A plethora of intercellular signals during Caenorhabditis elegans development.

Reproducible cell-cell interactions contribute to the invariance of Caenorhabditis elegans development and allow high resolution study of molecular mechanisms of intercellular signaling. A number of new cell interactions have been discovered in the past year. The power of nematode molecular genetics has been increased through several technical advances and the genome project, and these new approaches are now being successfully applied both to familiar and new signaling mechanisms.     

Regulation of with‐no‐lysine kinase signaling by Kelch‐like proteins

In 2001, with‐no‐lysine (WNK) kinases were identified as the genes responsible for the human hereditary hypertensive disease pseudohypoaldosteronism type II (PHAII). It took a further 6 years to clarify that WNK kinases participate in a signaling cascade with oxidative stress‐responsive gene 1 (OSR1), Ste20‐related proline‐alanine‐rich kinase (SPAK), and thiazide‐sensitive NaCl cotransporter (NCC) in the kidney and the constitutive activation of this signaling cascade is the molecular basis of PHAII. Since this discovery, the WNK–OSR1/SPAK–NCC signaling cascade has been shown to be involved not only in PHAII but also in the regulation of blood pressure under normal and pathogenic conditions, such as hyperinsulinemia. However, the molecular mechanisms of WNK kinase regulation by dietary and hormonal factors and by PHAII‐causing mutations remain poorly understood. In 2012, two additional genes responsible for PHAII, Kelch‐like 3 (KLHL3) and Cullin3, were identified. At the time of their discovery, the molecular mechanisms underlying the interaction between these genes and their involvement in PHAII were unknown. Here we review the pathophysiological roles of the WNK signaling cascade clarified to date and introduce a new mechanism of WNK kinase regulation by KLHL3 and Cullin3, which provides insight on previously unknown mechanisms of WNK kinase regulation.     

Root Defense Responses to Fungal Pathogens: A Molecular Perspective

This review will focus on the molecular and genetic mechanisms underlying defense responses of roots to fungal pathogens. Soil-borne pathogens, including Phytophthora, Pythium, Fusarium, and Bipolaris, represent major sources of biotic stress in the rhizosphere and roots of plants. Molecular recognition and signaling leading to effective resistance has been demonstrated to occur between host and Phytophthora, or Pythium. The hypersensitive response and apoptotic cell death, two oxidative processes that limit biotrophic pathogens, generally act to exacerbate disease symptoms induced by necrotrophic organisms. Although pathogenesis-related proteins can be expressed in roots during pathogen challenge, salicylic acid has not been implicated in root-mediated interactions. Jasmonic acid and ethylene have been found to mediate parallel as well as synergistic pathways that confer partial tolerance to necrotrophic pathogens, as well as induced systemic resistance to root and foliar pathogens. Genomics approaches are revealing new networks of defense-signaling pathways, and have the potential of elucidating those pathways that are important in root-defense responses.     

Dorsal-ventral signaling in limb development

In both Drosophila wings and vertebrate limbs, signaling between dorsal and ventral cells establishes an organizer that promotes limb formation. Significant progress has been made recently towards characterizing the signaling interactions that occur at the dorsal—ventral limb border. Studies of chicks have indicated that, as in Drosophila, this signaling process requires the participation of Fringe. Studies of Drosophila have indicated that Fringe functions by inhibiting the ability of Notch to be activated by one ligand, Serrate, while potentiating the ability of Notch to be activated by another ligand, Delta. Recent studies of both Drosophila and vertebrates have also shed new light on the signaling activity of the dorsal—ventral boundary limb organizer, and have highlighted how this organizer is maintained by feedback mechanisms with neighboring cells.     

The changing world of G protein-coupled receptors: from monomers to dimers and receptor mosaics with allosteric receptor–receptor interactions

Based on indications of direct physical interactions between neuropeptide and monoamine receptors in the early 1980s, the term receptor–receptor interactions was introduced and later on the term receptor heteromerization in the early 1990s. Allosteric mechanisms allow an integrative activity to emerge either intramolecularly in G protein-coupled receptor (GPCR) monomers or intermolecularly via receptor–receptor interactions in GPCR homodimers, heterodimers, and receptor mosaics. Stable heteromers of Class A receptors may be formed that involve strong high energy arginine–phosphate electrostatic interactions. These receptor–receptor interactions markedly increase the repertoire of GPCR recognition, signaling and trafficking in which the minimal signaling unit in the GPCR homomers appears to be one receptor and one G protein. GPCR homomers and GPCR assemblies are not isolated but also directly interact with other proteins to form horizontal molecular networks at the plasma membrane.     

Investigating the effect of key mutations on the conformational dynamics of toll‐like receptor dimers through molecular dynamics simulations and protein structure networks

The Toll‐like receptors (TLRs) are critical components of the innate immune system due to their ability to detect conserved pathogen‐associated molecular patterns, present in bacteria, viruses, and other microorganisms. Ligand detection by TLRs leads to a signaling cascade, mediated by interactions among TIR domains present in the receptors, the bridging adaptors and sorting adaptors. The BB loop is a highly conserved region present in the TIR domain and is crucial for mediating interactions among TIR domain‐containing proteins. Mutations in the BB loop of the Toll‐like receptors, such as the A795P mutation in TLR3 and the P712H mutation (Lps^d mutation) in TLR4, have been reported to disrupt or alter downstream signaling. While the phenotypic effect of these mutations is known, the underlying effect of these mutations on the structure, dynamics and interactions with other TIR domain‐containing proteins is not well understood. Here, we have attempted to investigate the effect of the BB loop mutations on the dimer form of TLRs, using TLR2 and TLR3 as case studies. Our results based on molecular dynamics simulations, protein–protein interaction analyses and protein structure network analyses highlight significant differences between the dimer interfaces of the wild‐type and mutant forms and provide a logical reasoning for the effect of these mutations on adaptor binding to TLRs. Furthermore, it also leads us to propose a hypothesis for the differential requirement of signaling and bridging adaptors by TLRs. This could aid in further understanding of the mechanisms governing such signaling pathways.     

Interactions of Paracoccidioides brasiliensis with host cells: recent advances

Host-fungal interactions are inherently complex and dynamic. In order to identify new microbial targets and develop more effective anti-fungal therapies, it is important to understand the cellular and molecular mechanisms of disease. Paracoccidioidomycosis provokes a variety of clinical symptoms, and Paracoccidioides brasiliensis can reach many tissues, but primarily attacks the lungs. The ability of the pathogen to interact with the host surface structures is essential to further colonization, invasion, and growth. Epithelial cells may represent the first host barrier or the preferential site of entry of the fungus. For this reason, interactions between P. brasiliensis and Vero/A549 epithelial cells were evaluated, with an emphasis on the adherence, induction of cytoskeletal alterations, and differential signaling activity of the various surface molecules. The adhesion to and invasion of epithelial cells by P. brasiliensis may represent strategies employed to thwart the initial host immune response, and may help in the subsequent dissemination of the pathogen throughout the body.     

Bacterial chemoreceptors: high-performance signaling in networked arrays

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.     

The RAS and YAP1 dance,who is leading?

The Hippo‐signaling effector YAP1 was recently found to compensate for oncogenic RAS in certain neoplasms, suggesting so far unanticipated molecular interplays between these major signaling routes. A new study in this issue of The EMBO Journal details KRAS‐dependent control of YAP1 stability as well as positive feedback regulation via the RAS/YAP1/EGFR‐ligand axis as novel molecular mechanisms that could become exploitable for therapeutic strategies.     

In vivo Rac/Rop localization as well as interaction with RhoGAP and RhoGDI in tobacco pollen tubes: analysis by low‐level expression of fluorescent fusion proteins and bimolecular fluorescence complementation

Polarized Rac/Rop GTPase signaling plays a key role in polar cell growth, which is essential for plant morphogenesis. The molecular and cellular mechanisms responsible for the polarization of Rac/Rop signaling during polar cell growth are only partially understood. Mutant variants of Rac/Rop GTPases lacking specific functions are important tools to investigate these mechanisms, and have been employed to develop a model suggesting that RhoGAP (GTPase activating protein) and RhoGDI (Guanine Nucleotide Dissociation Inhibitor) mediated recycling of Rac/Rop GTPases maintains apical polarization of Rac/Rop activity in pollen tubes, which elongate by ‘tip growth’ (an extreme form of polar cell growth). Despite the importance of these mutant variants for Rac/Rop functional characterization, their distinct intracellular distributions have not been thoroughly comparatively and quantitatively analyzed. Furthermore, support for the proposed RhoGAP and RhoGDI functions in apical polarization of Rac/Rop activity based on the analysis of in vivo interactions between these proteins and Rac/Rop GTPases has been missing. Here, extensive fluorescent protein tagging and bimolecular fluorescence complementation (BiFC) analyses are described of the intracellular distributions of wild type and mutant variants of the tobacco pollen tube Rac/Rop GTPase Nt‐Rac5, as well as of interactions of these Nt‐Rac5 variants with RhoGAP and RhoGDI proteins, in normally growing transiently transformed pollen tubes. Presented results substantially enhance our understanding of apical dynamics of pollen tube Rac/Rop signaling proteins, confirm previously proposed RhoGAP and RhoGDI functions in Rac/Rop polarization and provide important technical insights facilitating future in vivo protein localization and BiFC experiments in pollen tubes.     

Sexual incompatibility in Rosaceae fruit tree species: molecular interactions and evolutionary dynamics

Fruit crops have a growing economic importance worldwide and molecular genetics might be useful in solving many problems that arise during commercial production. One of the fields that have attracted intense attention is the molecular basis of self-incompatibility that may result in low fruit set. In tree fruits of the Rosaceae family, the incompatibility reactions take place between the pistil S-ribonuclease (S-RNase) and the pollen-expressed S-haplotype specific F-box (SFB) proteins. In most cases, the loss of self-incompatibility was associated with mutations in the S-RNase or SFB genes. A total of 27 non-functional S-haplotypes have been identified and characterized, most (24) of which emerged as a consequence of natural mutations. In the Prunoideae, most haplotypes are pollen-part mutants (50 %), while 8 are stylar-part mutants (36 %), one haplotype shows both pollen- and stylar-part mutations, and molecular changes for two haplotypes still have not been clarified. In contrast, non-functional natural haplotypes in the Maloideae are all stylar-part mutants. The analysis of such mutants may shed light on underlying molecular mechanisms as was the case with the establishment of the general inhibitor model that describes interactions between pollen and pistil S-proteins. However, several other molecules were supposed to contribute to the molecular interactions, at least in Solanaceae, a family with a similar self-incompatibility system. This review also endeavours to delineate the evolutionary implications of the S-locus mutations and collect limited data on non-S-locus molecular interactions and signaling events after self- and cross-pollination of fruit tree species.     

Subcellular targeting by membrane lipids

The reversible localization of signaling proteins to both the plasma and the internal membranes of cells is critical for the selective activation of downstream functions and depends on interactions with both proteins and membrane lipids. New structural and biochemical analyses of C1, C2, PH, FYVE, FERM and other domains have led to an unprecedented amount of information on the molecular interactions of these signaling proteins with regulatory lipids. A wave of studies using GFP-tagged membrane binding domains as reporters has led to new quantitative insights into the kinetics of these signaling mechanisms.     

How do digits emerge? – mathematical models of limb development

The mechanism that controls digit formation has long intrigued developmental and theoretical biologists, and many different models and mechanisms have been proposed. Here we review models of limb development with a specific focus on digit and long bone formation. Decades of experiments have revealed the basic signaling circuits that control limb development, and recent advances in imaging and molecular technologies provide us with unprecedented spatial detail and a broader view of the regulatory networks. Computational approaches are important to integrate the available information into a consistent framework that will allow us to achieve a deeper level of understanding, and that will help with the future planning and interpretation of complex experiments, paving the way to in silico genetics. Previous models of development had to be focused on very few, simple regulatory interactions. Algorithmic developments and increasing computing power now enable the generation and validation of increasingly realistic models that can be used to test old theories and uncover new mechanisms. Birth Defects Research (Part C) 102:1–12, 2014. © 2014 Wiley Periodicals, Inc.     

韧皮部取食昆虫诱导的植物防御反应

刺吸式昆虫与寄主植物之间具有特殊的生物互作关系。本文对刺吸式昆虫取食韧皮部诱导的植物防御反应类型、 防御物质变化、 信号途径以及植物反应转录组学研究等方面进行综述。韧皮部取食昆虫取食诱导的植物防御反应机制主要包括： (1)改变自身的营养状况; (2)产生有毒的次生化合物; (3)产生防御蛋白。防御反应与植物水杨酸、 茉莉酸、 乙烯等信号分子密切相关。研究表明, 刺吸式昆虫取食诱导的植物防御反应主要引发以水杨酸为主的信号途径, 但相关分子互作机制还有待明确。日益丰富的基因组资源和不断发展的分子生物学技术为揭示植物防御反应中信号分子的作用机制、 找出植物内生抗性的特异因子以及阐明诱导防御机制奠定了基础。了解刺吸式昆虫取食诱导的植物防御反应, 为深入理解植物-昆虫间协同进化关系提供了依据, 为害虫治理和抗虫植物的培育提供了新的思路。     

Yeast killer toxins,molecular mechanisms of their action and their applications

Killer toxins secreted by some yeast strains are the proteins that kill sensitive cells of the same or related yeast genera. In recent years, many new yeast species have been found to be able to produce killer toxins against the pathogenic yeasts, especially Candida albicans. Some of the killer toxins have been purified and characterized, and the genes encoding the killer toxins have been cloned and characterized. Many new targets including different components of cell wall, plasma membrane, tRNA, DNA and others in the sensitive cells for the killer toxin action have been identified so that the new molecular mechanisms of action have been elucidated. However, it is still unknown how some of the newly discovered killer toxins kill the sensitive cells. Studies on the killer phenomenon in yeasts have provided valuable insights into a number of fundamental aspects of eukaryotic cell biology and interactions of different eukaryotic cells. Elucidation of the molecular mechanisms of their action will be helpful to develop the strategies to fight more and more harmful yeasts.     

Bioelectromagnetic medicine: The role of resonance signaling

Only recently has the critical importance of electromagnetic (EM) field interactions in biology and medicine been recognized. We review the phenomenon of resonance signaling, discussing how specific frequencies modulate cellular function to restore or maintain health. The application of EM-tuned signals represents more than merely a new tool in information medicine. It can also be viewed in the larger context of EM medicine, the all-encompassing view that elevates the EM over the biochemical. The discovery by Zhadin that ultrasmall magnetic intensities are biologically significant suggests that EM signaling is endogenous to cell regulation, and consequently that the remarkable effectiveness of EM resonance treatments reflects a fundamental aspect of biological systems. The concept that organisms contain mechanisms for generating biologically useful electric signals is not new, dating back to the nineteenth century discovery of currents of injury by Matteucci. The corresponding modern-day version is that ion cyclotron resonance magnetic field combinations help regulate biological information. The next advance in medicine will be to discern and apply those EM signaling parameters acting to promote wellness, with decreasing reliance on marginal biochemical remediation and pharmaceuticals.     

Phototransduction in Drosophila

The Drosophila visual transduction is the fastest known G protein-coupled signaling cascade and has been served as a model for understanding the molecular mechanisms of other G protein-coupled signaling cascades. Numbers of components in visual transduction machinery have been identified. Based on the functional characterization of these genes, a model for Drosophila phototransduction has been outlined, including rhodopsin activation, phosphoinoside signaling, and the opening of TRP and TRPL channels. Recently, the characterization of mutants, showing slow termination, revealed the physiological significance and the mechanism of rapid termination of light response.     

Unique features of the rice blast resistance <Emphasis Type="Italic">Pish</Emphasis> locus revealed by large scale retrotransposon-tagging

Background  

R gene-mediated resistance is one of the most effective mechanisms of immunity against pathogens in plants. To date some components that regulate the primary steps of plant immunity have been isolated, however, the molecular dissection of defense signaling downstream of the R proteins remains to be completed. In addition, R genes are known to be highly variable, however, the molecular mechanisms responsible for this variability remain obscure.     

Construction of a dual affinity tagged allele of the Rb1 tumor suppressor gene in the mouse

Loss of Rb1 tumor suppressor gene function is involved in the genesis of most human cancers. Novel therapies targeting Rb1 have been slow to develop because of our incomplete understanding of its molecular mechanisms of action. Rb1 protein (pRb) binds a host of cellular genes and proteins, and these molecular interactions mediate its various functions. Given the potential complexity of these molecular interactions and the lack of established methods for pRb purification, it has been difficult to systematically identify gene and protein interactions relevant to tumor suppression in different tissues in vivo. To address this limitation, we have generated a dual affinity tagged Rb1 allele in the mouse. The tagged allele functions as wild type and the encoded protein can be purified by tandem affinity chromatography. This allele will facilitate identification and characterization of native pRb molecular interactions in any tissue accessible in the mouse. genesis 48:121–126, 2010. © 2009 Wiley‐Liss, Inc.