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Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [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: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
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Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
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Biziaev NS, Shuvalov AV, Alkalaeva EZ. HEMK-Like Methyltransferases in the Regulation of Cellular Processes. Mol Biol 2022. [DOI: 10.1134/s0026893322030025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuki T, Miwa K, Yamashita Y, Naito S, Fujiwara T. Translational Landscape of a C4 Plant, Sorghum bicolor, Under Normal and Sulfur-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:592-604. [PMID: 35166349 DOI: 10.1093/pcp/pcac023] [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: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling or Ribo-seq) has enabled genome-wide analysis of translation. Sorghum is a C4 cereal important not only as food but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Yet genome-wide translational profiles in sorghum are still missing. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 4,843 main open reading frames (ORFs) annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript and translation levels. Our study revealed the translational landscape of sorghum's response to sulfur and provides datasets that could serve as a fundamental resource to extend genetic research on sorghum, including studies on translational regulation.
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Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Haruka Aoyama
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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Shi Y, Yang X, Ye X, Feng J, Cheng T, Zhou X, Liu DX, Xu L, Wang J. The Methyltransferase HemK Regulates the Virulence and Nutrient Utilization of the Phytopathogenic Bacterium Xanthomonas citri Subsp. citri. Int J Mol Sci 2022; 23:ijms23073931. [PMID: 35409293 PMCID: PMC8999716 DOI: 10.3390/ijms23073931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), seriously affects fruit quality and yield, leading to significant economic losses around the world. Understanding the mechanism of Xcc virulence is important for the effective control of Xcc infection. In this report, we investigate the role of a protein named HemK in the regulation of the virulence traits of Xcc. The hemK gene was deleted in the Xcc jx-6 background, and the ΔhemK mutant phenotypically displayed significantly decreased motility, biofilm formation, extracellular enzymes, and polysaccharides production, as well as increased sensitivity to oxidative stress and high temperatures. In accordance with the role of HemK in the regulation of a variety of virulence-associated phenotypes, the deletion of hemK resulted in reduced virulence on citrus plants as well as a compromised hypersensitive response on a non-host plant, Nicotiana benthamiana. These results indicated that HemK is required for the virulence of Xcc. To characterize the regulatory effect of hemK deletion on gene expression, RNA sequencing analysis was conducted using the wild-type Xcc jx-6 strain and its isogenic ΔhemK mutant strain, grown in XVM2 medium. Comparative transcriptome analysis of these two strains revealed that hemK deletion specifically changed the expression of several virulence-related genes associated with the bacterial secretion system, chemotaxis, and quorum sensing, and the expression of various genes related to nutrient utilization including amino acid metabolism, carbohydrate metabolism, and energy metabolism. In conclusion, our results indicate that HemK plays an essential role in virulence, the regulation of virulence factor synthesis, and the nutrient utilization of Xcc.
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Affiliation(s)
- Yu Shi
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
| | - Xiaobei Yang
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
| | - Xiaoxin Ye
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
| | - Jiaying Feng
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
| | - Tianfang Cheng
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
| | - Xiaofan Zhou
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Ding Xiang Liu
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (L.X.); (J.W.)
| | - Junxia Wang
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (Y.S.); (X.Y.); (X.Y.); (J.F.); (T.C.); (X.Z.); (D.X.L.)
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (L.X.); (J.W.)
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Sotta N, Chiba Y, Miwa K, Takamatsu S, Tanaka M, Yamashita Y, Naito S, Fujiwara T. Global analysis of boron-induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG-stops in Arabidopsis shoots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1455-1467. [PMID: 33772920 DOI: 10.1111/tpj.15248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
We previously reported that ribosome stalling at AUG-stop sequences in the 5'-untranslated region plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1, which encodes a boron uptake transporter, in response to boron conditions in media. This ribosome stalling is triggered specifically by boric acid, but the mechanisms are unknown. Although upstream open reading frames (uORFs) are known in many cases to regulate translation through peptides encoded by the uORF, AUG-stop stalling does not involve any peptide synthesis. The unique feature of AUG-stops - that termination follows immediately after initiation - suggests a possible effect of boron on the translational process itself. However, the generality of AUG-stop-mediated translational regulation and the effect of boron on translation at the genome scale are not clear. Here, we conducted a ribosome profiling analysis to reveal the genome-wide regulation of translation in response to boron conditions in A. thaliana shoots. We identified hundreds of translationally regulated genes that function in various biological processes. Under high-boron conditions, transcripts with reduced translation efficiency were rich in uORFs, highlighting the importance of uORF-mediated translational regulation. We found 673 uORFs that had more frequent ribosome association. Moreover, transcripts that were translationally downregulated under high-boron conditions were rich in minimum uORFs (AUG-stops), suggesting that AUG-stops play a global role in the boron response. Metagene analysis revealed that boron increased the ribosome occupancy of stop codons, indicating that this element is involved in global translational termination processes.
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Affiliation(s)
- Naoyuki Sotta
- Graduate School of Agricultural and Life Science, University of Tokyo, Tokyo, 113-8657, Japan
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Seidai Takamatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Mayuki Tanaka
- Graduate School of Agricultural and Life Science, University of Tokyo, Tokyo, 113-8657, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Science, University of Tokyo, Tokyo, 113-8657, Japan
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Singh S, Kailasam S, Lo JC, Yeh KC. Histone H3 lysine4 trimethylation-regulated GRF11 expression is essential for the iron-deficiency response in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 230:244-258. [PMID: 33274450 DOI: 10.1111/nph.17130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 05/21/2023]
Abstract
Iron (Fe) homeostasis in plants is controlled by both transcription factors (TFs) and chromatin remodeling through histone modification. To date, few studies have reported the existence of histone modification in maintaining the Fe-deficiency response. However, the reports that do exist shed light on various histone modifications, but knowledge of the activation mark in Fe-deficiency response is lacking. By using a forward genetics approach, we identified a crucial allele for Fe-deficiency response, NON-RESPONSE TO Fe-DEFICIENCY2 (NRF2), previously described as EARLY FLOWERING8 (ELF8) associated with an activation mark on histone modification, histone H3 lysine4 trimethylation. In the nrf2-1 mutant, a point mutation at ELF8T404I , exhibits impaired expression of GENERAL REGULATORY FACTOR11 (GRF11) and downstream genes in the Fe-uptake pathway. In vivo chromatin immunoprecipitation revealed that in roots, NRF2/ELF8 is essential for the expression of GRF11 for Fe-deficiency response, whereas in shoots, NRF2/ELF8 regulates FLOWERING LOCUS C (FLC) expression for flowering time control. In summary, a key factor, NRF2/ELF8, involved in epigenetic regulation essential for both flowering time control and Fe-deficiency response is uncovered.
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Affiliation(s)
- Surjit Singh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Sakthivel Kailasam
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Jing-Chi Lo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuo-Chen Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan
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