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Yu Z, Wang J, Zhang C, Zhan Q, Shi L, Song B, Han D, Jiang J, Huang J, Ou X, Zhang Z, Lai J, Li QQ, Yang C. SIZ1-mediated SUMOylation of CPSF100 promotes plant thermomorphogenesis by controlling alternative polyadenylation. MOLECULAR PLANT 2024; 17:1392-1406. [PMID: 39066483 DOI: 10.1016/j.molp.2024.07.011] [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: 01/27/2024] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Under warm temperatures, plants adjust their morphologies for environmental adaption via precise gene expression regulation. However, the function and regulation of alternative polyadenylation (APA), an important fine-tuning of gene expression, remains unknown in plant thermomorphogenesis. In this study, we found that SUMOylation, a critical post-translational modification, is induced by a long-term treatment at warm temperatures via a SUMO ligase SIZ1 in Arabidopsis. Disruption of SIZ1 altered the global usage of polyadenylation signals and affected the APA dynamic of thermomorphogenesis-related genes. CPSF100, a key subunit of the CPSF complex for polyadenylation regulation, is SUMOylated by SIZ1. Importantly, we demonstrated that SUMOylation is essential for the function of CPSF100 in genome-wide polyadenylation site choice during thermomorphogenesis. Further analyses revealed that the SUMO conjugation on CPSF100 attenuates its interaction with two isoforms of its partner CPSF30, increasing the nuclear accumulation of CPSF100 for polyadenylation regulation. In summary, our study uncovers a regulatory mechanism of APA via SIZ1-mediated SUMOylation in plant thermomorphogenesis.
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Affiliation(s)
- Zhibo Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jun Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Cheng Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qiuna Zhan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Leqian Shi
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Bing Song
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Junwen Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaolin Ou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; Biomedical Science Division, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China.
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Mateo-Bonmatí E, Montez M, Maple R, Fiedler M, Fang X, Saalbach G, Passmore LA, Dean C. A CPF-like phosphatase module links transcription termination to chromatin silencing. Mol Cell 2024; 84:2272-2286.e7. [PMID: 38851185 PMCID: PMC7616277 DOI: 10.1016/j.molcel.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024]
Abstract
The interconnections between co-transcriptional regulation, chromatin environment, and transcriptional output remain poorly understood. Here, we investigate the mechanism underlying RNA 3' processing-mediated Polycomb silencing of Arabidopsis FLOWERING LOCUS C (FLC). We show a requirement for ANTHESIS PROMOTING FACTOR 1 (APRF1), a homolog of yeast Swd2 and human WDR82, known to regulate RNA polymerase II (RNA Pol II) during transcription termination. APRF1 interacts with TYPE ONE SERINE/THREONINE PROTEIN PHOSPHATASE 4 (TOPP4) (yeast Glc7/human PP1) and LUMINIDEPENDENS (LD), the latter showing structural features found in Ref2/PNUTS, all components of the yeast and human phosphatase module of the CPF 3' end-processing machinery. LD has been shown to co-associate in vivo with the histone H3 K4 demethylase FLOWERING LOCUS D (FLD). This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC.
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Affiliation(s)
- Eduardo Mateo-Bonmatí
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Pozuelo de Alarcón, Madrid 28223, Spain.
| | - Miguel Montez
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Xiaofeng Fang
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Gerhard Saalbach
- Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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Zhou L, Li K, Hunt AG. Natural variation in the plant polyadenylation complex. FRONTIERS IN PLANT SCIENCE 2024; 14:1303398. [PMID: 38317838 PMCID: PMC10839035 DOI: 10.3389/fpls.2023.1303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
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Affiliation(s)
| | | | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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Tabassum N, Ahmed HI, Parween S, Sheikh AH, Saad MM, Krattinger SG, Hirt H. Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome. MICROBIOME 2024; 12:11. [PMID: 38233870 PMCID: PMC10792890 DOI: 10.1186/s40168-023-01725-5] [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: 04/05/2023] [Accepted: 11/18/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity. RESULT We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response. CONCLUSION Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way. Video Abstract.
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Affiliation(s)
- Naheed Tabassum
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Sabiha Parween
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Arsheed H Sheikh
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Maged M Saad
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Heribert Hirt
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
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