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Tünnermann L, Colou J, Näsholm T, Gratz R. To have or not to have: expression of amino acid transporters during pathogen infection. PLANT MOLECULAR BIOLOGY 2022; 109:413-425. [PMID: 35103913 PMCID: PMC9213295 DOI: 10.1007/s11103-022-01244-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.
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Affiliation(s)
- Laura Tünnermann
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Justine Colou
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Torgny Näsholm
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Regina Gratz
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.
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2
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Berger N, Demolombe V, Hem S, Rofidal V, Steinmann L, Krouk G, Crabos A, Nacry P, Verdoucq L, Santoni V. Root Membrane Ubiquitinome under Short-Term Osmotic Stress. Int J Mol Sci 2022; 23:ijms23041956. [PMID: 35216074 PMCID: PMC8879470 DOI: 10.3390/ijms23041956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic-mediated stress. In this study, we used the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no ubiquitin (Ub) motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment but that it is putatively involved in protein internalization, as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub-conjugating enzymes, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.
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Affiliation(s)
- Nathalie Berger
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Vincent Demolombe
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Sonia Hem
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Valérie Rofidal
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Laura Steinmann
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
- Center for Computational and Theoretical Biology, University of Würzburg, 97070 Würzburg, Germany
| | - Gabriel Krouk
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Amandine Crabos
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Philippe Nacry
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Lionel Verdoucq
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
| | - Véronique Santoni
- BPMP, CNRS, INRAE, Institut Agro, University Montpellier, 34060 Montpellier, France; (N.B.); (V.D.); (S.H.); (V.R.); (L.S.); (G.K.); (A.C.); (P.N.); (L.V.)
- Correspondence:
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3
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Liu W, Liu Z, Mo Z, Guo S, Liu Y, Xie Q. ATG8-Interacting Motif: Evolution and Function in Selective Autophagy of Targeting Biological Processes. FRONTIERS IN PLANT SCIENCE 2021; 12:783881. [PMID: 34912364 PMCID: PMC8666691 DOI: 10.3389/fpls.2021.783881] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/28/2021] [Indexed: 05/26/2023]
Abstract
Autophagy is an evolutionarily conserved vacuolar process functioning in the degradation of cellular components for reuse. In plants, autophagy is generally activated upon stress and its regulation is executed by numbers of AuTophaGy-related genes (ATGs), of which the ATG8 plays a dual role in both biogenesis of autophagosomes and recruitment of ATG8-interacting motif (AIM) anchored selective autophagy receptors (SARs). Such motif is either termed as AIM or ubiquitin-interacting motif (UIM), corresponding to the LC3-interacting region (LIR)/AIM docking site (LDS) or the UIM docking site (UDS) of ATG8, respectively. To date, dozens of AIM or UIM containing SARs have been characterized. However, the knowledge of these motifs is still obscured. In this review, we intend to summarize the current understanding of SAR proteins and discuss the conservation and diversification of the AIMs/UIMs, expectantly providing new insights into the evolution of them in various biological processes in plants.
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Affiliation(s)
- Wanqing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zinan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
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4
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Jacott CN, Ridout CJ, Murray JD. Unmasking Mildew Resistance Locus O. TRENDS IN PLANT SCIENCE 2021; 26:1006-1013. [PMID: 34175219 DOI: 10.1016/j.tplants.2021.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Loss of Mildew Resistance Locus O (MLO) in barley confers durable resistance to powdery mildew fungi, which has led to its wide deployment in agriculture. Although MLO is a susceptibility factor, it has become nearly synonymous with powdery mildew resistance. However, MLO has been recently implicated in colonization by arbuscular mycorrhizal fungi and a fungal endophyte, confirming its importance for biotrophic interactions and in promoting symbiosis. Other MLO proteins are involved in essential sensory processes, particularly fertilization and thigmotropism. We propose external stimulus perception as a common theme in these interactions and consider a unified biochemical role, potentially relating to reactive oxygen species (ROS) and calcium regulation, for MLOs across tissues and processes.
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Affiliation(s)
- Catherine N Jacott
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Christopher J Ridout
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, CAS-araJIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Centre for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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5
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Jamsheer K M, Kumar M, Srivastava V. SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6042-6065. [PMID: 33693699 DOI: 10.1093/jxb/erab079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Manoj Kumar
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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6
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Gratz R, Ahmad I, Svennerstam H, Jämtgård S, Love J, Holmlund M, Ivanov R, Ganeteg U. Organic nitrogen nutrition: LHT1.2 protein from hybrid aspen (Populus tremula L. x tremuloides Michx) is a functional amino acid transporter and a homolog of Arabidopsis LHT1. TREE PHYSIOLOGY 2021; 41:1479-1496. [PMID: 33631788 PMCID: PMC8359683 DOI: 10.1093/treephys/tpab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.
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Affiliation(s)
- Regina Gratz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Iftikhar Ahmad
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Henrik Svennerstam
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Sandra Jämtgård
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Jonathan Love
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Mattias Holmlund
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, 40225 Düsseldorf, Germany
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7
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Alves HLS, Matiolli CC, Soares RC, Almadanim MC, Oliveira MM, Abreu IA. Carbon/nitrogen metabolism and stress response networks - calcium-dependent protein kinases as the missing link? JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4190-4201. [PMID: 33787877 PMCID: PMC8162629 DOI: 10.1093/jxb/erab136] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/29/2021] [Indexed: 05/04/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) play essential roles in plant development and stress responses. CDPKs have a conserved kinase domain, followed by an auto-inhibitory junction connected to the calmodulin-like domain that binds Ca2+. These structural features allow CDPKs to decode the dynamic changes in cytoplasmic Ca2+ concentrations triggered by hormones and by biotic and abiotic stresses. In response to these signals, CDPKs phosphorylate downstream protein targets to regulate growth and stress responses according to the environmental and developmental circumstances. The latest advances in our understanding of the metabolic, transcriptional, and protein-protein interaction networks involving CDPKs suggest that they have a direct influence on plant carbon/nitrogen (C/N) balance. In this review, we discuss how CDPKs could be key signaling nodes connecting stress responses with metabolic homeostasis, and acting together with the sugar and nutrient signaling hubs SnRK1, HXK1, and TOR to improve plant fitness.
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Affiliation(s)
- Hugo L S Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Cleverson C Matiolli
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Rafael C Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
- Correspondence:
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8
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Liu TY. Using Tripartite Split-sfGFP for the Study of Membrane Protein-Protein Interactions. Methods Mol Biol 2021; 2200:323-336. [PMID: 33175385 DOI: 10.1007/978-1-0716-0880-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The study of protein-protein interaction (PPI) is critical for understanding cellular processes within biological systems. The conventional biomolecular fluorescence complementation (BiFC) or bipartite split-fluorescent protein (FP) is a noninvasive fluorescent-based technique that enables direct visualization of PPI in living cells once the two nonfluorescent fragments are brought into close vicinity. However, BiFC can potentially lead to a high background noise arising from an inherent feature of the irreversible self-assembly of the nonfluorescent fragments. Recently, the newly developed tripartite split-sfGFP method was demonstrated to detect membrane PPIs in plant cells without spurious background signals even when fusion proteins are highly expressed and accessible to the compartments of interaction. Here we describe a protocol for using the ß-Estradiol-inducible tripartite split-sfGFP assay for side-by-side analyses of in vivo PPI along with in situ subcellular localization of fusion proteins in agroinfiltrated Nicotiana benthamiana leaves.
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Affiliation(s)
- Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
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9
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The Arabidopsis L-Type Amino Acid Transporter 5 (LAT5/PUT5) Is Expressed in the Phloem and Alters Seed Nitrogen Content When Knocked Out. PLANTS 2020; 9:plants9111519. [PMID: 33182302 PMCID: PMC7695346 DOI: 10.3390/plants9111519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 11/25/2022]
Abstract
The Arabidopsis L-type Amino Acid Transporter-5 (LAT5; At3g19553) was recently studied for its role in developmental responses such as flowering and senescence, under an assumption that it is a polyamine uptake transporter (PUT5). The LATs in Arabidopsis have a wide range of substrates, including amino acids and polyamines. This report extensively studied the organ and tissue-specific expression of the LAT5/PUT5 and investigated its role in mediating amino acid transport. Organ-specific quantitative RT-PCR detected LAT5/PUT5 transcripts in all organs with a relatively higher abundance in the leaves. Tissue-specific expression analysis identified GUS activity in the phloem under the LAT5/PUT5 promoter. In silico analysis identified both amino acid transporter and antiporter domains conserved in the LAT5/PUT5 protein. The physiological role of the LAT5/PUT5 was studied through analyzing a mutant line, lat5-1, under various growth conditions. The mutant lat5-1 seedlings showed increased sensitivity to exogenous leucine in Murashige and Skoog growth medium. In soil, the lat5-1 showed reduced leaf growth and altered nitrogen content in the seeds. In planta radio-labelled leucine uptake studies showed increased accumulation of leucine in the lat5-1 plants compared to the wild type when treated in the dark prior to the isotopic feeding. These studies suggest that LAT5/PUT5 plays a role in mediating amino acid transport.
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10
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Baune MC, Lansing H, Fischer K, Meyer T, Charton L, Linka N, von Schaewen A. The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum. THE PLANT CELL 2020; 32:1703-1726. [PMID: 32111666 PMCID: PMC7203913 DOI: 10.1105/tpc.19.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
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Affiliation(s)
- Marie-Christin Baune
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hannes Lansing
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Kerstin Fischer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Tanja Meyer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Lennart Charton
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicole Linka
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antje von Schaewen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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11
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Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ. Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PLANT PHYSIOLOGY 2019; 179:1893-1907. [PMID: 30679268 PMCID: PMC6446796 DOI: 10.1104/pp.18.01216] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/15/2019] [Indexed: 05/04/2023]
Abstract
Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted "structure-ome" and found a significant enrichment of real interactions for the top-ranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ∼2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/.
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Affiliation(s)
- Shaowei Dong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Vincent Lau
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Richard Song
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Yingzhou Wu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Teeratham Sivieng
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Hardeep Nahal
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Rose Oughtred
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- IBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
| | - Kara Dolinski
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- IBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
| | - Mike Tyers
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, 101H Price Hall, Mail Code: 0331, 170 Drillfield Drive, Blacksburg, Virginia 24061
| | - Björn Usadel
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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12
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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13
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Zhou JJ, Luo J. The PIN-FORMED Auxin Efflux Carriers in Plants. Int J Mol Sci 2018; 19:E2759. [PMID: 30223430 PMCID: PMC6164769 DOI: 10.3390/ijms19092759] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Auxin plays crucial roles in multiple developmental processes, such as embryogenesis, organogenesis, cell determination and division, as well as tropic responses. These processes are finely coordinated by the auxin, which requires the polar distribution of auxin within tissues and cells. The intercellular directionality of auxin flow is closely related to the asymmetric subcellular location of PIN-FORMED (PIN) auxin efflux transporters. All PIN proteins have a conserved structure with a central hydrophilic loop domain, which harbors several phosphosites targeted by a set of protein kinases. The activities of PIN proteins are finely regulated by diverse endogenous and exogenous stimuli at multiple layers-including transcriptional and epigenetic levels, post-transcriptional modifications, subcellular trafficking, as well as PINs' recycling and turnover-to facilitate the developmental processes in an auxin gradient-dependent manner. Here, the recent advances in the structure, evolution, regulation and functions of PIN proteins in plants will be discussed. The information provided by this review will shed new light on the asymmetric auxin-distribution-dependent development processes mediated by PIN transporters in plants.
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Affiliation(s)
- Jing-Jing Zhou
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jie Luo
- College of Horticulture and Forestry Science, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China.
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14
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Liu TY, Chou WC, Chen WY, Chu CY, Dai CY, Wu PY. Detection of membrane protein-protein interaction in planta based on dual-intein-coupled tripartite split-GFP association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:426-438. [PMID: 29451720 DOI: 10.1111/tpj.13874] [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: 09/02/2017] [Revised: 01/19/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Despite the great interest in identifying protein-protein interactions (PPIs) in biological systems, only a few attempts have been made at large-scale PPI screening in planta. Unlike biochemical assays, bimolecular fluorescence complementation allows visualization of transient and weak PPIs in vivo at subcellular resolution. However, when the non-fluorescent fragments are highly expressed, spontaneous and irreversible self-assembly of the split halves can easily generate false positives. The recently developed tripartite split-GFP system was shown to be a reliable PPI reporter in mammalian and yeast cells. In this study, we adapted this methodology, in combination with the β-estradiol-inducible expression cassette, for the detection of membrane PPIs in planta. Using a transient expression assay by agroinfiltration of Nicotiana benthamiana leaves, we demonstrate the utility of the tripartite split-GFP association in plant cells and affirm that the tripartite split-GFP system yields no spurious background signal even with abundant fusion proteins readily accessible to the compartments of interaction. By validating a few of the Arabidopsis PPIs, including the membrane PPIs implicated in phosphate homeostasis, we proved the fidelity of this assay for detection of PPIs in various cellular compartments in planta. Moreover, the technique combining the tripartite split-GFP association and dual-intein-mediated cleavage of polyprotein precursor is feasible in stably transformed Arabidopsis plants. Our results provide a proof-of-concept implementation of the tripartite split-GFP system as a potential tool for membrane PPI screens in planta.
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Affiliation(s)
- Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wen-Chun Chou
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-Yuan Chen
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ching-Yi Chu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chen-Yi Dai
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Pei-Yu Wu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
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Abstract
Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.
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Affiliation(s)
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;
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16
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Li S, Musungu B, Lightfoot D, Ji P. The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. Front Genet 2018; 9:104. [PMID: 29666630 PMCID: PMC5891612 DOI: 10.3389/fgene.2018.00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.
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Affiliation(s)
- Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Stoneville, MS, United States
| | - Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - David Lightfoot
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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17
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Liu F, Hu W, Vierstra RD. The Vacuolar Protein Sorting-38 Subunit of the Arabidopsis Phosphatidylinositol-3-Kinase Complex Plays Critical Roles in Autophagy, Endosome Sorting, and Gravitropism. FRONTIERS IN PLANT SCIENCE 2018; 9:781. [PMID: 29967628 PMCID: PMC6016017 DOI: 10.3389/fpls.2018.00781] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/23/2018] [Indexed: 05/02/2023]
Abstract
The family of phosphatidylinositols (PtdIns) plays essential roles in membrane identity and intracellular trafficking events. In animals and yeast, PtdIn-3-phosphate, which is particularly important for endosomal sorting, lysosomal/vacuolar transport and autophagy, is assembled by two conserved kinase complexes comprised of the catalytic VACUOLAR PROTEIN SORTING (VPS)-34 subunit, along with VPS15, AUTOPHAGY-RELATED (ATG)-6, and either ATG14 (complex I) or VPS38 (complex II). Here, we describe the Arabidopsis ortholog of VPS38 and show by interaction assays that it assembles into a tetrameric PtdIn-3 kinase complex II. Plants missing VPS38 are viable but have dampened pollen germination and heightened seed abortion, and display a dwarf rosette phenotype, with defects in leaf and vascular development and sucrose sensing. vps38 seeds accumulate irregular protein storage vesicles and suppress processing of storage proteins into their mature forms. Consistent with a role for PtdIn-3-phosphate in autophagy, vps38 mutants are hypersensitive to nitrogen and fixed-carbon starvation and show reduced autophagic transport of cargo into vacuoles. vps38 seedlings also have dampened root gravitropism, which is underpinned by aberrant vectoral auxin transport likely caused by defects in plasma membrane/endosome cycling of the PIN-FORMED family of auxin transporters necessary for asymmetric cell elongation. Collectively, this study places VPS38 and its class-III PtdIn-3 kinase complex at the nexus of numerous endosomal trafficking events important to plant growth and development.
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Affiliation(s)
- Fen Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
- *Correspondence: Richard D. Vierstra,
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18
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Kakar KU, Nawaz Z, Kakar K, Ali E, Almoneafy AA, Ullah R, Ren XL, Shu QY. Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles. BMC Genomics 2017; 18:869. [PMID: 29132315 PMCID: PMC5683364 DOI: 10.1186/s12864-017-4244-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
Background The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. Results In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i.e., IV-a and IV-b). The BoCNGC family is asymmetrically fractioned into the following three sub-genomes: least fractionated (14 genes), most fractionated-I (10), and most fractionated-II (2). The syntenic map of BoCNGC genes exhibited strong relationships with the model Arabidopsis thaliana and B. rapa CNGC genes and provided markers for defining the regions of conserved synteny among the three genomes. Both whole-genome triplication along with segmental and tandem duplications contributed to the expansion of this gene family. We predicted the characteristics of BoCNGCs regarding exon-intron organisations, motif compositions and post-translational modifications, which diversified their structures and functions. Using orthologous Arabidopsis CNGCs as a reference, we found that most CNGCs were associated with various protein–protein interaction networks involving CNGCs and other signalling and stress related proteins. We revealed that five microRNAs (i.e., bol-miR5021, bol-miR838d, bol-miR414b, bol-miR4234, and bol-miR_new2) have target sites in nine BoCNGC genes. The BoCNGC genes were differentially expressed in seven B. oleracea tissues including leaf, stem, callus, silique, bud, root and flower. The transcript abundance levels quantified by qRT-PCR assays revealed that BoCNGC genes from phylogenetic Groups I and IV were particularly sensitive to cold stress and infections with bacterial pathogen Xanthomonas campestris pv. campestris, suggesting their importance in abiotic and biotic stress responses. Conclusion Our comprehensive genome-wide analysis represents a rich data resource for studying new plant gene families. Our data may also be useful for breeding new B. oleracea cultivars with improved productivity, quality, and stress resistance. Electronic supplementary material The online version of this article (10.1186/s12864-017-4244-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaleem U Kakar
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.,Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Zarqa Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China.,Wuxi Hupper Bioseed Technology Academy Ltd., Wuxi, 214000, China
| | - Khadija Kakar
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Essa Ali
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Abdulwareth A Almoneafy
- Department of Biological sciences, College of Education and Science, Albaydaa University, Rada'a, Yemen
| | - Raqeeb Ullah
- Department of Environmental Sciences, Quaid -i- Azam University, Islamabad, Pakistan
| | - Xue-Liang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China. .,Guizhou Academy of Tobacco Science, Longtanba Road No. 29, Guanshanhu District, Guiyang, (550081), Guizhou, People's Republic of China.
| | - Qing-Yao Shu
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. .,Institute of Crop Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310029, China.
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19
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Bellati J, Champeyroux C, Hem S, Rofidal V, Krouk G, Maurel C, Santoni V. Novel Aquaporin Regulatory Mechanisms Revealed by Interactomics. Mol Cell Proteomics 2016; 15:3473-3487. [PMID: 27609422 PMCID: PMC5098044 DOI: 10.1074/mcp.m116.060087] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/31/2016] [Indexed: 12/22/2022] Open
Abstract
PIP1;2 and PIP2;1 are aquaporins that are highly expressed in roots and bring a major contribution to root water transport and its regulation by hormonal and abiotic factors. Interactions between cellular proteins or with other macromolecules contribute to forming molecular machines. Proteins that molecularly interact with PIP1;2 and PIP2;1 were searched to get new insights into regulatory mechanisms of root water transport. For that, a immuno-purification strategy coupled to protein identification and quantification by mass spectrometry (IP-MS) of PIPs was combined with data from the literature, to build thorough PIP1;2 and PIP2;1 interactomes, sharing about 400 interacting proteins. Such interactome revealed PIPs to behave as a platform for recruitment of a wide range of transport activities and provided novel insights into regulation of PIP cellular trafficking by osmotic and oxidative treatments. This work also pointed a role of lipid signaling in PIP function and enhanced our knowledge of protein kinases involved in PIP regulation. In particular we show that 2 members of the receptor-like kinase (RLK) family (RKL1 (At1g48480) and Feronia (At3g51550)) differentially modulate PIP activity through distinct molecular mechanisms. The overall work opens novel perspectives in understanding PIP regulatory mechanisms and their role in adjustment of plant water status.
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Affiliation(s)
- Jorge Bellati
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Chloé Champeyroux
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Sonia Hem
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Valérie Rofidal
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Gabriel Krouk
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Christophe Maurel
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
| | - Véronique Santoni
- From the ‡Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, F-34060 Montpellier, Cedex 2, France
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20
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Xing S, Wallmeroth N, Berendzen KW, Grefen C. Techniques for the Analysis of Protein-Protein Interactions in Vivo. PLANT PHYSIOLOGY 2016; 171:727-58. [PMID: 27208310 PMCID: PMC4902627 DOI: 10.1104/pp.16.00470] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 05/20/2023]
Abstract
Identifying key players and their interactions is fundamental for understanding biochemical mechanisms at the molecular level. The ever-increasing number of alternative ways to detect protein-protein interactions (PPIs) speaks volumes about the creativity of scientists in hunting for the optimal technique. PPIs derived from single experiments or high-throughput screens enable the decoding of binary interactions, the building of large-scale interaction maps of single organisms, and the establishment of cross-species networks. This review provides a historical view of the development of PPI technology over the past three decades, particularly focusing on in vivo PPI techniques that are inexpensive to perform and/or easy to implement in a state-of-the-art molecular biology laboratory. Special emphasis is given to their feasibility and application for plant biology as well as recent improvements or additions to these established techniques. The biology behind each method and its advantages and disadvantages are discussed in detail, as are the design, execution, and evaluation of PPI analysis. We also aim to raise awareness about the technological considerations and the inherent flaws of these methods, which may have an impact on the biological interpretation of PPIs. Ultimately, we hope this review serves as a useful reference when choosing the most suitable PPI technique.
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Affiliation(s)
- Shuping Xing
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Niklas Wallmeroth
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Kenneth W Berendzen
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Christopher Grefen
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
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21
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Xie Q, Tzfadia O, Levy M, Weithorn E, Peled-Zehavi H, Van Parys T, Van de Peer Y, Galili G. hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms. Autophagy 2016; 12:876-87. [PMID: 27071037 DOI: 10.1080/15548627.2016.1147668] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements-the presence of acidic amino acids and the absence of positively charged amino acids in certain positions-to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the Arabidopsis proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 in planta. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.
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Affiliation(s)
- Qingjun Xie
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel
| | - Oren Tzfadia
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel.,b Department of Plant Systems Biology , VIB , Ghent , Belgium.,c Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium.,d Bioinformatics Institute Ghent, Ghent University , Ghent , Belgium
| | - Matan Levy
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel
| | - Efrat Weithorn
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel
| | - Hadas Peled-Zehavi
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel
| | - Thomas Van Parys
- b Department of Plant Systems Biology , VIB , Ghent , Belgium.,c Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium.,d Bioinformatics Institute Ghent, Ghent University , Ghent , Belgium
| | - Yves Van de Peer
- b Department of Plant Systems Biology , VIB , Ghent , Belgium.,c Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium.,d Bioinformatics Institute Ghent, Ghent University , Ghent , Belgium.,e Genomics Research Institute (GRI), University of Pretoria , Pretoria , South Africa
| | - Gad Galili
- a Department of Plant and Environmental Science , Weizmann Institute of Science , Rehovotx , Israel
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22
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Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods ("omics") now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis). Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.
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Affiliation(s)
| | | | - Ueli Grossniklaus
- Department of Plant & Microbial Biology and Zurich-Basel Plant Science Center, University of ZurichZurich, Switzerland
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23
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Musungu B, Bhatnagar D, Brown RL, Fakhoury AM, Geisler M. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. Front Genet 2015; 6:201. [PMID: 26089837 PMCID: PMC4454876 DOI: 10.3389/fgene.2015.00201] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/21/2015] [Indexed: 12/30/2022] Open
Abstract
Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs) that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.
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Affiliation(s)
- Bryan Musungu
- Department of Plant Biology, Southern Illinois University Carbondale, IL, USA
| | - Deepak Bhatnagar
- Food and Feed Safety Research, Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service New Orleans, LA, USA
| | - Robert L Brown
- Food and Feed Safety Research, Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service New Orleans, LA, USA
| | - Ahmad M Fakhoury
- Department of Plant Soil and Agriculture Systems, Southern Illinois University Carbondale, IL, USA
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University Carbondale, IL, USA
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24
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Rosas-Santiago P, Lagunas-Gómez D, Barkla BJ, Vera-Estrella R, Lalonde S, Jones A, Frommer WB, Zimmermannova O, Sychrová H, Pantoja O. Identification of rice cornichon as a possible cargo receptor for the Golgi-localized sodium transporter OsHKT1;3. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2733-48. [PMID: 25750424 PMCID: PMC4986874 DOI: 10.1093/jxb/erv069] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Membrane proteins are synthesized and folded in the endoplasmic reticulum (ER), and continue their path to their site of residence along the secretory pathway. The COPII system has been identified as a key player for selecting and directing the fate of membrane and secretory cargo proteins. Selection of cargo proteins within the COPII vesicles is achieved by cargo receptors. The cornichon cargo receptor belongs to a conserved protein family found in eukaryotes that has been demonstrated to participate in the selection of integral membrane proteins as cargo for their correct targeting. Here it is demonstrated at the cellular level that rice cornichon OsCNIH1 interacts with OsHKT1;3 and, in yeast cells, enables the expression of the sodium transporter to the Golgi apparatus. Physical and functional HKT-cornichon interactions are confirmed by the mating-based split ubiquitin system, bimolecular fluorescence complementation, and Xenopus oocyte and yeast expression systems. The interaction between the two proteins occurs in the ER of plant cells and their co-expression in oocytes leads to the sequestration of the transporter in the ER. In the yeast cornichon mutant erv14, OsHKT1;3 is mistargeted, preventing the toxic effects of sodium transport in the cell observed in wild-type cells or in the erv14 mutant that co-expressed OsHKT1;3 with either OsCNIH1 or Erv14p. Identification and characterization of rice cornichon as a possible cargo receptor opens up the opportunity to improve our knowledge on membrane protein targeting in plant cells.
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Affiliation(s)
- Paul Rosas-Santiago
- Instituto de Biotecnología, Universidad Nacional de Autónoma de México, Cuernavaca, Morelos 62250, México Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Daniel Lagunas-Gómez
- Instituto de Biotecnología, Universidad Nacional de Autónoma de México, Cuernavaca, Morelos 62250, México
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional de Autónoma de México, Cuernavaca, Morelos 62250, México
| | - Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Alexander Jones
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Olga Zimmermannova
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Hana Sychrová
- Department of Membrane Transport, Institute of Physiology, Academy of Sciences of the Czech Republic, v.v.i., 142 20 Prague 4, Czech Republic
| | - Omar Pantoja
- Instituto de Biotecnología, Universidad Nacional de Autónoma de México, Cuernavaca, Morelos 62250, México
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25
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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26
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Li J, Zhang D. Quantitative Analysis of Protein‐Protein Interactions by Split Firefly Luciferase Complementation in Plant Protoplasts. ACTA ACUST UNITED AC 2014; 107:20.9.1-20.9.8. [DOI: 10.1002/0471142727.mb2009s107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian‐Feng Li
- Department of Molecular Biology, Massachusetts General Hospital Boston Massachusetts
| | - Dandan Zhang
- Department of Molecular Biology, Massachusetts General Hospital Boston Massachusetts
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27
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Rodrigues RB, Sabat G, Minkoff BB, Burch HL, Nguyen TT, Sussman MR. Expression of a translationally fused TAP-tagged plasma membrane proton pump in Arabidopsis thaliana. Biochemistry 2014; 53:566-78. [PMID: 24397334 PMCID: PMC3985734 DOI: 10.1021/bi401096m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The Arabidopsis thaliana plasma
membrane proton ATPase genes, AHA1 and AHA2, are the two most highly expressed isoforms of an 11 gene family
and are collectively essential for embryo development. We report the
translational fusion of a tandem affinity-purification tag to the
5′ end of the AHA1 open reading frame in a genomic clone. Stable
expression of TAP-tagged AHA1 in Arabidopsis rescues the embryonic lethal phenotype of endogenous double aha1/aha2 knockdowns. Western blots of SDS-PAGE and Blue
Native gels show enrichment of AHA1 in plasma membrane fractions and
indicate a hexameric quaternary structure. TAP-tagged AHA1 rescue
lines exhibited reduced vertical root growth. Analysis of the plasma
membrane and soluble proteomes identified several plasma membrane-localized
proteins with alterred abundance in TAP-tagged AHA1 rescue lines compared
to wild type. Using affinity-purification mass spectrometry, we uniquely
identified two additional AHA isoforms, AHA9 and AHA11, which copurified
with TAP-tagged AHA1. In conclusion, we have generated transgenic Arabidopsis lines in which a TAP-tagged AHA1 transgene
has complemented all essential endogenous AHA1 and AHA2 functions
and have shown that these plants can be used to purify AHA1 protein
and to identify in planta interacting proteins by
mass spectrometry.
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Affiliation(s)
- Rachel B Rodrigues
- Department of Biochemistry, Biotechnology Center, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
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28
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Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet 2013; 9:e1003840. [PMID: 24098147 PMCID: PMC3789834 DOI: 10.1371/journal.pgen.1003840] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. A commonly used method for this purpose is a top-down approach based on clustering the network into a range of densely connected segments, treating these segments as expression modules, and extracting promoter motifs from these modules. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via motif enrichment or motif position bias analysis. Our results indicate that motif position bias analysis is an effective tool for genome-wide motif analysis. Sub-networks containing the top ranked genes are extracted and analyzed for inherent gene expression modules. This approach identified novel expression modules for the G-box, W-box, site II, and MYB motifs from an Arabidopsis thaliana gene co-expression network based on the graphical Gaussian model. The novel expression modules include those involved in house-keeping functions, primary and secondary metabolism, and abiotic and biotic stress responses. In addition to confirmation of previously described modules, we identified modules that include new signaling pathways. To associate transcription factors that regulate genes in these co-expression modules, we developed a novel reporter system. Using this approach, we evaluated MYB transcription factor-promoter interactions within MYB motif modules. Gene co-expression networks unite genes with similar expression patterns. From these networks, gene co-expression modules can be identified. A specific family of transcription factor(s) may regulate the genes within a co-expression module. Thus, module identification is important to decipher the gene regulatory network. Previously, module identification relied on clustering the gene network into gene clusters that were then treated as modules. This represents a top-down approach. Here, we introduce a reverse approach aiming at identifying gene co-expression modules regulated by known promoter motifs. For a given promoter motif, we calculated the probability of each gene within the network to belong to a module regulated by that motif via motif enrichment analysis or motif position bias analysis. A sub-network containing the genes with a high probability of belonging to a motif driven module was then extracted from the gene co-expression network. From this sub-network, the modular structure can be identified via visual inspection. Our bottom-up approach recovered many known and novel modules for the G-box, MYB, W-box and site II elements motif, whose expression may be regulated by the transcription factors that bind to these motifs. Additionally, we developed a rapid transcription factor-promoter interaction screening system to validate predicted interactions.
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29
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Schmitz J, Tierbach A, Lenz H, Meschenmoser K, Knoop V. Membrane protein interactions between different Arabidopsis thaliana MRS2-type magnesium transporters are highly permissive. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2032-40. [DOI: 10.1016/j.bbamem.2013.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 05/06/2013] [Accepted: 05/22/2013] [Indexed: 12/25/2022]
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30
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Signal transfer in the plant plasma membrane: phospholipase A(2) is regulated via an inhibitory Gα protein and a cyclophilin. Biochem J 2013; 450:497-509. [PMID: 23252374 DOI: 10.1042/bj20120793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The plasma membrane of the California poppy is known to harbour a PLA2 (phospholipase A2) that is associated with the Gα protein which facilitates its activation by a yeast glycoprotein, thereby eliciting the biosynthesis of phytoalexins. To understand the functional architecture of the protein complex, we titrated purified plasma membranes with the Gα protein (native or recombinant) and found that critical amounts of this subunit keep PLA2 in a low-activity state from which it is released either by elicitor plus GTP or by raising the Gα concentration, which probably causes oligomerization of Gα, as supported by FRET (fluorescence resonance energy transfer)-orientated fluorescence imaging and a semiquantitative split-ubiquitin assay. All effects of Gα were blocked by specific antibodies. A low-Gα mutant showed elevated PLA2 activity and lacked the GTP-dependent stimulation by elicitor, but regained this capability after pre-incubation with Gα. The inhibition by Gα and the GTP-dependent stimulation of PLA2 were diminished by inhibitors of peptidylprolyl cis-trans isomerases. A cyclophilin was identified by sequence in the plasma membrane and in immunoprecipitates with anti-Gα antibodies. We conclude that soluble and target-associated Gα interact at the plasma membrane to build complexes of varying architecture and signal amplification. Protein-folding activity is probably required to convey conformational transitions from Gα to its target PLA2.
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31
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Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C. Plant protein interactomes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:161-87. [PMID: 23330791 DOI: 10.1146/annurev-arplant-050312-120140] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
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32
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Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. THE PLANT CELL 2012; 24:3859-75. [PMID: 23110892 PMCID: PMC3517224 DOI: 10.1105/tpc.112.100776] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/21/2012] [Accepted: 10/11/2012] [Indexed: 05/19/2023]
Abstract
Physiological responses, developmental programs, and cellular functions rely on complex networks of interactions at different levels and scales. Systems biology brings together high-throughput biochemical, genetic, and molecular approaches to generate omics data that can be analyzed and used in mathematical and computational models toward uncovering these networks on a global scale. Various approaches, including transcriptomics, proteomics, interactomics, and metabolomics, have been employed to obtain these data on the cellular, tissue, organ, and whole-plant level. We summarize progress on gene regulatory, cofunction, protein interaction, and metabolic networks. We also illustrate the main approaches that have been used to obtain these networks, with specific examples from Arabidopsis thaliana, and describe the pros and cons of each approach.
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Affiliation(s)
- George W. Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Siobhan M. Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Lars Hennig
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Seung Y. Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, United Kingdom
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33
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Tohge T, Fernie AR. Co-expression and co-responses: within and beyond transcription. FRONTIERS IN PLANT SCIENCE 2012; 3:248. [PMID: 23162560 PMCID: PMC3492870 DOI: 10.3389/fpls.2012.00248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/20/2012] [Indexed: 05/04/2023]
Abstract
Whole genome sequencing, the relative ease of transcript profiling by the use of microarrays and latterly RNA sequencing approaches have facilitated the capture of vast amounts of transcript data. However, despite the enormous progress made in gene annotation a substantial proportion of genes remain to be annotated at the functional level. Considerable progress has, however, been made by searching for transcriptional coordination between genes of known function and non-annotated genes on the premise that such co-expressed genes tend to be functionally related. Here we review progress made following this approach as well as its expansion to include phenotypic information from other levels of cellular organization such as proteomic and metabolomic data as well as physiological and developmental phenotypes.
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Affiliation(s)
- Takayuki Tohge
- *Correspondence: Takayuki Tohge, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany. e-mail:
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