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Cano-Ramirez DL, Panter PE, Takemura T, de Fraine TS, de Barros Dantas LL, Dekeya R, Barros-Galvão T, Paajanen P, Bellandi A, Batstone T, Manley BF, Tanaka K, Imamura S, Franklin KA, Knight H, Dodd AN. Low-temperature and circadian signals are integrated by the sigma factor SIG5. NATURE PLANTS 2023; 9:661-672. [PMID: 36997687 PMCID: PMC10119024 DOI: 10.1038/s41477-023-01377-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.
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Affiliation(s)
- Dora L Cano-Ramirez
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Tokiaki Takemura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | | | | | | - Annalisa Bellandi
- John Innes Centre, Norwich, UK
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, Université de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Tom Batstone
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Bethan F Manley
- School of Biological Sciences, University of Bristol, Bristol, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Japan
| | - Keara A Franklin
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Heather Knight
- Department of Biosciences, Durham University, Durham, UK
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2
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Korwin Krukowski P, Visentin I, Russo G, Minerdi D, Bendahmane A, Schubert A, Cardinale F. Transcriptome Analysis Points to BES1 as a Transducer of Strigolactone Effects on Drought Memory in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2023; 63:1873-1889. [PMID: 35489066 DOI: 10.1093/pcp/pcac058] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/09/2022] [Accepted: 04/29/2022] [Indexed: 05/21/2023]
Abstract
Strigolactones (SLs) are carotenoid-derived phytohormones governing a wide range of physiological processes, including drought-associated stomatal closure. We have previously shown in tomato that SLs regulate the so-called after-effect of drought, whereby stomatal conductance is not completely restored for some time during recovery after a drought spell, irrespective of the water potential. To ease the elucidation of its molecular underpinnings, we investigated whether this SL effect is conserved in Arabidopsis thaliana by contrasting the physiological performances of the wild-type with SL-depleted (more axillary growth 4, max4) and insensitive (dwarf 14, d14) mutants in a drought and recovery protocol. Physiological analyses showed that SLs are important to achieve a complete after-effect in A. thaliana, while transcriptome results suggested that the SL-dependent modulation of drought responses extends to a large subset (about 4/5) of genes displaying memory transcription patterns. Among these, we show that the activation of over 30 genes related to abscisic acid metabolism and signaling strongly depends on SL signaling. Furthermore, by using promoter-enrichment tools, we identified putative cis- and trans-acting factors that may be important in the SL-dependent and SL-independent regulation of genes during drought and recovery. Finally, in order to test the accuracy of our bioinformatic prediction, we confirmed one of the most promising transcription factor candidates mediating SL signaling effects on transcriptional drought memory-BRI-EMS SUPPRESSOR1 (BES1). Our findings reveal that SLs are master regulators of Arabidopsis transcriptional memory upon drought and that this role is partially mediated by the BES1 transcription factor.
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Affiliation(s)
- Paolo Korwin Krukowski
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
| | - Ivan Visentin
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
| | - Giulia Russo
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
| | - Daniela Minerdi
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
| | - Abdelhafid Bendahmane
- Biology Department, Institute of Plant Sciences-Paris-Saclay, CS80004, Gif-sur-Yvette Cedex 91192, France
| | - Andrea Schubert
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
| | - Francesca Cardinale
- PlantStressLab, DISAFA-University of Turin, Largo Paolo Braccini 2, Grugliasco (TO) I-10095, Italy
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Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes. Nat Commun 2022; 13:7440. [PMID: 36460634 PMCID: PMC9718756 DOI: 10.1038/s41467-022-35080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Light initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3's activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.
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Griffin JHC, Toledo-Ortiz G. Plant photoreceptors and their signalling components in chloroplastic anterograde and retrograde communication. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7126-7138. [PMID: 35640572 PMCID: PMC9675593 DOI: 10.1093/jxb/erac220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/18/2022] [Indexed: 05/27/2023]
Abstract
The red phytochrome and blue cryptochrome plant photoreceptors play essential roles in promoting genome-wide changes in nuclear and chloroplastic gene expression for photomorphogenesis, plastid development, and greening. While their importance in anterograde signalling has been long recognized, the molecular mechanisms involved remain under active investigation. More recently, the intertwining of the light signalling cascades with the retrograde signals for the optimization of chloroplast functions has been acknowledged. Advances in the field support the participation of phytochromes, cryptochromes, and key light-modulated transcription factors, including HY5 and the PIFs, in the regulation of chloroplastic biochemical pathways that produce retrograde signals, including the tetrapyrroles and the chloroplastic MEP-isoprenoids. Interestingly, in a feedback loop, the photoreceptors and their signalling components are targets themselves of these retrograde signals, aimed at optimizing photomorphogenesis to the status of the chloroplasts, with GUN proteins functioning at the convergence points. High light and shade are also conditions where the photoreceptors tune growth responses to chloroplast functions. Interestingly, photoreceptors and retrograde signals also converge in the modulation of dual-localized proteins (chloroplastic/nuclear) including WHIRLY and HEMERA/pTAC12, whose functions are required for the optimization of photosynthetic activities in changing environments and are proposed to act themselves as retrograde signals.
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Ferguson JN, Tidy AC, Murchie EH, Wilson ZA. The potential of resilient carbon dynamics for stabilizing crop reproductive development and productivity during heat stress. PLANT, CELL & ENVIRONMENT 2021; 44:2066-2089. [PMID: 33538010 DOI: 10.1111/pce.14015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/20/2023]
Abstract
Impaired carbon metabolism and reproductive development constrain crop productivity during heat stress. Reproductive development is energy intensive, and its requirement for respiratory substrates rises as associated metabolism increases with temperature. Understanding how these processes are integrated and the extent to which they contribute to the maintenance of yield during and following periods of elevated temperatures is important for developing climate-resilient crops. Recent studies are beginning to demonstrate links between processes underlying carbon dynamics and reproduction during heat stress, consequently a summation of research that has been reported thus far and an evaluation of purported associations are needed to guide and stimulate future research. To this end, we review recent studies relating to source-sink dynamics, non-foliar photosynthesis and net carbon gain as pivotal in understanding how to improve reproductive development and crop productivity during heat stress. Rapid and precise phenotyping during narrow phenological windows will be important for understanding mechanisms underlying these processes, thus we discuss the development of relevant high-throughput phenotyping approaches that will allow for more informed decision-making regarding future crop improvement.
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Affiliation(s)
- John N Ferguson
- Division of Plant & Crop Science, University of Nottingham, Leicestershire, UK
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Leicestershire, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Alison C Tidy
- Division of Plant & Crop Science, University of Nottingham, Leicestershire, UK
| | - Erik H Murchie
- Division of Plant & Crop Science, University of Nottingham, Leicestershire, UK
| | - Zoe A Wilson
- Division of Plant & Crop Science, University of Nottingham, Leicestershire, UK
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Sanjaya A, Kazama Y, Ishii K, Muramatsu R, Kanamaru K, Ohbu S, Abe T, Fujiwara MT. An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana. PLANTS (BASEL, SWITZERLAND) 2021; 10:848. [PMID: 33922223 PMCID: PMC8145761 DOI: 10.3390/plants10050848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 01/13/2023]
Abstract
Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.
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Affiliation(s)
- Alvin Sanjaya
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Ryohsuke Muramatsu
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan;
| | - Sumie Ohbu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Makoto T. Fujiwara
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
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Alameldin HF, Oh S, Hernandez AP, Montgomery BL. Nuclear-encoded sigma factor 6 (SIG6) is involved in the block of greening response in Arabidopsis thaliana. AMERICAN JOURNAL OF BOTANY 2020; 107:329-338. [PMID: 32002990 DOI: 10.1002/ajb2.1423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/24/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Light is critical in the ability of plants to accumulate chlorophyll. When exposed to far-red (FR) light and then grown in white light in the absence of sucrose, wild-type seedlings fail to green in a response known as the FR block of greening (BOG). This response is controlled by phytochrome A through repression of protochlorophyllide reductase-encoding (POR) genes by FR light coupled with irreversible plastid damage. Sigma (SIG) factors are nuclear-encoded proteins that contribute to plant greening and plastid development through regulating gene transcription in chloroplasts and impacting retrograde signaling from the plastid to nucleus. SIGs are regulated by phytochromes, and the expression of some SIG factors is reduced in phytochrome mutant lines, including phyA. Given the association of phyA with the FR BOG and its regulation of SIG factors, we investigated the potential regulatory role of SIG factors in the FR BOG response. METHODS We examined FR BOG responses in sig mutants, phytochrome-deficient lines, and mutant lines for several phy-associated factors. We quantified chlorophyll levels and examined expression of key BOG-associated genes. RESULTS Among six sig mutants, only the sig6 mutant significantly accumulated chlorophyll after FR BOG treatment, similar to the phyA mutant. SIG6 appears to control protochlorophyllide accumulation by contributing to the regulation of tetrapyrrole biosynthesis associated with glutamyl-tRNA reductase (HEMA1) function, select phytochrome-interacting factor genes (PIF4 and PIF6), and PENTA1, which regulates PORA mRNA translation after FR exposure. CONCLUSIONS Regulation of SIG6 plays a significant role in plant responses to FR exposure during the BOG response.
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Affiliation(s)
- Hussien F Alameldin
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, 12619, Egypt
| | - Sookyung Oh
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Alexandra P Hernandez
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Beronda L Montgomery
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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Oh S, Montgomery BL. Mesophyll-specific phytochromes impact chlorophyll light-harvesting complexes (LHCs) and non-photochemical quenching. PLANT SIGNALING & BEHAVIOR 2019; 14:1609857. [PMID: 31037997 PMCID: PMC6619949 DOI: 10.1080/15592324.2019.1609857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phytochromes regulate light-dependent plastid development and plant growth and development. Prior analyses demonstrated that phytochromes regulate expression of Sigma factor 2 (SIG2), which is involved in plastid transcription and coordinates expression of plastid- and nuclear-encoded genes involved in plastid development, as well as plant growth and development. Mutation of SIG2 impacts distinct aspects of photosynthesis, resulting in elevated levels of cyclic electron flow and nonphotochemical quenching (NPQ). As we initially identified SIG2 expression as misregulated in a line lacking phytochromes in mesophyll tissues (i.e., CAB3::pBVR lines), here we report on an investigation of whether photosynthetic parameters such as NPQ are also disrupted in CAB3::pBVR lines. We determined that a specific parameter of NPQ, i.e., energy-dependent quenching (qE) which is a rapidly induced photoprotective mechanism that dissipates stressful absorption of excess light energy during photosynthesis, is disrupted when mesophyll phytochromes are significantly depleted. The observed reduction in NPQ levels in strong CAB3::pBVR lines is associated with a reduction in the accumulation of Lhcb1 proteins and assembly or stability of light-harvesting complexes (LHCs), especially trimeric LHC. These results implicate mesophyll-localized phytochromes in a specific aspect of phytochrome-mediated NPQ, likely through regulation of chlorophyll synthesis and accumulation and the associated impacts on chlorophyll-protein complexes. This role is distinct from the impact of mesophyll phytochrome-dependent control of SIG2 and associated NPQ regulation.
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Affiliation(s)
- Sookyung Oh
- Department of Energy — Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Beronda L. Montgomery
- Department of Energy — Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- CONTACT Beronda L. Montgomery Department of Energy — Plant Research Laboratory, Michigan State University, 612 Wilson Road, Room 106, East Lansing, MI 48824, USA
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