Plant Proteomic Research

Plants, being sessile in nature, are constantly exposed to environmental challenges resulting in substantial yield loss. To cope with harsh environments, plants have developed a wide range of adaptation strategies involving morpho-anatomical, physiological, and biochemical traits. In recent years, there has been phenomenal progress in the understanding of plant responses to environmental cues at the protein level. This progress has been fueled by the advancement in mass spectrometry techniques, complemented with genome-sequence data and modern bioinformatics analysis with improved sample preparation and fractionation strategies. As proteins ultimately regulate cellular functions, it is perhaps of greater importance to understand the changes that occur at the protein-abundance level, rather than the modulation of mRNA expression. This Special Issue on "Plant Proteomic Research" brings together a selection of insightful papers that address some of these issues related to applications of proteomic techniques in elucidating master regulator proteins and the pathways associated with plant development and stress responses. This Issue includes four reviews and 13 original articles primarily on environmental proteomic studies

Plant Proteomic Research 4.0

As an important tool of systems biology, proteomics has enabled a deep understanding of different plant processes and functions. Complemented with genomic data, computational tools, and improved sample preparation strategies, proteomics has an unprecedented opportunity to characterize plant proteoforms in high spatial and temporal resolution. This special issue of Plant Proteomic Research 4.0 captures the recent advancements in proteomics and addresses the current challenges of plant stress response and resilience in the ever-changing climate. It contains 12 articles, including three reviews and nine original research articles. The three reviews deal with pollen phosphoproteomics, starch biosynthesis-related proteins and posttranslational modifications (PTMs) in rice developing seeds, and PTMs of waxy proteins in rice grain. The nine research articles include three related to temperature, two on water stress, two on salt stress, one on fungal pathogen, and the last one on field-grown potato apoplast proteome. The articles reflect the current frontiers of plant proteomics, focusing on themes of environmental stresses, proteoforms/PTMs, crop species, and new development in data-independent acquisition mass spectrometry. They provide readers insights into current technologies, their utility in understanding plant growth and resilience, as well as directions of proteomics in the frontiers of systems biology and synthetic biology

Legume Genetics and Biology

Legumes have played an important part as human food and animal feed in cropping systems since the dawn of agriculture. The legume family is arguably one of the most abundantly domesticated crop plant families. Their ability to symbiotically fix nitrogen and improve soil fertility has been rewarded since antiquity and makes them a key protein source. Pea was the original model organism used in Mendel´s discovery of the laws of inheritance, making it the foundation of modern plant genetics. This book based on Special Issue provides up-to-date information on legume biology, genetic advances, and the legacy of Mendel

Characterizing the transcriptional regulation of crassulacean acid metabolism in Kalanchoe

Due to the agricultural challenges posed by the prospect of a hotter drier climate understanding the molecular basis of plant water-use efficiency is of increasing importance. Species performing crassulacean acid metabolism (CAM) photosynthesis have evolved to be naturally water-use efficient primarily through shifting their carbon uptake to night to minimize water-loss. Relative to C3 and C4 photosynthesis species, CAM plants are enriched for rhythmic circadian clock-dependent regulation of metabolic processes. However, the transcriptional regulation of CAM remains largely uncharacterized. Using Kalanchoe fedtschenkoi, in which CAM develops along a leaf developmental gradient, candidate transcription factors with possible CAM-related functions were identified. The mRNA abundance of these transcription factors increases upon the transition from C3 photosynthesis to CAM and they appear to exhibit a circadian phase-dependent pattern of regulation. To better characterize the transcriptional control circuits underlying CAM, three such of these transcription factors, KfNF-YB3, KfHomeodomain-like, and KfMYB59 were selected for chromatin immunoprecipitation-sequencing (ChIP-seq). However, these experiments failed to identify enriched target genomic loci possibly as a consequence of the unique challenges of adapting experimental protocols designed for model C3 photosynthesis plant species to a succulent plant such as Kalanchoe. Additionally, this work focuses on elucidating the cis-regulatory elements and the trans-acting factors governing the transcriptional control of the phosphoenolpyruvate carboxylase gene (Ppc1) in Kalanchoe. Despite this enzyme’s importance in catalyzing the primary nocturnal fixation of CO2 in CAM species, the complex regulatory mechanisms underlying its expression are not well-studied. We examined the Kalanchoe Ppc1 promoter and identified numerous cis-regulatory elements on the basis of their sequence conservation with known regulatory modules. These individual elements along with two-hundred base pair region segments of the Kalanchoe Ppc1 promoter were used at bait probes in yeast one-hybrid (Y1H) assays. From this analysis, several high-confidence interacting transcriptional regulators were identified including ERF9, ERF106, TCP4, and PIF1. In silico examination of the Ppc1 promoter revealed likely binding sites for these factors based on homology to validated preferred binding sequences in Arabidopsis. The specific transcription factors identified through this work can now serve as the basis for further experiments to confirm interaction with the Ppc1 promoter and elucidate the nature of their regulatory effects. Overall, the work presented in this dissertation attempts to investigate the transcriptional control of crassulacean acid metabolism using the developmental CAM model Kalanchoe

Plant Stress Physiology

This book includes ten chapters addressing various aspects of plant stress physiology, including plant responses and tolerance to abiotic and biotic stress. These chapters summarize recent findings on the physiological and molecular mechanisms of stress tolerance. They also discuss approaches to enhancing plant productivity via stress tolerance mechanisms. This book is useful for undergraduate and graduate students, teachers, and researchers in the field of plant physiology and crop science

Molecular Aspects of Plant Salinity Stress and Tolerance

This book presents the advances in plant salinity stress and tolerance, including mechanistic insights revealed using powerful molecular tools and multi-omics and gene functions studied by genetic engineering and advanced biotechnological methods. Additionally, the use of plant growth-promoting rhizobacteria in the improvement of plant salinity tolerance and the underlying mechanisms and progress in breeding for salinity-tolerant rice are comprehensively discussed. Clearly, the published data have contributed to the significant progress in expanding our knowledge in the field of plant salinity stress and the results are valuable in developing salinity-stress-tolerant crops; in benefiting their quality and productivity; and eventually, in supporting the sustainability of the world food supply

Approaches in Enhancing Antioxidant Defense in Plants

This Special Issue, “Approaches in Enhancing Antioxidant Defense in Plants” published 13 original research works and a couple of review articles that discuss the various aspects of plant oxidative stress biology and ROS metabolism, as well as the physiological mechanisms and approaches to enhancing antioxidant defense and mitigating oxidative stress. These papers will serve as a foundation for plant oxidative stress tolerance and, in the long term, provide further research directions in the development of crop plants’ tolerance to abiotic stress in the era of climate change

Identification and Characterization of Salinity Tolerance Genes by Activation Tagging in Arabidopsis

Salinity often affects irrigated areas in arid and semi-arid regions of the world. The existence and accumulation of soluble salts in the soil layers limit the growth of crops essential for our food. Salt stress dramatically affects plant growth, plant development, as well as crop yield. Arabidopsis thaliana is the plant model that provides a comprehensive knowledge of plant development, genetics and physiology, and response to abiotic stresses such as salinity. The redundancy of genes due to duplication, even in the simple model genome of Arabidopsis, limits the value of knockout (KO) mutagenesis to provide complete information on gene function. ‘Gain-of-function’ mutants are an alternative genetic tool to identify gene functions for redundant genes, and those with small effect or that respond to an environmental condition. Transposon-mediated ‘activation tagging’ is an efficient genetic tool that can randomly generate ‘gain-of-function’ mutants for a large number of genes. In the method used here, the transposable element Enhancer-Inhibitor (En-I/dSpm) system of maize was modified to develop an activation tag (AT) mutant library in Arabidopsis. The mobile I-AT transposon contains a transcriptional enhancer, from the cauliflower mosaic virus (CaMV) 35S promoter, located close to the right border of the transposon. This I-AT element was mobilized to randomly insert into the plant genome by transposition from the T-DNA, and can give rise to mutants differing in the level of overexpression of the adjacent genes. Consequently, the gain-of-function dominant phenotypes generated are displayed by the I-AT plants due to enhanced expression of the gene(s) adjacent to the 35S enhancer. In this study, the I-AT library was used to screen for salt tolerance, identified by enhanced growth or biomass of the tagged mutants compared to the wild-type grown in saline conditions. A number of tagged salt tolerance candidate genes were identified flanking the I-AT insertion, and their tagged genes characterized for their role in salt tolerance

Plant Defense Mechanisms

Recent human migrations, technological advances, agricultural activities, and climate change-induced phenomenon have forced plants to increasingly adapt to new environments. This book highlights current morphological, anatomical, physiological, molecular, and genomic advances in plant defense mechanisms. These advances, including epigenetic mechanisms, have been linked to observed phenotypic plant plasticity. Researchers have found intriguing plant interactions and novel mechanisms, which have increased our understanding of how sessile plants adapt to and thrive in challenging environments. The studies in this book consider the resilience and sustainability of plant genomes and epigenomes and the role they will play in the next generation of food systems