1
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Mondal S, Pandey D, Singh SP. Chromatic acclimation in cyanobacteria renders robust photosynthesis and fitness in dynamic light environment: Recent advances and future perspectives. PHYSIOLOGIA PLANTARUM 2024; 176:e14536. [PMID: 39323055 DOI: 10.1111/ppl.14536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/27/2024]
Abstract
Cyanobacteria are photoautotrophic organisms that use light and water as a source of energy and electrons, respectively, to fix atmospheric carbon dioxide and release oxygen as a by-product during photosynthesis. However, photosynthesis and fitness of organisms are challenged by seasonal and diurnal fluctuations in light environments. Also, the distribution of cyanobacteria in a water column is subject to changes in the light regime. The quality and quantity of light change significantly in low and bright light environments that either limit photochemistry or result in photoinhibition due to an excess amount of light reaching reaction centers. Therefore, cyanobacteria have to adjust their light-harvesting machinery and cell morphology for the optimal harvesting of light. This adjustment of light-harvesting involves remodeling of the light-harvesting complex called phycobilisome or incorporation of chlorophyll molecules such as chlorophyll d and f into their light-harvesting machinery. Thus, photoacclimation responses of cyanobacteria at the level of pigment composition and cell morphology maximize their photosynthetic ability and fitness under a dynamic light environment. Cyanobacteria exhibit different types of photoacclimation responses that are commonly known as chromatic acclimation (CA). In this work, we discuss different types of CA reported in cyanobacteria and present a molecular mechanism of well-known type 3 CA where phycoerythrin and phycocyanin of phycobilisome changes according to light signals. We also include other aspects of type 3 CA that have been recently studied at a molecular level and highlight the importance of morphogenes, cytoskeleton, and carboxysome proteins. In summary, CA gives a unique competitive benefit to cyanobacteria by increasing their resource utilization ability and fitness.
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Affiliation(s)
- Soumila Mondal
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepa Pandey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shailendra P Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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2
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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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3
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Schmitt FJ, Friedrich T. Adaptation processes in Halomicronema hongdechloris, an example of the light-induced optimization of the photosynthetic apparatus on hierarchical time scales. FRONTIERS IN PLANT SCIENCE 2024; 15:1359195. [PMID: 39049856 PMCID: PMC11266139 DOI: 10.3389/fpls.2024.1359195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Oxygenic photosynthesis in Halomicronema hongdechloris, one of a series of cyanobacteria producing red-shifted Chl f, is adapted to varying light conditions by a range of diverse processes acting over largely different time scales. Acclimation to far-red light (FRL) above 700 nm over several days is mirrored by reversible changes in the Chl f content. In several cyanobacteria that undergo FRL photoacclimation, Chl d and Chl f are directly involved in excitation energy transfer in the antenna system, form the primary donor in photosystem I (PSI), and are also involved in electron transfer within photosystem II (PSII), most probably at the ChlD1 position, with efficient charge transfer happening with comparable kinetics to reaction centers containing Chl a. In H. hongdechloris, the formation of Chl f under FRL comes along with slow adaptive proteomic shifts like the rebuilding of the D1 complex on the time scale of days. On shorter time scales, much faster adaptation mechanisms exist involving the phycobilisomes (PBSs), which mainly contain allophycocyanin upon adaptation to FRL. Short illumination with white, blue, or red light leads to reactive oxygen species-driven mobilization of the PBSs on the time scale of seconds, in effect recoupling the PBSs with Chl f-containing PSII to re-establish efficient excitation energy transfer within minutes. In summary, H. hongdechloris reorganizes PSII to act as a molecular heat pump lifting excited states from Chl f to Chl a on the picosecond time scale in combination with a light-driven PBS reorganization acting on the time scale of seconds to minutes depending on the actual light conditions. Thus, structure-function relationships in photosynthetic energy and electron transport in H. hongdechloris including long-term adaptation processes cover 10-12 to 106 seconds, i.e., 18 orders of magnitude in time.
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Affiliation(s)
- Franz-Josef Schmitt
- Department of Physics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Thomas Friedrich
- Department of Bioenergetics, Technische Universität Berlin, Institute of Chemistry PC 14, Berlin, Germany
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4
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Nagae T, Fujita Y, Tsuchida T, Kamo T, Seto R, Hamada M, Aoyama H, Sato-Tomita A, Fujisawa T, Eki T, Miyanoiri Y, Ito Y, Soeta T, Ukaji Y, Unno M, Mishima M, Hirose Y. Green/red light-sensing mechanism in the chromatic acclimation photosensor. SCIENCE ADVANCES 2024; 10:eadn8386. [PMID: 38865454 PMCID: PMC11168458 DOI: 10.1126/sciadv.adn8386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/26/2024] [Indexed: 06/14/2024]
Abstract
Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.
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Affiliation(s)
- Takayuki Nagae
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yuya Fujita
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tatsuya Tsuchida
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Ryoka Seto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Masako Hamada
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Hiroshi Aoyama
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ayana Sato-Tomita
- Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Takahiro Soeta
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yutaka Ukaji
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjomachi, Saga 840-8502, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
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Guo R, Xu YL, Zhu JX, Scheer H, Zhao KH. Assembly of CpcL-phycobilisomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1207-1217. [PMID: 38319793 DOI: 10.1111/tpj.16666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024]
Abstract
CpcL-phycobilisomes (CpcL-PBSs) are a reduced type of phycobilisome (PBS) found in several cyanobacteria. They lack the traditional PBS terminal energy emitters, but still show the characteristic red-shifted fluorescence at ~670 nm. We established a method of assembling in vitro a rod-membrane linker protein, CpcL, with phycocyanin, generating complexes with the red-shifted spectral features of CpcL-PBSs. The red-shift arises from the interaction of a conserved key glutamine, Q57 of CpcL in Synechocystis sp. PCC 6803, with a single phycocyanobilin chromophore of trimeric phycocyanin at one of the three β82-sites. This chromophore is the terminal energy acceptor of CpcL-PBSs and donor to the photosystem(s). This mechanism also operates in PBSs from Acaryochloris marina MBIC11017. We then generated multichromic complexes harvesting light over nearly the complete visible range via the replacement of phycocyanobilin chromophores at sites α84 and β153 of phycocyanins by phycoerythrobilin and/or phycourobilin. The results demonstrate the rational design of biliprotein-based light-harvesting elements by engineering CpcL and phycocyanins, which broadens the light-harvesting range and accordingly improves the light-harvesting capacity and may be potentially applied in solar energy harvesting.
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Affiliation(s)
- Rui Guo
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ya-Li Xu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Jun-Xun Zhu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hugo Scheer
- Department Biologie I, Universität München, Menzinger Str. 67, D-80638, München, Germany
| | - Kai-Hong Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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6
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Stadnichuk IN, Krasilnikov PM. Relationship between non-photochemical quenching efficiency and the energy transfer rate from phycobilisomes to photosystem II. PHOTOSYNTHESIS RESEARCH 2024; 159:177-189. [PMID: 37328680 DOI: 10.1007/s11120-023-01031-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
The chromophorylated PBLcm domain of the ApcE linker protein in the cyanobacterial phycobilisome (PBS) serves as a bottleneck for Förster resonance energy transfer (FRET) from the PBS to the antennal chlorophyll of photosystem II (PS II) and as a redirection point for energy distribution to the orange protein ketocarotenoid (OCP), which is excitonically coupled to the PBLcm chromophore in the process of non-photochemical quenching (NPQ) under high light conditions. The involvement of PBLcm in the quenching process was first directly demonstrated by measuring steady-state fluorescence spectra of cyanobacterial cells at different stages of NPQ development. The time required to transfer energy from the PBLcm to the OCP is several times shorter than the time it takes to transfer energy from the PBLcm to the PS II, ensuring quenching efficiency. The data obtained provide an explanation for the different rates of PBS quenching in vivo and in vitro according to the half ratio of OCP/PBS in the cyanobacterial cell, which is tens of times lower than that realized for an effective NPQ process in solution.
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Affiliation(s)
- Igor N Stadnichuk
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya 35, 127726, Moscow, Russia.
| | - Pavel M Krasilnikov
- Biological Faculty of M.V., Lomonosov State University, Lenin Hills 12, 119991, Moscow, Russia
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7
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Rockwell NC, Lagarias JC. Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors. J Mol Biol 2024; 436:168313. [PMID: 37839679 PMCID: PMC11218821 DOI: 10.1016/j.jmb.2023.168313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The phytochrome superfamily comprises three groups of photoreceptors sharing a conserved GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) domain that uses a covalently attached linear tetrapyrrole (bilin) chromophore to sense light. Knotted red/far-red phytochromes are widespread in both bacteria and eukaryotes, but cyanobacteria also contain knotless red/far-red phytochromes and cyanobacteriochromes (CBCRs). Unlike typical phytochromes, CBCRs require only the GAF domain for bilin binding, chromophore ligation, and full, reversible photoconversion. CBCRs can sense a wide range of wavelengths (ca. 330-750 nm) and can regulate phototaxis, second messenger metabolism, and optimization of the cyanobacterial light-harvesting apparatus. However, the origins of CBCRs are not well understood: we do not know when or why CBCRs evolved, or what selective advantages led to retention of early CBCRs in cyanobacterial genomes. In the current work, we use the increasing availability of genomes and metagenome-assembled-genomes from early-branching cyanobacteria to explore the origins of CBCRs. We reaffirm the earliest branches in CBCR evolution. We also show that early-branching cyanobacteria contain late-branching CBCRs, implicating early appearance of CBCRs during cyanobacterial evolution. Moreover, we show that early-branching CBCRs behave as integrators of light and pH, providing a potential unique function for early CBCRs that led to their retention and subsequent diversification. Our results thus provide new insight into the origins of these diverse cyanobacterial photoreceptors.
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Affiliation(s)
- Nathan C Rockwell
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
| | - J Clark Lagarias
- 31 Briggs Hall, Department of Molecular and Cell Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA.
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8
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Gupta A, Pandey P, Gupta R, Tiwari S, Singh SP. Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1915-1930. [PMID: 38222287 PMCID: PMC10784256 DOI: 10.1007/s12298-023-01386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.
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Affiliation(s)
- Anjali Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Priyul Pandey
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Rinkesh Gupta
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Sapna Tiwari
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Shailendra Pratap Singh
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
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Larsen B, Hofmann R, Camacho IS, Clarke RW, Lagarias JC, Jones AR, Jones AM. Highlighter: An optogenetic system for high-resolution gene expression control in plants. PLoS Biol 2023; 21:e3002303. [PMID: 37733664 PMCID: PMC10513317 DOI: 10.1371/journal.pbio.3002303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
Optogenetic actuators have revolutionized the resolution at which biological processes can be controlled. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to function in the context of horticultural light environments. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter, a synthetic, light-gated gene expression system tailored for in planta function. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system. Analysis of a re-engineered CcaS in Escherichia coli demonstrated green/red photoswitching with phytochromobilin, a chromophore endogenous to plants, but also revealed a blue light response likely derived from a flavin-binding LOV-like domain. We deployed Highlighter in transiently transformed Nicotiana benthamiana for optogenetic control of fluorescent protein expression. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We implemented the system to demonstrate optogenetic control over plant immunity and pigment production through modulation of the spectral composition of broadband visible (white) light. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.
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Affiliation(s)
- Bo Larsen
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Roberto Hofmann
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ines S. Camacho
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - Richard W. Clarke
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California, United States of America
| | - Alex R. Jones
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, Teddington, United Kingdom
| | - Alexander M. Jones
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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Singh VK, Jha S, Rana P, Mishra S, Kumari N, Singh SC, Anand S, Upadhye V, Sinha RP. Resilience and Mitigation Strategies of Cyanobacteria under Ultraviolet Radiation Stress. Int J Mol Sci 2023; 24:12381. [PMID: 37569755 PMCID: PMC10419127 DOI: 10.3390/ijms241512381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Ultraviolet radiation (UVR) tends to damage key cellular machinery. Cells may adapt by developing several defence mechanisms as a response to such damage; otherwise, their destiny is cell death. Since cyanobacteria are primary biotic components and also important biomass producers, any drastic effects caused by UVR may imbalance the entire ecosystem. Cyanobacteria are exposed to UVR in their natural habitats. This exposure can cause oxidative stress which affects cellular morphology and vital processes such as cell growth and differentiation, pigmentation, photosynthesis, nitrogen metabolism, and enzyme activity, as well as alterations in the native structure of biomolecules such as proteins and DNA. The high resilience and several mitigation strategies adopted by a cyanobacterial community in the face of UV stress are attributed to the activation of several photo/dark repair mechanisms, avoidance, scavenging, screening, antioxidant systems, and the biosynthesis of UV photoprotectants, such as mycosporine-like amino acids (MAAs), scytonemin (Scy), carotenoids, and polyamines. This knowledge can be used to develop new strategies for protecting other organisms from the harmful effects of UVR. The review critically reports the latest updates on various resilience and defence mechanisms employed by cyanobacteria to withstand UV-stressed environments. In addition, recent developments in the field of the molecular biology of UV-absorbing compounds such as mycosporine-like amino acids and scytonemin and the possible role of programmed cell death, signal perception, and transduction under UVR stress are discussed.
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Affiliation(s)
- Varsha K. Singh
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
| | - Sapana Jha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
| | - Palak Rana
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
| | - Sonal Mishra
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
| | - Neha Kumari
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
| | - Suresh C. Singh
- Taurmed Technologies Pvt Ltd., 304, Pearl’s Business Park, Netaji Subhash Place, New Delhi 110034, India; (S.C.S.); (S.A.)
| | - Shekhar Anand
- Taurmed Technologies Pvt Ltd., 304, Pearl’s Business Park, Netaji Subhash Place, New Delhi 110034, India; (S.C.S.); (S.A.)
| | - Vijay Upadhye
- Department of Microbiology, Parul Institute of Applied Science, Center of Research for Development, Parul University, Vadodara 391760, India;
| | - Rajeshwar P. Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (V.K.S.); (S.J.); (P.R.); (S.M.); (N.K.)
- University Center for Research & Development (UCRD), Chandigarh University, Chandigarh 140413, India
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11
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Watanabe M, Ikeuchi M, Wilde A. The organization of the phycobilisome-photosystem I supercomplex depends on the ratio between two different phycobilisome linker proteins. Photochem Photobiol Sci 2023:10.1007/s43630-023-00397-2. [PMID: 36859522 DOI: 10.1007/s43630-023-00397-2] [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: 11/23/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
The phycobilisome (PBS) is an antenna protein complex in cyanobacteria, Glaucocystophytes, and red algae. In the standard PBS, the rod-core PBS, the rods are connected to the core by the rod-core linker protein CpcG. The rod-core PBS transfers the light energy mainly to photosystem (PS) II and to a lesser extent to PSI. Cyanobacteria assemble another type of PBS, the CpcL-PBS, which consists of only one rod. This rod-type PBS is connected to the thylakoid membrane by the linker protein CpcL and is a PSI-specific antenna. In the filamentous heterocyst-forming cyanobacterium Anabaena (Nostoc) sp. PCC 7120, the CpcL-PBS forms a complex with the tetrameric PSI (PBS-PSI supercomplex). The CpcL-PBS and the rod part of the rod-core PBS are identical except for the linker proteins CpcL and CpcG. How cells control the accumulation of the two different types of PBS is unknown. Here, we analyzed two mutant strains which either lack the major rod-core linker CpcG4 or overexpress the rod-membrane linker CpcL. In both mutant strains, more and larger PBS-PSI supercomplexes accumulated compared to the wild type. Our results suggest that CpcL and CpcG4 compete for the same phycobiliprotein pool, and therefore the CpcL/CpcG4 ratio determines the levels of PBS-PSI supercomplexes. We propose that the CpcL-PBS and the rod-core PBS fulfill distinct functions in light harvesting.
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Affiliation(s)
- Mai Watanabe
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany. .,Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo, 153-8902, Japan. .,Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan.
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Annegret Wilde
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
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12
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
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13
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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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14
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Li X, Jiang W, Qi Q, Liang Q. A Gene Circuit Combining the Endogenous I-E Type CRISPR-Cas System and a Light Sensor to Produce Poly-β-Hydroxybutyric Acid Efficiently. BIOSENSORS 2022; 12:bios12080642. [PMID: 36005038 PMCID: PMC9405541 DOI: 10.3390/bios12080642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022]
Abstract
‘Metabolic burden,’ which arises when introducing exogenic synthesizing pathways into a host strain, remains a challenging issue in metabolic engineering. Redirecting metabolic flux from cell growth to product synthesis at an appropriate culture timepoint is ideal for resolving this issue. In this report, we introduce optogenetics—which is capable of precise temporal and spatial control—as a genetic switch, accompanied by the endogenous type I-E CRISPRi system in Escherichia coli (E. coli) to generate a metabolic platform that redirects metabolic flux. Poly-β-hydroxybutyric acid (PHB) production was taken as an example to demonstrate the performance of this platform. A two-to-three-fold increase in PHB content was observed under green light when compared with the production of PHB under red light, confirming the regulatory activity of this platform and its potential to redirect metabolic flux to synthesize target products.
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Affiliation(s)
- Xiaomeng Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, Qingdao 266237, China
- The Second Laboratory of Lanzhou Institute of Biological Products Co., Ltd., No. 888, Yanchang Road, Lanzhou 730046, China
| | - Wei Jiang
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, No. 105, Jiefang Road, Jinan 250013, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, Qingdao 266237, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, Qingdao 266237, China
- Correspondence: ; Tel.: +86-13573163779
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15
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Chromatic Acclimation Processes and Their Relationships with Phycobiliprotein Complexes. Microorganisms 2022; 10:microorganisms10081562. [PMID: 36013980 PMCID: PMC9415938 DOI: 10.3390/microorganisms10081562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 12/02/2022] Open
Abstract
Chromatic acclimation (CA) is a widespread mechanism for optimizing the composition of phycobiliprotein complexes to maximize the cyanobacterial light capture efficiency. There are seven CA types, CA1-CA7, classified according to various photoregulatory pathways. Here, we use sequence analyses and bioinformatics to predict the presence of CA types according to three GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA)-containing photoreceptors, CcaS (cyanobacterial chromatic acclimation sensor), RcaE (regulator of chromatic adaptation), and RfpA (regulator for far-red photoacclimation). These photoreceptors were classified into three different phylogenetic groups leading different CA types in a diverse range of cyanobacteria. Combining with genomic information of phycobilisome compositions, the CA capabilities of various cyanobacteria were conjectured. Screening 65 accessible cyanobacterial genomes, we defined 19 cyanobacteria that have the capability to perform far-red light photoacclimation (FaRLiP) under the control of RfpA. Forty out of sixty-five cyanobacteria have the capability to perform green/red light photoacclimation, although they use different photoreceptors (RcaE and/or CcaS) and photoregulatory pathways. The reversible response of photoreceptors in CA regulation pathways trigged by changed light conditions reflects the flexibility of photoregulatory mechanisms in cyanobacteria and the putative independent evolutionary origin of photoacclimation types.
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16
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Reflections on Cyanobacterial Chromatic Acclimation: Exploring the Molecular Bases of Organismal Acclimation and Motivation for Rethinking the Promotion of Equity in STEM. Microbiol Mol Biol Rev 2022; 86:e0010621. [PMID: 35727025 PMCID: PMC9491170 DOI: 10.1128/mmbr.00106-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria are photosynthetic organisms that exhibit characteristic acclimation and developmental responses to dynamic changes in the external light environment. Photomorphogenesis is the tuning of cellular physiology, development, morphology, and metabolism in response to external light cues. The tuning of photosynthetic pigmentation, carbon fixation capacity, and cellular and filament morphologies to changes in the prevalent wavelengths and abundance of light have been investigated to understand the regulation and fitness implications of different aspects of cyanobacterial photomorphogenesis. Chromatic acclimation (CA) is the most common form of photomorphogenesis that has been explored in cyanobacteria. Multiple types of CA in cyanobacteria have been reported, and insights gained into the regulatory pathways and networks controlling some of these CA types. I examine the recent expansion of CA types that occur in nature and provide an overview of known regulatory factors involved in distinct aspects of cyanobacterial photomorphogenesis. Additionally, I explore lessons for cultivating success in scientific communities that can be drawn from a reflection on existing knowledge of and approaches to studying CA.
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17
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Identification of significant residues for intermediate accumulation in phycocyanobilin synthesis. Photochem Photobiol Sci 2022; 21:437-446. [PMID: 35394642 DOI: 10.1007/s43630-022-00198-z] [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: 12/28/2021] [Accepted: 02/28/2022] [Indexed: 10/18/2022]
Abstract
Phycocyanobilin, the primary pigment of both light perception and light-harvesting in cyanobacteria, is synthesized from biliverdin IXα (BV) through intermediate 181, 182-dihydrobiliverdin (181, 182-DHBV) by a phycocyanobilin:ferredoxin oxidoreductase (PcyA). In our previous study, we discovered two PcyA homologs (AmPcyAc and AmPcyAp) derived from Acaryochloris marina MBIC 11017 (A. marina) that exceptionally uses chlorophyll d as the primary photosynthetic pigment, absorbing longer wavelength far-red light than chlorophyll a, the photosynthetic pigment found in most cyanobacteria. Biochemical characterization of the two PcyA homologs identified functional diversification of these two enzymes: AmPcyAc provides 181, 182-DHBV, and PCB to the cyanobacteriochrome (CBCR) photoreceptors, whereas, AmPcyAp specifically provides PCB to the light-harvesting phycobilisome subunit. In this study, we focused on the residues necessary for 181, 182-DHBV supply to the CBCR photoreceptors by AmPcyAc. Based on the SyPcyA structure, we concentrated on the 30 residues that constitute the substrate-binding pocket. Among them, we discovered that Leu151 and Val225 in AmPcyAc were both substituted with isoleucine. During the enzymatic reaction, the SyPcyA variant molecule, possessing V225I and L151I replacements, accumulates the 181, 182-DHBV and supplies it to a CBCR molecule derived from A. marina. It is worth noting that the substitution of Val225 with isoleucine was specifically conserved among the Acaryochloris genus. Collectively, we propose that the specific evolution of PcyA among the Acaryochloris genus may correlate with the acquisition of Chl. d synthetic ability and growth in long-wavelength far-red light environments.
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18
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Okuda Y, Miyoshi R, Kamo T, Fujisawa T, Nagae T, Mishima M, Eki T, Hirose Y, Unno M. Raman Spectroscopy of an Atypical C15-E,syn Bilin Chromophore in Cyanobacteriochrome RcaE. J Phys Chem B 2022; 126:813-821. [DOI: 10.1021/acs.jpcb.1c09652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuji Okuda
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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19
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Takahashi M, Mikami K. Blue–red chromatic acclimation in the red alga Pyropia yezoensis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Noji T, Watanabe M, Dewa T, Itoh S, Ikeuchi M. Direct Energy Transfer from Allophycocyanin-Free Rod-Type CpcL-Phycobilisome to Photosystem I. J Phys Chem Lett 2021; 12:6692-6697. [PMID: 34260249 DOI: 10.1021/acs.jpclett.1c01763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phycobilisomes (PBSs) are photosynthetic antenna megacomplexes comprising pigment-binding proteins (cores and rods) joined with linker proteins. A rod-type PBS that does not have a core is connected to photosystem I (PSI) by a CpcL linker protein, which stabilizes a red-form of the phycocyanobilin (red-PCB) in the rod. However, quantitative information on the energy transfer from red-type PBS to PSI has not been determined. Herein, the isolated supercomplex of the rod-type PBS and the PSI tetramer from Anabaena sp. PCC 7120 were probed by time-resolved spectroscopy at 77 K and by decay-associated spectral analysis to show that red-PCB mediates the fast and efficient (time constant = 90 ps, efficiency = 95%) transfer of excitation energy from PCB to chlorophyll a (Chl a). According to the Förster energy transfer mechanism, this high efficiency corresponds to a 4 nm distance between red-PCB and Chl a, suggesting that β-84 PCB in the rod acts as red-PCB.
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Affiliation(s)
- Tomoyasu Noji
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Mai Watanabe
- 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, Saitama 332-0012, Japan
| | - Takehisa Dewa
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - 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, Saitama 332-0012, Japan
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21
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Ariyanti D, Ikebukuro K, Sode K. Artificial complementary chromatic acclimation gene expression system in Escherichia coli. Microb Cell Fact 2021; 20:128. [PMID: 34225717 PMCID: PMC8256508 DOI: 10.1186/s12934-021-01621-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/26/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The development of multiple gene expression systems, especially those based on the physical signals, such as multiple color light irradiations, is challenging. Complementary chromatic acclimation (CCA), a photoreversible process that facilitates the control of cellular expression using light of different wavelengths in cyanobacteria, is one example. In this study, an artificial CCA systems, inspired by type III CCA light-regulated gene expression, was designed by employing a single photosensor system, the CcaS/CcaR green light gene expression system derived from Synechocystis sp. PCC6803, combined with G-box (the regulator recognized by activated CcaR), the cognate cpcG2 promoter, and the constitutively transcribed promoter, the PtrcΔLacO promoter. RESULTS One G-box was inserted upstream of the cpcG2 promoter and a reporter gene, the rfp gene (green light-induced gene expression), and the other G-box was inserted between the PtrcΔLacO promoter and a reporter gene, the bfp gene (red light-induced gene expression). The Escherichia coli transformants with plasmid-encoded genes were evaluated at the transcriptional and translational levels under red or green light illumination. Under green light illumination, the transcription and translation of the rfp gene were observed, whereas the expression of the bfp gene was repressed. Under red light illumination, the transcription and translation of the bfp gene were observed, whereas the expression of the rfp gene was repressed. During the red and green light exposure cycles at every 6 h, BFP expression increased under red light exposure while RFP expression was repressed, and RFP expression increased under green light exposure while BFP expression was repressed. CONCLUSION An artificial CCA system was developed to realize a multiple gene expression system, which was regulated by two colors, red and green lights, using a single photosensor system, the CcaS/CcaR system derived from Synechocystis sp. PCC6803, in E. coli. The artificial CCA system functioned repeatedly during red and green light exposure cycles. These results demonstrate the potential application of this CCA gene expression system for the production of multiple metabolites in a variety of microorganisms, such as cyanobacteria.
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Affiliation(s)
- Dwi Ariyanti
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- Faculty of Biotechnology, Sumbawa University of Technology, Olat Maras, Moyo Hulu, Sumbawa, West Nusa Tenggara, 84371, Indonesia
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
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22
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Maeda K, Okuda Y, Enomoto G, Watanabe S, Ikeuchi M. Biosynthesis of a sulfated exopolysaccharide, synechan, and bloom formation in the model cyanobacterium Synechocystis sp. strain PCC 6803. eLife 2021; 10:66538. [PMID: 34127188 PMCID: PMC8205485 DOI: 10.7554/elife.66538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Extracellularpolysaccharides of bacteria contribute to biofilm formation, stress tolerance, and infectivity. Cyanobacteria, the oxygenic photoautotrophic bacteria, uniquely produce sulfated extracellular polysaccharides among bacteria to support phototrophic biofilms. In addition, sulfated polysaccharides of cyanobacteria and other organisms have been focused as beneficial biomaterial. However, very little is known about their biosynthesis machinery and function in cyanobacteria. Here, we found that the model cyanobacterium, Synechocystis sp. strain PCC 6803, formed bloom-like cell aggregates embedded in sulfated extracellular polysaccharides (designated as synechan) and identified whole set of genes responsible for synechan biosynthesis and its transcriptional regulation, thereby suggesting a model for the synechan biosynthesis apparatus. Because similar genes are found in many cyanobacterial genomes with wide variation, our findings may lead elucidation of various sulfated polysaccharides, their functions, and their potential application in biotechnology. Bacteria are single-cell microorganisms that can form communities called biofilms, which stick to surfaces such as rocks, plants or animals. Biofilms confer protection to bacteria and allow them to colonize new environments. The physical scaffold of biofilms is a viscous matrix made of several molecules, the main one being polysaccharides, complex carbohydrates formed by many monosaccharides (single sugar molecules) joined together. Cyanobacteria, also known as blue-green algae, are a type of bacteria that produce oxygen and use sunlight as an energy source, just as plants and algae do. Cyanobacteria produce extracellular polysaccharides that contain sulfate groups. These sulfated polysaccharides are also produced by animals and algae but are not common in other bacteria or plants. One possible role of sulfated, extracellular polysaccharides in cyanobacteria is keeping cells together in the floating aggregates found in cyanobacterial blooms. These are visible discolorations of the water caused by an overgrowth of cyanobacteria that occur in lakes, estuaries and coastal waters. However, little is known about how these polysaccharides are synthesized in cyanobacteria and what their natural role is. Maeda et al. found a strain of cyanobacteria that formed bloom-like aggregates that were embedded in sulfated extracellular polysaccharides. Using genetic engineering techniques, the researchers identified a set of genes responsible for producing a sulfated extracellular polysaccharide and regulating its levels. They also found that cell aggregates of cyanobacteria can float without having intracellular gas vesicles, which was previously thought to enable blooms to float. The results of the present study could have applications for human health, since many sulfated polysaccharides have antiviral, antitumor or anti-inflammatory properties, and similar genes are found in many cyanobacteria. In addition, these findings could be useful for controlling toxic cyanobacterial blooms, which are becoming increasingly problematic for society.
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Affiliation(s)
- Kaisei Maeda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Yukiko Okuda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.,Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
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23
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Sugimoto Y, Masuda S. In vivo localization and oligomerization of PixD and PixE for controlling phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2021; 67:54-58. [PMID: 33342920 DOI: 10.2323/jgam.2020.06.001] [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] [Indexed: 11/03/2022]
Abstract
Phototaxis is a phenomenon where cyanobacteria move toward a light source. Previous studies have shown that the blue-light-using-flavin (BLUF)-type photoreceptor PixD and the response regulator-like protein PixE control the phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. The pixD-null mutant moves away from light, whereas WT, pixE mutant, and pixD pixE double mutant move toward the light. This indicates that PixE functions downstream of PixD and influences the direction of movement. However, it is still unclear how the light signal received by PixD is transmitted to PixE, and then subsequently transmitted to the type IV pili motor mechanism. Here, we investigated intracellular localization and oligomerization of PixD and PixE to elucidate mechanisms of phototaxis regulation. Blue-native PAGE analysis, coupled with western blotting, indicated that most PixD exist as a dimer in soluble fractions, whereas PixE localized in ~250 kDa and ~450 kDa protein complexes in membrane fractions. When blue-native PAGE was performed after illuminating the membrane fractions with blue light, PixE levels in the ~250 kDa and ~450 kDa complexes were reduced and increased, respectively. These results suggest that PixE, localized in the ~450 kDa complex, controls activity of the motor ATPase PilB1 to regulate pilus motility.
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Affiliation(s)
- Yuki Sugimoto
- Department of Life Science and Technology, Tokyo Institute of Technology
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology
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24
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Unno M, Hirose Y, Mishima M, Kikukawa T, Fujisawa T, Iwata T, Tamogami J. Spectroscopic approach for exploring structure and function of photoreceptor proteins. Biophys Physicobiol 2021; 18:127-130. [PMID: 34178563 PMCID: PMC8214923 DOI: 10.2142/biophysico.bppb-v18.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan
| | - Masaki Mishima
- Department of Molecular Biophysics, Tokyo University of Pharmacy and Life Sciences, School of Pharmacy, Hachioji, Tokyo 192-0392, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tatsuya Iwata
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
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Kamo T, Eki T, Hirose Y. Pressurized Liquid Extraction of a Phycocyanobilin Chromophore and Its Reconstitution with a Cyanobacteriochrome Photosensor for Efficient Isotopic Labeling. PLANT & CELL PHYSIOLOGY 2021; 62:334-347. [PMID: 33386854 PMCID: PMC8112840 DOI: 10.1093/pcp/pcaa164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Linear tetrapyrrole compounds (bilins) are chromophores of the phytochrome and cyanobacteriochrome classes of photosensors and light-harvesting phycobiliproteins. Various spectroscopic techniques, such as resonance Raman, Fourier transform-infrared and nuclear magnetic resonance, have been used to elucidate the structures underlying their remarkable spectral diversity, in which the signals are experimentally assigned to specific structures using isotopically labeled bilin. However, current methods for isotopic labeling of bilins require specialized expertise, time-consuming procedures and/or expensive reagents. To address these shortcomings, we established a method for pressurized liquid extraction of phycocyanobilin (PCB) from the phycobiliprotein powder Lina Blue and also the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). PCB was efficiently cleaved in ethanol with three extractions (5 min each) under nitrogen at 125�C and 100 bars. A prewash at 75�C was effective for removing cellular pigments of Synechocystis without PCB cleavage. Liquid chromatography and mass spectrometry suggested that PCB was cleaved in the C3-E (majority) and C3-Z (partial) configurations. 15N- and 13C/15N-labeled PCBs were prepared from Synechocystis cells grown with NaH13CO3 and/or Na15NO3, the concentrations of which were optimized based on cell growth and pigmentation. Extracted PCB was reconstituted with a recombinant apoprotein of the cyanobacteriochrome-class photosensor RcaE. Yield of the photoactive holoprotein was improved by optimization of the expression conditions and cell disruption in the presence of Tween 20. Our method can be applied for the isotopic labeling of other PCB-binding proteins and for the commercial production of non-labeled PCB for food, cosmetic and medical applications.
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Affiliation(s)
- Takanari Kamo
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi, 441-8580 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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Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE. Proc Natl Acad Sci U S A 2021; 118:2024583118. [PMID: 33972439 DOI: 10.1073/pnas.2024583118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a "bucket" consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pK a, whereas they are directly hydrogen bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the "leaky bucket" structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.
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Altmayer S, Jähnigen S, Köhler L, Wiebeler C, Song C, Sebastiani D, Matysik J. Hydrogen Bond between a Tyrosine Residue and the C-Ring Propionate Has a Direct Influence on Conformation and Absorption of the Bilin Cofactor in Red/Green Cyanobacteriochromes. J Phys Chem B 2021; 125:1331-1342. [PMID: 33523656 DOI: 10.1021/acs.jpcb.0c08518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors of the phytochrome superfamily showing remarkable variability in the wavelengths of the first electronic transition-sometimes denoted as Q band-compared to canonical phytochromes. Both classes carry the same cofactor, a bilin, but the molecular basis for the wide variation of their absorption properties is still a matter of debate. The interaction between the cofactor and the surrounding protein moiety has been proposed as a possible tuning factor. Here, we address the impact of hydrogen-bonding interaction between the covalently bound tetrapyrrole cofactor (phycocyanobilin, PCB) and a conserved tyrosine residue (Y302) in the second GAF (cGMP-specific phosphodiesterase, adenylyl cyclases, and FhlA) domain of the red-/green-switching CBCR AnPixJ (AnPixJg2). In the wild type, AnPixJg2 shows absorption maxima of 648 and 543 nm for the dark-adapted (Pr) and photoproduct (Pg) states, respectively. The Y302F mutation leads to the occurrence of an additional absorption band at 687 nm, which is assigned to a new spectroscopically identified sub-state called PIII. Similar spectral changes result upon mutating the Y302F-homologue in another representative red-/green-switching CBCR, Slr1393g3. Molecular dynamics simulations on the dark-adapted state suggest that the removal of the hydrogen bond leads to an additional PCB sub-state differing in its A- and D-ring geometries. The origin of the Q band satellite in the dark-adapted state is discussed.
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Affiliation(s)
- Susanne Altmayer
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Sascha Jähnigen
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Lisa Köhler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Christian Wiebeler
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.,Leibniz-Institut für Oberflächenmodifizierung, Permoserstraße 15, 04318 Leipzig, Germany
| | - Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Daniel Sebastiani
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
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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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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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Walter JM, Coutinho FH, Leomil L, Hargreaves PI, Campeão ME, Vieira VV, Silva BS, Fistarol GO, Salomon PS, Sawabe T, Mino S, Hosokawa M, Miyashita H, Maruyama F, van Verk MC, Dutilh BE, Thompson CC, Thompson FL. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia. MICROBIAL ECOLOGY 2020; 80:249-265. [PMID: 32060621 DOI: 10.1007/s00248-019-01480-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
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Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Felipe H Coutinho
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Luciana Leomil
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo I Hargreaves
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mariana E Campeão
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Beatriz S Silva
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Giovana O Fistarol
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo S Salomon
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Masashi Hosokawa
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Hideaki Miyashita
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Marcel C van Verk
- Plant-Microbe Interactions, Bioinformatics, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, 373, CCS-IB-Biomar, Lab. de Microbiologia, Bloco A3, (Anexo), sl. 102, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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Villafani Y, Yang HW, Park YI. Color Sensing and Signal Transmission Diversity of Cyanobacterial Phytochromes and Cyanobacteriochromes. Mol Cells 2020; 43:509-516. [PMID: 32438780 PMCID: PMC7332365 DOI: 10.14348/molcells.2020.0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
To perceive fluctuations in light quality, quantity, and timing, higher plants have evolved diverse photoreceptors including UVR8 (a UV-B photoreceptor), cryptochromes, phototropins, and phytochromes (Phys). In contrast to plants, prokaryotic oxygen-evolving photosynthetic organisms, cyanobacteria, rely mostly on bilin-based photoreceptors, namely, cyanobacterial phytochromes (Cphs) and cyanobacteriochromes (CBCRs), which exhibit structural and functional differences compared with plant Phys. CBCRs comprise varying numbers of light sensing domains with diverse color-tuning mechanisms and signal transmission pathways, allowing cyanobacteria to respond to UV-A, visible, and far-red lights. Recent genomic surveys of filamentous cyanobacteria revealed novel CBCRs with broader chromophore-binding specificity and photocycle protochromicity. Furthermore, a novel Cph lineage has been identified that absorbs blue-violet/yellow-orange light. In this minireview, we briefly discuss the diversity in color sensing and signal transmission mechanisms of Cphs and CBCRs, along with their potential utility in the field of optogenetics.
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Affiliation(s)
- Yvette Villafani
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
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Kashimoto T, Miyake K, Sato M, Maeda K, Matsumoto C, Ikeuchi M, Toyooka K, Watanabe S, Kanesaki Y, Narikawa R. Acclimation process of the chlorophyll d-bearing cyanobacterium Acaryochloris marina to an orange light environment revealed by transcriptomic analysis and electron microscopic observation. J GEN APPL MICROBIOL 2020; 66:106-115. [PMID: 32147625 DOI: 10.2323/jgam.2019.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The cyanobacterium Acaryochloris marina MBIC 11017 (A. marina 11017) possesses chlorophyll d (Chl. d) peaking at 698 nm as photosystem reaction center pigments, instead of chlorophyll a (Chl. a) peaking at 665 nm. About 95% of the total chlorophylls is Chl. d in A. marina 11017. In addition, A. marina 11017 possesses phycobilisome (PBS) supercomplex to harvest orange light and to transfer the absorbing energy to the photosystems. In this context, A. marina 11017 utilizes both far-red and orange light as the photosynthetic energy source. In the present study, we incubated A. marina 11017 cells under monochromatic orange and far-red light conditions and performed transcriptional and morphological studies by RNA-seq analysis and electron microscopy. Cellular absorption spectra, transcriptomic profiles, and microscopic observations demonstrated that PBS was highly accumulated under an orange light condition relative to a far-red light condition. Notably, transcription of one cpcBA operon encoding the phycobiliprotein of the phycocyanin was up-regulated under the orange light condition, but another operon was constitutively expressed under both conditions, indicating functional diversification of these two operons for light harvesting. Taking the other observations into consideration, we could illustrate the photoacclimation processes of A. marina 11017 in response to orange and far-red light conditions in detail.
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Affiliation(s)
- Tomonori Kashimoto
- Department of Biological Science, Faculty of Science, Shizuoka University
| | - Keita Miyake
- Department of Biological Science, Faculty of Science, Shizuoka University
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science
| | - Kaisei Maeda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo.,Department of Bioscience, Tokyo University of Agriculture
| | | | - 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
| | | | | | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University.,NODAI Genome Research Center, Tokyo University of Agriculture
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency.,Research Institute of Green Science and Technology, Shizuoka University
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35
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Sanfilippo JE, Garczarek L, Partensky F, Kehoe DM. Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis. Annu Rev Microbiol 2020; 73:407-433. [PMID: 31500538 DOI: 10.1146/annurev-micro-020518-115738] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.
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Affiliation(s)
- Joseph E Sanfilippo
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08540, USA;
| | - Laurence Garczarek
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, CNRS UMR 7144, Sorbonne Université, 29680 Roscoff, France; ,
| | - Frédéric Partensky
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, CNRS UMR 7144, Sorbonne Université, 29680 Roscoff, France; ,
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
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Shi M, Chen L, Zhang W. Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics. Front Microbiol 2020; 11:403. [PMID: 32256471 PMCID: PMC7090099 DOI: 10.3389/fmicb.2020.00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/26/2020] [Indexed: 12/02/2022] Open
Abstract
Two-component signal transduction systems are still poorly functionally characterized in the model cyanobacterium Synechocystis sp. PCC 6803. To address the issue, a GC-MS based comparative metabolomic analysis was conducted on a library of 44 knockout mutants for the response regulators (RRs) in Synechocystis. The metabolomic profiling analysis showed that 7 RRs mutants, namely Δslr1909, Δsll1291, Δslr6040, Δsll1330, Δslr2024, Δslr1584, and Δslr1693, were significantly different at metabolomic level, although their growth patterns are similar to the wild type under the normal autotrophic growth condition, suggesting regulatory diversity of RRs at metabolite level in Synechocystis. Additionally, a detailed metabolomic analysis coupled with RT-PCR verification led to useful clues for possible function of these 7 RRs, which were found involved in regulation of multiple aspects of cellular metabolisms in Synechocystis. Moreover, an integrative metabolomic and evolutionary analysis of all RR showed that four groups of RR genes clustered together in both metabolomic and evolutionary trees, suggesting of possible functional conservation of these RRs during the evolutionary process. Meanwhile, six groups of RRs with close evolutionary origin were found with different metabolomic profiles, suggesting possible functional changes during evolution. In contrast, more than 10 groups of RR genes with different clustering patterns in the evolutionary tree were found clustered together in metabolomics-based tree, suggesting possible functional convergences during the evolution. This study provided a metabolomic view of RR function, and the most needed functional clues for further characterization of these regulatory proteins in Synechocystis.
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Affiliation(s)
- Mengliang Shi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
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Rockwell NC, Lagarias JC. Phytochrome evolution in 3D: deletion, duplication, and diversification. THE NEW PHYTOLOGIST 2020; 225:2283-2300. [PMID: 31595505 PMCID: PMC7028483 DOI: 10.1111/nph.16240] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/17/2019] [Indexed: 05/09/2023]
Abstract
Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.
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Miyake K, Fushimi K, Kashimoto T, Maeda K, Ni-Ni-Win, Kimura H, Sugishima M, Ikeuchi M, Narikawa R. Functional diversification of two bilin reductases for light perception and harvesting in unique cyanobacterium Acaryochloris marina MBIC 11017. FEBS J 2020; 287:4016-4031. [PMID: 31995844 DOI: 10.1111/febs.15230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Bilin pigments play important roles for both light perception and harvesting in cyanobacteria by binding to cyanobacteriochromes (CBCRs) and phycobilisomes (PBS), respectively. Among various cyanobacteria, Acaryochloris marina MBIC 11017 (A. marina 11017) exceptionally uses chlorophyll d as the main photosynthetic pigment absorbing longer wavelength light than the canonical pigment, chlorophyll a, indicating existence of a system to sense longer wavelength light than others. On the other hand, A. marina 11017 has the PBS apparatus to harvest short-wavelength orange light, similar to most cyanobacteria. Thus, A. marina 11017 might sense longer wavelength light and harvest shorter wavelength light by using bilin pigments. Phycocyanobilin (PCB) is the main bilin pigment of both systems. Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes PCB synthesis from biliverdin via the intermediate 181 ,182 -dihydrobiliverdin (181 ,182 -DHBV), resulting in the stepwise shortening of the absorbing wavelengths. In this study, we found that A. marina 11017 exceptionally encodes two PcyA homologs, AmPcyAc and AmPcyAp. AmPcyAc is encoded on the main chromosome with most photoreceptor genes, whereas AmPcyAp is encoded on a plasmid with PBS-related genes. High accumulation of 181 ,182 -DHBV for extended periods was observed during the reaction catalyzed by AmPcyAc, whereas 181 ,182 -DHBV was transiently accumulated for a short period during the reaction catalyzed by AmPcyAp. CBCRs could sense longer wavelength far-red light through 181 ,182 -DHBV incorporation, whereas PBS could only harvest orange light through PCB incorporation, suggesting functional diversification of PcyA as AmPcyAc and AmPcyAp to provide 181 ,182 -DHBV and PCB to the light perception and harvesting systems, respectively.
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Affiliation(s)
- Keita Miyake
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Tomonori Kashimoto
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Kaisei Maeda
- Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Ni-Ni-Win
- Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Hiroyuki Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Japan
| | - Masahiko Ikeuchi
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.,Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Japan
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Wiltbank LB, Kehoe DM. Diverse light responses of cyanobacteria mediated by phytochrome superfamily photoreceptors. Nat Rev Microbiol 2020; 17:37-50. [PMID: 30410070 DOI: 10.1038/s41579-018-0110-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyanobacteria are an evolutionarily and ecologically important group of prokaryotes. They exist in diverse habitats, ranging from hot springs and deserts to glaciers and the open ocean. The range of environments that they inhabit can be attributed in part to their ability to sense and respond to changing environmental conditions. As photosynthetic organisms, one of the most crucial parameters for cyanobacteria to monitor is light. Cyanobacteria can sense various wavelengths of light and many possess a range of bilin-binding photoreceptors belonging to the phytochrome superfamily. Vital cellular processes including growth, phototaxis, cell aggregation and photosynthesis are tuned to environmental light conditions by these photoreceptors. In this Review, we examine the physiological responses that are controlled by members of this diverse family of photoreceptors and discuss the signal transduction pathways through which these photoreceptors operate. We highlight specific examples where the activities of multiple photoreceptors function together to fine-tune light responses. We also discuss the potential application of these photosensing systems in optogenetics and synthetic biology.
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Affiliation(s)
- Lisa B Wiltbank
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, USA.
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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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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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Castillo-Hair SM, Baerman EA, Fujita M, Igoshin OA, Tabor JJ. Optogenetic control of Bacillus subtilis gene expression. Nat Commun 2019; 10:3099. [PMID: 31308373 PMCID: PMC6629627 DOI: 10.1038/s41467-019-10906-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis exhibits complex spatial and temporal gene expression signals. Although optogenetic tools are ideal for studying such processes, none has been engineered for this organism. Here, we port a cyanobacterial light sensor pathway comprising the green/red photoreversible two-component system CcaSR, two metabolic enzymes for production of the chromophore phycocyanobilin (PCB), and an output promoter to control transcription of a gene of interest into B. subtilis. Following an initial non-functional design, we optimize expression of pathway genes, enhance PCB production via a translational fusion of the biosynthetic enzymes, engineer a strong chimeric output promoter, and increase dynamic range with a miniaturized photosensor kinase. Our final design exhibits over 70-fold activation and rapid response dynamics, making it well-suited to studying a wide range of gene regulatory processes. In addition, the synthetic biology methods we develop to port this pathway should make B. subtilis easier to engineer in the future.
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Affiliation(s)
| | - Elliot A Baerman
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston, TX, 77004, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA.
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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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44
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Hirose Y, Chihong S, Watanabe M, Yonekawa C, Murata K, Ikeuchi M, Eki T. Diverse Chromatic Acclimation Processes Regulating Phycoerythrocyanin and Rod-Shaped Phycobilisome in Cyanobacteria. MOLECULAR PLANT 2019; 12:715-725. [PMID: 30818037 DOI: 10.1016/j.molp.2019.02.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Cyanobacteria have evolved various photoacclimation processes to perform oxygenic photosynthesis under different light environments. Chromatic acclimation (CA) is a widely recognized and ecologically important type of photoacclimation, whereby cyanobacteria alter the absorbing light colors of a supermolecular antenna complex called the phycobilisome. To date, several CA variants that regulate the green-absorbing phycoerythrin (PE) and/or the red-absorbing phycocyanin (PC) within the hemi-discoidal form of phycobilisome have been characterized. In this study, we identified a unique CA regulatory gene cluster encoding yellow-green-absorbing phycoerythrocyanin (PEC) and a rod-membrane linker protein (CpcL) for the rod-shaped form of phycobilisome. Using the cyanobacterium Leptolyngbya sp. PCC 6406, we revealed novel CA variants regulating PEC (CA7) and the rod-shaped phycobilisome (CA0), which maximize yellow-green light-harvesting capacity and balance the excitation of photosystems, respectively. Analysis of the distribution of CA gene clusters in 445 cyanobacteria genomes revealed eight CA variants responding to green and red light, which are classified based on the presence of PEC, PE, cpcL, and CA photosensor genes. Phylogenetic analysis further suggested that the emergence of CA7 was a single event and preceded that of heterocystous strains, whereas the acquisition of CA0 occurred multiple times. Taken together, these results offer novel insights into the diversity and evolution of the complex cyanobacterial photoacclimation mechanisms.
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Affiliation(s)
- Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
| | - Song Chihong
- National Institute for Physiological Sciences (NIPS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Mai Watanabe
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Chinatsu Yonekawa
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toshihiko Eki
- Department of Environmental and Life Sciences, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
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Osoegawa S, Miyoshi R, Watanabe K, Hirose Y, Fujisawa T, Ikeuchi M, Unno M. Identification of the Deprotonated Pyrrole Nitrogen of the Bilin-Based Photoreceptor by Raman Spectroscopy with an Advanced Computational Analysis. J Phys Chem B 2019; 123:3242-3247. [PMID: 30913882 DOI: 10.1021/acs.jpcb.9b00965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochrome and cyanobacteriochrome utilize a linear methine-bridged tetrapyrrole (bilin) to control numerous biological processes. They show a reversible photoconversion between two spectrally distinct states. This photocycle is initiated by a C═C double-bond photoisomerization of the bilin followed by its thermal relaxations with transient and/or stationary changes in the protonation state of the pyrrole moiety. However, it has never been identified which of the four pyrrole nitrogen atoms is deprotonated. Here, we report a resonance Raman spectroscopic study on cyanobacteriochrome RcaE, which has been proposed to contain a deprotonated bilin for its green-absorbing 15 Z state. The observed Raman spectra were well reproduced by a simulated structure whose bilin B ring is deprotonated, with the aid of molecular dynamics and quantum mechanics/molecular mechanics calculations. The results revealed that the deprotonation of B and C rings has the distinct effect on the overall bilin structure, which will be relevant to the color tuning and photoconversion mechanisms of the phytochrome superfamily. Furthermore, this study documents the ability of vibrational spectroscopy combined with the advanced spectral analysis to visualize a proton of a cofactor molecule embedded in a protein moiety.
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Affiliation(s)
- Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Kouhei Watanabe
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Yuu Hirose
- Department of Environmental and Life Sciences , Toyohashi University of Technology , Toyohashi , Aichi 441-8580 , Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology) , The University of Tokyo , Meguro, Tokyo 153-8902 , Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering , Saga University , Saga 840-8502 , Japan
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46
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Isolation and characterization of 1-palmitoyl-2-linoleoyl-sn-glycerol as a hormogonium-inducing factor (HIF) from the coralloid roots of Cycas revoluta (Cycadaceae). Sci Rep 2019; 9:4751. [PMID: 30894551 PMCID: PMC6426835 DOI: 10.1038/s41598-019-39647-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/29/2019] [Indexed: 11/27/2022] Open
Abstract
Coralloid roots are specialized tissues of cycads (Cycas revoluta) that are involved in symbioses with nitrogen-fixing Nostoc cyanobacteria. We found that a crude methanolic extract of coralloid roots induced differentiation of the filamentous cell aggregates of Nostoc species into motile hormogonia. Hence, the hormogonium-inducing factor (HIF) was chased using bioassay-based isolation, and the active principle was characterized as a mixture of diacylglycerols (DAGs), mainly composed of 1-palmitoyl-2-linoleoyl-sn-glycerol (1), 1-palmitoyl-2-oleoyl-sn-glycerol (2), 1-stearoyl-2-linolenoyl-sn-glycerol (3), and 1-stearoyl-2-linoleoyl-sn-glycerol (4). Enantioselectively synthesised compound 1 showed a clear HIF activity at 1 nmol (0.6 µg) disc−1 for the filamentous cells, whereas synthesised 2-linoleoyl-3-palmitoyl-sn-glycerol (1′) and 1-palmitoyl-2-linoleoyl-rac-glycerol (1/1′) were less active than 1. Conversely, synthesised 1-linoleoyl-2-palmitoyl-rac-glycerol (8/8′) which is an acyl positional isomer of compound 1 was inactive. In addition, neither 1-monoacylglycerols nor phospholipids structurally related to 1 showed HIF-like activities. As DAGs are protein kinase C (PKC) activators, 12-O-tetradecanoylphorbol-13-acetate (12), urushiol C15:3-Δ10,13,16 (13), and a skin irritant anacardic acid C15:1-Δ8 (14) were also examined for HIF-like activities toward the Nostoc cells. Neither 12 nor 13 showed HIF-like activities, whereas 14 showed an HIF-like activity at 1 nmol/disc. These findings appear to indicate that some DAGs act as hormogonium-inducing signal molecules for filamentous Nostoc cyanobacteria.
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47
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Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci U S A 2018; 115:E12378-E12387. [PMID: 30552139 DOI: 10.1073/pnas.1812871115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many cyanobacteria, which use light as an energy source via photosynthesis, have evolved the ability to guide their movement toward or away from a light source. This process, termed "phototaxis," enables organisms to localize in optimal light environments for improved growth and fitness. Mechanisms of phototaxis have been studied in the coccoid cyanobacterium Synechocystis sp. strain PCC 6803, but the rod-shaped Synechococcus elongatus PCC 7942, studied for circadian rhythms and metabolic engineering, has no phototactic motility. In this study we report a recent environmental isolate of S. elongatus, the strain UTEX 3055, whose genome is 98.5% identical to that of PCC 7942 but which is motile and phototactic. A six-gene operon encoding chemotaxis-like proteins was confirmed to be involved in phototaxis. Environmental light signals are perceived by a cyanobacteriochrome, PixJSe (Synpcc7942_0858), which carries five GAF domains that are responsive to blue/green light and resemble those of PixJ from Synechocystis Plate-based phototaxis assays indicate that UTEX 3055 uses PixJSe to sense blue and green light. Mutation of conserved functional cysteine residues in different GAF domains indicates that PixJSe controls both positive and negative phototaxis, in contrast to the multiple proteins that are employed for implementing bidirectional phototaxis in Synechocystis.
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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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Ong NT, Tabor JJ. A Miniaturized Escherichia coli Green Light Sensor with High Dynamic Range. Chembiochem 2018; 19:1255-1258. [PMID: 29420866 DOI: 10.1002/cbic.201800007] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 12/16/2022]
Abstract
Genetically engineered photoreceptors enable unrivaled control over gene expression. Previously, we ported the Synechocystis PCC 6803 CcaSR two-component system, which is activated by green light and deactivated by red, into Escherichia coli, resulting in a sensor with a sixfold dynamic range. Later, we optimized pathway protein expression levels and the output promoter sequence to decrease transcriptional leakiness and to increase the dynamic range to approximately 120-fold. These CcaSR v 1.0 and v 2.0 systems have been used for precise quantitative, temporal, and spatial control of gene expression for a variety of applications. Recently, other workers deleted two PAS domains of unknown function from the CcaS sensor histidine kinase in a system similar to CcaSR v 1.0. Here we apply these deletions to CcaSR v 2.0, resulting in a v 3.0 light sensor with an output four times less leaky and a dynamic range of nearly 600-fold. We demonstrate that the PAS domain deletions have no deleterious effect on CcaSR green light sensitivity or response dynamics. CcaSR v 3.0 is the best-performing engineered bacterial green light sensor available, and should have broad applications in fundamental and synthetic biology studies.
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Affiliation(s)
- Nicholas T Ong
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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Scarbath-Evers LK, Jähnigen S, Elgabarty H, Song C, Narikawa R, Matysik J, Sebastiani D. Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy. Phys Chem Chem Phys 2018; 19:13882-13894. [PMID: 28513754 DOI: 10.1039/c7cp01218g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental 13C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.
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Affiliation(s)
- Laura Katharina Scarbath-Evers
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.
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