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Wang L, Zhang J, Wang R, Huang Z, Cui R, Zhu H, Yang Y, Zhang D. Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max). Funct Integr Genomics 2023; 23:37. [PMID: 36639600 DOI: 10.1007/s10142-023-00966-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.
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Affiliation(s)
- Li Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinyu Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongwen Huang
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
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2
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Langella E, Di Fiore A, Alterio V, Monti SM, De Simone G, D’Ambrosio K. α-CAs from Photosynthetic Organisms. Int J Mol Sci 2022; 23:ijms231912045. [PMID: 36233343 PMCID: PMC9570166 DOI: 10.3390/ijms231912045] [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: 07/26/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous enzymes that catalyze the reversible carbon dioxide hydration reaction. Among the eight different CA classes existing in nature, the α-class is the largest one being present in animals, bacteria, protozoa, fungi, and photosynthetic organisms. Although many studies have been reported on these enzymes, few functional, biochemical, and structural data are currently available on α-CAs isolated from photosynthetic organisms. Here, we give an overview of the most recent literature on the topic. In higher plants, these enzymes are engaged in both supplying CO2 at the Rubisco and determining proton concentration in PSII membranes, while in algae and cyanobacteria they are involved in carbon-concentrating mechanism (CCM), photosynthetic reactions and in detecting or signaling changes in the CO2 level in the environment. Crystal structures are only available for three algal α-CAs, thus not allowing to associate specific structural features to cellular localizations or physiological roles. Therefore, further studies on α-CAs from photosynthetic organisms are strongly needed to provide insights into their structure–function relationship.
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3
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Rozov SM, Deineko EV. Increasing the Efficiency of the Accumulation of Recombinant Proteins in Plant Cells: The Role of Transport Signal Peptides. PLANTS (BASEL, SWITZERLAND) 2022; 11:2561. [PMID: 36235427 PMCID: PMC9572730 DOI: 10.3390/plants11192561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. The main systems of the protein transport across membranes of the endoplasmic reticulum and endosymbiotic organelles are reviewed here, as are the major types and structure of the signal sequences targeting proteins to the endoplasmic reticulum and its derivatives, to plastids, and to mitochondria. The role of protein targeting to certain cell organelles depending on specific features of recombinant proteins and the effect of this targeting on the protein yield are discussed, in addition to the main directions of the search for signal sequences based on their primary structure. This knowledge makes it possible not only to predict a protein localization in the cell but also to reveal the most efficient sequences with potential biotechnological utility.
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Malebary SJ, Alzahrani E, Khan YD. A comprehensive tool for accurate identification of methyl-Glutamine sites. J Mol Graph Model 2021; 110:108074. [PMID: 34768228 DOI: 10.1016/j.jmgm.2021.108074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
Methylation is a biochemical process involved in nearly all of the human body functions. Glutamine is considered an indispensable amino acid that is susceptible to methylation via post-translational modification (PTM). Modern research has proved that methylation plays a momentous role in the progression of most types of cancers. Therefore, there is a need for an effective method to predict glutamine sites vulnerable to methylation accurately and inexpensively. The motive of this study is the formulation of an accurate method that could predict such sites with high accuracy. Various computationally intelligent classifiers were employed for their formulation and evaluation. Rigorous validations prove that deep learning performs best as compared to other classifiers. The accuracy (ACC) and the area under the receiver operating curve (AUC) obtained by 10-fold cross-validation was 0.962 and 0.981, while with the jackknife testing, it was 0.968 and 0.980, respectively. From these results, it is concluded that the proposed methodology works sufficiently well for the prediction of methyl-glutamine sites. The webserver's code, developed for the prediction of methyl-glutamine sites, is freely available at https://github.com/s20181080001/WebServer.git. The code can easily be set up by any intermediate-level Python user.
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Affiliation(s)
- Sharaf J Malebary
- Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, P.O. Box 344, Rabigh, 21911, Saudi Arabia.
| | - Ebraheem Alzahrani
- Department of Mathematics, Faculty of Science, King Abdulaziz University, P. O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Yaser Daanial Khan
- Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore, Pakistan.
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5
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Post-translational modifications in tumor-associated carbonic anhydrases. Amino Acids 2021; 54:543-558. [PMID: 34436666 DOI: 10.1007/s00726-021-03063-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022]
Abstract
Human carbonic anhydrases IX (hCA IX) and XII (hCA XII) are two proteins associated with tumor formation and development. These enzymes have been largely investigated both from a biochemical and a functional point of view. However, limited data are currently available on the characterization of their post-translational modifications (PTMs) and the functional implication of these structural changes in the tumor environment. In this review, we summarize existing literature data on PTMs of hCA IX and hCA XII, such as disulphide bond formation, phosphorylation, O-/N-linked glycosylation, acetylation and ubiquitination, highlighting, when possible, their specific role in cancer pathological processes.
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Di Fiore A, Supuran CT, Scaloni A, De Simone G. Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. J Enzyme Inhib Med Chem 2021; 35:1450-1461. [PMID: 32648529 PMCID: PMC7470082 DOI: 10.1080/14756366.2020.1781846] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human carbonic anhydrases (CAs) have become a well-recognized target for the design of inhibitors and activators with biomedical applications. Accordingly, an enormous amount of literature is available on their biochemical, functional and structural aspects. Nevertheless post-translational modifications (PTMs) occurring on these enzymes and their functional implications have been poorly investigated so far. To fill this gap, in this review we have analysed all PTMs occurring on human CAs, as deriving from the search in dedicated databases, showing a widespread occurrence of modification events in this enzyme family. By combining these data with sequence alignments, inspection of 3 D structures and available literature, we have summarised the possible functional implications of these PTMs. Although in some cases a clear correlation between a specific PTM and the CA function has been highlighted, many modification events still deserve further dedicated studies.
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Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-National Research Council, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Sesto Fiorentino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
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Burlacot A, Burlacot F, Li-Beisson Y, Peltier G. Membrane Inlet Mass Spectrometry: A Powerful Tool for Algal Research. FRONTIERS IN PLANT SCIENCE 2020; 11:1302. [PMID: 33013952 PMCID: PMC7500362 DOI: 10.3389/fpls.2020.01302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/11/2020] [Indexed: 05/15/2023]
Abstract
Since the first great oxygenation event, photosynthetic microorganisms have continuously shaped the Earth's atmosphere. Studying biological mechanisms involved in the interaction between microalgae and cyanobacteria with the Earth's atmosphere requires the monitoring of gas exchange. Membrane inlet mass spectrometry (MIMS) has been developed in the early 1960s to study gas exchange mechanisms of photosynthetic cells. It has since played an important role in investigating various cellular processes that involve gaseous compounds (O2, CO2, NO, or H2) and in characterizing enzymatic activities in vitro or in vivo. With the development of affordable mass spectrometers, MIMS is gaining wide popularity and is now used by an increasing number of laboratories. However, it still requires an important theory and practical considerations to be used. Here, we provide a practical guide describing the current technical basis of a MIMS setup and the general principles of data processing. We further review how MIMS can be used to study various aspects of algal research and discuss how MIMS will be useful in addressing future scientific challenges.
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Feng CY, Chen ZF, Pei LL, Ma SX, Nie HM, Zheng SW, Sun S, Xing GM. Genome-wide identification, phylogeny, and expression analysis of the CA gene family in tomato. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1715832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Chao-Yang Feng
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Zhi-Feng Chen
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Ling-Ling Pei
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Su-Xian Ma
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Hong-Mei Nie
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Shao-Wen Zheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Sheng Sun
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
| | - Guo-Ming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Collaborative Innovation Center for Improving the Quality and Efficiency of Greenhouse Vegetable in Shanxi Province, Taigu County, China
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Muthamilselvan T, Kim JS, Cheong G, Hwang I. Production of recombinant proteins through sequestration in chloroplasts: a strategy based on nuclear transformation and post-translational protein import. PLANT CELL REPORTS 2019; 38:825-833. [PMID: 31139894 DOI: 10.1007/s00299-019-02431-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 05/17/2023]
Abstract
Recently, plants have emerged as a lucrative alternative system for the production of recombinant proteins, as recombinant proteins produced in plants are safer and cheaper than those produced in bacteria and animal cell-based production systems. To obtain high yields in plants, recombinant proteins are produced in chloroplasts using different strategies. The first strategy is based on chloroplast transformation, followed by gene expression and translation in chloroplasts. This has proven to be a powerful approach for the production of proteins at high levels. The second approach is based on nuclear transformation, followed by post-translational import of proteins from the cytosol into chloroplasts. In the nuclear transformation approach, foreign genes are stably integrated into the nuclear genome or transiently expressed in the nucleus by non-integrating T-DNA. Although this approach also has great potential for protein production at high levels, it has not been thoroughly investigated. In this review, we focus on nuclear transformation-based protein expression and its subsequent sequestration in chloroplasts, and summarize the different strategies used for high-level production of recombinant proteins. We also discuss future directions for further improvements in protein production in chloroplasts through nuclear transformation-based gene expression.
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Affiliation(s)
- Thangarasu Muthamilselvan
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea
| | - Jung Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea
| | - Gangwon Cheong
- Department of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea.
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10
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Rivera-Perez C, Magallanes-Dominguez C, Dominguez-Beltran RV, Ojeda-Ramirez de Areyano JJ, Hernandez-Saavedra NY. Biochemical and molecular characterization of N66 from the shell of Pinctada mazatlanica. PeerJ 2019; 7:e7212. [PMID: 31293836 PMCID: PMC6599672 DOI: 10.7717/peerj.7212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022] Open
Abstract
Mollusk shell mineralization is a tightly controlled process made by shell matrix proteins (SMPs). However, the study of SMPs has been limited to a few model species. In this study, the N66 mRNA of the pearl oyster Pinctada mazatlanica was cloned and functionally characterized. The full sequence of the N66 mRNA comprises 1,766 base pairs, and encodes one N66 protein. A sequence analysis revealed that N66 contained two carbonic anhydrase (CA) domains, a NG domain and several glycosylation sites. The sequence showed similarity to the CA VII but also with its homolog protein nacrein. The native N66 protein was isolated from the shell and identified by mass spectrometry, the peptide sequence matched to the nucleotide sequence obtained. Native N66 is a glycoprotein with a molecular mass of 60-66 kDa which displays CA activity and calcium carbonate precipitation ability in presence of different salts. Also, a recombinant form of N66 was produced in Escherichia coli, and functionally characterized. The recombinant N66 displayed higher CA activity and crystallization capability than the native N66, suggesting that the lack of posttranslational modifications in the recombinant N66 might modulate its activity.
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Affiliation(s)
- Crisalejandra Rivera-Perez
- Department of Fisheries Ecology, CONACyT-Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | - Catalina Magallanes-Dominguez
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | | | - Josafat Jehu Ojeda-Ramirez de Areyano
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
| | - Norma Y. Hernandez-Saavedra
- Department of Fisheries Ecology, Molecular Genetics Laboratory, Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, Baja California Sur, Mexico
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11
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Razzak MA, Lee J, Lee DW, Kim JH, Yoon HS, Hwang I. Expression of seven carbonic anhydrases in red alga Gracilariopsis chorda and their subcellular localization in a heterologous system, Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:147-159. [PMID: 30446790 DOI: 10.1007/s00299-018-2356-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/07/2018] [Indexed: 05/07/2023]
Abstract
Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.
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Affiliation(s)
- Md Abdur Razzak
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Jeong Hee Kim
- Department of Biochemistry and Molecular Biology, College of Dentistry, Kyung Hee University, Seoul, 130-701, South Korea
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, 130-701, South Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, 37673, South Korea.
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea.
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12
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LaBrant E, Barnes AC, Roston RL. Lipid transport required to make lipids of photosynthetic membranes. PHOTOSYNTHESIS RESEARCH 2018; 138:345-360. [PMID: 29961189 DOI: 10.1007/s11120-018-0545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/20/2018] [Indexed: 05/21/2023]
Abstract
Photosynthetic membranes provide much of the usable energy for life on earth. To produce photosynthetic membrane lipids, multiple transport steps are required, including fatty acid export from the chloroplast stroma to the endoplasmic reticulum, and lipid transport from the endoplasmic reticulum to the chloroplast envelope membranes. Transport of hydrophobic molecules through aqueous space is energetically unfavorable and must be catalyzed by dedicated enzymes, frequently on specialized membrane structures. Here, we review photosynthetic membrane lipid transport to the chloroplast in the context of photosynthetic membrane lipid synthesis. We independently consider the identity of transported lipids, the proteinaceous transport components, and membrane structures which may allow efficient transport. Recent advances in lipid transport of chloroplasts, bacteria, and other systems strongly suggest that lipid transport is achieved by multiple mechanisms which include membrane contact sites with specialized protein machinery. This machinery is likely to include the TGD1, 2, 3 complex with the TGD5 and TGD4/LPTD1 systems, and may also include a number of proteins with domains similar to other membrane contact site lipid-binding proteins. Importantly, the likelihood of membrane contact sites does not preclude lipid transport by other mechanisms including vectorial acylation and vesicle transport. Substantial progress is needed to fully understand all photosynthetic membrane lipid transport processes and how they are integrated.
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Affiliation(s)
- Evan LaBrant
- Department of Biochemistry, University of Nebraska-Lincoln, 1901 Vine St, Lincoln, NE, 68588, USA
| | - Allison C Barnes
- Department of Biochemistry, University of Nebraska-Lincoln, 1901 Vine St, Lincoln, NE, 68588, USA
| | - Rebecca L Roston
- Department of Biochemistry, University of Nebraska-Lincoln, 1901 Vine St, Lincoln, NE, 68588, USA.
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Inomata T, Baslam M, Masui T, Koshu T, Takamatsu T, Kaneko K, Pozueta-Romero J, Mitsui T. Proteomics Analysis Reveals Non-Controlled Activation of Photosynthesis and Protein Synthesis in a Rice npp1 Mutant under High Temperature and Elevated CO₂ Conditions. Int J Mol Sci 2018; 19:ijms19092655. [PMID: 30205448 PMCID: PMC6165220 DOI: 10.3390/ijms19092655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 11/26/2022] Open
Abstract
Rice nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides including ADP-glucose and ATP. Under high temperature and elevated CO2 conditions (HT + ECO2), the npp1 knockout rice mutant displayed rapid growth and high starch content phenotypes, indicating that NPP1 exerts a negative effect on starch accumulation and growth. To gain further insight into the mechanisms involved in the NPP1 downregulation induced starch overaccumulation, in this study we conducted photosynthesis, leaf proteomic, and chloroplast phosphoproteomic analyses of wild-type (WT) and npp1 plants cultured under HT + ECO2. Photosynthesis in npp1 leaves was significantly higher than in WT. Additionally, npp1 leaves accumulated higher levels of sucrose than WT. The proteomic analyses revealed upregulation of proteins related to carbohydrate metabolism and the protein synthesis system in npp1 plants. Further, our data indicate the induction of 14-3-3 proteins in npp1 plants. Our finding demonstrates a higher level of protein phosphorylation in npp1 chloroplasts, which may play an important role in carbohydrate accumulation. Together, these results offer novel targets and provide additional insights into carbohydrate metabolism regulation under ambient and adverse conditions.
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Affiliation(s)
- Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Marouane Baslam
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Takahiro Masui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Tsutomu Koshu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Takeshi Takamatsu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Mutiloako Etorbidea Zenbaki Gabe, 31192 Mutiloabeti, Nafarroa, Spain.
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
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14
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Jeong IS, Lee S, Bonkhofer F, Tolley J, Fukudome A, Nagashima Y, May K, Rips S, Lee SY, Gallois P, Russell WK, Jung HS, von Schaewen A, Koiwa H. Purification and characterization of Arabidopsis thaliana oligosaccharyltransferase complexes from the native host: a protein super-expression system for structural studies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:131-145. [PMID: 29385647 DOI: 10.1111/tpj.13847] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/31/2017] [Accepted: 01/15/2018] [Indexed: 05/18/2023]
Abstract
The oligosaccharyltransferase (OT) complex catalyzes N-glycosylation of nascent secretory polypeptides in the lumen of the endoplasmic reticulum. Despite their importance, little is known about the structure and function of plant OT complexes, mainly due to lack of efficient recombinant protein production systems suitable for studies on large plant protein complexes. Here, we purified Arabidopsis OT complexes using the tandem affinity-tagged OT subunit STAUROSPORINE AND TEMPERATURE SENSITIVE3a (STT3a) expressed by an Arabidopsis protein super-expression platform. Mass-spectrometry analysis of the purified complexes identified three essential OT subunits, OLIGOSACCHARYLTRANSFERASE1 (OST1), HAPLESS6 (HAP6), DEFECTIVE GLYCOSYLATION1 (DGL1), and a number of ribosomal subunits. Transmission-electron microscopy showed that STT3a becomes incorporated into OT-ribosome super-complexes formed in vivo, demonstrating that this expression/purification platform is suitable for analysis of large protein complexes. Pairwise in planta interaction analyses of individual OT subunits demonstrated that all subunits identified in animal OT complexes are conserved in Arabidopsis and physically interact with STT3a. Genetic analysis of newly established OT subunit mutants for OST1 and DEFENDER AGAINST APOTOTIC DEATH (DAD) family genes revealed that OST1 and DAD1/2 subunits are essential for the plant life cycle. However, mutations in these individual isoforms produced much milder growth/underglycosylation phenotypes than previously reported for mutations in DGL1, OST3/6 and STT3a.
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Affiliation(s)
- In Sil Jeong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
- Department of Biomedical Engineering College of Creative Convergence Engineering, Catholic Kwandong University, Gangneung, Gangwon-do, 25601, South Korea
| | - Sangmin Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, South Korea
| | - Florian Bonkhofer
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Jordan Tolley
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Akihito Fukudome
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yukihiro Nagashima
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Kimberly May
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Stephan Rips
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Sang Y Lee
- Division of Applied Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Patrick Gallois
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester, M13 9PT, UK
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas-Medical Branch, Oxford Rd, Galveston, TX, 77555, USA
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, South Korea
| | - Antje von Schaewen
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149, Münster, Germany
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
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15
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Oikawa K, Inomata T, Hirao Y, Yamamoto T, Baslam M, Kaneko K, Mitsui T. Proteomic Analysis of Rice Golgi Membranes Isolated by Floating Through Discontinuous Sucrose Density Gradient. Methods Mol Biol 2018; 1696:91-105. [PMID: 29086398 DOI: 10.1007/978-1-4939-7411-5_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Golgi apparatus is an endomembrane system organelle and has roles in glycosylation, sorting, and secretion of proteins in the secretory pathway. It has a central function in living organism and is also essential for plant growth. Proteomic approaches to identify the Golgi membrane proteins have been performed in cell suspension cultures and many Golgi membrane-associated proteins were found, whereas it has well established in rice seedling yet. In this chapter, our recent improving published methods for isolated rice Golgi membranes by floating through a discontinuous sucrose density gradient are provided in detail with proteomic analyses.
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Affiliation(s)
- Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Marouane Baslam
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Kentaro Kaneko
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan.
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan.
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16
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Bu TT, Shen J, Chao Q, Shen Z, Yan Z, Zheng HY, Wang BC. Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using Concanavalin A lectin affinity chromatography and a nano-LC-MS/MS-based iTRAQ approach. PLANT CELL REPORTS 2017; 36:1943-1958. [PMID: 28942497 DOI: 10.1007/s00299-017-2209-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
The identification of N -glycosylated proteins with information about changes in the level of N -glycosylation during de-etiolation provides a database that will aid further research on plant N -glycosylation and de-etiolation. N-glycosylation is one of the most prominent and abundant protein post-translational modifications in all eukaryotes and in plants it plays important roles in development, stress tolerance and immune responses. Because light-induced de-etiolation is one of the most dramatic developmental processes known in plants, seedlings undergoing de-etiolation are an excellent model for investigating dynamic proteomic profiles. Here, we present a comprehensive, quantitative N-glycoproteomic profile of maize seedlings undergoing 12 h of de-etiolation obtained using Concanavalin A (Con A) lectin affinity chromatography enrichment coupled with a nano-LC-MS/MS-based iTRAQ approach. In total, 1084 unique N-glycopeptides carrying 909 N-glycosylation sites and corresponding to 609 proteins were identified and quantified, including 186 N-glycosylation sites from 162 proteins that were significantly regulated over the course of the 12 h de-etiolation period. Based on hierarchical clustering analysis, the significantly regulated N-glycopeptides were divided into seven clusters that showed different N-glycosylation patterns during de-etiolation. We found no obvious difference in the enriched MapMan bincode categories for each cluster, and these clustered significantly regulated N-glycoproteins (SRNPs) are enriched in miscellaneous, protein, cell wall and signaling, indicating that although the N-glycosylation regulation patterns of these SRNPs might differ, they are involved in similar biological processes. Overall, this study represents the first large-scale quantitative N-glycoproteome of the model C4 plant, maize, which is one of the most important cereal and biofuel crops. Our results greatly expand the maize N-glycoproteomic database and also shed light on the potential roles of N-glycosylation modification during the greening of maize leaves.
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Affiliation(s)
- Tian-Tian Bu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Shen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qing Chao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhuo Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Yan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Yan Zheng
- Center for Advanced Biotechnology and Medicine, Robert-Wood Johnson Medical School-Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Bai-Chen Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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17
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Hartings S, Paradies S, Karnuth B, Eisfeld S, Mehsing J, Wolff C, Levey T, Westhoff P, Meierhoff K. The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants. PLANT PHYSIOLOGY 2017; 174:1807-1824. [PMID: 28572458 PMCID: PMC5490910 DOI: 10.1104/pp.17.00401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/31/2017] [Indexed: 05/22/2023]
Abstract
To understand the biogenesis of the thylakoid membrane in higher plants and to identify auxiliary proteins required to build up this highly complex membrane system, we have characterized the allelic nuclear mutants high chlorophyll fluorescence222-1 (hcf222-1) and hcf222-2 and isolated the causal gene by map-based cloning. In the ethyl methanesulfonate-induced mutant hcf222-1, the accumulation of the cytochrome b6f (Cytb6f) complex was reduced to 30% compared with the wild type. Other thylakoid membrane complexes accumulated to normal levels. The T-DNA knockout mutant hcf222-2 showed a more severe defect with respect to thylakoid membrane proteins and accumulated only 10% of the Cytb6f complex, accompanied by a reduction in photosystem II, the photosystem II light-harvesting complex, and photosystem I. HCF222 encodes a protein of 99 amino acids in Arabidopsis (Arabidopsis thaliana) that has similarities to the cysteine-rich zinc-binding domain of DnaJ chaperones. The insulin precipitation assay demonstrated that HCF222 has disulfide reductase activity in vitro. The protein is conserved in higher plants and bryophytes but absent in algae and cyanobacteria. Confocal fluorescence microscopy showed that a fraction of HCF222-green fluorescent protein was detectable in the endoplasmic reticulum but that it also could be recognized in chloroplasts. A fusion construct of HCF222 containing a plastid transit peptide targets the protein into chloroplasts and was able to complement the mutational defect. These findings indicate that the chloroplast-targeted HCF222 is indispensable for the maturation and/or assembly of the Cytb6f complex and is very likely involved in thiol-disulfide biochemistry at the thylakoid membrane.
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Affiliation(s)
- Stephanie Hartings
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Susanne Paradies
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Bianca Karnuth
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Sabrina Eisfeld
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Jasmin Mehsing
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Christian Wolff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Tatjana Levey
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Peter Westhoff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Karin Meierhoff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
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18
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Floryszak-Wieczorek J, Arasimowicz-Jelonek M. The multifunctional face of plant carbonic anhydrase. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 112:362-368. [PMID: 28152407 DOI: 10.1016/j.plaphy.2017.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
Although most studies on the ubiquitous enzyme carbonic anhydrase (CA) have indicated its significant role in plants to facilitate the diffusion of CO2 to the site of inorganic carbon fixation, it is becoming increasingly likely that carbonic anhydrase isoforms also have diverse unexplored functions in plant cells. This review lays emphasis on additional roles of CA associated with many physiological, biochemical and structural changes in plant metabolism. The presented findings have revealed essential functions of CA isoforms in plant adjustment to both abiotic and biotic agents and developmental stimuli. However, sometimes it is difficult to separate the non-photosynthetic from the photosynthetic-related role of CAs during post-stress impaired metabolism, and the preventive CA outcome might be due to the effect of these enzymes on improvement of photosynthetic capacity. Finally, taking into account the experimental evidence, the direct and indirect functional roles of CAs in mitigating negative effects of environmental conditions are presented.
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19
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Dixon DP, Van Ekeris L, Linser PJ. Characterization of Carbonic Anhydrase 9 in the Alimentary Canal of Aedes aegypti and Its Relationship to Homologous Mosquito Carbonic Anhydrases. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:E213. [PMID: 28230813 PMCID: PMC5334767 DOI: 10.3390/ijerph14020213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 01/22/2023]
Abstract
In the mosquito midgut, luminal pH regulation and cellular ion transport processes are important for the digestion of food and maintenance of cellular homeostasis. pH regulation in the mosquito gut is affected by the vectorial movement of the principal ions including bicarbonate/carbonate and protons. As in all metazoans, mosquitoes employ the product of aerobic metabolism carbon dioxide in its bicarbonate/carbonate form as one of the major buffers of cellular and extracellular pH. The conversion of metabolic carbon dioxide to bicarbonate/carbonate is accomplished by a family of enzymes encoded by the carbonic anhydrase gene family. This study characterizes Aedes aegypti carbonic anhydrases using bioinformatic, molecular, and immunohistochemical methods. Our analyses show that there are fourteen Aedes aegypti carbonic anhydrase genes, two of which are expressed as splice variants. The carbonic anhydrases were classified as either integral membrane, peripheral membrane, mitochondrial, secreted, or soluble cytoplasmic proteins. Using polymerase chain reaction and Western blotting, one of the carbonic anhydrases, Aedes aegypti carbonic anhydrase 9, was analyzed and found in each life stage, male/female pupae, male/female adults, and in the female posterior midgut. Next, carbonic anhydrase 9 was analyzed in larvae and adults using confocal microscopy and was detected in the midgut regions. According to our analyses, carbonic anhydrase 9 is a soluble cytoplasmic enzyme found in the alimentary canal of larvae and adults and is expressed throughout the life cycle of the mosquito. Based on previous physiological analyses of adults and larvae, it appears AeCA9 is one of the major carbonic anhydrases involved in producing bicarbonate/carbonate which is involved in pH regulation and ion transport processes in the alimentary canal. Detailed understanding of the molecular bases of ion homeostasis in mosquitoes will provide targets for novel mosquito control strategies into the new millennium.
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Affiliation(s)
- Daniel P Dixon
- The Whitney Laboratory, University of Florida, Saint Augustine, FL 32080, USA.
- The Anastasia Mosquito Control District, St. Augustine Florida, Saint Augustine, FL 32092, USA.
| | - Leslie Van Ekeris
- The Whitney Laboratory, University of Florida, Saint Augustine, FL 32080, USA.
| | - Paul J Linser
- The Whitney Laboratory, University of Florida, Saint Augustine, FL 32080, USA.
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20
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Durnford DG, Schwartzbach SD. Protein Targeting to the Plastid of Euglena. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:183-205. [PMID: 28429323 DOI: 10.1007/978-3-319-54910-1_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The lateral transfer of photosynthesis between kingdoms through endosymbiosis is among the most spectacular examples of evolutionary innovation. Euglena, which acquired a chloroplast indirectly through an endosymbiosis with a green alga, represents such an example. As with other endosymbiont-derived plastids from eukaryotes, there are additional membranes that surround the organelle, of which Euglena has three. Thus, photosynthetic genes that were transferred from the endosymbiont to the host nucleus and whose proteins are required in the new plastid, are now faced with targeting and plastid import challenges. Early immunoelectron microscopy data suggested that the light-harvesting complexes, photosynthetic proteins in the thylakoid membrane, are post-translationally targeted to the plastid via the Golgi apparatus, an unexpected discovery at the time. Proteins targeted to the Euglena plastid have complex, bipartite presequences that direct them into the endomembrane system, through the Golgi apparatus and ultimately on to the plastid, presumably via transport vesicles. From transcriptome sequencing, dozens of plastid-targeted proteins were identified, leading to the identification of two different presequence structures. Both have an amino terminal signal peptide followed by a transit peptide for plastid import, but only one of the two classes of presequences has a third domain-the stop transfer sequence. This discovery implied two different transport mechanisms; one where the protein was fully inserted into the lumen of the ER and another where the protein remains attached to, but effectively outside, the endomembrane system. In this review, we will discuss the biochemical and bioinformatic evidence for plastid targeting, discuss the evolution of the targeting system, and ultimately provide a working model for the targeting and import of proteins into the plastid of Euglena.
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Affiliation(s)
- Dion G Durnford
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, Canada, E3B 5A3
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21
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Maksimov V, Nakamura M, Wildhaber T, Nanni P, Ramström M, Bergquist J, Hennig L. The H3 chaperone function of NASP is conserved in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:425-436. [PMID: 27402088 DOI: 10.1111/tpj.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Histones are abundant cellular proteins but, if not incorporated into chromatin, they are usually bound by histone chaperones. Here, we identify Arabidopsis NASP as a chaperone for histones H3.1 and H3.3. NASP interacts in vitro with monomeric H3.1 and H3.3 as well as with histone H3.1-H4 and H3.3-H4 dimers. However, NASP does not bind to monomeric H4. NASP shifts the equilibrium between histone dimers and tetramers towards tetramers but does not interact with tetramers in vitro. Arabidopsis NASP promotes [H3-H4]2 tetrasome formation, possibly by providing preassembled histone tetramers. However, NASP does not promote disassembly of in vitro preassembled tetrasomes. In contrast to its mammalian homolog, Arabidopsis NASP is a predominantly nuclear protein. In vivo, NASP binds mainly monomeric H3.1 and H3.3. Pulldown experiments indicated that NASP may also interact with the histone chaperone MSI1 and a HSC70 heat shock protein.
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Affiliation(s)
- Vladimir Maksimov
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Thomas Wildhaber
- Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057, Zurich, Switzerland
| | - Margareta Ramström
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
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22
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Dąbrowska-Bronk J, Komar DN, Rusaczonek A, Kozłowska-Makulska A, Szechyńska-Hebda M, Karpiński S. β-carbonic anhydrases and carbonic ions uptake positively influence Arabidopsis photosynthesis, oxidative stress tolerance and growth in light dependent manner. JOURNAL OF PLANT PHYSIOLOGY 2016; 203:44-54. [PMID: 27316917 DOI: 10.1016/j.jplph.2016.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 06/06/2023]
Abstract
Carbonic anhydrases (CAs) catalyse reversible interconversion of CO2 and water into bicarbonate and protons and regulate concentration of CO2 around photosynthetic enzymes. In higher plants the CAs are divided into three distinct classes α, β and γ, with members off each of them being involved in CO2 uptake, fixation or recycling. The most abundant group is βCAs. In C4 plants they are localized in the cytosol of mesophyll cells and catalyse first step of carbon concentration pathway. C3 plants contain orthologues genes encoding βCAs's, however their functions are unknown. Given the importance of βCAs in the present study we analysed the effect of carbonic ions, selected orthologues βCAs's gene expression and βCAs enzymatic activity on Arabidopsis photosynthesis, growth and cell death in different light conditions. Plants fertilised with 0.5-3mM sodium bicarbonate had a significantly increased number of leaves, improved fresh and dry weight and reduced cell death (cellular ion leakage). This effect was dependent on provided photon flux density and photoperiod. Higher content of carbonic ions also stimulated photoprotective mechanisms such as non-photochemical quenching and foliar content of photoprotective pigments (neoxanthin, violaxanthin and carotenes). Function of various βCAs genes examined in null βcas mutants showed to be complementary and additive, and confirm results of fertilizing experiments. Taken together, regulation of βCAs gene expression and enzymatic activities are important for optimal plant growth and probably can be one of the factor influencing a switch between C3 and C4 photosynthesis mode in variable light conditions. Therefore, biotechnological amelioration of βCAs activity in economically important plants and their fertilisation with carbonic ions may lead to improved photosynthetic efficiency and further crop productivity.
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Affiliation(s)
- Joanna Dąbrowska-Bronk
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Dorota Natalia Komar
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Anna Rusaczonek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Anna Kozłowska-Makulska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Magdalena Szechyńska-Hebda
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland.
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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23
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Baslam M, Oikawa K, Kitajima-Koga A, Kaneko K, Mitsui T. Golgi-to-plastid trafficking of proteins through secretory pathway: Insights into vesicle-mediated import toward the plastids. PLANT SIGNALING & BEHAVIOR 2016; 11:e1221558. [PMID: 27700755 PMCID: PMC5058459 DOI: 10.1080/15592324.2016.1221558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/31/2016] [Accepted: 08/01/2016] [Indexed: 05/22/2023]
Abstract
The diversity of protein targeting pathways to plastids and their regulation in response to developmental and metabolic status is a key issue in the regulation of cellular function in plants. The general import pathways that target proteins into and across the plastid envelope with changes in gene expression are critical for plant development by regulating the response to physiological and metabolic changes within the cell. Glycoprotein targeting to complex plastids involves routing through the secretory pathway, among others. However, the mechanisms of trafficking via this system remain poorly understood. The present article discusses our results in site-specific N-glycosylation of nucleotide pyrophosphatase/phosphodiesterases (NPPs) glycoproteins and highlights protein delivery in Golgi/plastid pathway via the secretory pathway. Furthermore, we outline the hypotheses that explain the mechanism for importing vesicles trafficking with nucleus-encoded proteins into plastids.
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Affiliation(s)
- Marouane Baslam
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Aya Kitajima-Koga
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
- CONTACT Toshiaki Mitsui Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 9502181, R3T 2N2 Japan
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24
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Trotta A, Suorsa M, Rantala M, Lundin B, Aro EM. Serine and threonine residues of plant STN7 kinase are differentially phosphorylated upon changing light conditions and specifically influence the activity and stability of the kinase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:484-94. [PMID: 27214592 DOI: 10.1111/tpj.13213] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 05/22/2023]
Abstract
STN7 kinase catalyzes the phosphorylation of the globally most common membrane proteins, the light-harvesting complex II (LHCII) in plant chloroplasts. STN7 itself possesses one serine (Ser) and two threonine (Thr) phosphosites. We show that phosphorylation of the Thr residues protects STN7 against degradation in darkness, low light and red light, whereas increasing light intensity and far red illumination decrease phosphorylation and induce STN7 degradation. Ser phosphorylation, in turn, occurs under red and low intensity white light, coinciding with the client protein (LHCII) phosphorylation. Through analysis of the counteracting LHCII phosphatase mutant tap38/pph1, we show that Ser phosphorylation and activation of the STN7 kinase for subsequent LHCII phosphorylation are heavily affected by pre-illumination conditions. Transitions between the three activity states of the STN7 kinase (deactivated in darkness and far red light, activated in low and red light, inhibited in high light) are shown to modulate the phosphorylation of the STN7 Ser and Thr residues independently of each other. Such dynamic regulation of STN7 kinase phosphorylation is crucial for plant growth and environmental acclimation.
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Affiliation(s)
- Andrea Trotta
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20520, Finland
| | - Marjaana Suorsa
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20520, Finland
| | - Marjaana Rantala
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20520, Finland
| | - Björn Lundin
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20520, Finland.
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25
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Kaneko K, Takamatsu T, Inomata T, Oikawa K, Itoh K, Hirose K, Amano M, Nishimura SI, Toyooka K, Matsuoka K, Pozueta-Romero J, Mitsui T. N-Glycomic and Microscopic Subcellular Localization Analyses of NPP1, 2 and 6 Strongly Indicate that trans-Golgi Compartments Participate in the Golgi to Plastid Traffic of Nucleotide Pyrophosphatase/Phosphodiesterases in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:1610-28. [PMID: 27335351 PMCID: PMC4970613 DOI: 10.1093/pcp/pcw089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/26/2016] [Indexed: 05/02/2023]
Abstract
Nucleotide pyrophosphatase/phosphodiesterases (NPPs) are widely distributed N-glycosylated enzymes that catalyze the hydrolytic breakdown of numerous nucleotides and nucleotide sugars. In many plant species, NPPs are encoded by a small multigene family, which in rice are referred to NPP1-NPP6 Although recent investigations showed that N-glycosylated NPP1 is transported from the endoplasmic reticulum (ER)-Golgi system to the chloroplast through the secretory pathway in rice cells, information on N-glycan composition and subcellular localization of other NPPs is still lacking. Computer-assisted analyses of the amino acid sequences deduced from different Oryza sativa NPP-encoding cDNAs predicted all NPPs to be secretory glycoproteins. Confocal fluorescence microscopy observation of cells expressing NPP2 and NPP6 fused with green fluorescent protein (GFP) revealed that NPP2 and NPP6 are plastidial proteins. Plastid targeting of NPP2-GFP and NPP6-GFP was prevented by brefeldin A and by the expression of ARF1(Q71L), a dominant negative mutant of ADP-ribosylation factor 1 that arrests the ER to Golgi traffic, indicating that NPP2 and NPP6 are transported from the ER-Golgi to the plastidial compartment. Confocal laser scanning microscopy and high-pressure frozen/freeze-substituted electron microscopy analyses of transgenic rice cells ectopically expressing the trans-Golgi marker sialyltransferase fused with GFP showed the occurrence of contact of Golgi-derived membrane vesicles with cargo and subsequent absorption into plastids. Sensitive and high-throughput glycoblotting/mass spectrometric analyses showed that complex-type and paucimannosidic-type glycans with fucose and xylose residues occupy approximately 80% of total glycans of NPP1, NPP2 and NPP6. The overall data strongly indicate that the trans-Golgi compartments participate in the Golgi to plastid trafficking and targeting mechanism of NPPs.
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Affiliation(s)
- Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Takeshi Takamatsu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Kimiko Itoh
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Kazuko Hirose
- Graduate School of Advanced Life Science, Frontier Research Center for Post-genomic Science and Technology, Hokkaido University, Sapporo, 001-0021 Japan
| | - Maho Amano
- Graduate School of Advanced Life Science, Frontier Research Center for Post-genomic Science and Technology, Hokkaido University, Sapporo, 001-0021 Japan
| | - Shin-Ichiro Nishimura
- Graduate School of Advanced Life Science, Frontier Research Center for Post-genomic Science and Technology, Hokkaido University, Sapporo, 001-0021 Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Kanagawa, 230-0045 Japan
| | - Ken Matsuoka
- Laboratory of Plant Nutrition, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Mutiloako etorbidea zenbaki gabe, 31192 Mutiloabeti, Nafarroa, Spain
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
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26
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Horiuchi R, Hirotsu N, Miyanishi N. N-glycan transition of the early developmental stage in Oryza sativa. Biochem Biophys Res Commun 2016; 477:426-32. [DOI: 10.1016/j.bbrc.2016.06.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
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27
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Meyer MT, McCormick AJ, Griffiths H. Will an algal CO2-concentrating mechanism work in higher plants? CURRENT OPINION IN PLANT BIOLOGY 2016; 31:181-8. [PMID: 27194106 DOI: 10.1016/j.pbi.2016.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/17/2016] [Accepted: 04/21/2016] [Indexed: 05/19/2023]
Abstract
Many algae use a biophysical carbon concentrating mechanism for active accumulation and retention of inorganic carbon within chloroplasts, with CO2 fixation by RuBisCO within a micro-compartment, the pyrenoid. Engineering such mechanisms into higher plant chloroplasts is a possible route to augment RuBisCO operating efficiency and photosynthetic rates. Significant progress has been made recently in characterising key algal transporters and identifying factors responsible for the aggregation of RuBisCO into the pyrenoid. Several transporters have now also been successfully incorporated into higher plant chloroplasts. Consistent with the predictions from modelling, regulation of higher plant plastidic carbonic anhydrases and some form of RuBisCO aggregation will be needed before the mechanism delivers potential benefits. Key research priorities include a better understanding of the regulation of the algal carbon concentrating mechanism, advancing the fundamental characterisation of known components, evaluating whether higher plant chloroplasts can accommodate a pyrenoid, and, ultimately, testing transgenic lines under realistic growth conditions.
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Affiliation(s)
- Moritz T Meyer
- Department of Plant Sciences, University of Cambridge, CB2 3EA, UK
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, CB2 3EA, UK.
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28
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DiMario RJ, Quebedeaux JC, Longstreth DJ, Dassanayake M, Hartman MM, Moroney JV. The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO2. PLANT PHYSIOLOGY 2016; 171:280-93. [PMID: 26993617 PMCID: PMC4854698 DOI: 10.1104/pp.15.01990] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/16/2016] [Indexed: 05/23/2023]
Abstract
Carbonic anhydrases (CAs) are zinc metalloenzymes that interconvert CO2 and HCO3 (-) In plants, both α- and β-type CAs are present. We hypothesize that cytoplasmic βCAs are required to modulate inorganic carbon forms needed in leaf cells for carbon-requiring reactions such as photosynthesis and amino acid biosynthesis. In this report, we present evidence that βCA2 and βCA4 are the two most abundant cytoplasmic CAs in Arabidopsis (Arabidopsis thaliana) leaves. Previously, βCA4 was reported to be localized to the plasma membrane, but here, we show that two forms of βCA4 are expressed in a tissue-specific manner and that the two proteins encoded by βCA4 localize to two different regions of the cell. Comparing transfer DNA knockout lines with wild-type plants, there was no reduction in the growth rates of the single mutants, βca2 and βca4 However, the growth rate of the double mutant, βca2βca4, was reduced significantly when grown at 200 μL L(-1) CO2 The reduction in growth of the double mutant was not linked to a reduction in photosynthetic rate. The amino acid content of leaves from the double mutant showed marked reduction in aspartate when compared with the wild type and the single mutants. This suggests the cytoplasmic CAs play an important but not previously appreciated role in amino acid biosynthesis.
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Affiliation(s)
- Robert J DiMario
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Jennifer C Quebedeaux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - David J Longstreth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - Monica M Hartman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808
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29
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Shiraya T, Mori T, Maruyama T, Sasaki M, Takamatsu T, Oikawa K, Itoh K, Kaneko K, Ichikawa H, Mitsui T. Golgi/plastid-type manganese superoxide dismutase involved in heat-stress tolerance during grain filling of rice. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:1251-63. [PMID: 25586098 PMCID: PMC6680209 DOI: 10.1111/pbi.12314] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/19/2014] [Indexed: 05/20/2023]
Abstract
Superoxide dismutase (SOD) is widely assumed to play a role in the detoxification of reactive oxygen species caused by environmental stresses. We found a characteristic expression of manganese SOD 1 (MSD1) in a heat-stress-tolerant cultivar of rice (Oryza sativa). The deduced amino acid sequence contains a signal sequence and an N-glycosylation site. Confocal imaging analysis of rice and onion cells transiently expressing MSD1-YFP showed MSD1-YFP in the Golgi apparatus and plastids, indicating that MSD1 is a unique Golgi/plastid-type SOD. To evaluate the involvement of MSD1 in heat-stress tolerance, we generated transgenic rice plants with either constitutive high expression or suppression of MSD1. The grain quality of rice with constitutive high expression of MSD1 grown at 33/28 °C, 12/12 h, was significantly better than that of the wild type. In contrast, MSD1-knock-down rice was markedly susceptible to heat stress. Quantitative shotgun proteomic analysis indicated that the overexpression of MSD1 up-regulated reactive oxygen scavenging, chaperone and quality control systems in rice grains under heat stress. We propose that the Golgi/plastid MSD1 plays an important role in adaptation to heat stress.
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Affiliation(s)
- Takeshi Shiraya
- Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Taiki Mori
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Tatsuya Maruyama
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Maiko Sasaki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Takeshi Takamatsu
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Kimiko Itoh
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Kentaro Kaneko
- Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
| | - Hiroaki Ichikawa
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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30
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Lannoo N, Van Damme EJM. Review/N-glycans: The making of a varied toolbox. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:67-83. [PMID: 26398792 DOI: 10.1016/j.plantsci.2015.06.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 05/23/2023]
Abstract
Asparagine (N)-linked protein glycosylation is one of the most crucial, prevalent, and complex co- and post-translational protein modifications. It plays a pivotal role in protein folding, quality control, and endoplasmic reticulum (ER)-associated degradation (ERAD) as well as in protein sorting, protein function, and in signal transduction. Furthermore, glycosylation modulates many important biological processes including growth, development, morphogenesis, and stress signaling processes. As a consequence, aberrant or altered N-glycosylation is often associated with reduced fitness, diseases, and disorders. The initial steps of N-glycan synthesis at the cytosolic side of the ER membrane and in the lumen of the ER are highly conserved. In contrast, the final N-glycan processing in the Golgi apparatus is organism-specific giving rise to a wide variety of carbohydrate structures. Despite our vast knowledge on N-glycans in yeast and mammals, the modus operandi of N-glycan signaling in plants is still largely unknown. This review will elaborate on the N-glycosylation biosynthesis pathway in plants but will also critically assess how N-glycans are involved in different signaling cascades, either active during normal development or upon abiotic and biotic stresses.
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Affiliation(s)
- Nausicaä Lannoo
- Lab Biochemistry and Glycobiology, Department Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Els J M Van Damme
- Lab Biochemistry and Glycobiology, Department Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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31
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Lehtimäki N, Koskela MM, Mulo P. Posttranslational Modifications of Chloroplast Proteins: An Emerging Field. PLANT PHYSIOLOGY 2015; 168:768-75. [PMID: 25911530 PMCID: PMC4741338 DOI: 10.1104/pp.15.00117] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/29/2015] [Indexed: 05/19/2023]
Abstract
Posttranslational modifications of proteins are key effectors of enzyme activity, protein interactions, targeting, and turnover rate, but despite their importance, they are still poorly understood in plants. Although numerous reports have revealed the regulatory role of protein phosphorylation in photosynthesis, various other protein modifications have been identified in chloroplasts only recently. It is known that posttranslational N(α)-acetylation occurs in both nuclear- and plastid-encoded chloroplast proteins, but the physiological significance of this acetylation is not yet understood. Lysine acetylation affects the localization and activity of key metabolic enzymes, and it may work antagonistically or cooperatively with lysine methylation, which also occurs in chloroplasts. In addition, tyrosine nitration may help regulate the repair cycle of photosystem II, while N-glycosylation determines enzyme activity of chloroplastic carbonic anhydrase. This review summarizes the progress in the research field of posttranslational modifications of chloroplast proteins and points out the importance of these modifications in the regulation of chloroplast metabolism.
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Affiliation(s)
- Nina Lehtimäki
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Minna M Koskela
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Paula Mulo
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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32
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Liu H, Yang Q, Fan C, Zhao X, Wang X, Zhou Y. Transcriptomic basis of functional difference and coordination between seeds and the silique wall of Brassica napus during the seed-filling stage. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:186-199. [PMID: 25711826 DOI: 10.1016/j.plantsci.2015.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
The silique of oilseed rape (Brassica napus) is a composite organ including seeds and the silique wall (SW) that possesses distinctly physiological, biochemical and functional differentiations. Yet, the molecular events controlling such differences between the SW and seeds, as well as their coordination during silique development at transcriptional level are largely unknown. Here, we identified large sets of differentially expressed genes in the SW and seeds of siliques at 21-22 days after flowering with a Brassica 95K EST microarray. At this particular stage, there were 3278 SW preferentially expressed genes and 2425 seed preferentially expressed genes. Using the MapMan visualization software, genes differentially regulated in various metabolic pathways and sub-pathways between the SW and seeds were revealed. Photosynthesis and transport-related genes were more actively transcripted in the SW, while those involved in lipid metabolism were more active in seeds during the seed filling stage. On the other hand, genes involved in secondary metabolisms were selectively regulated in the SW and seeds. Large numbers of transcription factors were identified to be differentially expressed between the SW and seeds, suggesting a complex pattern of transcriptional control in these two organs. Furthermore, most genes discussed in categories or pathways showed a similar expression pattern through 21 DAF to 42 DAF. Our results thus provide insights into the coordination of seeds and the SW in the developing silique at the transcriptional levels, which will facilitate the functional studies of important genes for improving B. napus seed productivity and quality.
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Affiliation(s)
- Han Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoqin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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33
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Benlloch R, Shevela D, Hainzl T, Grundström C, Shutova T, Messinger J, Samuelsson G, Sauer-Eriksson AE. Crystal structure and functional characterization of photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2015; 167:950-62. [PMID: 25617045 PMCID: PMC4348767 DOI: 10.1104/pp.114.253591] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/16/2015] [Indexed: 05/22/2023]
Abstract
In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates. The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place in photosystem II (PSII). Recent studies show that in higher plants, HCO3 (-) increases PSII activity by acting as a mobile acceptor of the protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested to improve proton removal from PSII, possibly by rapid reformation of HCO3 (-) from CO2. In this study, we investigated the interplay between PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometry measurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen under illumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and 2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature not previously observed in α-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 function with dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3 (-) on PSII activity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSII preparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at low pH and CO2 concentration.
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Affiliation(s)
- Reyes Benlloch
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Dmitriy Shevela
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Tobias Hainzl
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Christin Grundström
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Tatyana Shutova
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Johannes Messinger
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - Göran Samuelsson
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
| | - A Elisabeth Sauer-Eriksson
- Department of Forest Genetics and Plant Physiology (R.B) and Department of Plant Physiology (T.S., G.S.), Umeå Plant Science Centre, and Department of Chemistry, Chemistry Biology Centre (D.S., T.H., C.G., J.M., A.E.S.-E.), Umeå University, SE-90187 Umea, Sweden
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34
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Bajsa J, Pan Z, Duke SO. Cantharidin, a protein phosphatase inhibitor, strongly upregulates detoxification enzymes in the Arabidopsis proteome. JOURNAL OF PLANT PHYSIOLOGY 2015; 173:33-40. [PMID: 25462076 DOI: 10.1016/j.jplph.2014.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/19/2014] [Accepted: 09/07/2014] [Indexed: 06/04/2023]
Abstract
Cantharidin, a potent inhibitor of plant serine/threonine protein phosphatases (PPPs), is highly phytotoxic and dramatically affects the transcriptome in Arabidopsis. To investigate the effect of cantharidin on the Arabidopsis proteome, a combination of two-dimensional difference gel electrophoresis (2-D DIGE) and matrix-assisted laser desorption ionization time-of-flight (MALDI/TOF) mass spectrometry was employed for protein profiling. Multivariate statistical analysis identified 75 significant differential spots corresponding to 59 distinct cantharidin-responsive proteins, which were representative of different biological processes, cellular components, and molecular functions categories. The majority of identified proteins localized in the chloroplast had a significantly decreased presence, especially proteins involved in photosynthesis. Detoxification enzymes, especially glutathione-S-transferases (GSTs), were the most upregulated group (ca. 1.5- to 3.3-fold). Given that the primary role of GSTs is involved in the process of detoxification of both xenobiotic and endobiotic compounds, the induction of GSTs suggests that cantharidin promoted inhibition of PPPs may lead to defense-like responses through regulation of GST enzymes as well as other metabolic pathways.
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Affiliation(s)
- Joanna Bajsa
- USDA, ARS, Natural Products Utilization Research Unit, Cochran Research Center, University, MS 38677, USA
| | - Zhiqiang Pan
- USDA, ARS, Natural Products Utilization Research Unit, Cochran Research Center, University, MS 38677, USA
| | - Stephen O Duke
- USDA, ARS, Natural Products Utilization Research Unit, Cochran Research Center, University, MS 38677, USA.
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35
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Shen J, Ding Y, Gao C, Rojo E, Jiang L. N-linked glycosylation of AtVSR1 is important for vacuolar protein sorting in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:977-92. [PMID: 25293377 DOI: 10.1111/tpj.12696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 05/18/2023]
Abstract
Vacuolar sorting receptors (VSRs) in Arabidopsis mediate the sorting of soluble proteins to vacuoles in the secretory pathway. The VSRs are post-translationally modified by the attachment of N-glycans, but the functional significance of such a modification remains unknown. Here we have studied the role(s) of glycosylation in the stability, trafficking and vacuolar protein transport of AtVSR1 in Arabidopsis protoplasts. AtVSR1 harbors three complex-type N-glycans, which are located in the N-terminal 'PA domain', the central region and the C-terminal epidermal growth factor repeat domain, respectively. We have demonstrated that: (i) the N-glycans do not affect the targeting of AtVSR1 to pre-vacuolar compartments (PVCs) and its vacuolar degradation; and (ii) N-glycosylation alters the binding affinity of AtVSR1 to cargo proteins and affects the transport of cargo into the vacuole. Hence, N-glycosylation of AtVSR1 plays a critical role in its function as a VSR in plants.
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Affiliation(s)
- Jinbo Shen
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Tian L, Okita TW. mRNA-based protein targeting to the endoplasmic reticulum and chloroplasts in plant cells. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:77-85. [PMID: 25282588 DOI: 10.1016/j.pbi.2014.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 09/15/2014] [Indexed: 05/12/2023]
Abstract
The targeting of proteins to subcellular organelles is specified by the presence of signal/leader peptide sequences normally located on the N-terminus. In the past two decades, messenger RNA (mRNA) localization, a pathway driven by cis-acting localization elements within the RNA sequence, has emerged as an alternative mechanism for protein targeting to specific locations in the cytoplasm, on the endoplasmic reticulum or to mitochondria and chloroplasts. In this review, we will summarize studies on mRNA-based protein targeting to the endoplasmic reticulum and chloroplast within plant cells.
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Affiliation(s)
- Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
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Heiny SR, Pautz S, Recker M, Przyborski JM. Protein Traffic to thePlasmodium falciparumApicoplast: Evidence for a Sorting Branch Point at the Golgi. Traffic 2014; 15:1290-304. [DOI: 10.1111/tra.12226] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 09/08/2014] [Accepted: 09/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Sabrina R. Heiny
- Parasitology, FB Biology, Philipps University Marburg; Karl von Frisch Straße 8; 35043 Marburg Germany
| | - Sabine Pautz
- Parasitology, FB Biology, Philipps University Marburg; Karl von Frisch Straße 8; 35043 Marburg Germany
| | - Mario Recker
- College of Engineering, Mathematics and Physical Sciences; University of Exeter; North Park Road Exeter UK
| | - Jude M. Przyborski
- Parasitology, FB Biology, Philipps University Marburg; Karl von Frisch Straße 8; 35043 Marburg Germany
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Spijkerman E, Stojkovic S, Beardall J. CO2 acquisition in Chlamydomonas acidophila is influenced mainly by CO2, not phosphorus, availability. PHOTOSYNTHESIS RESEARCH 2014; 121:213-221. [PMID: 24906887 DOI: 10.1007/s11120-014-0016-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 05/19/2014] [Indexed: 06/03/2023]
Abstract
The extremophilic green microalga Chlamydomonas acidophila grows in very acidic waters (pH 2.3-3.4), where CO2 is the sole inorganic carbon source. Previous work has revealed that the species can accumulate inorganic carbon (Ci) and exhibits high affinity CO2 utilization under low-CO2 (air-equilibrium) conditions, similar to organisms with an active CO2 concentrating mechanism (CCM), whereas both processes are down-regulated under high CO2 (4.5 % CO2) conditions. Responses of this species to phosphorus (Pi)-limited conditions suggested a contrasting regulation of the CCM characteristics. Therefore, we measured external carbonic anhydrase (CAext) activities and protein expression (CAH1), the internal pH, Ci accumulation, and CO2-utilization in cells adapted to high or low CO2 under Pi-replete and Pi-limited conditions. Results reveal that C. acidophila expressed CAext activity and expressed a protein cross-reacting with CAH1 (the CAext from Chlamydomonas reinhardtii). Although the function of this CA remains unclear, CAext activity and high affinity CO2 utilization were the highest under low CO2 conditions. C. acidophila accumulated Ci and expressed the CAH1 protein under all conditions tested, and C. reinhardtii also contained substantial amounts of CAH1 protein under Pi-limitation. In conclusion, Ci utilization is optimized in C. acidophila under ecologically relevant conditions, which may enable optimal survival in its extreme Ci- and Pi-limited habitat. The exact physiological and biochemical acclimation remains to be further studied.
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Affiliation(s)
- Elly Spijkerman
- Universität Potsdam, Am Neuen Palais 10, 14469, Potsdam, Germany,
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Bushey DF, Bannon GA, Delaney BF, Graser G, Hefford M, Jiang X, Lee TC, Madduri KM, Pariza M, Privalle LS, Ranjan R, Saab-Rincon G, Schafer BW, Thelen JJ, Zhang JX, Harper MS. Characteristics and safety assessment of intractable proteins in genetically modified crops. Regul Toxicol Pharmacol 2014; 69:154-70. [DOI: 10.1016/j.yrtph.2014.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/07/2014] [Accepted: 03/15/2014] [Indexed: 10/25/2022]
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Lehneck R, Elleuche S, Pöggeler S. The filamentous ascomyceteSordaria macrosporacan survive in ambient air without carbonic anhydrases. Mol Microbiol 2014; 92:931-44. [DOI: 10.1111/mmi.12607] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Ronny Lehneck
- Institute of Microbiology and Genetics; Department of Genetics of Eukaryotic Microorganisms; Georg-August-University Göttingen; Göttingen Germany
| | - Skander Elleuche
- Institute of Technical Microbiology; Hamburg University of Technology; Hamburg Germany
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics; Department of Genetics of Eukaryotic Microorganisms; Georg-August-University Göttingen; Göttingen Germany
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Shaurya A, Dubicki KI, Hof F. Chemical agents for binding post-translationally methylated lysines and arginines. Supramol Chem 2014. [DOI: 10.1080/10610278.2013.872786] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Alok Shaurya
- Department of Chemistry, University of Victoria, Victoria, BC, Canada V8W3V6
| | - Krystyn I. Dubicki
- Department of Chemistry, University of Victoria, Victoria, BC, Canada V8W3V6
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, BC, Canada V8W3V6
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Ruiz-May E, Hucko S, Howe KJ, Zhang S, Sherwood RW, Thannhauser TW, Rose JKC. A comparative study of lectin affinity based plant N-glycoproteome profiling using tomato fruit as a model. Mol Cell Proteomics 2014; 13:566-79. [PMID: 24198434 PMCID: PMC3916654 DOI: 10.1074/mcp.m113.028969] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 10/20/2013] [Indexed: 12/22/2022] Open
Abstract
Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be determined whether certain lectins, or combinations of lectins are optimal for plant N-glycoproteome profiling; or whether specific lectins show preferential association with particular N-glycosylation sites or N-glycan structures. We describe here a comparative study of three mannose-binding lectins, concanavalin A, snowdrop lectin, and lentil lectin, to profile the N-glycoproteome of mature green stage tomato (Solanum lycopersicum) fruit pericarp. Through coupling lectin affinity chromatography with a shotgun proteomics strategy, we identified 448 putative N-glycoproteins, whereas a parallel lectin affinity chromatography plus hydrophilic interaction chromatography analysis revealed 318 putative N-glycosylation sites on 230 N-glycoproteins, of which 100 overlapped with the shotgun analysis, as well as 17 N-glycan structures. The use of multiple lectins substantially increased N-glycoproteome coverage and although there were no discernible differences in the structures of N-glycans, or the charge, isoelectric point (pI) or hydrophobicity of the glycopeptides that differentially bound to each lectin, differences were observed in the amino acid frequency at the -1 and +1 subsites of the N-glycosylation sites. We also demonstrated an alternative and complementary in planta recombinant expression strategy, followed by affinity MS analysis, to identify the putative N-glycan structures of glycoproteins whose abundance is too low to be readily determined by a shotgun approach, and/or combined with deglycosylation for predicted deamidated sites, using a xyloglucan-specific endoglucanase inhibitor protein as an example.
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Affiliation(s)
- Eliel Ruiz-May
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
| | - Simon Hucko
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Kevin J. Howe
- §USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Sheng Zhang
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | - Robert W. Sherwood
- ¶Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Ithaca, New York 14853
| | | | - Jocelyn K. C. Rose
- From the ‡Department of Plant Biology, Cornell University, Ithaca, New York 14853
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Kaneko K, Inomata T, Masui T, Koshu T, Umezawa Y, Itoh K, Pozueta-Romero J, Mitsui T. Nucleotide pyrophosphatase/phosphodiesterase 1 exerts a negative effect on starch accumulation and growth in rice seedlings under high temperature and CO2 concentration conditions. PLANT & CELL PHYSIOLOGY 2014; 55:320-32. [PMID: 24092883 PMCID: PMC3913438 DOI: 10.1093/pcp/pct139] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleotide pyrophosphatase/phosphodiesterase (NPP) is a widely distributed enzymatic activity occurring in both plants and mammals that catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides. Unlike mammalian NPPs, the physiological function of plant NPPs remains largely unknown. Using a complete rice NPP1-encoding cDNA as a probe, in this work we have screened a rice shoot cDNA library and obtained complete cDNAs corresponding to six NPP genes (NPP1-NPP6). As a first step to clarify the role of NPPs, recombinant NPP1, NPP2 and NPP6 were purified from transgenic rice cells constitutively expressing NPP1, NPP2 and NPP6, respectively, and their enzymatic properties were characterized. NPP1 and NPP6 exhibited hydrolytic activities toward ATP, UDP-glucose and the starch precursor molecule, ADP-glucose, whereas NPP2 did not recognize nucleotide sugars as substrates, but hydrolyzed UDP, ADP and adenosine 5'-phosphosulfate. To gain insight into the physiological function of rice NPP1, an npp1 knockout mutant was characterized. The ADP-glucose hydrolytic activities in shoots of npp1 rice seedlings were 8% of those of the wild type (WT), thus indicating that NPP1 is a major determinant of ADP-glucose hydrolytic activity in rice shoots. Importantly, when seedlings were cultured at 160 Pa CO2 under a 28°C/23°C (12 h light/12 h dark) regime, npp1 shoots and roots were larger than those of wild-type (WT) seedlings. Furthermore, the starch content in the npp1 shoots was higher than that of WT shoots. Growth and starch accumulation were also enhanced under an atmospheric CO2 concentration (40 Pa) when plants were cultured under a 33°C/28°C regime. The overall data strongly indicate that NPP1 exerts a negative effect on plant growth and starch accumulation in shoots, especially under high CO2 concentration and high temperature conditions.
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Affiliation(s)
- Kentaro Kaneko
- Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
- These authors contributed equally to this work
| | - Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
- These authors contributed equally to this work
| | - Takahiro Masui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Tsutomu Koshu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Yukiho Umezawa
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Kimiko Itoh
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra). Mutiloako etorbidea zenbaki gabe, 31192 Mutiloabeti, Nafarroa, Spain
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181 Japan
- *Corresponding author: E-mail, ; Fax, +81-25-262-6641
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Kaneko K, Shiraya T, Mitsui T, Nishimura SI. Rapid and high-throughput N-glycomic analysis of plant glycoproteins. Methods Mol Biol 2014; 1072:645-653. [PMID: 24136553 DOI: 10.1007/978-1-62703-631-3_44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Glycoprotein is a major element in higher organisms including mammalians and plants. It is widely accepted that variation in cellular N-glycome is related to modulation in dynamic cellular mechanisms such as cell-cell adhesion, cell activation, and malignant alterations in mammalian cells. However, the physiological importance of glycan modification of glycoproteins in plant cells is still a matter of dispute. Therefore, a comprehensive and high-throughput analysis of N-glycome in plant glycoproteins is needed. Here, an application of the glycoblotting-mass spectrometry technique to plant glycoprotein research is described.
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Affiliation(s)
- Kentaro Kaneko
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
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Peschke M, Hempel F. Glycoprotein import: a common feature of complex plastids? PLANT SIGNALING & BEHAVIOR 2013; 8:26050. [PMID: 24220152 PMCID: PMC4091080 DOI: 10.4161/psb.26050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
Complex plastids evolved by secondary endosymbiosis and are, in contrast to primary plastids, surrounded by 3 or 4 envelope membranes. Recently, we provided evidence that in diatoms proteins exist that get N-glycosylated during transport across the outermost membrane of the complex plastid. This gives rise to unique questions on the transport mechanisms of these bulky proteins, which get transported across up to 3 further membranes into the plastid stroma. Here we discuss our results in an evolutionary context and speculate about the existence of plastidal glycoproteins in other organisms with complex plastids.
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Affiliation(s)
- Madeleine Peschke
- Department of Cell Biology of the Philipps University Marburg; Marburg, Germany
- Current Affiliation: Department of Biomolecular Mechanisms; Max-Planck-Institute for Medical Research; Heidelberg, Germany
| | - Franziska Hempel
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO); Marburg, Germany
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Gagat P, Bodył A, Mackiewicz P. How protein targeting to primary plastids via the endomembrane system could have evolved? A new hypothesis based on phylogenetic studies. Biol Direct 2013; 8:18. [PMID: 23845039 PMCID: PMC3716720 DOI: 10.1186/1745-6150-8-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 07/02/2013] [Indexed: 01/21/2023] Open
Abstract
Background It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-encoded proteins initially were imported into the new organelle. Most proteins targeted to primary plastids carry a transit peptide and are transported post-translationally using Toc and Tic translocons. There are, however, several proteins with N-terminal signal peptides that are directed to higher plant plastids in vesicles derived from the endomembrane system (ES). The existence of these proteins inspired a hypothesis that all nuclear-encoded, plastid-targeted proteins initially carried signal peptides and were targeted to the ancestral primary plastid via the host ES. Results We present the first phylogenetic analyses of Arabidopsis thaliana α-carbonic anhydrase (CAH1), Oryza sativa nucleotide pyrophosphatase/phosphodiesterase (NPP1), and two O. sativa α-amylases (αAmy3, αAmy7), proteins that are directed to higher plant primary plastids via the ES. We also investigated protein disulfide isomerase (RB60) from the green alga Chlamydomonas reinhardtii because of its peculiar dual post- and co-translational targeting to both the plastid and ES. Our analyses show that these proteins all are of eukaryotic rather than cyanobacterial origin, and that their non-plastid homologs are equipped with signal peptides responsible for co-translational import into the host ES. Our results indicate that vesicular trafficking of proteins to primary plastids evolved long after the cyanobacterial endosymbiosis (possibly only in higher plants) to permit their glycosylation and/or transport to more than one cellular compartment. Conclusions The proteins we analyzed are not relics of ES-mediated protein targeting to the ancestral primary plastid. Available data indicate that Toc- and Tic-based translocation dominated protein import into primary plastids from the beginning. Only a handful of host proteins, which already were targeted through the ES, later were adapted to reach the plastid via the vesicular trafficking. They represent a derived class of higher plant plastid-targeted proteins with an unusual evolutionary history. Reviewers This article was reviewed by Prof. William Martin, Dr. Philippe Deschamps (nominated by Dr. Purificacion Lopez-Garcia) and Dr Simonetta Gribaldo.
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Affiliation(s)
- Przemysław Gagat
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Przybyszewskiego 63/77, Wrocław 51-148, Poland
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Abstract
Diatoms are microalgae that possess so-called "complex plastids," which evolved by secondary endosymbiosis and are surrounded by four membranes. Thus, in contrast to primary plastids, which are surrounded by only two membranes, nucleus-encoded proteins of complex plastids face additional barriers, i.e., during evolution, mechanisms had to evolve to transport preproteins across all four membranes. This study reveals that there exist glycoproteins not only in primary but also in complex plastids, making transport issues even more complicated, as most translocation machineries are not believed to be able to transport bulky proteins. We show that plastidal reporter proteins with artificial N-glycosylation sites are indeed glycosylated during transport into the complex plastid of the diatom Phaeodactylum tricornutum. Additionally, we identified five endogenous glycoproteins, which are transported into different compartments of the complex plastid. These proteins get N-glycosylated during transport across the outermost plastid membrane and thereafter are transported across the second, third, and fourth plastid membranes in the case of stromal proteins. The results of this study provide insights into the evolutionary pressure on translocation mechanisms and pose unique questions on the operating mode of well-known transport machineries like the translocons of the outer/inner chloroplast membranes (Toc/Tic).
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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Divol F, Couch D, Conéjéro G, Roschzttardtz H, Mari S, Curie C. The Arabidopsis YELLOW STRIPE LIKE4 and 6 transporters control iron release from the chloroplast. THE PLANT CELL 2013; 25:1040-1055. [PMID: 23512854 DOI: 10.1105/tpc112107672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In most plant cell types, the chloroplast represents the largest sink for iron, which is both essential for chloroplast metabolism and prone to cause oxidative damage. Here, we show that to buffer the potentially harmful effects of iron, besides ferritins for storage, the chloroplast is equipped with specific iron transporters that respond to iron toxicity by removing iron from the chloroplast. We describe two transporters of the YELLOW STRIPE1-LIKE family from Arabidopsis thaliana, YSL4 and YSL6, which are likely to fulfill this function. Knocking out both YSL4 and YSL6 greatly reduces the plant's ability to cope with excess iron. Biochemical and immunolocalization analyses showed that YSL6 resides in the chloroplast envelope. Elemental analysis and histochemical staining indicate that iron is trapped in the chloroplasts of the ysl4 ysl6 double mutants, which also accumulate ferritins. Also, vacuolar iron remobilization and NRAMP3/4 expression are inhibited. Furthermore, ubiquitous expression of YSL4 or YSL6 dramatically reduces plant tolerance to iron deficiency and decreases chloroplastic iron content. These data demonstrate a fundamental role for YSL4 and YSL6 in managing chloroplastic iron. YSL4 and YSL6 expression patterns support their physiological role in detoxifying iron during plastid dedifferentiation occurring in embryogenesis and senescence.
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Affiliation(s)
- Fanchon Divol
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5004/Institut National de la Recherche Agronomique/SupAgro/Université Montpellier 1, F-34060 Montpellier cedex 2, France
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50
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Divol F, Couch D, Conéjéro G, Roschzttardtz H, Mari S, Curie C. The Arabidopsis YELLOW STRIPE LIKE4 and 6 transporters control iron release from the chloroplast. THE PLANT CELL 2013; 25:1040-55. [PMID: 23512854 PMCID: PMC3634676 DOI: 10.1105/tpc.112.107672] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/20/2013] [Accepted: 02/26/2013] [Indexed: 05/18/2023]
Abstract
In most plant cell types, the chloroplast represents the largest sink for iron, which is both essential for chloroplast metabolism and prone to cause oxidative damage. Here, we show that to buffer the potentially harmful effects of iron, besides ferritins for storage, the chloroplast is equipped with specific iron transporters that respond to iron toxicity by removing iron from the chloroplast. We describe two transporters of the YELLOW STRIPE1-LIKE family from Arabidopsis thaliana, YSL4 and YSL6, which are likely to fulfill this function. Knocking out both YSL4 and YSL6 greatly reduces the plant's ability to cope with excess iron. Biochemical and immunolocalization analyses showed that YSL6 resides in the chloroplast envelope. Elemental analysis and histochemical staining indicate that iron is trapped in the chloroplasts of the ysl4 ysl6 double mutants, which also accumulate ferritins. Also, vacuolar iron remobilization and NRAMP3/4 expression are inhibited. Furthermore, ubiquitous expression of YSL4 or YSL6 dramatically reduces plant tolerance to iron deficiency and decreases chloroplastic iron content. These data demonstrate a fundamental role for YSL4 and YSL6 in managing chloroplastic iron. YSL4 and YSL6 expression patterns support their physiological role in detoxifying iron during plastid dedifferentiation occurring in embryogenesis and senescence.
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