Living organisms continuously monitor, interpret, and respond to their environments. They do so through an assortment of mechanisms, but the focus of this doctoral dissertation is on two strikingly prevalent mechanisms: calcium signaling and protein phosphoregulation. These two processes are linked through the activities of calcium-regulated protein kinases and phosphatases. This dissertation focuses on calcium signaling processes in plants and the role that calcium-decoding protein kinases, the elusive upstream calcium signal- coding complexes, and the downstream target proteins play in plant environmental responses. The described research builds upon recent advances in the field of plant genomics, merging bioinformatic methods with experimental approaches. Notably, much of the research utilizes genomic and transcriptomic data from an emerging model plant species, the moss Physcomitrella patens. Because all land plants are evolutionarily related, insights from mosses – an early-diverging plant lineage – are useful to classify proteins and assess functional conservation or divergence. In addition to synthesizing relevant published research, this dissertation describes the phylogenomic classification of a family of plant-specific calcium sensors known as calcineurin B-like proteins (CBLs) and their associated protein kinases (CIPKs). Plants feature several families of protein kinases that share a similar overall architecture: an N-terminal serine/threonine kinase domain coupled to a C-terminal autoinhibitory region. Some of these protein kinase families are either directly or indirectly regulated by calcium, the latter exemplified by CIPKs. Calcium-dependent protein kinases (CDPKs) are directly regulated by calcium through calcium-binding EF-hand domains in the autoinhibitory region. Both CIPKs and CDPKs constitute multi- gene families in all sequenced land plant genomes. In contrast, calcium/calmodulin-dependent protein kinases (CCaMKs) are found as single-copy genes in most sequenced plant genomes and have been evolutionarily lost in certain plant lineages, including the preeminent model plant Arabidopsis. The accepted rationale for the inferred independent losses of CCaMK loci has been that CCaMKs fulfill obligate functions in plant-microbe symbioses that are incompatible with some plant lineages due to relatively recent evolutionary events. During the course of characterizing CIPKs, the unexpected observation that Physcomitrella – which is incompetent for canonical plant-microbe symbioses – contains two loci encoding CCaMKs prompted an investigation into CCaMK function in mosses. Through implementation and refinement of a gain- of-function approach in Physcomitrella, this doctoral research demonstrated that activation of a Physcomitrella CCaMK (CCaMK1) was associated with formation of brood cells, a type of stress-induced asexual propagule formed by mosses. In legumes, CCaMK regulates CYCLOPS, a novel type of transcription factor, by phosphorylating it at two sites in its autoinhibitory region. Physcomitrella contains a single CYCLOPS homolog that interacts with CCaMK1 and shows strong sequence conservation at the two key phosphosites identified by prior work in legumes. Expression of a modified form of Physcomitrella CYCLOPS containing two putative phosphomimetic substitutions at these sites also likewise elicited brood cell formation. These observations suggest that Physcomitrella CCaMK and CYCLOPS homologs operate in a similar manner to the legume CCaMK-CYCLOPS module; yet in Physcomitrella, the module tends to a disparate function. This dissertation further describes efforts to identify ion channels that function in calcium signal-coding processes. These efforts contributed to the identification of a novel family of putative cation channels through a combination of heterologous expression, electrophysiological techniques, and bioinformatic approaches. This doctoral dissertation encompasses a broad range of interconnected processes involved in calcium signal generation and interpretation in biology, and the field stands to address many unanswered questions detailed here. To that end, prospective ideas for further investigation are provided in the concluding remarks.

Plants cannot move away from their environments. As a result, all plants that have survived to date have evolved sophisticated signaling mechanisms that allow them to perceive, respond, and adapt to constantly changing environmental conditions. Among the many cellular processes that respond to environmental changes, elevation of calcium levels is by far the most universal messenger that matches primary signals to cellular responses. Yet it remains unclear how calcium, a simple cation, translates so many different signals into distinct responses - how is the “specificity” of signal-response coupling encoded within the calcium changes? This book will attempt to answer this question by describing the cellular and molecular mechanisms underlying the coding and decoding of calcium signals in plant cells.

A comprehensive review of stress signaling in plants using genomics and functional genomic approaches Improving agricultural production and meeting the needs of a rapidly growing global population requires crop systems capable of overcoming environmental stresses. Understanding the role of different signaling components in plant stress regulation is vital to developing crops which can withstand abiotic and biotic stresses without loss of crop yield and productivity. Emphasizing genomics and functional genomic approaches, Protein Kinases and Stress Signaling in Plants is a comprehensive review of cutting-edge research on stress perception, signal transduction, and stress response generation. Detailed chapters cover a broad range of topics central to improving agricultural production developing crop systems capable of overcoming environmental stresses to meet the needs of a rapidly growing global population. This book describes the field of protein kinases and stress signaling with a special emphasis on functional genomics. It presents a highly valuable contribution in the field of stress perception, signal transduction and generation of responses against one or multiple stress signals. This timely resource: Summarizes the role of various kinases involved in stress management Enumerates the role of TOR, GSK3-like kinase, SnRK kinases in different physiological conditions Examines mitogen-activated protein kinases (MAPKs) in different stresses Describes the different aspects of calcium signaling under different stress conditions Examines photo-activated kinases (PAPKs) in varying light conditions Briefs the presence of tyrosine kinases in plants Highlights the cellular functions of receptor ]like protein kinases (RLKs) Possible implication of these kinases in developing stress tolerant crops Protein Kinases and Stress Signaling in Plants: Functional Genomic Perspective is an essential resource for researchers and students in the fields of plant molecular biology and signal transduction, plant responses to stress, plant cell signaling, plant protein kinases, plant biotechnology, transgenic plants and stress biology.

The regulation of the phosphorylation/dephosphorylation process, resulting in “cellular switches” that monitor normal plant physiology, growth and development, has immense potential in crop systems. With much of the information in the nascent stages, coming largely from Arabidopsis and rice particularly, the use of cell biology, genetic screens, biochemical approaches aided by an omics approach should help unravel the detail functional information available about signaling pathways in plants. The regulation could be exploited to develop crop varieties better equipped to handle changing environments and enhance agricultural productivity. In the post-genomic era, one of the major challenges is investigation and understanding of multiple genes and gene families regulating a particular physiological and developmental aspect of plant life cycle. One of the important physiological processes is regulation of stress response, which leads to adaptation or adjustment in response to adverse stimuli. With the holistic understanding of the signaling pathways involving phosphatases, one gene family or multiple genes or gene families, plant biologist can lay a foundation for designing and generating future crops, which can withstand the higher degree of environmental stresses. Especially abiotic stresses, which are the major cause of crop loss throughout the world without losing crop yield and productivity. This book incorporates the contributions from leading plant biologists in the field of stress-mediated dephosphorylation by phosphatases as an important task to elucidate the aspects of stress signaling by functional genomic approaches.

Plant Cold Acclimation: Methods and Protocols details many of the methods and protocols commonly used to study plant cold acclimation and freezing tolerance, breeding, genetics, physiology or molecular biology, or any combination of these specialties. Chapters focus on interdisciplinary approaches, experimental methods, and concepts from different areas of science. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Cold Acclimation: Methods and Protocols seeks to help not only new researchers starting in this field, but also those already working in a particular area of cold acclimation and freezing tolerance research who are looking to expand their range of experimental approaches.

This book will shed light on the effect of salt stress on plants development, proteomics, genomics, genetic engineering, and plant adaptations, among other topics. Understanding the molecular basis will be helpful in developing selection strategies for improving salinity tolerance. The book will cover around 25 chapters with contributors from all over the world.

​In this fast moving field the main goal of this volume is to provide up-to-date information on the molecular and functional properties and pharmacology of mammalian TRP channels. Leading experts in the field describe properties of a single TRP protein/channel or portray more general principles of TRP function and important pathological situations linked to mutations of TRP genes or their altered expression. Thereby this volume on Transient Receptor Potential (TRP) Channels provides valuable information for readers with different expectations and backgrounds, for those who are approaching this field of research as well as for those wanting to make a trip to TRPs.