCRs reversibly sense two light qualities. We also found that AM1_1870g4 possesses a GDCF motif in which the Asp residue is swapped with the next Gly residue within the DXCF motif. Site-directed mutagenesis revealed that this swap is essential for the light power-sensing function of AM1_1870g4. This is the first report of a blue-light power sensor from the CBCR superfamily and of photoperception without Z/E isomerization among the bilin-based photoreceptors.
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Affiliation(s)
- Masumi Hasegawa
- From the Department of Biological Science, Faculty of Science, and
| | - Keiji Fushimi
- From the Department of Biological Science, Faculty of Science, and.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Keita Miyake
- From the Department of Biological Science, Faculty of Science, and
| | - Takahiro Nakajima
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.,the Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, and
| | - Yuki Oikawa
- From the Department of Biological Science, Faculty of Science, and
| | - Gen Enomoto
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.,the Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, and
| | - Moritoshi Sato
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.,the Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, and
| | - Masahiko Ikeuchi
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.,the Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, and
| | - Rei Narikawa
- From the Department of Biological Science, Faculty of Science, and .,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.,the Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya, Suruga-ku, Shizuoka 422-8529
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Hydrophobic Residues near the Bilin Chromophore-Binding Pocket Modulate Spectral Tuning of Insert-Cys Subfamily Cyanobacteriochromes. Sci Rep 2017; 7:40576. [PMID: 28094296 PMCID: PMC5240096 DOI: 10.1038/srep40576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are a subfamily of phytochrome photoreceptors found exclusively in photosynthetic cyanobacteria. Four CBCRs containing a second Cys in the insert region (insert-Cys) have been identified from the nonheterocystous cyanobacterium Microcoleus B353 (Mbr3854g4 and Mbl3738g2) and the nitrogen fixing, heterocystous cyanobacterium Nostoc punctiforme (NpF2164g3 and NpR1597g2). These insert-Cys CBCRs can sense light in the near-UV to orange range, but key residues responsible for tuning their colour sensitivity have not been reported. In the present study, near-UV/Green (UG) photosensors Mbr3854g4 (UG1) and Mbl3738g2 (UG2) were chosen for further spectroscopic analysis of their spectral sensitivity and tuning. Consistent with most dual-Cys CBCRs, both UGs formed a second thioether linkage to the phycocyanobilin (PCB) chromophore via the insert-Cys. This bond is subject to breakage and relinkage during forward and reverse photoconversions. Variations in residues equivalent to Phe that are in close contact with the PCB chromophore D-ring in canonical red/green CBCRs are responsible for tuning the light absorption peaks of both dark and photoproducts. This is the first time these key residues that govern light absorption in insert-Cys family CBCRs have been identified and characterised.
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Fushimi K, Rockwell NC, Enomoto G, Ni-Ni-Win, Martin SS, Gan F, Bryant DA, Ikeuchi M, Lagarias JC, Narikawa R. Cyanobacteriochrome Photoreceptors Lacking the Canonical Cys Residue. Biochemistry 2016; 55:6981-6995. [PMID: 27935696 DOI: 10.1021/acs.biochem.6b00940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that sense near-ultraviolet to far-red light. Like the distantly related phytochromes, all CBCRs reported to date have a conserved Cys residue (the "canonical Cys" or "first Cys") that forms a thioether linkage to C31 of the linear tetrapyrrole (bilin) chromophore. Detection of ultraviolet, violet, and blue light is performed by at least three subfamilies of two-Cys CBCRs that require both the first Cys and a second Cys that forms a second covalent linkage to C10 of the bilin. In the well-characterized DXCF subfamily, the second Cys is part of a conserved Asp-Xaa-Cys-Phe motif. We here report novel CBCRs lacking the first Cys but retaining the DXCF Cys as part of a conserved Asp-Xaa-Cys-Ile-Pro (DXCIP) motif. Phylogenetic analysis demonstrates that DXCIP CBCRs are a sister to a lineage of DXCF CBCR domains from phototaxis sensors. Three such DXCIP CBCR domains (cce_4193g1, Cyan8802_2776g1, and JSC1_24240) were characterized after recombinant expression in Escherichia coli engineered to produce phycocyanobilin. All three covalently bound bilin and showed unidirectional photoconversion in response to green light. Spectra of acid-denatured proteins in the dark-adapted state do not correspond to those of known bilins. One DXCIP CBCR, cce_4193g1, exhibited very rapid dark reversion consistent with a function as a power sensor. However, Cyan8802_2776g1 exhibited slower dark reversion and would not have such a function. The full-length cce_4193 protein also possesses a DXCF CBCR GAF domain (cce_4193g2) with a covalently bound phycoviolobilin chromophore and a blue/green photocycle. Our studies indicate that CBCRs need not contain the canonical Cys residue to function as photochromic light sensors and that phototaxis proteins containing DXCIP CBCRs may potentially perceive both light quality and light intensity.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University , Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan
| | - Ni-Ni-Win
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Fei Gan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802 United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802 United States.,Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717 United States
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University , Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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31
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Ma Q, Zhou N, Zhou M. Energy transfer between fusion biliproteins co-expressed with phycobiliprotein in Escherichia coli. Protein Expr Purif 2016; 126:84-88. [DOI: 10.1016/j.pep.2016.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 12/20/2022]
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32
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Rockwell NC, Martin SS, Lagarias JC. Identification of Cyanobacteriochromes Detecting Far-Red Light. Biochemistry 2016; 55:3907-19. [DOI: 10.1021/acs.biochem.6b00299] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
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33
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Abstract
Certain cyanobacteria look green if grown in red light and vice versa. This dramatic color change, called complementary chromatic adaptation (CCA), is caused by alterations of the major colored light-harvesting proteins. A major controller of CCA is the cyanobacteriochrome (CBCR) RcaE, a red-green reversible photoreceptor that triggers a complex signal transduction pathway. Now, a new study demonstrates that CCA is also modulated by DpxA, a CBCR that senses yellow and teal (greenish blue) light. DpxA acts to expand the range of wavelengths that can impact CCA, by fine-tuning the process. This dual control of CCA might positively impact the fitness of cells growing in the shade of competing algae or in a water column where light levels and spectral quality change gradually with depth. This discovery adds to the growing number of light-responsive phenomena controlled by multiple CBCRs. Furthermore, the diverse CBCRs which are exclusively found in cyanobacteria have significant biotechnological potential.
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34
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Fushimi K, Nakajima T, Aono Y, Yamamoto T, Ni-Ni-Win, Ikeuchi M, Sato M, Narikawa R. Photoconversion and Fluorescence Properties of a Red/Green-Type Cyanobacteriochrome AM1_C0023g2 That Binds Not Only Phycocyanobilin But Also Biliverdin. Front Microbiol 2016; 7:588. [PMID: 27242674 PMCID: PMC4876366 DOI: 10.3389/fmicb.2016.00588] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 01/09/2023] Open
Abstract
Cyanobacteriochromes (CBCRs) are distantly related to the red/far-red responsive phytochromes. Red/green-type CBCRs are widely distributed among various cyanobacteria. The red/green-type CBCRs covalently bind phycocyanobilin (PCB) and show red/green reversible photoconversion. Recent studies revealed that some red/green-type CBCRs from chlorophyll d-bearing cyanobacterium Acaryochloris marina covalently bind not only PCB but also biliverdin (BV). The BV-binding CBCRs show far-red/orange reversible photoconversion. Here, we identified another CBCR (AM1_C0023g2) from A. marina that also covalently binds not only PCB but also BV with high binding efficiencies, although BV chromophore is unstable in the presence of urea. Replacement of Ser334 with Gly resulted in significant improvement in the yield of the BV-binding holoprotein, thereby ensuring that the mutant protein is a fine platform for future development of optogenetic switches. We also succeeded in detecting near-infrared fluorescence from mammalian cells harboring PCB-binding AM1_C0023g2 whose fluorescence quantum yield is 3.0%. Here the PCB-binding holoprotein is shown as a platform for future development of fluorescent probes.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University Shizuoka, Japan
| | - Takahiro Nakajima
- Graduate School of Arts and Sciences, University of Tokyo Tokyo, Japan
| | - Yuki Aono
- Graduate School of Arts and Sciences, University of Tokyo Tokyo, Japan
| | - Tatsuro Yamamoto
- Department of Biological Science, Faculty of Science, Shizuoka University Shizuoka, Japan
| | - Ni-Ni-Win
- Graduate School of Arts and Sciences, University of Tokyo Tokyo, Japan
| | - Masahiko Ikeuchi
- Graduate School of Arts and Sciences, University of TokyoTokyo, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology AgencySaitama, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, University of Tokyo Tokyo, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University Shizuoka, Japan
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35
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Cho SM, Jeoung SC, Song JY, Kupriyanova EV, Pronina NA, Lee BW, Jo SW, Park BS, Choi SB, Song JJ, Park YI. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353. J Biol Chem 2015; 290:28502-28514. [PMID: 26405033 DOI: 10.1074/jbc.m115.669150] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found.
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Affiliation(s)
- Sung Mi Cho
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Sae Chae Jeoung
- Center for Advanced Measurement and Instrumentation, Korea Research Institute of Standards and Science, Daejeon 305-340, Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Natalia A Pronina
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | | | | | - Beom-Seok Park
- The Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Wanju 565-851, Korea.
| | - Sang-Bong Choi
- School of Biotechnology and Environmental Engineering, Myongji University, Yongin 449-728, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
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36
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Anders K, Essen LO. The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Curr Opin Struct Biol 2015; 35:7-16. [PMID: 26241319 DOI: 10.1016/j.sbi.2015.07.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 11/17/2022]
Abstract
Bilin-dependent GAF domain photoreceptors cover the whole spectrum of light with their absorbance properties. They can be divided into three groups according to the domain architecture of their photosensory module. Group I and Group II harbor phytochromes with PAS-GAF-PHY and GAF-PHY domain architecture, respectively. Group III consists of stand-alone GAF domain photoreceptors, the cyanobacteriochromes. Crystal structures of all three groups are now available to shed light on possible downstream signaling pathways. Structures of Group I and III photoreceptors in both states display changes in the secondary structures during photoconversion. The knowledge about the photoconversion in phytochromes and CBCRs make them promising targets for applications in life science and synthetic biology.
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Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany.
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37
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Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation. Proc Natl Acad Sci U S A 2015; 112:8082-7. [PMID: 26080423 DOI: 10.1073/pnas.1504228112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that have diverse spectral properties and domain compositions. Although large numbers of CBCR genes exist in cyanobacterial genomes, no studies have assessed whether multiple CBCRs work together. We recently showed that the diguanylate cyclase (DGC) activity of the CBCR SesA from Thermosynechococcus elongatus is activated by blue-light irradiation and that, when irradiated, SesA, via its product cyclic dimeric GMP (c-di-GMP), induces aggregation of Thermosynechococcus vulcanus cells at a temperature that is suboptimum for single-cell viability. For this report, we first characterize the photobiochemical properties of two additional CBCRs, SesB and SesC. Blue/teal light-responsive SesB has only c-di-GMP phosphodiesterase (PDE) activity, which is up-regulated by teal light and GTP. Blue/green light-responsive SesC has DGC and PDE activities. Its DGC activity is enhanced by blue light, whereas its PDE activity is enhanced by green light. A ΔsesB mutant cannot suppress cell aggregation under teal-green light. A ΔsesC mutant shows a less sensitive cell-aggregation response to ambient light. ΔsesA/ΔsesB/ΔsesC shows partial cell aggregation, which is accompanied by the loss of color dependency, implying that a nonphotoresponsive DGC(s) producing c-di-GMP can also induce the aggregation. The results suggest that SesB enhances the light color dependency of cell aggregation by degrading c-di-GMP, is particularly effective under teal light, and, therefore, seems to counteract the induction of cell aggregation by SesA. In addition, SesC seems to improve signaling specificity as an auxiliary backup to SesA/SesB activities. The coordinated action of these three CBCRs highlights why so many different CBCRs exist.
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38
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Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Hydrophobic Pocket for the C15-E,anti Chromophore in the Photoproduct. Biochemistry 2015; 54:3772-83. [DOI: 10.1021/acs.biochem.5b00438] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
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39
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Narikawa R, Fushimi K, Ni-Ni-Win, Ikeuchi M. Red-shifted red/green-type cyanobacteriochrome AM1_1870g3 from the chlorophyll d-bearing cyanobacterium Acaryochloris marina. Biochem Biophys Res Commun 2015; 461:390-5. [DOI: 10.1016/j.bbrc.2015.04.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 12/23/2022]
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40
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Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Protonated Bilin Ring System in Both Photostates. Biochemistry 2015; 54:2581-600. [DOI: 10.1021/bi501548t] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
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41
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Rockwell NC, Martin SS, Gan F, Bryant DA, Lagarias JC. NpR3784 is the prototype for a distinctive group of red/green cyanobacteriochromes using alternative Phe residues for photoproduct tuning. Photochem Photobiol Sci 2015; 14:258-69. [DOI: 10.1039/c4pp00336e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report chromophore–protein interactions used by cyanobacteriochrome NpR3784 and related proteins for spectral tuning of the green-absorbing photoproduct state. These interactions are distinct from those used by canonical red/green cyanobacteriochromes.
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Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
| | - Shelley S. Martin
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
| | - Fei Gan
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- University Park
- USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- University Park
- USA
- Department of Chemistry and Biochemistry
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
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42
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Rockwell NC, Martin SS, Lagarias JC. Identification of DXCF cyanobacteriochrome lineages with predictable photocycles. Photochem Photobiol Sci 2015; 14:929-41. [DOI: 10.1039/c4pp00486h] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two specialized subgroups of cyanobacteriochromes with predictable green/blue and blue/orange photocycles are defined by these studies.
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Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
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43
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Pennacchietti F, Losi A, Xu XL, Zhao KH, Gärtner W, Viappiani C, Cella F, Diaspro A, Abbruzzetti S. Photochromic conversion in a red/green cyanobacteriochrome from Synechocystis PCC6803: quantum yields in solution and photoswitching dynamics in living E. coli cells. Photochem Photobiol Sci 2015; 14:229-37. [DOI: 10.1039/c4pp00337c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochromic conversion in GAF3 has been followed in solution and in E. coli cells.
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Affiliation(s)
| | - Aba Losi
- Dipartimento di Fisica e Scienze della Terra “Macedonio Melloni”
- Università di Parma
- Parma
- Italy
| | - Xiu-ling Xu
- Max-Planck-Institute for Chemical Energy Conversion
- D-45470 Mülheim
- Germany
| | - Kai-hong Zhao
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- PR China
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion
- D-45470 Mülheim
- Germany
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra “Macedonio Melloni”
- Università di Parma
- Parma
- Italy
- NEST
| | | | - Alberto Diaspro
- Fondazione Istituto Italiano di Tecnologia
- 16163 Genova
- Italy
- Nikon Imaging Center
- Fondazione Istituto Italiano di Tecnologia
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44
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Lim S, Rockwell NC, Martin SS, Dallas JL, Lagarias JC, Ames JB. Photoconversion changes bilin chromophore conjugation and protein secondary structure in the violet/orange cyanobacteriochrome NpF2164g3' [corrected]. Photochem Photobiol Sci 2014; 13:951-62. [PMID: 24745038 DOI: 10.1039/c3pp50442e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to phytochromes. All CBCRs examined to date utilize a conserved Cys residue to form a covalent thioether linkage to the bilin chromophore. In the insert-Cys CBCR subfamily, a second conserved Cys can covalently link to the bilin C10 methine bridge, allowing detection of near-UV to blue light. The best understood insert-Cys CBCR is the violet/orange CBCR NpF2164g3 from Nostoc punctiforme, which has a stable second linkage in the violet-absorbing dark state. Photoconversion of NpF2164g3 leads to elimination of the second linkage and formation of an orange-absorbing photoproduct. We recently reported NMR chemical shift assignments for the orange-absorbing photoproduct state of NpF2164g3. We here present equivalent information for its violet-absorbing dark state. In both photostates, NpF2164g3 is monomeric in solution and regions containing the two conserved Cys residues essential for photoconversion are structurally disordered. In contrast to blue light receptors such as phototropin, NpF2164g3 is less structurally ordered in the dark state than in the photoproduct. The insert-Cys insertion loop and C-terminal helix exhibit light-dependent structural changes. Moreover, a motif containing an Asp residue also found in other CBCRs and in phytochromes adopts a random-coil structure in the dark state but a stable α-helix structure in the photoproduct. NMR analysis of the chromophore is consistent with a less ordered dark state, with A-ring resonances only resolved in the photoproduct. The C10 atom of the bilin chromophore exhibits a drastic change in chemical shift upon photoconversion, changing from 34.5 ppm (methylene) in the dark state to 115 ppm (methine) in the light-activated state. Our results provide structural insight into the two-Cys photocycle of NpF2164g3 and the structurally diverse mechanisms used for light perception by the larger phytochrome superfamily.
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Affiliation(s)
- Sunghyuk Lim
- Department of Chemistry, University of California, Davis, CA 95616, USA.
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45
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Narikawa R, Enomoto G, Ni-Ni-Win, Fushimi K, Ikeuchi M. A New Type of Dual-Cys Cyanobacteriochrome GAF Domain Found in Cyanobacterium Acaryochloris marina, Which Has an Unusual Red/Blue Reversible Photoconversion Cycle. Biochemistry 2014; 53:5051-9. [DOI: 10.1021/bi500376b] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rei Narikawa
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department
of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku,
Shizuoka 422-8529, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Gen Enomoto
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Ni-Ni-Win
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Keiji Fushimi
- Department
of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku,
Shizuoka 422-8529, Japan
| | - Masahiko Ikeuchi
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho
Kawaguchi, Saitama 332-0012, Japan
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46
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Enomoto G, Nomura R, Shimada T, Ni-Ni-Win, Narikawa R, Ikeuchi M. Cyanobacteriochrome SesA is a diguanylate cyclase that induces cell aggregation in Thermosynechococcus. J Biol Chem 2014; 289:24801-9. [PMID: 25059661 DOI: 10.1074/jbc.m114.583674] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteria have unique photoreceptors, cyanobacteriochromes, that show diverse spectral properties to sense near-UV/visible lights. Certain cyanobacteriochromes have been shown to regulate cellular phototaxis or chromatic acclimation of photosynthetic pigments. Some cyanobacteriochromes have output domains involved in bacterial signaling using a second messenger cyclic dimeric GMP (c-di-GMP), but its role in cyanobacteria remains elusive. Here, we characterize the recombinant Tlr0924 from a thermophilic cyanobacterium Thermosynechococcus elongatus, which was expressed in a cyanobacterial system. The protein reversibly photoconverts between blue- and green-absorbing forms, which is consistent with the protein prepared from Escherichia coli, and has diguanylate cyclase activity, which is enhanced 38-fold by blue light compared with green light. Therefore, Tlr0924 is a blue light-activated diguanylate cyclase. The protein's relatively low affinity (10.5 mM) for Mg(2+), which is essential for diguanylate cyclase activity, suggests that Mg(2+) might also regulate c-di-GMP signaling. Finally, we show that blue light irradiation under low temperature is responsible for Thermosynechococcus vulcanus cell aggregation, which is abolished when tlr0924 is disrupted, suggesting that Tlr0924 mediates blue light-induced cell aggregation by producing c-di-GMP. Given our results, we propose the name "sesA (sessility-A)" for tlr0924. This is the first report for cyanobacteriochrome-dependent regulation of a sessile/planktonic lifestyle in cyanobacteria via c-di-GMP.
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Affiliation(s)
- Gen Enomoto
- From the Department of Life Sciences (Biology), Graduate School of Arts and Sciences, and
| | - Ryouhei Nomura
- Department of Biological Science, Graduate School of Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902
| | - Takashi Shimada
- the Life Science Research Center, Shimadzu Corp., 3-1 Kanda-Nishikicho, Chiyoda-ku, Tokyo 108-8639, and
| | - Ni-Ni-Win
- From the Department of Life Sciences (Biology), Graduate School of Arts and Sciences, and
| | - Rei Narikawa
- From the Department of Life Sciences (Biology), Graduate School of Arts and Sciences, and PRESTO and
| | - Masahiko Ikeuchi
- From the Department of Life Sciences (Biology), Graduate School of Arts and Sciences, and Department of Biological Science, Graduate School of Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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47
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Rockwell NC, Martin SS, Gulevich AG, Lagarias JC. Conserved Phenylalanine Residues Are Required for Blue-Shifting of Cyanobacteriochrome Photoproducts. Biochemistry 2014; 53:3118-30. [DOI: 10.1021/bi500037a] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Alexander G. Gulevich
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
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48
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Gottlieb SM, Kim PW, Corley SC, Madsen D, Hanke SJ, Chang CW, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Primary and Secondary Photodynamics of the Violet/Orange Dual-Cysteine NpF2164g3 Cyanobacteriochrome Domain from Nostoc punctiforme. Biochemistry 2014; 53:1029-40. [DOI: 10.1021/bi4015538] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sean M. Gottlieb
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Scott C. Corley
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dorte Madsen
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Samuel J. Hanke
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Che-Wei Chang
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Nathan C. Rockwell
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department of Chemistry and ‡Department of
Molecular and Cell Biology, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
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49
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Gottlieb SM, Kim PW, Rockwell NC, Hirose Y, Ikeuchi M, Lagarias JC, Larsen DS. Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon. Biochemistry 2013; 52:8198-208. [DOI: 10.1021/bi400946q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean M. Gottlieb
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Nathan C. Rockwell
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Yuu Hirose
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Masahiko Ikeuchi
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
- Department
of Life Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - J. Clark Lagarias
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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50
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Velazquez Escobar F, Utesch T, Narikawa R, Ikeuchi M, Mroginski MA, Gärtner W, Hildebrandt P. Photoconversion mechanism of the second GAF domain of cyanobacteriochrome AnPixJ and the cofactor structure of its green-absorbing state. Biochemistry 2013; 52:4871-80. [PMID: 23808413 DOI: 10.1021/bi400506a] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriochromes are members of the phytochrome superfamily. In contrast to classical phytochromes, these small photosensors display a considerable variability of electronic absorption maxima. We have studied the light-induced conversions of the second GAF domain of AnPixJ, AnPixJg2, a phycocyanobilin-binding protein from the cyanobacterium Anabaena PCC 7120, using low-temperature resonance Raman spectroscopy combined with molecular dynamics simulations. AnPixJg2 is formed biosynthetically as a red-absorbing form (Pr) and can be photoconverted into a green-absorbing form (Pg). Forward and backward phototransformations involve the same reaction sequences and intermediates of similar cofactor structures as the corresponding processes in canonical phytochromes, including a transient cofactor deprotonation. Whereas the cofactor of the Pr state shows far-reaching similarities to the Pr states of classical phytochromes, the Pg form displays significant upshifts of the methine bridge stretching frequencies concomitant to the hypsochromically shifted absorption maximum. However, the cofactor in Pg is protonated and adopts a conformation very similar to the Pfr state of classical phytochromes. The spectral differences are probably related to an increased solvent accessibility of the chromophore which may reduce the π-electron delocalization in the phycocyanobilin and thus raise the energies of the first electronic transition and the methine bridge stretching modes. Molecular dynamics simulations suggest that the Z → E photoisomerization of the chromophore at the C-D methine bridge alters the interactions with the nearby Trp90 which in turn may act as a gate, allowing the influx of water molecules into the chromophore pocket. Such a mechanism of color tuning AnPixJg2 is unique among the cyanobacteriochromes studied so far.
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Affiliation(s)
- Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin , Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
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