Special Issue "Plant Proteomics"

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A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (30 June 2014)

Special Issue Editors

Guest Editor
Prof. Dr. Setsuko Komatsu

National Institute of Crop Science, Kannondai 2-1-18, Tsukuba 305-8518, Japan
Fax: +81 29 838 8694
Interests: plant proteomics; plant biotechnology; plant physiology; abiotic stress
Guest Editor
Dr. Zahed Hossain

Department of Botany, University of Kalyani, West Bengal, India
Fax: +91 33 2582 8282
Interests: plant proteomics; plant stress biology; abiotic stress response; plant antioxidant defence

Special Issue Information

Dear Colleagues,

Proteomics, the high-throughput “omic” technique has validated its role in precise identification and characterization of individual components of plant protein networks. A comprehensive understanding of plant response mechanism is essential to elucidate the key factors affecting plant performance under adverse conditions. Various proteomic approaches that are being exploited extensively for elucidating plant response largely include gel-based and mass spectrometry-based methods that involve both label-based and label-free protein quantification. Despite of limitations in identifying low-abundance and hydrophobic proteins, exceedingly large or small proteins, as well as basic proteins, gel-based method has been accepted as a global tool to unravel the underlying molecular mechanism of stress signal perception and transduction in plant defense responses. Moreover, recent advances in the mass spectrometry-based approaches provide a better opportunity to dissect stress signaling cascades. Nevertheless, complete protein extraction from different plant organs or subcellular organelles is the most challenging facet of plant proteome analysis. Furthermore, protein-protein interactions and post-translational modifications provide deeper insight into protein molecular function. We welcome submissions of original research papers and review articles addressing recent advancements as well as strengths and shortcomings of various proteomic approaches and diverse applications of plant proteomic techniques to get new insights of plant molecular responses to various biotic and abiotic challenges.

Prof. Dr. Setsuko Komatsu
Dr. Zahed Hossain
Guest Editors

Submission

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Keywords

  • plant proteomics
  • methodologies for plant proteomics
  • application of plant proteomics

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Published Papers (12 papers)

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Research

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Open AccessArticle Enhanced Synthesis of Antioxidant Enzymes, Defense Proteins and Leghemoglobin in Rhizobium-Free Cowpea Roots after Challenging with Meloydogine incognita
Proteomes 2014, 2(4), 527-549; doi:10.3390/proteomes2040527
Received: 8 August 2014 / Revised: 22 October 2014 / Accepted: 13 November 2014 / Published: 26 November 2014
Cited by 1 | PDF Full-text (1786 KB) | HTML Full-text | XML Full-text
Abstract
The root knot nematodes (RKN), Meloydogine spp., particularly Meloidogyne incognita and Meloidogyne javanica species, parasitize several plant species and are responsible for large annual yield losses all over the world. Only a few available chemical nematicides are still authorized for RKN control [...] Read more.
The root knot nematodes (RKN), Meloydogine spp., particularly Meloidogyne incognita and Meloidogyne javanica species, parasitize several plant species and are responsible for large annual yield losses all over the world. Only a few available chemical nematicides are still authorized for RKN control owing to environmental and health reasons. Thus, plant resistance is currently considered the method of choice for controlling RKN, and research performed on the molecular interactions between plants and nematodes to identify genes of interest is of paramount importance. The present work aimed to identify the differential accumulation of root proteins of a resistant cowpea genotype (CE-31) inoculated with M. incognita (Race 3) in comparison with mock-inoculated control, using 2D electrophoresis assay, mass spectrometry identification and gene expression analyses by RT-PCR. The results showed that at least 22 proteins were differentially represented in response to RKN challenge of cowpea roots mainly within 4–6 days after inoculation. Amongst the up-represented proteins were SOD, APX, PR-1, β-1,3-glucanase, chitinases, cysteine protease, secondary metabolism enzymes, key enzymes involved in ethylene biosynthesis, proteins involved in MAPK pathway signaling and, surprisingly, leghemoglobin in non-rhizobium-bacterized cowpea. These findings show that an important rearrangement in the resistant cowpea root proteome occurred following challenge with M. incognita. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
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Open AccessArticle Quantitative Proteomics of the Root of Transgenic Wheat Expressing TaBWPR-1.2 Genes in Response to Waterlogging
Proteomes 2014, 2(4), 485-500; doi:10.3390/proteomes2040485
Received: 10 July 2014 / Revised: 20 October 2014 / Accepted: 22 October 2014 / Published: 4 November 2014
Cited by 1 | PDF Full-text (1632 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation [...] Read more.
Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation and plant regeneration efficiencies and expression variability and instability. Earlier, we found two cDNAs encoding WL stress-responsive wheat pathogenesis-related proteins 1.2 (TaBWPR-1.2), TaBWPR-1.2#2 and TaBWPR-1.2#13. Using microprojectile bombardment, both cDNAs were introduced into “Bobwhite”. Despite low transformation efficiency, four independent T2 homozygous lines for each gene were isolated, where transgenes were ubiquitously and variously expressed. The highest transgene expression was obtained in Ubi:TaBWPR-1.2#2 L#11a and Ubi:TaBWPR-1.2#13 L#4a. Using quantitative proteomics, the root proteins of L#11a were analyzed to explore possible physiological pathways regulated by TaBWPR-1.2 under normal and waterlogged conditions. In L#11a, the abundance of proteasome subunit alpha type-3 decreased under normal conditions, whereas that of ferredoxin precursor and elongation factor-2 increased under waterlogged conditions in comparison with normal plants. Proteomic results suggest that L#11a is one of the engineered wheat plants where TaBWPR-1.2#2 is most probably involved in proteolysis, protein synthesis and alteration in the energy pathway in root tissues via the above proteins in order to gain metabolic adjustment to WL. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
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Open AccessArticle Proteomic Analysis of Responsive Proteins Induced in Japanese Birch Plantlet Treated with Salicylic Acid
Proteomes 2014, 2(3), 323-340; doi:10.3390/proteomes2030323
Received: 1 February 2014 / Revised: 26 May 2014 / Accepted: 10 June 2014 / Published: 1 July 2014
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Abstract
The present study was performed to unravel the mechanisms of systemic acquired resistance (SAR) establishment and resistance signaling pathways against the canker-rot fungus (Inonotus obliquus strain IO-U1) infection in Japanese birch plantlet No.8. Modulation of protein-profile induced by salicylic acid (SA)-administration [...] Read more.
The present study was performed to unravel the mechanisms of systemic acquired resistance (SAR) establishment and resistance signaling pathways against the canker-rot fungus (Inonotus obliquus strain IO-U1) infection in Japanese birch plantlet No.8. Modulation of protein-profile induced by salicylic acid (SA)-administration was analyzed, and SA-responsive proteins were identified. In total, 5 specifically expressed, 3 significantly increased, and 3 significantly decreased protein spots were identified using liquid chromatography/tandem mass spectrometry (LC/MS/MS) and the sequence tag method. These proteins were malate dehydrogenase, succinate dehydrogenase, phosphoglycerate kinase, diaminopimalate decarboxylase, arginase, chorismate mutase, cyclophilin, aminopeptidase, and unknown function proteins. These proteins are considered to be involved in SAR-establishment mechanisms in the Japanese birch plantlet No 8. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
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Open AccessArticle Alterations in Soluble Class III Peroxidases of Maize Shoots by Flooding Stress
Proteomes 2014, 2(3), 303-322; doi:10.3390/proteomes2030303
Received: 2 April 2014 / Revised: 28 May 2014 / Accepted: 28 May 2014 / Published: 26 June 2014
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Abstract
Due to changing climate, flooding (waterlogged soils and submergence) becomes a major problem in agriculture and crop production. In the present study, the effect of waterlogging was investigated on peroxidases of maize (Zea mays L.) leaves. The plants showed typical adaptations [...] Read more.
Due to changing climate, flooding (waterlogged soils and submergence) becomes a major problem in agriculture and crop production. In the present study, the effect of waterlogging was investigated on peroxidases of maize (Zea mays L.) leaves. The plants showed typical adaptations to flooding stress, i.e., alterations in chlorophyll a/b ratios and increased basal shoot diameter. Seven peroxidase bands could be detected by first dimension modified SDS-PAGE and 10 bands by first dimension high resolution Clear Native Electrophoresis that altered in dependence on plant development and time of waterlogging. Native isoelectric focusing revealed three acidic to neutral and four alkaline guaiacol peroxidases that could be further separated by high resolution Clear Native Electrophorese in the second dimension. One neutral peroxidase (pI 7.0) appeared to be down-regulated within four hours after flooding, whereas alkaline peroxidases (pI 9.2, 8.0 and 7.8) were up-regulated after 28 or 52 h. Second dimensions revealed molecular masses of 133 kDa and 85 kDa for peroxidases at pI 8.0 and 7.8, respectively. Size exclusion chromatography revealed native molecular masses of 30–58 kDa for peroxidases identified as class III peroxidases and ascorbate peroxidases by mass spectrometry. Possible functions of these peroxidases in flooding stress will be discussed. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
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Open AccessArticle Protein Profiling Reveals Novel Proteins in Pollen and Pistil of W22 (ga1; Ga1) in Maize
Proteomes 2014, 2(2), 258-271; doi:10.3390/proteomes2020258
Received: 8 February 2014 / Revised: 8 April 2014 / Accepted: 21 April 2014 / Published: 5 May 2014
Cited by 1 | PDF Full-text (553 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active roles in limiting gene flow among maize populations and between maize and teosinte. This study was carried out to identify proteins and investigate the mechanism of gametophytic factors [...] Read more.
Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active roles in limiting gene flow among maize populations and between maize and teosinte. This study was carried out to identify proteins and investigate the mechanism of gametophytic factors using protein analysis. W22 (ga1); which did not carry a gametophytic factor and W22 (Ga1), a near iso-genic line, were used for the proteome investigation. SDS-PAGE was executed to investigate proteins in the pollen and pistil of W22 (ga1) and W22 (Ga1). A total of 44 differentially expressed proteins were identified in the pollen and pistil on SDS-PAGE using LTQ-FTICR MS. Among the 44 proteins, a total of 24 proteins were identified in the pollen of W22 (ga1) and W22 (Ga1) whereas 20 differentially expressed proteins were identified from the pistil of W22 (ga1) and W22 (Ga1). However, in pollen, 2 proteins were identified only in the W22 (ga1) and 12 proteins only in the W22 (Ga1) whereas 10 proteins were confirmed from the both of W22 (ga1) and W22 (Ga1). In contrary, 10 proteins were appeared only in the pistil of W22 (ga1) and 7 proteins from W22 (Ga1) while 3 proteins confirmed in the both of W22 (ga1) and W22 (Ga1). Moreover, the identified proteins were generally involved in hydrolase activity, nucleic acid binding and nucleotide binding. These results help to reveal the mechanism of gametophytic factors and provide a valuable clue for the pollen and pistil research in maize. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessArticle Proteomic Profiling of Sugar Beet (Beta vulgaris) Leaves during Rhizomania Compatible Interactions
Proteomes 2014, 2(2), 208-223; doi:10.3390/proteomes2020208
Received: 16 January 2014 / Revised: 15 March 2014 / Accepted: 27 March 2014 / Published: 9 April 2014
Cited by 3 | PDF Full-text (521 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), severely impacts sugar beet (Beta vulgaris) production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors [...] Read more.
Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), severely impacts sugar beet (Beta vulgaris) production throughout the world, and is widely prevalent in most production regions. Initial efforts to characterize proteome changes focused primarily on identifying putative host factors that elicit resistant interactions with BNYVV, but as resistance breaking strains become more prevalent, effective disease control strategies will require the application of novel methods based on better understanding of disease susceptibility and symptom development. Herein, proteomic profiling was conducted on susceptible sugar beet, infected with two strains of BNYVV, to clarify the types of proteins prevalent during compatible virus-host plant interactions. Total protein was extracted from sugar beet leaf tissue infected with BNYVV, quantified, and analyzed by mass spectrometry. A total of 203 proteins were confidently identified, with a predominance of proteins associated with photosynthesis and energy, metabolism, and response to stimulus. Many proteins identified in this study are typically associated with systemic acquired resistance and general plant defense responses. These results expand on relatively limited proteomic data available for sugar beet and provide the ground work for additional studies focused on understanding the interaction of BNYVV with sugar beet. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessArticle Effect of Aluminum Treatment on Proteomes of Radicles of Seeds Derived from Al-Treated Tomato Plants
Proteomes 2014, 2(2), 169-190; doi:10.3390/proteomes2020169
Received: 18 February 2014 / Revised: 4 March 2014 / Accepted: 6 March 2014 / Published: 28 March 2014
Cited by 4 | PDF Full-text (1017 KB) | HTML Full-text | XML Full-text
Abstract
Aluminum (Al) toxicity is a major constraint to plant growth and crop yield in acid soils. Tomato cultivars are especially susceptible to excessive Al3+ accumulated in the root zone. In this study, tomato plants were grown in a hydroponic culture system [...] Read more.
Aluminum (Al) toxicity is a major constraint to plant growth and crop yield in acid soils. Tomato cultivars are especially susceptible to excessive Al3+ accumulated in the root zone. In this study, tomato plants were grown in a hydroponic culture system supplemented with 50 µM AlK(SO4)2. Seeds harvested from Al-treated plants contained a significantly higher Al content than those grown in the control hydroponic solution. In this study, these Al-enriched tomato seeds (harvested from Al-treated tomato plants) were germinated in 50 µM AlK(SO4)2 solution in a homopiperazine-1,4-bis(2-ethanesulfonic acid) buffer (pH 4.0), and the control solution which contained the buffer only. Proteomes of radicles were analyzed quantitatively by mass spectrometry employing isobaric tags for relative and absolute quantitation (iTRAQ®). The proteins identified were assigned to molecular functional groups and cellular metabolic pathways using MapMan. Among the proteins whose abundance levels changed significantly were: a number of transcription factors; proteins regulating gene silencing and programmed cell death; proteins in primary and secondary signaling pathways, including phytohormone signaling and proteins for enhancing tolerance to abiotic and biotic stress. Among the metabolic pathways, enzymes in glycolysis and fermentation and sucrolytic pathways were repressed. Secondary metabolic pathways including the mevalonate pathway and lignin biosynthesis were induced. Biological reactions in mitochondria seem to be induced due to an increase in the abundance level of mitochondrial ribosomes and enzymes in the TCA cycle, electron transport chains and ATP synthesis. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessArticle PAPE (Prefractionation-Assisted Phosphoprotein Enrichment): A Novel Approach for Phosphoproteomic Analysis of Green Tissues from Plants
Proteomes 2013, 1(3), 254-274; doi:10.3390/proteomes1030254
Received: 15 October 2013 / Revised: 28 November 2013 / Accepted: 28 November 2013 / Published: 5 December 2013
Cited by 2 | PDF Full-text (1532 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Phosphorylation is an important post-translational protein modification with regulatory roles in diverse cellular signaling pathways. Despite recent advances in mass spectrometry, the detection of phosphoproteins involved in signaling is still challenging, as protein phosphorylation is typically transient and/or occurs at low levels. [...] Read more.
Phosphorylation is an important post-translational protein modification with regulatory roles in diverse cellular signaling pathways. Despite recent advances in mass spectrometry, the detection of phosphoproteins involved in signaling is still challenging, as protein phosphorylation is typically transient and/or occurs at low levels. In green plant tissues, the presence of highly abundant proteins, such as the subunits of the RuBisCO complex, further complicates phosphoprotein analysis. Here, we describe a simple, but powerful, method, which we named prefractionation-assisted phosphoprotein enrichment (PAPE), to increase the yield of phosphoproteins from Arabidopsis thaliana leaf material. The first step, a prefractionation via ammonium sulfate precipitation, not only depleted RuBisCO almost completely, but, serendipitously, also served as an efficient phosphoprotein enrichment step. When coupled with a subsequent metal oxide affinity chromatography (MOAC) step, the phosphoprotein content was highly enriched. The reproducibility and efficiency of phosphoprotein enrichment was verified by phospho-specific staining and, further, by mass spectrometry, where it could be shown that the final PAPE fraction contained a significant number of known and additionally novel (potential) phosphoproteins. Hence, this facile two-step procedure is a good prerequisite to probe the phosphoproteome and gain deeper insight into plant phosphorylation-based signaling events. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
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Review

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Open AccessReview Proteomics Advances in the Understanding of Pollen–Pistil Interactions
Proteomes 2014, 2(4), 468-484; doi:10.3390/proteomes2040468
Received: 25 July 2014 / Revised: 22 September 2014 / Accepted: 23 September 2014 / Published: 29 September 2014
Cited by 1 | PDF Full-text (1110 KB) | HTML Full-text | XML Full-text
Abstract
The first key point to the successful pollination and fertilization in plants is the pollen-pistil interaction, referring to the cellular and molecular levels, which mainly involve the haploid pollen and the diploid pistil. The process is defined as “siphonogamy”, which starts from [...] Read more.
The first key point to the successful pollination and fertilization in plants is the pollen-pistil interaction, referring to the cellular and molecular levels, which mainly involve the haploid pollen and the diploid pistil. The process is defined as “siphonogamy”, which starts from the capture of pollen by the epidermis of stigma and ends up with the fusion of sperm with egg. So far, the studies of the pollen-pistil interaction have been explicated around the self-compatibility and self-incompatibility (SI) process in different species from the molecular genetics and biochemistry to cellular and signal levels, especially the mechanism of SI system. Among them, numerous proteomics studies based on the advanced technologies from gel-system to gel-free system were conducted, focusing on the interaction, in order to uncover the mechanism of the process. The current review mainly focuses on the recent developments in proteomics of pollen-pistil interaction from two aspects: self-incompatible and compatible pollination. It might provide a comprehensive insight on the proteins that were involved in the regulation of pollen-pistil interaction. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessReview Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways?
Proteomes 2014, 2(2), 224-242; doi:10.3390/proteomes2020224
Received: 3 February 2014 / Revised: 8 April 2014 / Accepted: 8 April 2014 / Published: 17 April 2014
Cited by 9 | PDF Full-text (1459 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving [...] Read more.
Plant cell wall proteomics has been a very dynamic field of research for about fifteen years. A full range of strategies has been proposed to increase the number of identified proteins and to characterize their post-translational modifications. The protocols are still improving to enlarge the coverage of cell wall proteomes. Comparisons between these proteomes have been done based on various working strategies or different physiological stages. In this review, two points are highlighted. The first point is related to data analysis with an overview of the cell wall proteomes already described. A large body of data is now available with the description of cell wall proteomes of seventeen plant species. CWP contents exhibit particularities in relation to the major differences in cell wall composition and structure between these plants and between plant organs. The second point is related to methodology and concerns the present limitations of the coverage of cell wall proteomes. Because of the variety of cell wall structures and of the diversity of protein/polysaccharide and protein/protein interactions in cell walls, some CWPs can be missing either because they are washed out during the purification of cell walls or because they are covalently linked to cell wall components. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessReview Potentiality of Soybean Proteomics in Untying the Mechanism of Flood and Drought Stress Tolerance
Proteomes 2014, 2(1), 107-127; doi:10.3390/proteomes2010107
Received: 17 November 2013 / Revised: 26 February 2014 / Accepted: 27 February 2014 / Published: 7 March 2014
Cited by 8 | PDF Full-text (808 KB) | HTML Full-text | XML Full-text
Abstract
Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world’s most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to [...] Read more.
Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world’s most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to abiotic stressors including flood and drought. Irrespective of the kind and severity of the water stress, soybean exhibits a tight control over the carbon metabolism to meet the cells required energy demand for alleviating stress effects. The present review summarizes the major proteomic findings related to changes in soybean proteomes in response to flood and drought stresses to get a clear insight into the complex mechanisms of stress tolerance. Furthermore, advantages and disadvantages of different protein extraction protocols and challenges and future prospects of soybean proteome study are discussed in detail to comprehend the underlying mechanism of water stress acclimation. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available
Open AccessReview Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses
Proteomes 2014, 2(1), 85-106; doi:10.3390/proteomes2010085
Received: 30 October 2013 / Revised: 21 February 2014 / Accepted: 21 February 2014 / Published: 4 March 2014
Cited by 11 | PDF Full-text (1548 KB) | HTML Full-text | XML Full-text
Abstract
Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors [...] Read more.
Responses to biotic stress in plants lead to dramatic reprogramming of gene expression, favoring stress responses at the expense of normal cellular functions. Transcription factors are master regulators of gene expression at the transcriptional level, and controlling the activity of these factors alters the transcriptome of the plant, leading to metabolic and phenotypic changes in response to stress. The functional analysis of interactions between transcription factors and other proteins is very important for elucidating the role of these transcriptional regulators in different signaling cascades. In this review, we present an overview of protein-protein interactions for the six major families of transcription factors involved in plant defense: basic leucine zipper containing domain proteins (bZIP), amino-acid sequence WRKYGQK (WRKY), myelocytomatosis related proteins (MYC), myeloblastosis related proteins (MYB), APETALA2/ ETHYLENE-RESPONSIVE ELEMENT BINDING FACTORS (AP2/EREBP) and no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF), and cup-shaped cotyledon (CUC) (NAC). We describe the interaction partners of these transcription factors as molecular responses during pathogen attack and the key components of signal transduction pathways that take place during plant defense responses. These interactions determine the activation or repression of response pathways and are crucial to understanding the regulatory networks that modulate plant defense responses. Full article
(This article belongs to the Special Issue Plant Proteomics) Print Edition available

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