1
|
Yang C, Li X, Yang L, Chen S, Liao J, Li K, Zhou J, Shen W, Zhuang X, Bai M, Bassham DC, Gao C. A positive feedback regulation of SnRK1 signaling by autophagy in plants. Mol Plant 2023; 16:1192-1211. [PMID: 37408307 DOI: 10.1016/j.molp.2023.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/02/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.
Collapse
Affiliation(s)
- Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China; Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xibao Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lianming Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shunquan Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Kailin Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Zhou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Mingyi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| |
Collapse
|
2
|
Jeong EY, Seo PJ, Woo JC, Park CM. AKIN10 delays flowering by inactivating IDD8 transcription factor through protein phosphorylation in Arabidopsis. BMC Plant Biol 2015; 15:110. [PMID: 25929516 PMCID: PMC4416337 DOI: 10.1186/s12870-015-0503-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/23/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sugar plays a central role as a source of carbon metabolism and energy production and a signaling molecule in diverse growth and developmental processes and environmental adaptation in plants. It is known that sugar metabolism and allocation between different physiological functions is intimately associated with flowering transition in many plant species. The INDETERMINATE DOMAIN (IDD)-containing transcription factor IDD8 regulates flowering time by modulating sugar metabolism and transport under sugar-limiting conditions in Arabidopsis. Meanwhile, it has been reported that SUCROSE NONFERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1), which acts as a sensor of cellular energy metabolism, is activated by sugar deprivation. Notably, SnRK1-overexpressing plants and IDD8-deficient mutants exhibit similar phenotypes, including delayed flowering, suggesting that SnRK1 is involved in the IDD8-mediated metabolic control of flowering. RESULTS We examined whether the sugar deprivation-sensing SnRK1 is functionally associated with IDD8 in flowering time control through biochemical and molecular genetic approaches. Overproduction of AKIN10, the catalytic subunit of SnRK1, delayed flowering in Arabidopsis, as was observed in IDD8-deficient idd8-3 mutant. We found that AKIN10 interacts with IDD8 in the nucleus. Consequently, AKIN10 phosphorylates IDD8 primarily at two serine (Ser) residues, Ser-178 and Ser-182, which reside in the fourth zinc finger (ZF) domain that mediates DNA binding and protein-protein interactions. AKIN10-mediated phosphorylation did not affect the subcellular localization and DNA-binding property of IDD8. Instead, the transcriptional activation activity of the phosphorylated IDD8 was significantly reduced. Together, these observations indicate that AKIN10 antagonizes the IDD8 function in flowering time control, a notion that is consistent with the delayed flowering phenotypes of AKIN10-overexpressing plants and idd8-3 mutant. CONCLUSION Our data show that SnRK1 and its substrate IDD8 constitute a sugar metabolic pathway that mediates the timing of flowering under sugar deprivation conditions. In this signaling scheme, the SnRK1 signals are directly integrated into the IDD8-mediated gene regulatory network that governs flowering transition in response to fluctuations in sugar metabolism, further supporting the metabolic control of flowering.
Collapse
Affiliation(s)
- Eun-Young Jeong
- Department of Chemistry, Seoul National University, Seoul, 151-742, South Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 151-742, South Korea.
| | - Je Chang Woo
- Department of Biological Science, Mokpo National University, Jeonnam, 534-729, South Korea.
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, South Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, South Korea.
| |
Collapse
|
3
|
Ramon M, Ruelens P, Li Y, Sheen J, Geuten K, Rolland F. The hybrid four-CBS-domain KINβγ subunit functions as the canonical γ subunit of the plant energy sensor SnRK1. Plant J 2013; 75:11-25. [PMID: 23551663 PMCID: PMC6599549 DOI: 10.1111/tpj.12192] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/15/2013] [Accepted: 03/26/2013] [Indexed: 05/17/2023]
Abstract
The AMPK/SNF1/SnRK1 protein kinases are a family of ancient and highly conserved eukaryotic energy sensors that function as heterotrimeric complexes. These typically comprise catalytic α subunits and regulatory β and γ subunits, the latter function as the energy-sensing modules of animal AMPK through adenosine nucleotide binding. The ability to monitor accurately and adapt to changing environmental conditions and energy supply is essential for optimal plant growth and survival, but mechanistic insight in the plant SnRK1 function is still limited. In addition to a family of γ-like proteins, plants also encode a hybrid βγ protein that combines the Four-Cystathionine β-synthase (CBS)-domain (FCD) structure in γ subunits with a glycogen-binding domain (GBD), typically found in β subunits. We used integrated functional analyses by ectopic SnRK1 complex reconstitution, yeast mutant complementation, in-depth phylogenetic reconstruction, and a seedling starvation assay to show that only the hybrid KINβγ protein that recruited the GBD around the emergence of the green chloroplast-containing plants, acts as the canonical γ subunit required for heterotrimeric complex formation. Mutagenesis and truncation analysis further show that complex interaction in plant cells and γ subunit function in yeast depend on both a highly conserved FCD and a pre-CBS domain, but not the GBD. In addition to novel insight into canonical AMPK/SNF/SnRK1 γ subunit function, regulation and evolution, we provide a new classification of plant FCD genes as a convenient and reliable tool to predict regulatory partners for the SnRK1 energy sensor and novel FCD gene functions.
Collapse
Affiliation(s)
- Matthew Ramon
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, B-3001, Leuven, Belgium
| | - Philip Ruelens
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, B-3001, Leuven, Belgium
| | - Yi Li
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, B-3001, Leuven, Belgium
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative, Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Koen Geuten
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, B-3001, Leuven, Belgium
| | - Filip Rolland
- Laboratory of Molecular Plant Biology, KU Leuven Department of Biology, B-3001, Leuven, Belgium
| |
Collapse
|
4
|
Paul MJ, Jhurreea D, Zhang Y, Primavesi LF, Delatte T, Schluepmann H, Wingler A. Upregulation of biosynthetic processes associated with growth by trehalose 6-phosphate. Plant Signal Behav 2010; 5:386-92. [PMID: 20139731 PMCID: PMC2958589 DOI: 10.4161/psb.5.4.10792] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 11/25/2009] [Indexed: 05/17/2023]
Abstract
Trehalose 6-phosphate (T6P), the precursor of trehalose, is a signaling molecule in plants with strong effects on metabolism, growth and development. We recently showed that in growing tissues T6P is an inhibitor of SnRK1 of the SNF1-related group of protein kinases. SnRK1 acts as transcriptional integrator in response to carbon and energy supply. In microarray experiments on seedlings of transgenic Arabidopsis with elevated T6P content we found that expression of SnRK1 marker genes was affected in a manner to be predicted by inhibition of SnRK1 by T6P in vivo. A large number of genes involved in reactions that utilize carbon, e.g., UDP-glucose dehydrogenase genes involved in cell wall synthesis, were upregulated. T6P was also found to affect developmental signaling pathways, probably in a SnRK1-independent manner. This includes upregulation of genes encoding UDP-glycosyltransferases that are involved in the glycosylation of hormones. In addition, genes involved in auxin response and light signaling were affected. Many of these genes belong to pathways that link the circadian clock to plant growth and development. The overall pattern of changes in gene expression supports a role for T6P in coordinating carbon supply with biosynthetic process involved in growth and development.
Collapse
Affiliation(s)
- Matthew J Paul
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK.
| | | | | | | | | | | | | |
Collapse
|
5
|
Hummel M, Rahmani F, Smeekens S, Hanson J. Sucrose-mediated translational control. Ann Bot 2009; 104:1-7. [PMID: 19376782 PMCID: PMC2706714 DOI: 10.1093/aob/mcp086] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 12/18/2008] [Accepted: 03/05/2009] [Indexed: 05/20/2023]
Abstract
BACKGROUND Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally. RECENT PROGRESS Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress. CONCLUSIONS Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.
Collapse
Affiliation(s)
- Maureen Hummel
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Fatima Rahmani
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sjef Smeekens
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Centre for BioSystems Genomics, POB 98, 6700 AB, Wageningen, The Netherlands
| | - Johannes Hanson
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Centre for BioSystems Genomics, POB 98, 6700 AB, Wageningen, The Netherlands
- For correspondence. Email
| |
Collapse
|