1
|
Zhang D, Ma S, Liu Z, Yang Y, Yang W, Zeng H, Su H, Yang Y, Zhang W, Zhang J, Ku L, Ren Z, Chen Y. ZmABF4-ZmVIL2/ZmFIP37 module enhances drought tolerance in maize seedlings. PLANT, CELL & ENVIRONMENT 2024; 47:3605-3618. [PMID: 38747469 DOI: 10.1111/pce.14954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/14/2024] [Accepted: 05/05/2024] [Indexed: 08/16/2024]
Abstract
Drought, as a primary environmental factor, imposes significant constraints on developmental processes and productivity of plants. PHDs were identified as stress-responsive genes in a wide range of eukaryotes. However, the regulatory mechanisms governing PHD genes in maize under abiotic stress conditions are still largely unknown and require further investigation. Here, we identified a mutant, zmvil2, in the EMS mutant library with a C to T mutation in the exon of the Zm00001d053875 (VIN3-like protein 2, ZmVIL2), resulting in premature termination of protein coding. ZmVIL2 belongs to PHD protein family. Compared to WT, zmvil2 mutant exhibited increased sensitivity to drought stress. Consistently, overexpression of ZmVIL2 enhances drought resistance in maize. Y2H, BiFC, and Co-IP experiments revealed that ZmVIL2 directly interacts with ZmFIP37 (FKBP12-interacting protein of 37). zmfip37 knockout mutants also exhibit decreased drought tolerance. Interestingly, we demonstrated that ZmABF4 directly binds to the ZmVIL2 promoter to enhance its activity in yeast one hybrid (Y1H), electrophoretic mobility shift assay (EMSA) and dual luciferase reporter assays. Therefore, we uncovered a novel model ZmABF4-ZmVIL2/ZmFIP37 that promotes drought tolerance in maize. Overall, these findings have enriched the knowledge of the functions of PHD genes in maize and provides genetic resources for breeding stress-tolerant maize varieties.
Collapse
Affiliation(s)
- Dongling Zhang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Shixiang Ma
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhixue Liu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuwei Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenjing Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Haixia Zeng
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Huihui Su
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yang Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wanjun Zhang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jing Zhang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lixia Ku
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhenzhen Ren
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| |
Collapse
|
2
|
Zhang H, Xiong X, Guo K, Zheng M, Cao T, Yang Y, Song J, Cen J, Zhang J, Jiang Y, Feng S, Tian L, Li X. A rapid aureochrome opto-switch enables diatom acclimation to dynamic light. Nat Commun 2024; 15:5578. [PMID: 38956103 PMCID: PMC11219949 DOI: 10.1038/s41467-024-49991-7] [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: 08/28/2023] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.
Collapse
Affiliation(s)
- Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaofeng Xiong
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Kangning Guo
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiaojiao Song
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jie Cen
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiahuan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| |
Collapse
|
3
|
Madhuri S, Lepetit B, Fürst AH, Kroth PG. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components. PLANTS (BASEL, SWITZERLAND) 2024; 13:1465. [PMID: 38891274 PMCID: PMC11174801 DOI: 10.3390/plants13111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.
Collapse
Affiliation(s)
| | | | | | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany; (S.M.); (B.L.); (A.H.F.)
| |
Collapse
|
4
|
Coesel SN. More than a photoreceptor: aureochromes are intrinsic to the diatom light-regulated transcriptional network. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1786-1790. [PMID: 38534187 DOI: 10.1093/jxb/erae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
This article comments on:
Im SH, Lepetit B, Mosesso N, Shrestha S, Weiss L, Nymark M, Roellig R, Wilhelm C, Isono E, Kroth PG. 2024. Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum. Journal of Experimental Botany 75, 1834–1851.
Collapse
Affiliation(s)
- Sacha N Coesel
- School of Oceanography, University of Washington, Seattle, WA, USA
| |
Collapse
|
5
|
Im SH, Lepetit B, Mosesso N, Shrestha S, Weiss L, Nymark M, Roellig R, Wilhelm C, Isono E, Kroth PG. Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1834-1851. [PMID: 38066674 DOI: 10.1093/jxb/erad478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2, PtAureo1a, and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties.
Collapse
Affiliation(s)
- Soo Hyun Im
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
- Molecular Stress Physiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany
| | - Niccolò Mosesso
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sandeep Shrestha
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Laura Weiss
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marianne Nymark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Robert Roellig
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Erika Isono
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| |
Collapse
|
6
|
Im SH, Madhuri S, Lepetit B, Kroth PG. Functional demonstration of Aureochrome 1a proteasomal degradation after blue light incubation in the diatom Phaeodactylum tricornutum. JOURNAL OF PLANT PHYSIOLOGY 2024; 292:154148. [PMID: 38101100 DOI: 10.1016/j.jplph.2023.154148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Aureochromes (AUREOs) are both blue light photoreceptors and transcription factors found in diatoms and related algal groups that play a critical role in regulating gene and cell physiology. One of the AUREOs in the diatom Phaeodactylum tricornutum, PtAUREO1a, has been demonstrated to significantly influence global cellular transcription upon blue light exposure. PtAUREO1a itself is highly regulated on the gene transcription level, depending on the light conditions. However, little is known about the proteostasis of PtAUREO1a in vivo. In this study, we used quantitative immunoblot analysis to examine PtAUREO1a levels under different light conditions as well as in the presence of inhibitors for translation and proteolysis. Our results demonstrate that PtAUREO1a is rapidly degraded in response to blue light exposure after red light acclimation, while the protein has an extended protein half-life in white light conditions. Moreover, the data provide the first in vivo evidence for a functional ubiquitin-proteasome system in the model diatom P. tricornutum. Our findings provide a theoretical basis for studies on protein degradation mechanisms and the regulation of PtAUREO1a, suggesting that changing light conditions can have an impact on the PtAUREO1a protein amount by directly affecting its protein stability.
Collapse
Affiliation(s)
- Soo Hyun Im
- Plant Ecophysiology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| | - Shvaita Madhuri
- Plant Ecophysiology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany; Molecular Stress Physiology, Institute of Biological Sciences, University of Rostock, 18059, Rostock, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| |
Collapse
|
7
|
Genome-Wide Identification and Analysis of the Aureochrome Gene Family in Saccharina japonica and a Comparative Analysis with Six Other Algae. PLANTS 2022; 11:plants11162088. [PMID: 36015392 PMCID: PMC9416419 DOI: 10.3390/plants11162088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Aureochrome (AUREO) is a kind of blue light photoreceptor with both LOV and bZIP structural domains, identified only in Stramenopiles. It functions as a transcription factor that responds to blue light, playing diverse roles in the growth, development, and reproduction of Stramenopiles. Most of its functions are currently unknown, especially in the economically important alga S. japonica farmed on a large scale. This study provided a comprehensive analysis of the characteristics of AUREO gene families in seven algae, focusing on the AUREOs of S. japonica. AUREO genes were strictly identified from seven algal genomes. Then AUREO phylogenetic tree was constructed from 44 conserved AUREO genes collected. These AUREO genes were divided into five groups based on phylogenetic relationships. A total of 28 genes unnamed previously were named according to the phylogenetic tree. A large number of different cis-acting elements, especially bZIP transcription factors, were discovered upstream of AUREO genes in brown algae. Different intron/exon structural patterns were identified among all AUREOs. Transcriptomic data indicated that the expression of Sj AUREO varied significantly during the different development stages of S. japonica gametophytes. Periodic rhythms of light induction experiments indicate that Sj AUREO existed in a light-dependent circadian expression pattern, differing from other similar studies in the past. This may indicate that blue light affects gametophyte development through AUREO as a light signal receptor. This study systematically identified and analyzed the AUREO gene family in seven representative brown algae, which lay a good foundation for further study and understanding of AUERO functions in agal growth and development.
Collapse
|
8
|
Tsuji A, Yamashita H, Hisatomi O, Abe M. Dimerization processes for light-regulated transcription factor Photozipper visualized by high-speed atomic force microscopy. Sci Rep 2022; 12:12903. [PMID: 35941201 PMCID: PMC9359980 DOI: 10.1038/s41598-022-17228-6] [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: 04/09/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Dimerization is critical for transcription factors (TFs) to bind DNA and regulate a wide variety of cellular functions; however, the molecular mechanisms remain to be completely elucidated. Here, we used high-speed atomic force microscopy (HS-AFM) to observe the dimerization process for a photoresponsive TF Photozipper (PZ), which consists of light–oxygen–voltage-sensing (LOV) and basic-region-leucine-zipper (bZIP) domains. HS-AFM visualized not only the oligomeric states of PZ molecules forming monomers and dimers under controlled dark–light conditions but also the domain structures within each molecule. Successive AFM movies captured the dimerization process for an individual PZ molecule and the monomer–dimer reversible transition during dark–light cycling. Detailed AFM images of domain structures in PZ molecules demonstrated that the bZIP domain entangled under dark conditions was loosened owing to light illumination and fluctuated around the LOV domain. These observations revealed the role of the bZIP domain in the dimerization processes of a TF.
Collapse
Affiliation(s)
- Akihiro Tsuji
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Osaka, Japan.
| | - Osamu Hisatomi
- Graduate School of Science, Osaka University, Osaka, Japan
| | - Masayuki Abe
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| |
Collapse
|
9
|
Poliner E, Busch AWU, Newton L, Kim YU, Clark R, Gonzalez-Martinez SC, Jeong BR, Montgomery BL, Farré EM. Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. PLANT PHYSIOLOGY 2022; 189:906-921. [PMID: 35166829 PMCID: PMC9157131 DOI: 10.1093/plphys/kiac052] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
Nannochloropsis oceanica, like other stramenopile microalgae, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs) such as eicosapentaenoic acid (EPA). We observed that fatty acid desaturases (FADs) involved in LC-PUFA biosynthesis were among the strongest blue light-induced genes in N. oceanica CCMP1779. Blue light was also necessary for maintaining LC-PUFA levels in CCMP1779 cells, and growth under red light led to a reduction in EPA content. Aureochromes are stramenopile-specific proteins that contain a light-oxygen-voltage (LOV)-sensing domain that associates with a flavin mononucleotide and is able to sense blue light. These proteins also contain a basic leucine zipper DNA-binding motif and can act as blue light-regulated transcription factors by associating with an E-box like motif, which we found enriched in the promoters of blue light-induced genes. We demonstrated that, in vitro, two CCMP1779 aureochromes were able to absorb blue light. Moreover, the loss or reduction of the expression of any of the three aureochrome genes led to a decrease in the blue light-specific induction of several FADs in CCMP1779. EPA content was also significantly reduced in NoAUREO2 and NoAUREO4 mutants. Taken together, our results indicate that aureochromes mediate blue light-dependent regulation of LC-PUFA content in N. oceanica CCMP1779 cells.
Collapse
Affiliation(s)
- Eric Poliner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan, USA
| | - Andrea W U Busch
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Young Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Rachel Clark
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | | | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandon Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QiBEBT), Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Author for correspondence: (E.M.F.)
| |
Collapse
|
10
|
Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
Collapse
|
11
|
Transmission of light signals from the light-oxygen-voltage core via the hydrophobic region of the β-sheet surface in aureochrome-1. Sci Rep 2021; 11:11995. [PMID: 34099847 PMCID: PMC8184817 DOI: 10.1038/s41598-021-91497-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/21/2021] [Indexed: 12/05/2022] Open
Abstract
Light-Oxygen-Voltage (LOV) domains are responsible for detecting blue light (BL) and regulating the activities of effector domains in various organisms. Photozipper (PZ), an N-terminally truncated aureochrome-1 protein, contains a LOV domain and a basic leucin zipper (bZIP) domain and plays a role as a light-activatable transcription factor. PZ is monomeric in the dark state and undergoes non-covalent dimerization upon illumination with BL, subsequently increasing its affinity for the target DNA. To clarify the molecular mechanism of aureochromes, we prepared site-directed mutants of PZ and performed quantitative analyses in the dark and light states. Although the amino acid substitutions in the hinge region between the LOV core and A’α helix had minor effects on the dimerization and DNA-binding properties of PZ, the substitutions in the β-sheet region of the LOV core and in the A’α helix significantly affected these properties. We found that light signals are transmitted from the LOV core to the effector bZIP domain via the hydrophobic residues on the β-sheet. The light-induced conformational change possibly deforms the hydrophobic regions of the LOV core and induces the detachment of the A’α helix to expose the dimerization surface, likely activating the bZIP domain in a light-dependent manner.
Collapse
|
12
|
Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
Collapse
Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | | |
Collapse
|
13
|
Mann M, Serif M, Wrobel T, Eisenhut M, Madhuri S, Flachbart S, Weber APM, Lepetit B, Wilhelm C, Kroth PG. The Aureochrome Photoreceptor PtAUREO1a Is a Highly Effective Blue Light Switch in Diatoms. iScience 2020; 23:101730. [PMID: 33235981 PMCID: PMC7670200 DOI: 10.1016/j.isci.2020.101730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023] Open
Abstract
Aureochromes represent a unique type of blue light photoreceptors that possess a blue light sensing flavin-binding LOV-domain and a DNA-binding bZIP domain, thus being light-driven transcription factors. The diatom Phaeodactylum tricornutum, a member of the essential marine primary producers, possesses four aureochromes (PtAUREO1a, 1b, 1c, 2). Here we show a dramatic change in the global gene expression pattern of P. tricornutum wild-type cells after a shift from red to blue light. About 75% of the genes show significantly changed transcript levels already after 10 and 60 min of blue light exposure, which includes genes of major transcription factors as well as other photoreceptors. Very surprisingly, this light-induced regulation of gene expression is almost completely inhibited in independent PtAureo1a knockout lines. Such a massive and fast transcriptional change depending on one single photoreceptor is so far unprecedented. We conclude that PtAUREO1a plays a key role in diatoms upon blue light exposure. Blue light induces a very fast transcriptional response in the diatom P. tricornutum This strong response is almost completely inhibited when Aureochrome 1a is absent The results imply a key role of PtAureo1a in blue light-induced responses in diatoms
Collapse
Affiliation(s)
- Marcus Mann
- Institut für Biologie, Universität Leipzig, 04009 Leipzig, Germany
| | - Manuel Serif
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Thomas Wrobel
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Marion Eisenhut
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Shvaita Madhuri
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Samantha Flachbart
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Bernard Lepetit
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | | | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
14
|
Goett-Zink L, Klocke JL, Bögeholz LAK, Kottke T. In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells. J Biol Chem 2020; 295:11729-11741. [PMID: 32580943 PMCID: PMC7450117 DOI: 10.1074/jbc.ra120.013091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.
Collapse
Affiliation(s)
- Lukas Goett-Zink
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Lena A K Bögeholz
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
15
|
Farré EM. The brown clock: circadian rhythms in stramenopiles. PHYSIOLOGIA PLANTARUM 2020; 169:430-441. [PMID: 32274814 DOI: 10.1111/ppl.13104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Circadian clocks allow organisms to anticipate environmental changes associated with the diurnal light/dark cycle. Circadian oscillators have been described in plants and green algae, cyanobacteria, animals and fungi, however, little is known about the circadian clocks of photosynthetic eukaryotes outside the green lineage. Stramenopiles are a diverse group of secondary endosymbionts whose plastid originated from a red alga. Photosynthetic stramenopiles, which include diatoms and brown algae, play key roles in biogeochemical cycles and are important components of marine ecosystems. Genome annotation efforts indicated the presence of a novel type of oscillator in these organisms and the first circadian clock component in a stramenopile has been recently discovered. This review summarizes the phenotypic characterization of circadian rhythms in stramenopiles and current efforts to determine the mechanisms of this 'brown clock'. The elucidation of this brown clock will enable a deeper understanding of the role of self-sustained oscillations in the adaptation to life in marine environments.
Collapse
Affiliation(s)
- Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
16
|
Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
Collapse
Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| |
Collapse
|
17
|
Hepp S, Trauth J, Hasenjäger S, Bezold F, Essen LO, Taxis C. An Optogenetic Tool for Induced Protein Stabilization Based on the Phaeodactylum tricornutum Aureochrome 1a Light-Oxygen-Voltage Domain. J Mol Biol 2020; 432:1880-1900. [PMID: 32105734 DOI: 10.1016/j.jmb.2020.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 02/14/2020] [Indexed: 01/02/2023]
Abstract
Control of cellular events by optogenetic tools is a powerful approach to manipulate cellular functions in a minimally invasive manner. A common problem posed by the application of optogenetic tools is to tune the activity range to be physiologically relevant. Here, we characterized a photoreceptor of the light-oxygen-voltage (LOV) domain family of Phaeodactylum tricornutum aureochrome 1a (AuLOV) as a tool for increasing protein stability under blue light conditions in budding yeast. Structural studies of AuLOVwt, the variants AuLOVM254, and AuLOVW349 revealed alternative dimer association modes for the dark state, which differ from previously reported AuLOV dark-state structures. Rational design of AuLOV-dimer interface mutations resulted in an optimized optogenetic tool that we fused to the photoactivatable adenylyl cyclase from Beggiatoa sp. This synergistic light-regulation approach using two photoreceptors resulted in an optimized, photoactivatable adenylyl cyclase with a cyclic adenosine monophosphate production activity that matches the physiological range of Saccharomyces cerevisiae. Overall, we enlarged the optogenetic toolbox for yeast and demonstrated the importance of fine-tuning the optogenetic tool activity for successful application in cells.
Collapse
Affiliation(s)
- Sebastian Hepp
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany; Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany.
| | - Christof Taxis
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| |
Collapse
|
18
|
Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
Collapse
Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
19
|
bHLH-PAS protein RITMO1 regulates diel biological rhythms in the marine diatom Phaeodactylum tricornutum. Proc Natl Acad Sci U S A 2019; 116:13137-13142. [PMID: 31171659 PMCID: PMC6600994 DOI: 10.1073/pnas.1819660116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Periodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. Alteration of RITMO1 expression levels and timing by ectopic overexpression results in lines with deregulated diurnal gene expression profiles compared with the wild-type cells. Reduced gene expression oscillations are also observed in these lines in continuous darkness, showing that the regulation of rhythmicity by RITMO1 is not directly dependent on light inputs. We also describe strong diurnal rhythms of cellular fluorescence in wild-type cells, which persist in continuous light conditions, indicating the existence of an endogenous circadian clock in diatoms. The altered rhythmicity observed in RITMO1 overexpression lines in continuous light supports the involvement of this protein in circadian rhythm regulation. Phylogenetic analysis reveals a wide distribution of RITMO1-like proteins in the genomes of diatoms as well as in other marine algae, which may indicate a common function in these phototrophs. This study adds elements to our understanding of diatom biology and offers perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but under-investigated, branch of the tree of life.
Collapse
|
20
|
Kalvaitis ME, Johnson LA, Mart RJ, Rizkallah P, Allemann RK. A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation. Biochemistry 2019; 58:2608-2616. [PMID: 31082213 PMCID: PMC7007005 DOI: 10.1021/acs.biochem.9b00255] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Light-oxygen-voltage
(LOV) domains are increasingly used to engineer
photoresponsive biological systems. While the photochemical cycle
is well documented, the allosteric mechanism by which formation of
a cysteinyl-flavin adduct leads to activation is unclear. Via replacement
of flavin mononucleotide (FMN) with 5-deazaflavin mononucleotide (5dFMN)
in the Aureochrome1a (Au1a) transcription factor from Ochromonas
danica, a thermally stable cysteinyl-5dFMN adduct was generated.
High-resolution crystal structures (<2 Å) under different
illumination conditions with either FMN or 5dFMN chromophores reveal
three conformations of the highly conserved glutamine 293. An allosteric
hydrogen bond network linking the chromophore via Gln293 to the auxiliary
A′α helix is observed. With FMN, a “flip”
of the Gln293 side chain occurs between dark and lit states. 5dFMN
cannot hydrogen bond through the C5 position and proved to be unable
to support Au1a domain dimerization. Under blue light, the Gln293
side chain instead “swings” away in a conformation distal
to the chromophore and not previously observed in existing LOV domain
structures. Together, the multiple side chain conformations of Gln293
and functional analysis of 5dFMN provide new insight into the structural
requirements for LOV domain activation.
Collapse
Affiliation(s)
- Mindaugas E Kalvaitis
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Luke A Johnson
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Robert J Mart
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| | - Pierre Rizkallah
- School of Medicine , University Hospital Wales , Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Rudolf K Allemann
- School of Chemistry , Cardiff University , Park Place , Cardiff CF10 3AT , United Kingdom
| |
Collapse
|
21
|
Bannister S, Böhm E, Zinn T, Hellweg T, Kottke T. Arguments for an additional long-lived intermediate in the photocycle of the full-length aureochrome 1c receptor: A time-resolved small-angle X-ray scattering study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:034701. [PMID: 31263739 PMCID: PMC6588521 DOI: 10.1063/1.5095063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Aureochromes (AUREO) act as blue-light photoreceptors in algae. They consist of a light-, oxygen-, voltage-sensitive (LOV) domain and a DNA-binding basic region/leucine zipper. Illumination of the flavin cofactor in LOV leads to the formation of an adduct, followed by global structural changes. Here, we first applied UV/vis spectroscopy to characterize the photocycle of full-length aureochrome 1c (PtAUREO1c) from the diatom Phaeodactylum tricornutum. With a time constant of 850 s and a quantum yield of 23%, PtAUREO1c reveals a faster recovery time and a much lower sensitivity toward light than PtAUREO1a, pointing to its role as a high light sensor in vivo. UV/vis spectroscopy offers details on the local recovery of the flavin chromophore. However, kinetic information on the global structural recovery of full-length AUREO or any other multidomain LOV protein is missing. This information is essential not least for the photoreceptors' applications as optogenetic devices. Therefore, we established a procedure to apply small-angle X-ray scattering on PtAUREO1c in a time-resolved manner employing an in-house setup. In combination with UV/vis spectroscopy under similar conditions, we revealed a discrepancy between the recovery of the global protein structure and the adduct lifetime. Accordingly, we propose to supplement the photocycle by an intermediate state (I447), which decays with a time constant of about 800 s and prolongs the lifetime of the signaling state.
Collapse
Affiliation(s)
- Saskia Bannister
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Thomas Zinn
- ESRF–The European Synchrotron, 71, Avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| |
Collapse
|
22
|
Tateyama S, Kobayashi I, Hisatomi O. Target Sequence Recognition by a Light-Activatable Basic Leucine Zipper Factor, Photozipper. Biochemistry 2018; 57:6615-6623. [PMID: 30388362 DOI: 10.1021/acs.biochem.8b00995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photozipper (PZ) is a light-activatable basic leucine zipper (bZIP) protein composed of a bZIP domain and a light-oxygen-voltage-sensing domain of aureochrome-1. Blue light induces dimerization and subsequently increases the affinity of PZ for the target DNA sequence. We prepared site-directed PZ mutants in which Asn131 (N131) in the basic region was substituted with Ala and Gln. N131 mutants showed spectroscopic and dimerization properties almost identical to those of wild-type PZ and an increase in helical content in the presence of the target sequence. Quantitative analyses by an electrophoretic mobility shift assay and quartz crystal microbalance (QCM) measurements demonstrated that the half-maximal effective concentrations of N131 mutants to bind to the target sequence were significantly higher than those of PZ. QCM data also revealed that N131 substitutions accelerated the dissociation without affecting the association, suggesting that a base-specific interaction of N131 occurred after the association between PZ and DNA. Activation of PZ by illumination decreased both the standard errors and the unstable period of QCM data. Optical control of transcription factors will provide new knowledge of the recognition of the target sequence.
Collapse
Affiliation(s)
- Samu Tateyama
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Itsuki Kobayashi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science , Osaka University , Toyonaka , Osaka 560-0043 , Japan
| |
Collapse
|
23
|
Matiiv AB, Chekunova EM. Aureochromes - Blue Light Receptors. BIOCHEMISTRY (MOSCOW) 2018; 83:662-673. [PMID: 30195323 DOI: 10.1134/s0006297918060044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A variety of living organisms including bacteria, fungi, animals, and plants use blue light (BL) to adapt to changing ambient light. Photosynthetic forms (plants and algae) require energy of light for photosynthesis, movements, development, and regulation of activity. Several complex light-sensitive systems evolved in eukaryotic cells to use the information of light efficiently with photoreceptors selectively absorbing various segments of the solar spectrum, being the first components in the light signal transduction chain. They are most diverse in algae. Photosynthetic stramenopiles, which received chloroplasts from red algae during secondary symbiosis, play an important role in ecosystems and aquaculture, being primary producers. These taxa acquired the ability to use BL for regulation of such processes as phototropism, chloroplast photo-relocation movement, and photomorphogenesis. A new type of BL receptor - aureochrome (AUREO) - was identified in Vaucheria frigida in 2007. AUREO consists of two domains: bZIP (basic-region leucine zipper) domain and LOV (light-oxygen-voltage-sensing) domain, and thus this photoreceptor is a BL-sensitive transcription factor. This review presents current data on the structure, mechanisms of action, and biochemical features of aureochromes.
Collapse
Affiliation(s)
- A B Matiiv
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia
| | - E M Chekunova
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia.
| |
Collapse
|
24
|
Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779. ACS Synth Biol 2018; 99:112-127. [PMID: 29518315 PMCID: PMC6616531 DOI: 10.1111/tpj.14314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 04/25/2023]
Abstract
Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).
Collapse
Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
| | - Tomomi Takeuchi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Zhi-Yan Du
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan
- Biochemistry and Molecular Department, Michigan State University, East Lansing, Michigan
- Plant Biology Department, Michigan State University, East Lansing, Michigan
| | - Eva M. Farré
- Plant Biology Department, Michigan State University, East Lansing, Michigan
- Corresponding Author: Eva M. Farré (), Phone: +1-517-353-5215
| |
Collapse
|
25
|
Iuliano JN, Gil AA, Laptenok SP, Hall CR, Collado JT, Lukacs A, Hag Ahmed SA, Abyad J, Daryaee T, Greetham GM, Sazanovich IV, Illarionov B, Bacher A, Fischer M, Towrie M, French JB, Meech SR, Tonge PJ. Variation in LOV Photoreceptor Activation Dynamics Probed by Time-Resolved Infrared Spectroscopy. Biochemistry 2018; 57:620-630. [PMID: 29239168 PMCID: PMC5801046 DOI: 10.1021/acs.biochem.7b01040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The light, oxygen, voltage (LOV) domain proteins are blue light photoreceptors that utilize a noncovalently bound flavin mononucleotide (FMN) cofactor as the chromophore. The modular nature of these proteins has led to their wide adoption in the emerging fields of optogenetics and optobiology, where the LOV domain has been fused to a variety of output domains leading to novel light-controlled applications. In this work, we extend our studies of the subpicosecond to several hundred microsecond transient infrared spectroscopy of the isolated LOV domain AsLOV2 to three full-length photoreceptors in which the LOV domain is fused to an output domain: the LOV-STAS protein, YtvA, the LOV-HTH transcription factor, EL222, and the LOV-histidine kinase, LovK. Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate. However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain. While the rate of adduct formation varies by only 3.6-fold among the proteins, the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
Collapse
Affiliation(s)
- James N. Iuliano
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Agnieszka A. Gil
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | | | | | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, U.K
- Department of Biophysics, Medical School, University of Pecs, Szigeti út 12, 7624 Pecs, Hungary
| | - Safaa A. Hag Ahmed
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Jenna Abyad
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Igor V. Sazanovich
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Boris Illarionov
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Adelbert Bacher
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Markus Fischer
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, U.K
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| |
Collapse
|
26
|
Nakatani Y, Hisatomi O. Quantitative analyses of the equilibria among DNA complexes of a blue-light-regulated bZIP module, Photozipper. Biophys Physicobiol 2018; 15:8-17. [PMID: 29450110 PMCID: PMC5812316 DOI: 10.2142/biophysico.15.0_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/28/2023] Open
Abstract
Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida. Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light–oxygen–voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states. DNA binding by PZ was sequence-specific and light-dependent. The half-maximal effective concentration of PZ for binding to the target DNA sequence was ~40 nM in the light, which was >10-fold less than the value in the dark. By contrast, the dimeric PZ-S2C variant (with intermolecular disulfide bonds) had higher affinity for the target sequence, with dissociation constants of ~4 nM, irrespective of the light conditions. Substitutions of Glu159 and Lys164 in the leucine zipper region decreased the affinity of PZ for the target sequence, especially in the light, suggesting that these residues form inter-helical salt bridges between leucine zipper regions, stabilizing the dimer–DNA complex. Our quantitative analyses of the equilibria in PZ–DNA-complex formation suggest that the blue-light-induced dimerization of LOV domains and coiled-coil formation by leucine zipper regions are the primary determinants of the affinity of PZ for the target sequence.
Collapse
Affiliation(s)
- Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
27
|
Duanmu D, Rockwell NC, Lagarias JC. Algal light sensing and photoacclimation in aquatic environments. PLANT, CELL & ENVIRONMENT 2017; 40:2558-2570. [PMID: 28245058 PMCID: PMC5705019 DOI: 10.1111/pce.12943] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 05/05/2023]
Abstract
Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m-2 s-1 . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.
Collapse
Affiliation(s)
- Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| | - Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| |
Collapse
|
28
|
König S, Eisenhut M, Bräutigam A, Kurz S, Weber APM, Büchel C. The Influence of a Cryptochrome on the Gene Expression Profile in the Diatom Phaeodactylum tricornutum under Blue Light and in Darkness. PLANT & CELL PHYSIOLOGY 2017; 58:1914-1923. [PMID: 29016997 DOI: 10.1093/pcp/pcx127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Diatoms, albeit being only distantly related with higher plants, harbor a plant-like cryptochrome (CryP) that was proposed to act as a photoreceptor required for the regulation of some photosynthetic proteins. Plant cryptochromes are involved in the regulation of developmental processes relevant only to multicellular organisms. Their role in the unicellular diatoms to date is mostly enigmatic. To elucidate the function of this plant-like cryptochrome in a unicellular species, we examined the role of CryP in the regulation of transcription in the diatom Phaeodactylum tricornutum by comparative RNA-seq of wild type and CryP knock-down mutants, under prolonged darkness and one hour after onset of blue light. In total, mRNAs of 12,298 genes were identified and more than 70% of the genes could be sorted into functional bins. CryP influenced groups of transcripts in three different ways: some transcripts displayed altered expression under blue light only, others independent of the light condition, and, surprisingly, some were influenced by CryP only in darkness. Genes regulated in any condition were distributed over almost all functional categories. CryP exerted an influence on two other photoreceptors: the genes encoding phytochrome and CPF1, another cryptochrome, which were down-regulated by CryP independent of the light condition. However, the regulatory responses of the affected photoreceptors on transcriptional output were independent. The influence of CryP on the expression of other photoreceptors hints to the existence of a regulatory signaling network in diatoms that includes several cryptochromes and phytochrome, whereby CryP acts as a regulator of transcript abundance under light as well as in darkness.
Collapse
Affiliation(s)
- Sarah König
- Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Bräutigam
- IPK Gatersleben, Network Analysis and Modeling, Corrensstrasse 3, 06466 Seeland, Germany
| | - Samantha Kurz
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Claudia Büchel
- Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| |
Collapse
|
29
|
Affiliation(s)
- Maria Mittag
- Friedrich Schiller University Jena, Jena, Germany.
| | | |
Collapse
|
30
|
Essen LO, Franz S, Banerjee A. Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:27-37. [PMID: 28756992 DOI: 10.1016/j.jplph.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Blue-light reception plays a pivotal role for algae to adapt to changing environmental conditions. In this review we summarize the current structural and mechanistic knowledge about flavin-dependent algal photoreceptors. We especially focus on the cryptochrome and aureochrome type photoreceptors in the context of their evolutionary divergence. Despite similar photochemical characteristics to orthologous photoreceptors from higher plants and animals the algal blue-light photoreceptors have developed a set of unique structural and mechanistic features that are summarized below.
Collapse
Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology, Philipps-University, 35043 Marburg, Germany.
| | - Sophie Franz
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| | - Ankan Banerjee
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| |
Collapse
|
31
|
Kroth PG, Wilhelm C, Kottke T. An update on aureochromes: Phylogeny - mechanism - function. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:20-26. [PMID: 28797596 DOI: 10.1016/j.jplph.2017.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 05/20/2023]
Abstract
Light is important for algae, as it warrants metabolic independence via photosynthesis. In addition to the absorption of light by the photosystems, algae possess a variety of specific photoreceptors that allow the quantification of the light fluxes as well as the assessment of light qualities. About a decade ago, aureochromes have been described in the xanthophyte alga Vaucheria frigida. These proteins represent a new type of blue light photoreceptor as they possess both a light-oxygen-voltage (LOV) domain for light reception as well as a basic region leucine zipper (bZIP) domain for DNA binding, indicating that they represent light-driven transcription factors. Aureochromes so far have been detected only in a single group of algae, photosynthetic stramenopiles, but not in any other prokaryotic or eukaryotic organisms. Recent biophysical work on aureochromes in the absence and the presence of DNA revealed the mechanism of allosteric communication between the sensor and effector domains despite their unusual inversed arrangement. Different molecular models have been proposed to describe the effect of light on DNA binding. Functional characterization of mutants of the diatom Phaeodactylum tricornutum, in which the aureochrome genes have been silenced or deleted, indicate that different aureochromes may have different functions, being involved in central processes like light acclimation and regulation of the cell cycle.
Collapse
Affiliation(s)
- Peter G Kroth
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
| | - Christian Wilhelm
- Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| |
Collapse
|
32
|
Kottke T, Oldemeyer S, Wenzel S, Zou Y, Mittag M. Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:4-14. [PMID: 28619534 DOI: 10.1016/j.jplph.2017.05.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.
Collapse
Affiliation(s)
- Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Yong Zou
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
| |
Collapse
|
33
|
König S, Juhas M, Jäger S, Kottke T, Büchel C. The cryptochrome-photolyase protein family in diatoms. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:15-19. [PMID: 28720252 DOI: 10.1016/j.jplph.2017.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
The cryptochrome - photolyase family (CPF) consists of homologous flavoproteins having completely different functions involving DNA repair, circadian rhythm and/or photoreception. From the original photolyases, working either as (6-4) or cyclobutane pyrimidine dimer photolyases, the animal- and plant-type cryptochromes, respectively, evolved and also the more intermediate DASH cryptochromes. Whereas animal cryptochromes work mostly in clock-related functions, plant cryptochromes are also directly involved in developmental processes such as hypocotyl elongation or flower induction. In diatoms, all types of cryptochromes and photolyases were predicted from genome sequences. However, up to now only two proteins have been characterised in more detail, CPF1 and CryP. CPF1 is related to animal-type cryptochromes, but works as a (6-4) photolyase in addition to having photoreceptor functions. It was shown to interact with the CLOCK:Bmal1 heterodimer in a heterologous system, and thus is probably involved in clock-related processes. Moreover, CPF1 directly influences transcription. The latter was also true for CryP, which is a cryptochrome distantly related to plant-type cryptochromes. In addition, CryP influences light-harvesting protein accumulation. For all diatom cryptochromes, down-stream signalling has to proceed via interaction partners different from the classical proteins involved in cryptochrome signalling in higher plants, because these candidates are missing in diatoms.
Collapse
Affiliation(s)
- Sarah König
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Matthias Juhas
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie Jäger
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany.
| |
Collapse
|
34
|
Mann M, Serif M, Jakob T, Kroth PG, Wilhelm C. PtAUREO1a and PtAUREO1b knockout mutants of the diatom Phaeodactylum tricornutum are blocked in photoacclimation to blue light. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:44-48. [PMID: 28610707 DOI: 10.1016/j.jplph.2017.05.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 05/20/2023]
Abstract
Aureochromes are blue light receptors specifically found in photosynthetic Stramenopiles (algae). Four different Aureochromes have been identified in the marine diatom Phaeodactylum tricornutum (PtAUREO 1a, 1b, 1c, and 2). Since blue light is necessary for high light acclimation in diatoms, it has been hypothesized that Aureochromes might play an important role in the light acclimation capacity of diatoms. This hypothesis was supported by an RNAi knockdown line of PtAUREO1a, which showed a phenotype different from wild type cells when grown in either blue or red light. Here, we show for the first time the phenotype and the photoacclimation reaction of TALEN-mediated knockout mutants of PtAUREO1a and PtAUREO1b, clearly proving the necessity of Aureochromes for light acclimation under blue light. However, both mutants do also show specific differences in their respective phenotypes. Hence, PtAUREO1a and 1b are not functionally redundant in photoacclimation to blue light, and their specific contribution needs to be clarified further.
Collapse
Affiliation(s)
- Marcus Mann
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany.
| | - Manuel Serif
- Plant Ecophysiology, Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Torsten Jakob
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| |
Collapse
|
35
|
Jaubert M, Bouly JP, Ribera d'Alcalà M, Falciatore A. Light sensing and responses in marine microalgae. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:70-77. [PMID: 28456112 DOI: 10.1016/j.pbi.2017.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
Marine eukaryotic phytoplankton are major contributors to global primary production. To adapt and thrive in the oceans, phytoplankton relies on a variety of light-regulated responses and light-acclimation capacities probably driven by sophisticated photoregulatory mechanisms. A plethora of photoreceptor-like sequences from marine microalgae have been identified in omics approaches. Initial studies have revealed that some algal photoreceptors are similar to those known in plants. In addition, new variants with different spectral tuning and algal-specific light sensors have also been found, changing current views and perspectives on how photoreceptor structure and function have diversified in phototrophs experiencing different environmental conditions.
Collapse
Affiliation(s)
- Marianne Jaubert
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Laboratory of Ecology and Evolution of Plankton, Villa Comunale, 80121 Naples, Italy.
| | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France.
| |
Collapse
|
36
|
Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
Collapse
Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
| |
Collapse
|
37
|
Akiyama Y, Nakasone Y, Nakatani Y, Hisatomi O, Terazima M. Time-Resolved Detection of Light-Induced Dimerization of Monomeric Aureochrome-1 and Change in Affinity for DNA. J Phys Chem B 2016; 120:7360-70. [PMID: 27404115 DOI: 10.1021/acs.jpcb.6b05760] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aureochrome (Aureo) is a recently discovered blue light sensor protein initially from Vaucheria frigida, in which it controls blue light-dependent branch formation and/or development of a sex organ by a light-dependent change in the affinity for DNA. Although photochemical reactions of Aureo-LOV (LOV is a C-terminal light-oxygen-voltage domain) and the N-terminal truncated construct containing a bZIP (N-terminal basic leucine zipper domain) and a LOV domain have previously been reported, the reaction kinetics of the change in affinity for DNA have never been elucidated. The reactions of Aureo where the cysteines are replaced by serines (AureoCS) as well as the kinetics of the change in affinity for a target DNA are investigated in the time-domain. The dimerization rate constant is obtained as 2.8 × 10(4) M(-1) s(-1), which suggests that the photoinduced dimerization occurs in the LOV domain and the bZIP domain dimerizes using the interaction with DNA. Surprisingly, binding with the target DNA is completed very quickly, 7.7 × 10(4) M(-1) s(-1), which is faster than the protein dimerization rate. It is proposed that the nonspecific electrostatic interaction, which is observed as a weak binding with DNA, may play a role in the efficient searching for the target sequence within the DNA.
Collapse
Affiliation(s)
- Yuki Akiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Yoichi Nakatani
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Osamu Hisatomi
- Department of Earth and Space Science, Graduate School of Science, Osaka University , Osaka 560-0043, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| |
Collapse
|