1
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Deng Q, Hong X, Xia Y, Gong Z, Dai H, Chen J, Feng Y, Zhang J, Xie X, Li N, Shen X, Hu J, Zhang Q, Lang X, Pan R. Comprehensive identification of plant peroxisome targeting signal type 1 tripeptides. THE NEW PHYTOLOGIST 2024. [PMID: 38975665 DOI: 10.1111/nph.19955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Affiliation(s)
- Qianwen Deng
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
- Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xiao Hong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuqing Xia
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
| | - Zhicheng Gong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
| | - Huaxin Dai
- Beijing Life Science Academy, Changping, Beijing, 102209, China
| | - Jiarong Chen
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yanlei Feng
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
| | - Jianfeng Zhang
- Beijing Life Science Academy, Changping, Beijing, 102209, China
| | - Xiaodong Xie
- Beijing Life Science Academy, Changping, Beijing, 102209, China
| | - Nannan Li
- Zhejiang Laboratory, Hangzhou, 311121, China
| | - Xingxing Shen
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
| | - Qiang Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
| | - Xuye Lang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
| | - Ronghui Pan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, 311215, China
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2
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Deng Q, Jiang H, Hu J, Pan R. Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation. Methods Mol Biol 2024; 2792:265-275. [PMID: 38861094 DOI: 10.1007/978-1-0716-3802-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially restricted manner. The subcellular localization of proteins is largely determined by their intrinsic targeting signals, which are mainly constituted by short peptides. A complete organelle targeting signal may contain a core signal (CoreS) as well as auxiliary signals (AuxiS). However, the AuxiS is often not as well characterized as the CoreS. Peroxisomes house many key steps in photorespiration, besides other crucial functions in plants. Peroxisome targeting signal type 1 (PTS1), which is carried by most peroxisome matrix proteins, was initially recognized as a C-terminal tripeptide with a "canonical" consensus of [S/A]-[K/R]-[L/M]. Many studies have shown the existence of auxiliary targeting signals upstream of PTS1, but systematic characterizations are lacking. Here, we designed an analytical strategy to characterize the auxiliary targeting signals for plant peroxisomes using large datasets and statistics followed by experimental validations. This method may also be applied to deciphering the auxiliary targeting signals for other organelles, whose organellar targeting depends on a core peptide with assistance from a nearby auxiliary signal.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Zhijiang Lab, Hangzhou, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Ronghui Pan
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
- Zhijiang Lab, Hangzhou, China.
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3
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Zhang Y, Wang X, Wang X, Wang Y, Liu J, Wang S, Li W, Jin Y, Akhter D, Chen J, Hu J, Pan R. Bioinformatic analysis of short-chain dehydrogenase/reductase proteins in plant peroxisomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1180647. [PMID: 37360717 PMCID: PMC10288848 DOI: 10.3389/fpls.2023.1180647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
Peroxisomes are ubiquitous eukaryotic organelles housing not only many important oxidative metabolic reactions, but also some reductive reactions that are less known. Members of the short-chain dehydrogenase/reductase (SDR) superfamily, which are NAD(P)(H)-dependent oxidoreductases, play important roles in plant peroxisomes, including the conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid (IAA), auxiliary β-oxidation of fatty acids, and benzaldehyde production. To further explore the function of this family of proteins in the plant peroxisome, we performed an in silico search for peroxisomal SDR proteins from Arabidopsis based on the presence of peroxisome targeting signal peptides. A total of 11 proteins were discovered, among which four were experimentally confirmed to be peroxisomal in this study. Phylogenetic analyses showed the presence of peroxisomal SDR proteins in diverse plant species, indicating the functional conservation of this protein family in peroxisomal metabolism. Knowledge about the known peroxisomal SDRs from other species also allowed us to predict the function of plant SDR proteins within the same subgroup. Furthermore, in silico gene expression profiling revealed strong expression of most SDR genes in floral tissues and during seed germination, suggesting their involvement in reproduction and seed development. Finally, we explored the function of SDRj, a member of a novel subgroup of peroxisomal SDR proteins, by generating and analyzing CRISPR/Cas mutant lines. This work provides a foundation for future research on the biological activities of peroxisomal SDRs to fully understand the redox control of peroxisome functions.
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Affiliation(s)
- Yuchan Zhang
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Zhejiang Lab, Hangzhou, China
| | - Xiaowen Wang
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Xinyu Wang
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yukang Wang
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jun Liu
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Saisai Wang
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Weiran Li
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yijun Jin
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Delara Akhter
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Jiarong Chen
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, United States
| | - Ronghui Pan
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Zhejiang Lab, Hangzhou, China
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4
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Kunze M. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa. Methods Mol Biol 2023; 2643:391-404. [PMID: 36952201 DOI: 10.1007/978-1-0716-3048-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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5
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Muhammad D, Smith KA, Bartel B. Plant peroxisome proteostasis-establishing, renovating, and dismantling the peroxisomal proteome. Essays Biochem 2022; 66:229-242. [PMID: 35538741 PMCID: PMC9375579 DOI: 10.1042/ebc20210059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/28/2022]
Abstract
Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with transcriptional regulation of peroxisomal protein genes and the synthesis, trafficking, import, and folding of peroxisomal proteins. The saga continues with assembly and disaggregation by chaperones and degradation via proteases or the proteasome. The story concludes with organelle recycling via autophagy. Some of these processes as well as the proteins that facilitate them are peroxisome-specific, while others are shared among organelles. Our understanding of translational regulation of plant peroxisomal protein transcripts and proteins necessary for pexophagy remain based in findings from other models. Recent strides to elucidate transcriptional control, membrane dynamics, protein trafficking, and conditions that induce peroxisome turnover have expanded our knowledge of plant peroxisomal proteostasis. Here we review our current understanding of the processes and proteins necessary for plant peroxisome proteostasis-the emergence, maintenance, and clearance of the peroxisomal proteome.
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Affiliation(s)
| | - Kathryn A Smith
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
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Tarafdar S, Chowdhary G. Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. Front Cell Dev Biol 2022; 10:909604. [PMID: 35912119 PMCID: PMC9328179 DOI: 10.3389/fcell.2022.909604] [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: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisomes are small, single-membrane specialized organelles present in all eukaryotic organisms. The peroxisome is one of the nodal centers of reactive oxygen species homeostasis in plants, which are generated in a high amount due to various stress conditions. Over the past decade, there has been extensive study on peroxisomal proteins and their signaling pathways in the model plant Arabidopsis thaliana, and a lot has been deciphered. However, not much impetus has been given to studying the peroxisome proteome of economically important crops. Owing to the significance of peroxisomes in the physiology of plants during normal and stress conditions, understating its proteome is of much importance. Hence, in this paper, we have made a snapshot of putative peroxisomal matrix proteins in the economically important vegetable crop tomato (Solanum lycopersicum, (L.) family Solanaceae). First, a reference peroxisomal matrix proteome map was generated for Arabidopsis thaliana using the available proteomic and localization studies, and proteins were categorized into various groups as per their annotations. This was used to create the putative peroxisomal matrix proteome map for S. lycopersicum. The putative peroxisome proteome in S. lycopersicum retains the basic framework: the bulk of proteins had peroxisomal targeting signal (PTS) type 1, a minor group had PTS2, and the catalase family retained its characteristic internal PTS. Apart from these, a considerable number of S. lycopersicum orthologs did not contain any “obvious” PTS. The number of PTS2 isoforms was found to be reduced in S. lycopersicum. We further investigated the PTS1s in the case of both the plant species and generated a pattern for canonical and non-canonical PTS1s. The number of canonical PTS1 proteins was comparatively lesser in S. lycopersicum. The non-canonical PTS1s were found to be comparable in both the plant species; however, S. lycopersicum showed greater diversity in the composition of the signal tripeptide. Finally, we have tried to address the lacunas and probable strategies to fill those gaps.
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7
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Deng Q, Li H, Feng Y, Xu R, Li W, Zhu R, Akhter D, Shen X, Hu J, Jiang H, Pan R. Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large-scale in silico and in vivo analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:567-582. [PMID: 35603488 PMCID: PMC9542071 DOI: 10.1111/tpj.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/01/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C-terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large-scale and in-depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low-frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated in vivo. Follow-up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a 'basic-nonpolar-basic' pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - He Li
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Yanlei Feng
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - Ruonan Xu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Weiran Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Rui Zhu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Delara Akhter
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- Department of Genetics and Plant BreedingSylhet Agricultural UniversitySylhet3100Bangladesh
| | - Xingxing Shen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology DepartmentMichigan State UniversityEast LansingMichigan48824USA
| | - Hangjin Jiang
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Ronghui Pan
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
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8
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Kataya A, Gautam N, Jamshed M, Muench DG, Samuel MA, Thelen JJ, Moorhead GB. Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals. Front Cell Dev Biol 2022; 10:745883. [PMID: 35242755 PMCID: PMC8886021 DOI: 10.3389/fcell.2022.745883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Peroxisomes are eukaryotic specific organelles that perform diverse metabolic functions including fatty acid β-oxidation, reactive species metabolism, photorespiration, and responses to stress. However, the potential regulation of these functions by post-translational modifications, including protein phosphorylation, has had limited study. Recently, we identified and catalogued a large number of peroxisomal phosphorylated proteins, implicating the presence of protein kinases in this organelle. Here, we employed available prediction models coupled with sequence conservation analysis to identify 31 protein kinases from the Arabidopsis kinome (all protein kinases) that contain a putative, non-canonical peroxisomal targeting signal type 1 (PTS1). From this, twelve C-terminal domain-PTS1s were demonstrated to be functional in vivo, targeting enhanced yellow fluorescent protein to peroxisomes, increasing the list of presumptive peroxisomal protein kinases to nineteen. Of the twelve protein kinases with functional PTS1s, we obtained full length clones for eight and demonstrated that seven target to peroxisomes in vivo. Screening homozygous mutants of the presumptive nineteen protein kinases revealed one candidate (GPK1) that harbors a sugar-dependence phenotype, suggesting it is involved in regulating peroxisomal fatty acid β-oxidation. These results present new opportunities for investigating the regulation of peroxisome functions.
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Affiliation(s)
- Amr Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nitija Gautam
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Rudić J, Dragićević MB, Momčilović I, Simonović AD, Pantelić D. In Silico Study of Superoxide Dismutase Gene Family in Potato and Effects of Elevated Temperature and Salicylic Acid on Gene Expression. Antioxidants (Basel) 2022; 11:antiox11030488. [PMID: 35326138 PMCID: PMC8944489 DOI: 10.3390/antiox11030488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Potato (Solanum tuberosum L.) is the most important vegetable crop globally and is very susceptible to high ambient temperatures. Since heat stress causes the accumulation of reactive oxygen species (ROS), investigations regarding major enzymatic components of the antioxidative system are of the essence. Superoxide dismutases (SODs) represent the first line of defense against ROS but detailed in silico analysis and characterization of the potato SOD gene family have not been performed thus far. We have analyzed eight functional SOD genes, three StCuZnSODs, one StMnSOD, and four StFeSODs, annotated in the updated version of potato genome (Spud DB DM v6.1). The StSOD genes and their respective proteins were analyzed in silico to determine the exon-intron organization, splice variants, cis-regulatory promoter elements, conserved domains, signals for subcellular targeting, 3D-structures, and phylogenetic relations. Quantitative PCR analysis revealed higher induction of StCuZnSODs (the major potato SODs) and StFeSOD3 in thermotolerant cultivar Désirée than in thermosensitive Agria and Kennebec during long-term exposure to elevated temperature. StMnSOD was constitutively expressed, while expression of StFeSODs was cultivar-dependent. The effects of salicylic acid (10−5 M) on StSODs expression were minor. Our results provide the basis for further research on StSODs and their regulation in potato, particularly in response to elevated temperatures.
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Kang BH, Anderson CT, Arimura SI, Bayer E, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM, Chapman KD, Dünser K, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Kleine-Vehn J, Wang P, Zolman BK. A glossary of plant cell structures: Current insights and future questions. THE PLANT CELL 2022; 34:10-52. [PMID: 34633455 PMCID: PMC8846186 DOI: 10.1093/plcell/koab247] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.
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Affiliation(s)
- Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d'Ornon F-33140, France
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortifruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 29071, Spain
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Kai Dünser
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Yangnan Gu
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yu Tang
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jürgen Kleine-Vehn
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri, St. Louis, St. Louis, Missouri 63121, USA
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11
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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Sandalio LM, Peláez-Vico MA, Molina-Moya E, Romero-Puertas MC. Peroxisomes as redox-signaling nodes in intracellular communication and stress responses. PLANT PHYSIOLOGY 2021; 186:22-35. [PMID: 33587125 PMCID: PMC8154099 DOI: 10.1093/plphys/kiab060] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
Abstract
Peroxisomes are redox nodes playing a diverse range of roles in cell functionality and in the perception of and responses to changes in their environment.
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Affiliation(s)
- Luisa M Sandalio
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín-CSIC, Profesor Albareda 1, 18008 Granada, Spain
- Author for communication:
| | - Maria Angeles Peláez-Vico
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín-CSIC, Profesor Albareda 1, 18008 Granada, Spain
| | - Eliana Molina-Moya
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín-CSIC, Profesor Albareda 1, 18008 Granada, Spain
| | - Maria C Romero-Puertas
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín-CSIC, Profesor Albareda 1, 18008 Granada, Spain
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Kechasov D, de Grahl I, Endries P, Reumann S. Evolutionary Maintenance of the PTS2 Protein Import Pathway in the Stramenopile Alga Nannochloropsis. Front Cell Dev Biol 2020; 8:593922. [PMID: 33330478 PMCID: PMC7710942 DOI: 10.3389/fcell.2020.593922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The stramenopile alga Nannochloropsis evolved by secondary endosymbiosis of a red alga by a heterotrophic host cell and emerged as a promising organism for biotechnological applications, such as the production of polyunsaturated fatty acids and biodiesel. Peroxisomes play major roles in fatty acid metabolism but experimental analyses of peroxisome biogenesis and metabolism in Nannochloropsis are not reported yet. In fungi, animals, and land plants, soluble proteins of peroxisomes are targeted to the matrix by one of two peroxisome targeting signals (type 1, PTS1, or type 2, PTS2), which are generally conserved across kingdoms and allow the prediction of peroxisomal matrix proteins from nuclear genome sequences. Because diatoms lost the PTS2 pathway secondarily, we investigated its presence in the stramenopile sister group of diatoms, the Eustigmatophyceae, represented by Nannochloropsis. We detected a full-length gene of a putative PEX7 ortholog coding for the cytosolic receptor of PTS2 proteins and demonstrated its expression in Nannochloropsis gaditana. The search for predicted PTS2 cargo proteins in N. gaditana yielded several candidates. In vivo subcellular targeting analyses of representative fusion proteins in different plant expression systems demonstrated that two predicted PTS2 domains were indeed functional and sufficient to direct a reporter protein to peroxisomes. Peroxisome targeting of the predicted PTS2 cargo proteins was further confirmed in Nannochloropsis oceanica by confocal and transmission electron microscopy. Taken together, the results demonstrate for the first time that one group of stramenopile algae maintained the import pathway for PTS2 cargo proteins. To comprehensively map and model the metabolic capabilities of Nannochloropsis peroxisomes, in silico predictions needs to encompass both the PTS1 and the PTS2 matrix proteome.
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Affiliation(s)
- Dmitry Kechasov
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Pierre Endries
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
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Kataya ARA, Elshobaky A, Heidari B, Dugassa NF, Thelen JJ, Lillo C. Multi-targeted trehalose-6-phosphate phosphatase I harbors a novel peroxisomal targeting signal 1 and is essential for flowering and development. PLANTA 2020; 251:98. [PMID: 32306103 PMCID: PMC7214503 DOI: 10.1007/s00425-020-03389-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/10/2020] [Indexed: 05/13/2023]
Abstract
This work reveals information about new peroxisomal targeting signals type 1 and identifies trehalose-6-phosphate phosphatase I as multitargeted and is implicated in plant development, reproduction, and stress response. A putative, non-canonical peroxisomal targeting signal type 1 (PTS1) Pro-Arg-Met > was identified in the extreme C-terminus of trehalose-6-phosphate phosphatase (TPP)I. TPP catalyzes the final step of trehalose synthesis, and the enzyme was previously characterized to be nuclear only (Krasensky et al. in Antioxid Redox Signal 21(9):1289-1304, 2014). Here we show that the TPPI C-terminal decapeptide ending with Pro-Arg-Met > or Pro-Lys-Met > can indeed function as a PTS1. Upon transient expression in two plant expression systems, the free C- or N-terminal end led to the full-length TPPI targeting to peroxisomes and plastids, respectively. The nucleus and nucleolus targeting of the full-length TPPI was observed in both cases. The homozygous T-DNA insertion line of TPPI showed a pleiotropic phenotype including smaller leaves, shorter roots, delayed flowering, hypersensitivity to salt, and a sucrose dependent seedling development. Our results identify novel PTS1s, and TPPI as a protein multi-targeted to peroxisomes, plastids, nucleus, and nucleolus. Altogether our findings implicate an essential role for TPPI in development, reproduction, and cell signaling.
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Affiliation(s)
- Amr R A Kataya
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway.
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Ahmed Elshobaky
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Behzad Heidari
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nemie-Feyissa Dugassa
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
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Pan R, Liu J, Wang S, Hu J. Peroxisomes: versatile organelles with diverse roles in plants. THE NEW PHYTOLOGIST 2020; 225:1410-1427. [PMID: 31442305 DOI: 10.1111/nph.16134] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/08/2019] [Indexed: 05/18/2023]
Abstract
Peroxisomes are small, ubiquitous organelles that are delimited by a single membrane and lack genetic material. However, these simple-structured organelles are highly versatile in morphology, abundance and protein content in response to various developmental and environmental cues. In plants, peroxisomes are essential for growth and development and perform diverse metabolic functions, many of which are carried out coordinately by peroxisomes and other organelles physically interacting with peroxisomes. Recent studies have added greatly to our knowledge of peroxisomes, addressing areas such as the diverse proteome, regulation of division and protein import, pexophagy, matrix protein degradation, solute transport, signaling, redox homeostasis and various metabolic and physiological functions. This review summarizes our current understanding of plant peroxisomes, focusing on recent discoveries. Current problems and future efforts required to better understand these organelles are also discussed. An improved understanding of peroxisomes will be important not only to the understanding of eukaryotic cell biology and metabolism, but also to agricultural efforts aimed at improving crop performance and defense.
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Affiliation(s)
- Ronghui Pan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jun Liu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Saisai Wang
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
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