1
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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 DOI: 10.1016/j.jmb.2023.168313] [Citation(s) in RCA: 0] [Impact Index Per Article: 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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2
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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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Toida K, Kushida W, Yamamoto H, Yamamoto K, Ishii K, Uesaka K, Kanaly RA, Kutsuna S, Ihara K, Fujita Y, Iwasaki H. The GGDEF protein Dgc2 suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana. Microbiol Spectr 2023; 11:e0483722. [PMID: 37655901 PMCID: PMC10581220 DOI: 10.1128/spectrum.04837-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Colony pattern formations of bacteria with motility manifest complicated morphological self-organization phenomena. Leptolyngbya boryana is a filamentous cyanobacterium, which has been used as a genetic model organism for studying metabolism including photosynthesis and nitrogen fixation. A widely used type strain [wild type (WT) in this article] of this species has not been reported to show any motile activity. However, we isolated a spontaneous mutant strain that shows active motility (gliding activity) to give rise to complicated colony patterns, including comet-like wandering clusters and disk-like rotating vortices on solid media. Whole-genome resequencing identified multiple mutations in the genome of the mutant strain. We confirmed that inactivation of the candidate gene dgc2 (LBDG_02920) in the WT background was sufficient to give rise to motility and morphologically complex colony patterns. This gene encodes a protein containing the GGDEF motif which is conserved at the catalytic domain of diguanylate cyclase (DGC). Although DGC has been reported to be involved in biofilm formation, the dgc2 mutant significantly facilitated biofilm formation, suggesting a role for the dgc2 gene in suppressing both gliding motility and biofilm formation. Thus, Leptolyngbya is expected to be an excellent genetic model for studying dynamic colony pattern formation and to provide novel insights into the role of DGC family genes in biofilm formation. IMPORTANCE Self-propelled bacteria often exhibit complex collective behaviors, such as formation of dense-moving clusters, which are exemplified by wandering comet-like and rotating disk-like colonies; however, the molecular details of how these structures are formed are scant. We found that a strain of the filamentous cyanobacterium Leptolyngbya deficient in the GGDEF protein gene dgc2 elicits motility and complex and dynamic colony pattern formation, including comet-like and disk-like clusters. Although c-di-GMP has been reported to activate biofilm formation in some bacterial species, disruption of dgc2 unexpectedly enhanced it, suggesting a novel role for this GGDEF protein for inhibiting both colony pattern formation and biofilm formation.
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Affiliation(s)
- Kazuma Toida
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Wakana Kushida
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Hiroki Yamamoto
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kyoka Yamamoto
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kaichi Ishii
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Robert A. Kanaly
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Shinsuke Kutsuna
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hideo Iwasaki
- Department of Electrical Engineering and Bioscience, Graduate School of Sciences and Engineering, TWIns, Waseda University, Tokyo, Japan
- metaPhorest, Bioaesthetics Platform, Waseda University, Tokyo, Japan
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4
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Enomoto G, Wallner T, Wilde A. Control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP. MICROLIFE 2023; 4:uqad019. [PMID: 37223735 PMCID: PMC10124867 DOI: 10.1093/femsml/uqad019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/01/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide-derived signalling molecules control a wide range of cellular processes in all organisms. The bacteria-specific cyclic dinucleotide c-di-GMP plays a crucial role in regulating motility-to-sessility transitions, cell cycle progression, and virulence. Cyanobacteria are phototrophic prokaryotes that perform oxygenic photosynthesis and are widespread microorganisms that colonize almost all habitats on Earth. In contrast to photosynthetic processes that are well understood, the behavioural responses of cyanobacteria have rarely been studied in detail. Analyses of cyanobacterial genomes have revealed that they encode a large number of proteins that are potentially involved in the synthesis and degradation of c-di-GMP. Recent studies have demonstrated that c-di-GMP coordinates many different aspects of the cyanobacterial lifestyle, mostly in a light-dependent manner. In this review, we focus on the current knowledge of light-regulated c-di-GMP signalling systems in cyanobacteria. Specifically, we highlight the progress made in understanding the most prominent behavioural responses of the model cyanobacterial strains Thermosynechococcus vulcanus and Synechocystis sp. PCC 6803. We discuss why and how cyanobacteria extract crucial information from their light environment to regulate ecophysiologically important cellular responses. Finally, we emphasize the questions that remain to be addressed.
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Affiliation(s)
- Gen Enomoto
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Wallner
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
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5
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Frenkel A, Zecharia E, Gómez-Pérez D, Sendersky E, Yegorov Y, Jacob A, Benichou JIC, Stierhof YD, Parnasa R, Golden SS, Kemen E, Schwarz R. Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein. NPJ Biofilms Microbiomes 2023; 9:10. [PMID: 36864092 PMCID: PMC9981879 DOI: 10.1038/s41522-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
Cyanobacterial biofilms are ubiquitous and play important roles in diverse environments, yet, understanding of the processes underlying the development of these aggregates is just emerging. Here we report cell specialization in formation of Synechococcus elongatus PCC 7942 biofilms-a hitherto unknown characteristic of cyanobacterial social behavior. We show that only a quarter of the cell population expresses at high levels the four-gene ebfG-operon that is required for biofilm formation. Almost all cells, however, are assembled in the biofilm. Detailed characterization of EbfG4 encoded by this operon revealed cell-surface localization as well as its presence in the biofilm matrix. Moreover, EbfG1-3 were shown to form amyloid structures such as fibrils and are thus likely to contribute to the matrix structure. These data suggest a beneficial 'division of labor' during biofilm formation where only some of the cells allocate resources to produce matrix proteins-'public goods' that support robust biofilm development by the majority of the cells. In addition, previous studies revealed the operation of a self-suppression mechanism that depends on an extracellular inhibitor, which supresses transcription of the ebfG-operon. Here we revealed inhibitor activity at an early growth stage and its gradual accumulation along the exponential growth phase in correlation with cell density. Data, however, do not support a threshold-like phenomenon known for quorum-sensing in heterotrophs. Together, data presented here demonstrate cell specialization and imply density-dependent regulation thereby providing deep insights into cyanobacterial communal behavior.
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Affiliation(s)
- Alona Frenkel
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Eli Zecharia
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Daniel Gómez-Pérez
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Eleonora Sendersky
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Yevgeni Yegorov
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Avi Jacob
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Jennifer I. C. Benichou
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - York-Dieter Stierhof
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Rami Parnasa
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Susan S. Golden
- grid.266100.30000 0001 2107 4242Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA ,grid.266100.30000 0001 2107 4242Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | - Eric Kemen
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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6
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Nakane D. Live Cell Imaging of the Twitching Motility of Cyanobacteria by High-Resolution Microscopy. Methods Mol Biol 2023; 2646:255-263. [PMID: 36842120 DOI: 10.1007/978-1-0716-3060-0_20] [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] [Indexed: 04/28/2023]
Abstract
Many cyanobacteria show directional movement either toward or away from light sources. The cell movement, also known as twitching motility, is usually driven by type IV pili (T4P), a bacterial molecular machine. The machine generates a propulsion force through repeated cycles of extension and retraction of pilus filaments. Here, I describe a phototaxis assay for observing Synechocystis sp. PCC6803 and Thermosynechococcus vulcanus at the single-cell level with optical microscopy. By adding fluorescent beads, I also describe a method how to visualize the asymmetric activation of T4P during phototaxis.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan.
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7
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Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium. NPJ Biofilms Microbiomes 2022; 8:80. [PMID: 36253388 PMCID: PMC9576798 DOI: 10.1038/s41522-022-00340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/23/2022] [Indexed: 11/08/2022] Open
Abstract
Proteomic studies on cyanobacterial biofilms can be an effective approach to unravel metabolic pathways involved in biofilm formation and, consequently, obtain more efficient biofouling control strategies. Biofilm development by the filamentous cyanobacterium Toxifilum sp. LEGE 06021 was evaluated on different surfaces, glass and perspex, and at two significant shear rates for marine environments (4 s-1 and 40 s-1). Higher biofilm development was observed at 4 s-1. Overall, about 1877 proteins were identified, and differences in proteome were more noticeable between hydrodynamic conditions than those found between surfaces. Twenty Differentially Expressed Proteins (DEPs) were found between 4 s-1 vs. 40 s-1. On glass, some of these DEPs include phage tail proteins, a carotenoid protein, cyanophynase glutathione-dependent formaldehyde dehydrogenase, and the MoaD/ThiS family protein, while on perspex, DEPs include transketolase, dihydroxy-acid dehydratase, iron ABC transporter substrate-binding protein and protein NusG. This study contributes to developing a standardized protocol for proteomic analysis of filamentous cyanobacterial biofilms. This kind of proteomic analysis can also be useful for different research fields, given the broad spectrum of promising secondary metabolites and added-value compounds produced by cyanobacteria, as well as for the development of new antibiofilm strategies.
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8
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Jang J, Reed PMM, Rauscher S, Woolley GA. Point (S-to-G) Mutations in the W(S/G)GE Motif in Red/Green Cyanobacteriochrome GAF Domains Enhance Thermal Reversion Rates. Biochemistry 2022; 61:1444-1455. [PMID: 35759789 DOI: 10.1021/acs.biochem.2c00060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors consisting of single or tandem GAF (cGMP-phosphodiesterase/adenylate cyclase/FhlA) domains that bind bilin chromophores. Canonical red/green CBCR GAF domains are a well-characterized subgroup of the expanded red/green CBCR GAF domain family that binds phycocyanobilin (PCB) and converts between a thermally stable red-absorbing Pr state and a green-absorbing Pg state. The rate of thermal reversion from Pg to Pr varies widely among canonical red/green CBCR GAF domains, with half-lives ranging from days to seconds. Since the thermal reversion rate is an important parameter for the application of CBCR GAF domains as optogenetic tools, the molecular factors controlling the thermal reversion rate are of particular interest. Here, we report that point mutations in a well-conserved W(S/G)GE motif alter reversion rates in canonical red/green CBCR GAF domains in a predictable manner. Specifically, S-to-G mutations enhance thermal reversion rates, while the reverse, G-to-S mutations slow thermal reversion. Despite the distance (>10 Å) of the mutation site from the chromophore, molecular dynamics simulations and nuclear magnetic resonance (NMR) analyses suggest that the presence of a glycine residue allows the formation of a water bridge that alters the conformational dynamics of chromophore-interacting residues, leading to enhanced Pg to Pr thermal reversion.
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Affiliation(s)
- Jaewan Jang
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - P Maximilian M Reed
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Sarah Rauscher
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, L5L 1C6, Canada.,Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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9
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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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10
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Nakane D, Enomoto G, Bähre H, Hirose Y, Wilde A, Nishizaka T. Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-dependent process with high spatial resolution. eLife 2022; 11:73405. [PMID: 35535498 PMCID: PMC9090330 DOI: 10.7554/elife.73405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB, and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Direct visualization of type IV pilus filaments revealed that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
| | - Gen Enomoto
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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11
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Park J, Lee H, Dinh TB, Choi S, De Saeger J, Depuydt S, Brown MT, Han T. Commercial Potential of the Cyanobacterium Arthrospira maxima: Physiological and Biochemical Traits and the Purification of Phycocyanin. BIOLOGY 2022; 11:biology11050628. [PMID: 35625356 PMCID: PMC9138259 DOI: 10.3390/biology11050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary Arthrospira maxima is an unbranched, filamentous cyanobacterium rich in important cellular products such as vitamins, minerals, iron, essential amino acids, essential fatty acids, and protein, which has made it one of the most important commercial photoautotrophs. To optimize the growth conditions for the production of target compounds and to ensure profitability in commercial applications, the effects of pH and temperature were investigated. A. maxima has been shown to be tolerant to a range of pH conditions and to exhibit hyper-accumulation of phycoerythrin and allophycocyanin at low temperatures. These traits may offer significant advantages for future exploitation, especially in outdoor cultivation with fluctuating pH and temperature. Our study also demonstrated a new method for the purification of phycocyanin from A. maxima by using by ultrafiltration, ion-exchange chromatography, and gel filtration, producing PC at 1.0 mg·mL−1 with 97.6% purity. Abstract Arthrospira maxima is a natural source of fine chemicals for multiple biotechnological applications. We determined the optimal environmental conditions for A. maxima by measuring its relative growth rate (RGR), pigment yield, and photosynthetic performance under different pH and temperature conditions. RGR was highest at pH 7–9 and 30 °C. Chlorophyll a, phycocyanin, maximal quantum yield (Fv/Fm), relative maximal electron transport rate (rETRmax), and effective quantum yield (ΦPSII) were highest at pH 7–8 and 25 °C. Interestingly, phycoerythrin and allophycocyanin content was highest at 15 °C, which may be the lowest optimum temperature reported for phycobiliprotein production in the Arthrospira species. A threestep purification of phycocyanin (PC) by ultrafiltration, ion-exchange chromatography, and gel filtration resulted in a 97.6% purity of PC.
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Affiliation(s)
- Jihae Park
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea;
| | - Hojun Lee
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
| | - Thai Binh Dinh
- Department of Cosmetic Science and Management, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
| | - Soyeon Choi
- Department of Marine Science, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium;
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea;
| | - Murray T. Brown
- School of Marine Science & Engineering, Plymouth University, Plymouth PL4 8AA, Devon, UK;
| | - Taejun Han
- Development & Planning Office, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Korea; (J.P.); (H.L.)
- Department of Marine Science, Incheon National University, 119, Academy-ro, Incheon 22012, Korea;
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, 9000 Ghent, Belgium
- Correspondence:
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12
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Kameda M, Kanaly RA, Harada M, Aoki S, Tukada H, Kutsuna S. Quantification of cyanobacterial cyclic di-guanosine monophosphate (c-di-GMP) by liquid chromatography electrospray ionization tandem mass spectrometry. J Microbiol Methods 2022; 196:106468. [DOI: 10.1016/j.mimet.2022.106468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 12/27/2022]
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13
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Suban S, Sendersky E, Golden SS, Schwarz R. Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:218-229. [PMID: 35172394 PMCID: PMC9306852 DOI: 10.1111/1758-2229.13050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/03/2022] [Indexed: 05/03/2023]
Abstract
A biofilm inhibiting mechanism operates in the cyanobacterium Synechococcus elongatus. Here, we demonstrate that the glycosyltransferase homologue, Ogt, participates in the inhibitory process - inactivation of ogt results in robust biofilm formation. Furthermore, a mutational approach shows requirement of the glycosyltransferase activity for biofilm inhibition. This enzyme is necessary for glycosylation of the pilus subunit and for adequate pilus formation. In contrast to wild-type culture in which most cells exhibit several pili, only 25% of the mutant cells are piliated, half of which possess a single pilus. In spite of this poor piliation, natural DNA competence was similar to that of wild-type; therefore, we propose that the unglycosylated pili facilitate DNA transformation. Additionally, conditioned medium from wild-type culture, which contains a biofilm inhibiting substance(s), only partially blocks biofilm development by the ogt-mutant. Thus, we suggest that inactivation of ogt affects multiple processes including production or secretion of the inhibitor as well as the ability to sense or respond to it.
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Affiliation(s)
- Shiran Suban
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Susan S. Golden
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCA92093USA
- Center for Circadian BiologyUniversity of California, San DiegoLa JollaCA92093USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
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14
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Rockwell NC, Moreno MV, Martin SS, Lagarias JC. Protein-chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes. Photochem Photobiol Sci 2022; 21:471-491. [PMID: 35411484 PMCID: PMC9609751 DOI: 10.1007/s43630-022-00213-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Photoreceptors in the phytochrome superfamily use 15,16-photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties. Canonical phytochromes include master regulators of plant growth and development in which light signals trigger interconversion between a red-absorbing 15Z dark-adapted state and a metastable, far-red-absorbing 15E photoproduct state. Distantly related cyanobacteriochromes (CBCRs) carry out a diverse range of photoregulatory functions in cyanobacteria and exhibit considerable spectral diversity. One widespread CBCR subfamily typically exhibits a red-absorbing 15Z dark-adapted state similar to that of phytochrome that gives rise to a distinct green-absorbing 15E photoproduct. This red/green CBCR subfamily also includes red-inactive examples that fail to undergo photoconversion, providing an opportunity to study protein-chromophore interactions that either promote photoisomerization or block it. In this work, we identified a conserved lineage of red-inactive CBCRs. This enabled us to identify three substitutions sufficient to block photoisomerization in photoactive red/green CBCRs. The resulting red-inactive variants faithfully replicated the fluorescence and circular dichroism properties of naturally occurring examples. Converse substitutions restored photoconversion in naturally red-inactive CBCRs. This work thus identifies protein-chromophore interactions that control the fate of the excited-state population in red/green cyanobacteriochromes.
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Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
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15
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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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16
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Xu HF, Dai GZ, Wang YJ, Cheng C, Shang JL, Li RH, Liu K, Duanmu D, Qiu BS. Expansion of bilin-based red light sensors in the subaerial desert cyanobacterium Nostoc flagelliforme. Environ Microbiol 2022; 24:2047-2058. [PMID: 35172392 DOI: 10.1111/1462-2920.15932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022]
Abstract
Light is the crucial environmental signal for desiccation-tolerant cyanobacteria to activate photosynthesis and prepare for desiccation at dawn. However, the photobiological characteristics of desert cyanobacteria adaptation to one of the harshest habitats on Earth remain unresolved. In this study, we surveyed the genome of a subaerial desert cyanobacterium Nostoc flagelliforme and identified two phytochromes and seven cyanobacteriochromes (CBCRs) with one or more bilin-binding GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains. Biochemical and spectroscopic analyses of 69 purified GAF-containing proteins from recombinant phycocyanobilin (PCB), biliverdin or phycoerythrobilin-producing Escherichia coli indicated that nine of these proteins bind chromophores. Further investigation revealed that 11 GAFs form covalent adducts responsive to near-UV and visible light: eight GAFs contained PCB chromophores, three GAFs contained biliverdin chromophores and one contained the PCB isomer, phycoviolobilin. Interestingly, COO91_03972 is the first-ever reported GAF-only CBCR capable of sensing five wavelengths of light. Bioinformatics and biochemical analyses revealed that residue P132 of COO91_03972 is essential for chromophore binding to dual-cysteine CBCRs. Furthermore, the complement of N. flagelliforme CBCRs is enriched in red light sensors. We hypothesize that these sensors are critical for the acclimatization of N. flagelliforme to weak light environments at dawn.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Jie Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chao Cheng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ren-Han Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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17
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Huang M, Zhang JY, Zeng X, Zhang CC. c-di-GMP Homeostasis Is Critical for Heterocyst Development in Anabaena sp. PCC 7120. Front Microbiol 2021; 12:793336. [PMID: 34925302 PMCID: PMC8682488 DOI: 10.3389/fmicb.2021.793336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/09/2021] [Indexed: 12/04/2022] Open
Abstract
c-di-GMP is a ubiquitous bacterial signal regulating various physiological process. Anabaena PCC 7120 (Anabaena) is a filamentous cyanobacterium able to form regularly-spaced heterocysts for nitrogen fixation, in response to combined-nitrogen deprivation in 24h. Anabaena possesses 16 genes encoding proteins for c-di-GMP metabolism, and their functions are poorly characterized, except all2874 (cdgS) whose deletion causes a decrease in heterocyst frequency 48h after nitrogen starvation. We demonstrated here that c-di-GMP levels increased significantly in Anabaena after combined-nitrogen starvation. By inactivating each of the 16 genes, we found that the deletion of all1175 (cdgSH) led to an increase of heterocyst frequency 24h after nitrogen stepdown. A double mutant ΔcdgSHΔcdgS had an additive effect over the single mutants in regulating heterocyst frequency, indicating that the two genes acted at different time points for heterocyst spacing. Biochemical and genetic data further showed that the functions of CdgSH and CdgS in the setup or maintenance of heterocyst frequency depended on their opposing effects on the intracellular levels of c-di-GMP. Finally, we demonstrated that heterocyst differentiation was completely inhibited when c-di-GMP levels became too high or too low. Together, these results indicate that the homeostasis of c-di-GMP level is important for heterocyst differentiation in Anabaena.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.,Institut AMU-WUT, Aix-Marseille University and Wuhan University of Technology, Wuhan, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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18
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Blain-Hartung M, Rockwell NC, Lagarias JC. Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases. PLANT PHYSIOLOGY 2021; 187:632-645. [PMID: 34608946 PMCID: PMC8491021 DOI: 10.1093/plphys/kiab240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/02/2021] [Indexed: 05/03/2023]
Abstract
Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves-affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.
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Affiliation(s)
- Matthew Blain-Hartung
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- Author for communication:
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19
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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20
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Romeu MJ, Domínguez-Pérez D, Almeida D, Morais J, Araújo MJ, Osório H, Campos A, Vasconcelos V, Mergulhão FJ. Quantitative proteomic analysis of marine biofilms formed by filamentous cyanobacterium. ENVIRONMENTAL RESEARCH 2021; 201:111566. [PMID: 34181917 DOI: 10.1016/j.envres.2021.111566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial molecular biology can identify pathways that affect the adhesion and settlement of biofouling organisms and, consequently, obtain novel antifouling strategies for marine applications. Proteomic analyses can provide an essential understanding of how cyanobacteria adapt to different environmental settings. However, only a few qualitative studies have been performed in some cyanobacterial strains. Considering the limited knowledge about protein expression in cyanobacteria in different growing conditions, a quantitative proteomic analysis by LC-MS/MS of biofilm cells from a filamentous strain was performed. Biofilms were also analysed through standard methodologies for following cyanobacterial biofilm development. Biofilms were formed on glass and perspex at two relevant hydrodynamic conditions for marine environments (average shear rates of 4 s-1 and 40 s-1). Biofilm development was higher at 4 s-1 and no significant differences were found between surfaces. Proteomic analysis identified 546 proteins and 41 were differentially expressed. Differences in protein expression were more noticeable between biofilms formed on glass and perspex at 4 s-1. When comparing biofilms formed on different surfaces, results suggest that biofilm development may be related to the expression of several proteins like a beta-propeller domain-containing protein, chaperone DnaK, SLH domain-containing proteins, an OMF family outer membrane protein, and/or additional uncharacterized proteins. Regarding the hydrodynamic effect, biofilm development can be related to SOD enzyme expression, to proteins related to photosynthetic processes and to a set of uncharacterized proteins with calcium binding domains, disordered proteins, and others involved in electron transfer activity. Studies that combine distinct approaches are essential for finding new targets for antibiofilm agents. The characterisation performed in this work provides new insights into how shear rate and surface affect cyanobacterial biofilm development and how cyanobacteria adapt to these different environmental settings from a macroscopic standpoint to a proteomics context.
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Affiliation(s)
- M J Romeu
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - D Domínguez-Pérez
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - D Almeida
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - J Morais
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - M J Araújo
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - H Osório
- i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto, IPATIMUP, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal; Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - A Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - V Vasconcelos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - F J Mergulhão
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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21
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Böhm C, Todorović N, Balasso M, Gourinchas G, Winkler A. The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains. J Mol Biol 2021; 433:167092. [PMID: 34116122 PMCID: PMC7615318 DOI: 10.1016/j.jmb.2021.167092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Protein dynamics play a major role for the catalytic function of enzymes, the interaction of protein complexes or signal integration in regulatory proteins. In the context of multi-domain proteins involved in light-regulation of enzymatic effectors, the central role of conformational dynamics is well established. Light activation of sensory modules is followed by long-range signal transduction to different effectors; rather than domino-style structural rearrangements, a complex interplay of functional elements is required to maintain functionality. One family of such sensor-effector systems are red-light-regulated phytochromes that control diguanylate cyclases involved in cyclic-dimeric-GMP formation. Based on structural and functional studies of one prototypic family member, the central role of the coiled-coil sensor-effector linker was established. Interestingly, subfamilies with different linker lengths feature strongly varying biochemical characteristics. The dynamic interplay of the domains involved, however, is presently not understood. Here we show that the PHY domain dimer interface plays an essential role in signal integration, and that a functional coupling with the coiled-coil linker element is crucial. Chimaeras of two biochemically different family members highlight the phytochrome-spanning helical spine as an essential structural element involved in light-dependent upregulation of enzymatic turnover. However, isolated structural elements can frequently not be assigned to individual characteristics, which further emphasises the importance of global conformational dynamics. Our results provide insights into the intricate processes at play during light signal integration and transduction in these photosensory systems and thus provide additional guidelines for a more directed design of novel sensor-effector combinations with potential applications as optogenetic tools.
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Affiliation(s)
- Cornelia Böhm
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Nikolina Todorović
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Marco Balasso
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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22
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Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
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Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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23
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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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24
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Kharadi RR, Sundin GW. Cyclic-di-GMP Regulates Autoaggregation Through the Putative Peptidoglycan Hydrolase, EagA, and Regulates Transcription of the znuABC Zinc Uptake Gene Cluster in Erwinia amylovora. Front Microbiol 2020; 11:605265. [PMID: 33281804 PMCID: PMC7705223 DOI: 10.3389/fmicb.2020.605265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022] Open
Abstract
Erwinia amylovora is the causal agent of fire blight, an economically impactful disease that affects apple and pear production worldwide. E. amylovora pathogenesis is comprised of distinct type III secretion-dependent and biofilm-dependent stages. Alterations in the intracellular levels of cyclic-di-GMP (c-di-GMP) regulate the transition between the different stages of infection in E. amylovora. We previously reported that hyper-elevation of c-di-GMP levels in E. amylovora Ea1189, resulting from the deletion of all three c-di-GMP specific phosphodiesterase genes (Ea1189ΔpdeABC), resulted in an autoaggregation phenotype. The two major exopolysaccharides, amylovoran and cellulose, were also shown to partially contribute to autoaggregation. In this study, we aimed to identify the c-di-GMP dependent factor(s) that contributes to autoaggregation. We conducted a transposon mutant screen in Ea1189ΔpdeABC and selected for loss of autoaggregation. Our search identified a peptidoglycan hydrolase, specifically, a D, D-endopeptidase of the metallopeptidase class, EagA (Erwiniaaggregation factor A), that was found to physiologically contribute to autoaggregation in a c-di-GMP dependent manner. The production of amylovoran was also positively affected by EagA levels. An eagA deletion mutant (Ea1189ΔeagA) was significantly reduced in virulence compared to the wild type E. amylovora Ea1189. eagA is part of the znuABC zinc uptake gene cluster and is located within an operon downstream of znuA. The znuAeagA/znuCB gene cluster was transcriptionally regulated by elevated levels of c-di-GMP as well as by the zinc-dependent transcriptional repressor Zur. We also observed that with an influx of Zn2+ in the environment, the transcription of the znuAeagA/znuBC gene cluster is regulated by both Zur and a yet to be characterized c-di-GMP dependent pathway.
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Affiliation(s)
- Roshni R Kharadi
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - George W Sundin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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25
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Conradi FD, Mullineaux CW, Wilde A. The Role of the Cyanobacterial Type IV Pilus Machinery in Finding and Maintaining a Favourable Environment. Life (Basel) 2020; 10:life10110252. [PMID: 33114175 PMCID: PMC7690835 DOI: 10.3390/life10110252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Type IV pili (T4P) are proteinaceous filaments found on the cell surface of many prokaryotic organisms and convey twitching motility through their extension/retraction cycles, moving cells across surfaces. In cyanobacteria, twitching motility is the sole mode of motility properly characterised to date and is the means by which cells perform phototaxis, the movement towards and away from directional light sources. The wavelength and intensity of the light source determine the direction of movement and, sometimes in concert with nutrient conditions, act as signals for some cyanobacteria to form mucoid multicellular assemblages. Formation of such aggregates or flocs represents an acclimation strategy to unfavourable environmental conditions and stresses, such as harmful light conditions or predation. T4P are also involved in natural transformation by exogenous DNA, secretion processes, and in cellular adaptation and survival strategies, further cementing the role of cell surface appendages. In this way, cyanobacteria are finely tuned by external stimuli to either escape unfavourable environmental conditions via phototaxis, exchange genetic material, and to modify their surroundings to fit their needs by forming multicellular assemblies.
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Affiliation(s)
- Fabian D. Conradi
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (F.D.C.); (C.W.M.)
| | - Conrad W. Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (F.D.C.); (C.W.M.)
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg; Germany
- Correspondence:
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26
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Revealing the origin of multiphasic dynamic behaviors in cyanobacteriochrome. Proc Natl Acad Sci U S A 2020; 117:19731-19736. [PMID: 32759207 DOI: 10.1073/pnas.2001114117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteriochromes are photoreceptors in cyanobacteria that exhibit a wide spectral coverage and unique photophysical properties from the photoinduced isomerization of a linear tetrapyrrole chromophore. Here, we integrate femtosecond-resolved fluorescence and transient-absorption methods and unambiguously showed the significant solvation dynamics occurring at the active site from a few to hundreds of picoseconds. These motions of local water molecules and polar side chains are continuously convoluted with the isomerization reaction, leading to a nonequilibrium processes with continuous active-site motions. By mutations of critical residues at the active site, the modified local structures become looser, resulting in faster solvation relaxations and isomerization reaction. The observation of solvation dynamics is significant and critical to the correct interpretation of often-observed multiphasic dynamic behaviors, and thus the previously invoked ground-state heterogeneity may not be relevant to the excited-state isomerization reaction.
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27
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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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28
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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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29
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Arakaki A, Matsumoto T, Shimura N, Maeda Y, Yoshino T, Matsumoto M, Kisailus D, Tanaka T. Analysis of UV irradiation-induced cell settling of an oleaginous diatom, Fistulifera solaris, for efficient biomass recovery. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Enomoto G, Kamiya A, Okuda Y, Narikawa R, Ikeuchi M. Tlr0485 is a cAMP-activated c-di-GMP phosphodiesterase in a cyanobacterium Thermosynechococcus. J GEN APPL MICROBIOL 2020; 66:147-152. [PMID: 32224605 DOI: 10.2323/jgam.2020.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Second messenger molecules are crucial components of environmental signaling systems to integrate multiple inputs and elicit physiological responses. Among various kinds of second messengers, cyclic nucleotides cAMP and cyclic di-GMP (c-di-GMP) play pivotal roles in bacterial environmental responses. However, how these signaling systems are interconnected for a concerted regulation of cellular physiology remains elusive. In a thermophilic cyanobacterium Thermosynechococcus vulcanus strain RKN, incident light color is sensed by cyanobacteriochrome photoreceptors to transduce the light information to the levels of c-di-GMP, which induces cellular aggregation probably via cellulose synthase activation. Herein, we identified that Tlr0485, which is composed of a cGMP-specific phosphodiesterases, adenylate cyclases, and FhlA (GAF) domain and an HD-GYP domain, is a cAMP-activated c-di-GMP phosphodiesterase. We also show biochemical evidence that the two class-III nucleotide cyclases, Cya1 and Cya2, are both adenylate cyclases to produce cAMP in T. vulcanus. The prevalence of cAMP-activated c-di-GMP phosphodiesterase genes in cyanobacterial genomes suggests that the direct crosstalk between cAMP and c-di-GMP signaling systems may be crucial for cyanobacterial environmental responses.
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Affiliation(s)
- Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo.,Institute for Biology III, Faculty of Biology, University of Freiburg
| | - Ayako Kamiya
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo
| | - Yukiko Okuda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo
| | - Rei Narikawa
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency.,Department of Biological Science, Faculty of Science, Shizuoka University
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency.,Faculty of Education and Integrated Arts and Sciences, Waseda University
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31
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Chen M, Xu CY, Wang X, Ren CY, Ding J, Li L. Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa. BMC Genomics 2020; 21:217. [PMID: 32151246 PMCID: PMC7063779 DOI: 10.1186/s12864-020-6591-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/19/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. RESULTS Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.97 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. CONCLUSIONS Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism.
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Affiliation(s)
- Meng Chen
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Chun-Yang Xu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Xu Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Chong-Yang Ren
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Jiao Ding
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan, China
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32
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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: 57] [Impact Index Per Article: 14.3] [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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33
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Blue-/Green-Light-Responsive Cyanobacteriochromes Are Cell Shade Sensors in Red-Light Replete Niches. iScience 2020; 23:100936. [PMID: 32146329 PMCID: PMC7063230 DOI: 10.1016/j.isci.2020.100936] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/31/2020] [Accepted: 02/20/2020] [Indexed: 11/23/2022] Open
Abstract
Cyanobacteriochrome (CBCRs) photoreceptors show various photochemical properties, but their ecophysiological functions remain elusive. Here, we report that the blue/green CBCRs SesA/B/C can serve as physiological sensors of cell density. Because cyanobacterial cells show lower transmittance of blue light than green light, higher cell density gives more green-light-enriched irradiance to cells. The cell-density-dependent suppression of cell aggregation under blue-/green-mixed light and white light conditions support this idea. Such a sensing mechanism may provide information about the cell position in cyanobacterial mats in hot springs, the natural habitat of Thermosynechococcus. This cell-position-dependent SesA/B/C-mediated regulation of cellular sessility (aggregation) might be ecophysiologically essential for the reorganization and growth of phototrophic mats. We also report that the green-light-induced dispersion of cell aggregates requires red-light-driven photosynthesis. Blue/green CBCRs might work as shade detectors in a different niche than red/far-red phytochromes, which may be why CBCRs have evolved in cyanobacteria. Blue- and green-light-sensing cyanobacteriochromes can be sensors of cell density They may provide information about the cell position in microbial mats Green-light-induced dispersion of aggregates needs red-light-driven photosynthesis Cyanobacteriochromes might work in a different niche than red/far-red phytochromes
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34
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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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35
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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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36
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Wright TA, Jiang L, Park JJ, Anderson WA, Chen G, Hallberg ZF, Nan B, Hammond MC. Second messengers and divergent HD-GYP phosphodiesterases regulate 3',3'-cGAMP signaling. Mol Microbiol 2019; 113:222-236. [PMID: 31665539 DOI: 10.1111/mmi.14412] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2019] [Indexed: 12/16/2022]
Abstract
3',3'-cyclic GMP-AMP (cGAMP) is the third cyclic dinucleotide (CDN) to be discovered in bacteria. No activators of cGAMP signaling have yet been identified, and the signaling pathways for cGAMP have been inferred to display a narrow distribution based upon the characterized synthases, DncV and Hypr GGDEFs. Here, we report that the ubiquitous second messenger cyclic AMP (cAMP) is an activator of the Hypr GGDEF enzyme GacB from Myxococcus xanthus. Furthermore, we show that GacB is inhibited directly by cyclic di-GMP, which provides evidence for cross-regulation between different CDN pathways. Finally, we reveal that the HD-GYP enzyme PmxA is a cGAMP-specific phosphodiesterase (GAP) that promotes resistance to osmotic stress in M. xanthus. A signature amino acid change in PmxA was found to reprogram substrate specificity and was applied to predict the presence of non-canonical HD-GYP phosphodiesterases in many bacterial species, including phyla previously not known to utilize cGAMP signaling.
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Affiliation(s)
- Todd A Wright
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
| | - Lucy Jiang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - James J Park
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Wyatt A Anderson
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ge Chen
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Zachary F Hallberg
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Ming C Hammond
- Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
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37
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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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Factors Controlling Floc Formation and Structure in the Cyanobacterium Synechocystis sp. Strain PCC 6803. J Bacteriol 2019; 201:JB.00344-19. [PMID: 31262837 PMCID: PMC6755745 DOI: 10.1128/jb.00344-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Motile strains of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803 readily aggregate into flocs, or floating multicellular assemblages, when grown in liquid culture. As described here, we used confocal imaging to probe the structure of these flocs, and we developed a quantitative assay for floc formation based on fluorescence imaging of 6-well plates. The flocs are formed from strands of linked cells, sometimes packed into dense clusters but also containing voids with very few cells. Cells within the dense clusters show signs of nutrient stress, as judged by the subcellular distribution of green fluorescent protein (GFP)-tagged Vipp1 protein. We analyzed the effects on flocculation of a series of mutations that alter piliation and motility, including Δhfq, ΔpilB1, ΔpilT1, and ΔushA mutations and deletion mutations affecting major and minor pilins. The extent of flocculation is increased in the hyperpiliated ΔpilT1 mutant, but active cycles of pilus extension and retraction are not required for flocculation. Deletion of PilA1, the major subunit of type IV pili, has no effect on flocculation; however, flocculation is lost in mutants lacking an operon coding for the minor pilins PilA9 to -11. Therefore, minor pilins appear crucial for flocculation. We show that flocculation is a tightly regulated process that is promoted by blue light perception by the cyanobacteriochrome Cph2. Floc formation also seems to be a highly cooperative process. A proportion of nonflocculating Δhfq cells can be incorporated into wild-type flocs, but the presence of a high proportion of Δhfq cells disrupts the large-scale architecture of the floc.IMPORTANCE Some bacteria form flocs, which are multicellular floating assemblages of many thousands of cells. Flocs have been relatively little studied compared to surface-adherent biofilms, but flocculation could play many physiological roles, be a crucial factor in marine carbon burial, and enable more efficient biotechnological cell harvesting. We studied floc formation and architecture in the model cyanobacterium Synechocystis sp. strain PCC 6803, using mutants to identify specific cell surface structures required for floc formation. We show that floc formation is regulated by blue and green light perceived by the photoreceptor Cph2. The flocs have a characteristic structure based on strands of linked cells aggregating into dense clusters. Cells within the dense clusters show signs of nutrient stress, pointing to a disadvantage of floc formation.
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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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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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41
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Kuang S, Yuan Y, Wu Z, Peng R. Expression, purification and characterization of diguanylate cyclase from Rhodococcus ruber. Protein Expr Purif 2019; 163:105441. [PMID: 31195084 DOI: 10.1016/j.pep.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Abstract
Diguanylate cyclases (DGCs) were responsible for the synthesis of second messenger cyclic di-guanosine monophosphate (c-di-GMP), which were involved in various physiological activities of bacterial species. Here, a full-length DGC from Rhodococcus ruber SD3 fused with glutathione-S-transferase (GST) was expressed in E. coli and purified by glutathione agarose resin. The apparent molecular mass of one subunit of the purified diguanylate cyclase with GST tag (GST-DGC) was estimated to be 71.9 kDa by SDS-PAGE, which was approximately in accordance with the theoretical value of 73.0 kDa. The sequence of GST-DGC was confirmed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The blue native PAGE indicated that GST-DGC formed octamer. The optimum pH and temperature for GST-DGC activity were 8.0 and 47 °C, respectively. The fusion protein exhibited high thermostability, and 94% of activity was retained when the protein was incubated at 87 °C for 1 h. Moreover, the fusion protein showed pH stability. The Km, Vmax and Kcat values for GST-DGC enzyme were 9.8 μM, 0.7 μM/min and 1.3 S-1. Some ions such as Zn2+, Mn2+, Fe2+, Ni2+ and Co2+ had inhibitory effects on the activity of the protein, while other ions such as Mg2+, K+ and Na+ slightly activated the protein. The fusion protein also showed rather high stability in the presence of toluene, cyclohexane and n-hexane.
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Affiliation(s)
- Sufang Kuang
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Yuan Yuan
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Zhonghao Wu
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Ren Peng
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China.
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42
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Allen R, Rittmann BE, Curtiss R. Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures. Appl Environ Microbiol 2019; 85:e02192-18. [PMID: 30709828 PMCID: PMC6585507 DOI: 10.1128/aem.02192-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
Phototrophic biofilms are key to nutrient cycling in natural environments and bioremediation technologies, but few studies describe biofilm formation by pure (axenic) cultures of a phototrophic microbe. The cyanobacterium Synechocystis sp. strain PCC 6803 (here Synechocystis) is a model microorganism for the study of oxygenic photosynthesis and biofuel production. We report here that wild-type (WT) Synechocystis caused extensive biofilm formation in a 2,000-liter outdoor nonaxenic photobioreactor under conditions attributed to nutrient limitation. We developed a biofilm assay and found that axenic Synechocystis forms biofilms of cells and extracellular material but only when cells are induced by an environmental signal, such as a reduction in the concentration of growth medium BG11. Mutants lacking cell surface structures, namely type IV pili and the S-layer, do not form biofilms. To further characterize the molecular mechanisms of cell-cell binding by Synechocystis, we also developed a rapid (8-h) axenic aggregation assay. Mutants lacking type IV pili were unable to aggregate, but mutants lacking a homolog to Wza, a protein required for type 1 exopolysaccharide export in Escherichia coli, had a superbinding phenotype. In WT cultures, 1.2× BG11 medium induced aggregation to the same degree as 0.8× BG11 medium. Overall, our data support that Wza-dependent exopolysaccharide is essential to maintain stable, uniform suspensions of WT Synechocystis cells in unmodified growth medium and that this mechanism is counteracted in a pilus-dependent manner under altered BG11 concentrations.IMPORTANCE Microbes can exist as suspensions of individual cells in liquids and also commonly form multicellular communities attached to surfaces. Surface-attached communities, called biofilms, can confer antibiotic resistance to pathogenic bacteria during infections and establish food webs for global nutrient cycling in the environment. Phototrophic biofilm formation is one of the earliest phenotypes visible in the fossil record, dating back over 3 billion years. Despite the importance and ubiquity of phototrophic biofilms, most of what we know about the molecular mechanisms, genetic regulation, and environmental signals of biofilm formation comes from studies of heterotrophic bacteria. We aim to help bridge this knowledge gap by developing new assays for Synechocystis, a phototrophic cyanobacterium used to study oxygenic photosynthesis and biofuel production. With the aid of these new assays, we contribute to the development of Synechocystis as a model organism for the study of axenic phototrophic biofilm formation.
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Affiliation(s)
- Rey Allen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Bruce E Rittmann
- School of Sustainable Engineering and the Built Environment, Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
| | - Roy Curtiss
- School of Life Sciences, Biodesign Swette Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, Arizona, USA
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43
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Fushimi K, Enomoto G, Ikeuchi M, Narikawa R. Distinctive Properties of Dark Reversion Kinetics between Two Red/Green-Type Cyanobacteriochromes and their Application in the Photoregulation of cAMP Synthesis. Photochem Photobiol 2018; 93:681-691. [PMID: 28500699 DOI: 10.1111/php.12732] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/07/2016] [Indexed: 12/13/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors that bind to a linear tetrapyrrole within a conserved cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domain and exhibit reversible photoconversion. Red/green-type CBCR GAF domains that photoconvert between red- (Pr) and green-absorbing (Pg) forms occur widely in various cyanobacteria. A putative phototaxis regulator, AnPixJ, contains multiple red/green-type CBCR GAF domains. We previously reported that AnPixJ's second domain (AnPixJg2) but not its fourth domain (AnPixJg4) shows red/green reversible photoconversion. Herein, we found that AnPixJg4 showed Pr-to-Pg photoconversion and rapid Pg-to-Pr dark reversion, whereas AnPixJg2 showed a barely detectable dark reversion. Site-directed mutagenesis revealed the involvement of six residues in Pg stability. Replacement at the Leu294/Ile660 positions of AnPixJg2/AnPixJg4 showed the highest influence on dark reversion kinetics. AnPixJg2_DR6, wherein the six residues of AnPixJg2 were entirely replaced with those of AnPixJg4, showed a 300-fold faster dark reversion than that of the wild type. We constructed chimeric proteins by fusing the GAF domains with adenylate cyclase catalytic regions, such as AnPixJg2-AC, AnPixJg4-AC and AnPixJg2_DR6-AC. We detected successful enzymatic activation under red light for both AnPixJg2-AC and AnPixJg2_DR6-AC, and repression under green light for AnPixJg2-AC and under dark incubation for AnPixJg2_DR6-AC. These results provide platforms to develop cAMP synthetic optogenetic tools.
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Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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44
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Gourinchas G, Heintz U, Winkler A. Asymmetric activation mechanism of a homodimeric red light-regulated photoreceptor. eLife 2018; 7:34815. [PMID: 29869984 PMCID: PMC6005682 DOI: 10.7554/elife.34815] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/03/2018] [Indexed: 12/18/2022] Open
Abstract
Organisms adapt to environmental cues using diverse signaling networks. In order to sense and integrate light for regulating various biological functions, photoreceptor proteins have evolved in a modular way. This modularity is targeted in the development of optogenetic tools enabling the control of cellular events with high spatiotemporal precision. However, the limited understanding of signaling mechanisms impedes the rational design of innovative photoreceptor-effector couples. Here, we reveal molecular details of signal transduction in phytochrome-regulated diguanylyl cyclases. Asymmetric structural changes of the full-length homodimer result in a functional heterodimer featuring two different photoactivation states. Structural changes around the cofactors result in a quasi-translational rearrangement of the distant coiled-coil sensor-effector linker. Eventually, this regulates enzymatic activity by modulating the dimer interface of the output domains. Considering the importance of phytochrome heterodimerization in plant signaling, our mechanistic details of asymmetric photoactivation in a bacterial system reveal novel aspects of the evolutionary adaptation of phytochromes.
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Affiliation(s)
| | - Udo Heintz
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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45
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Agostoni M, Logan-Jackson AR, Heinz ER, Severin GB, Bruger EL, Waters CM, Montgomery BL. Homeostasis of Second Messenger Cyclic-di-AMP Is Critical for Cyanobacterial Fitness and Acclimation to Abiotic Stress. Front Microbiol 2018; 9:1121. [PMID: 29896182 PMCID: PMC5986932 DOI: 10.3389/fmicb.2018.01121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/11/2018] [Indexed: 12/11/2022] Open
Abstract
Second messengers are intracellular molecules regulated by external stimuli known as first messengers that are used for rapid organismal responses to dynamic environmental changes. Cyclic di-AMP (c-di-AMP) is a relatively newly discovered second messenger implicated in cell wall homeostasis in many pathogenic bacteria. C-di-AMP is synthesized from ATP by diadenylyl cyclases (DAC) and degraded by specific c-di-AMP phosphodiesterases (PDE). C-di-AMP DACs and PDEs are present in all sequenced cyanobacteria, suggesting roles for c-di-AMP in the physiology and/or development of these organisms. Despite conservation of these genes across numerous cyanobacteria, the functional roles of c-di-AMP in cyanobacteria have not been well-investigated. In a unique feature of cyanobacteria, phylogenetic analysis indicated that the broadly conserved DAC, related to CdaA/DacA, is always co-associated in an operon with genes critical for controlling cell wall synthesis. To investigate phenotypes regulated by c-di-AMP in cyanobacteria, we overexpressed native DAC (sll0505) and c-di-AMP PDE (slr0104) genes in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis) to increase and decrease intracellular c-di-AMP levels, respectively. DAC- and PDE-overexpression strains, showed abnormal aggregation phenotypes, suggesting functional roles for regulating c-di-AMP homeostasis in vivo. As c-di-AMP may be implicated in osmotic responses in cyanobacteria, we tested whether sorbitol and NaCl stresses impacted expression of sll0505 and slr0104 or intracellular c-di-AMP levels in Synechocystis. Additionally, to determine the range of cyanobacteria in which c-di-AMP may function, we assessed c-di-AMP levels in two unicellular cyanobacteria, i.e., Synechocystis and Synechococcus elongatus PCC 7942, and two filamentous cyanobacteria, i.e., Fremyella diplosiphon and Anabaena sp. PCC 7120. C-di-AMP levels responded differently to abiotic stress signals in distinct cyanobacteria strains, whereas salt stress uniformly impacted another second messenger cyclic di-GMP in cyanobacteria. Together, these results suggest regulation of c-di-AMP homeostasis in cyanobacteria and implicate a role for the second messenger in maintaining cellular fitness in response to abiotic stress.
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Affiliation(s)
- Marco Agostoni
- Cell and Molecular Biology Graduate Program, Michigan State University, East Lansing, MI, United States.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Alshaé R Logan-Jackson
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Emily R Heinz
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Geoffrey B Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Eric L Bruger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Christopher M Waters
- Cell and Molecular Biology Graduate Program, Michigan State University, East Lansing, MI, United States.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Beronda L Montgomery
- Cell and Molecular Biology Graduate Program, Michigan State University, East Lansing, MI, United States.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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46
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Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria. Methods Mol Biol 2018; 1657:169-186. [PMID: 28889294 DOI: 10.1007/978-1-4939-7240-1_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Signaling pathways involving second messenger c-di-GMP regulate various aspects of bacterial physiology and behavior. We describe the use of a red light-activated diguanylate cyclase (c-di-GMP synthase) and a blue light-activated c-di-GMP phosphodiesterase (hydrolase) for manipulating intracellular c-di-GMP levels in bacterial cells. We illustrate the application of these enzymes in regulating several c-di-GMP-dependent phenotypes, i.e., motility and biofilm phenotypes in E. coli and chemotactic behavior in the alphaproteobacterium Azospirillum brasilense. We expect these light-activated enzymes to be also useful in regulating c-di-GMP-dependent processes occurring at the fast timescale, for spatial control of bacterial populations, as well as for analyzing c-di-GMP-dependent phenomena at the single-cell level.
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47
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Etzl S, Lindner R, Nelson MD, Winkler A. Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications. J Biol Chem 2018; 293:9078-9089. [PMID: 29695503 PMCID: PMC5995499 DOI: 10.1074/jbc.ra118.003069] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/21/2018] [Indexed: 12/02/2022] Open
Abstract
Genetically targeting biological systems to control cellular processes with light is the concept of optogenetics. Despite impressive developments in this field, underlying molecular mechanisms of signal transduction of the employed photoreceptor modules are frequently not sufficiently understood to rationally design new optogenetic tools. Here, we investigate the requirements for functional coupling of red light–sensing phytochromes with non-natural enzymatic effectors by creating a series of constructs featuring the Deinococcus radiodurans bacteriophytochrome linked to a Synechocystis guanylate/adenylate cyclase. Incorporating characteristic structural elements important for cyclase regulation in our designs, we identified several red light–regulated fusions with promising properties. We provide details of one light-activated construct with low dark-state activity and high dynamic range that outperforms previous optogenetic tools in vitro and expands our in vivo toolkit, as demonstrated by manipulation of Caenorhabditis elegans locomotor activity. The full-length crystal structure of this phytochrome-linked cyclase revealed molecular details of photoreceptor–effector coupling, highlighting the importance of the regulatory cyclase element. Analysis of conformational dynamics by hydrogen–deuterium exchange in different functional states enriched our understanding of phytochrome signaling and signal integration by effectors. We found that light-induced conformational changes in the phytochrome destabilize the coiled-coil sensor–effector linker, which releases the cyclase regulatory element from an inhibited conformation, increasing cyclase activity of this artificial system. Future designs of optogenetic functionalities may benefit from our work, indicating that rational considerations for the effector improve the rate of success of initial designs to obtain optogenetic tools with superior properties.
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Affiliation(s)
- Stefan Etzl
- From the Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Robert Lindner
- the Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany, and
| | - Matthew D Nelson
- the Department of Biology, Saint Joseph's University, Philadelphia, Pennsylvania 19131
| | - Andreas Winkler
- From the Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria,
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48
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Maeda K, Tamura J, Okuda Y, Narikawa R, Midorikawa T, Ikeuchi M. Genetic identification of factors for extracellular cellulose accumulation in the thermophilic cyanobacterium Thermosynechococcus vulcanus: proposal of a novel tripartite secretion system. Mol Microbiol 2018; 109:121-134. [PMID: 29688612 DOI: 10.1111/mmi.13977] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/12/2018] [Indexed: 12/19/2022]
Abstract
Cells of the thermophilic cyanobacterium Thermosynechococcus vulcanus strain RKN (NIES-2134) aggregate and produce extracellular cellulose under induced conditions of blue light and low temperature, and both aggregation and cellulose production require the cellulose synthase Tll0007 (XcsA) and photosensory diguanylate cyclases. However, overexpression of both the cellulose synthase and a constitutively active diguanylate cyclase was not sufficient to induce cellulose-mediated cell aggregation under normal growth conditions. Synteny analysis and gene knockout revealed that two putative genes, hlyD-like tlr0903 (xcsB) and endoglucanase-like tlr1902 (xcsC), are linked to tll0007, although they are located apart from tll0007 in the T. vulcanus genome. Gene knockdown revealed that tlr1605 (tolC) was essential for the cellulose-mediated cell aggregation. Low temperature induced marked upregulation of tlr0903, and overexpression of both tlr0903 (but not tlr1902) and diguanylate cyclase resulted in the strong cell aggregation and cellulose accumulation under normal conditions. Based on these and phylogenetic analysis, we propose that the cyanobacterial extracellular cellulose production is due to a novel variant of the bacterial tripartite secretion system.
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Affiliation(s)
- Kaisei Maeda
- Department of Life Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Jyunya Tamura
- Department of Life Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Yukiko Okuda
- Department of Life Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Takafumi Midorikawa
- Department of Life Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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49
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Blain-Hartung M, Rockwell NC, Moreno MV, Martin SS, Gan F, Bryant DA, Lagarias JC. Cyanobacteriochrome-based photoswitchable adenylyl cyclases (cPACs) for broad spectrum light regulation of cAMP levels in cells. J Biol Chem 2018; 293:8473-8483. [PMID: 29632072 DOI: 10.1074/jbc.ra118.002258] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Indexed: 12/18/2022] Open
Abstract
Class III adenylyl cyclases generate the ubiquitous second messenger cAMP from ATP often in response to environmental or cellular cues. During evolution, soluble adenylyl cyclase catalytic domains have been repeatedly juxtaposed with signal-input domains to place cAMP synthesis under the control of a wide variety of these environmental and endogenous signals. Adenylyl cyclases with light-sensing domains have proliferated in photosynthetic species depending on light as an energy source, yet are also widespread in nonphotosynthetic species. Among such naturally occurring light sensors, several flavin-based photoactivated adenylyl cyclases (PACs) have been adopted as optogenetic tools to manipulate cellular processes with blue light. In this report, we report the discovery of a cyanobacteriochrome-based photoswitchable adenylyl cyclase (cPAC) from the cyanobacterium Microcoleus sp. PCC 7113. Unlike flavin-dependent PACs, which must thermally decay to be deactivated, cPAC exhibits a bistable photocycle whose adenylyl cyclase could be reversibly activated and inactivated by blue and green light, respectively. Through domain exchange experiments, we also document the ability to extend the wavelength-sensing specificity of cPAC into the near IR. In summary, our work has uncovered a cyanobacteriochrome-based adenylyl cyclase that holds great potential for the design of bistable photoswitchable adenylyl cyclases to fine-tune cAMP-regulated processes in cells, tissues, and whole organisms with light across the visible spectrum and into the near IR.
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Affiliation(s)
- Matthew Blain-Hartung
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Nathan C Rockwell
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Marcus V Moreno
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Shelley S Martin
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Fei Gan
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, and
| | - Donald A Bryant
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, and.,the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - J Clark Lagarias
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616,
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Tlr1612 is the major repressor of cell aggregation in the light-color-dependent c-di-GMP signaling network of Thermosynechococcus vulcanus. Sci Rep 2018; 8:5338. [PMID: 29593349 PMCID: PMC5871770 DOI: 10.1038/s41598-018-23628-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/16/2018] [Indexed: 11/08/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is a bacterial second messenger involved in sessile/motile lifestyle transitions. We previously reported that c-di-GMP is a crucial inducer of cell aggregation of the cyanobacterium Thermosynechococcus vulcanus. The three cooperating cyanobacteriochrome photoreceptors (SesA/B/C) regulate cell aggregation in a light color-dependent manner by synthesizing/degrading c-di-GMP. Although a variety of c-di-GMP signaling proteins are encoded in cyanobacterial genomes, how c-di-GMP signaling networks are organized remains elusive. Here we experimentally demonstrate that the cellulose synthase Tll0007, which is essential for cell aggregation, binds c-di-GMP although the affinity is low (Kd = 63.9 ± 5.1 µM). We also show that SesA-the main trigger of cell aggregation-is subject to strict product feedback inhibition (IC50 = 1.07 ± 0.13 µM). These results suggest that SesA-produced c-di-GMP may not directly bind to Tll0007. We therefore systematically analyzed all 10 of the genes encoding proteins containing a c-di-GMP synthesis/degradation domain. We identified Tlr1612, harboring both domains, as the major repressor of cell aggregation under the repressing teal-green light irradiation. tlr1612 acts downstream of sesA and is not regulated transcriptionally by light color, suggesting that Tlr1612 may be involved in c-di-GMP amplification in the signaling cascade. Post-transcriptional control is likely crucial for the light-regulated c-di-GMP signaling.
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