The RLK/Pelle family of kinases

The RLK/Pelle class of proteins kinases is composed of over 600 members in Arabidopsis. Many of the proteins in this family are receptor-like kinases (RLK), while others have lost their extracellular domains and are found as cytoplasmic kinases. Proteins in this family that are RLKs have a variety of extracellular domains that drive function in a large number of processes, from cell wall interactions to disease resistance to developmental control. This review will briefly cover the major subclasses of RLK/Pelle proteins and their roles. In addition, two specific groups on RLKs will be discussed in detail, relating recent findings in Arabidopsis and how well these conclusions have been able to be translated to agronomically important species. Finally, some details on kinase activity and signal transduction will be addressed, along with the mystery of RLK/Pelle members lacking kinase enzymatic activity.     

Challenges and progress towards understanding the role of effectors in plant-fungal interactions

Both mutualistic and biotrophic pathogenic fungi rely on living host plants for growth and reproduction and must modify host cell structure and function for successful infection. The deployment of a diverse set of secreted virulence determinants referred to as 'effectors', many of which are directly delivered into the host cell, is postulated to be the key to host infection. This review provides a snapshot of the current progress in fungal effector biology. Recent genome sequencing of rust and powdery mildew obligate biotrophs has provided insight into the repertoires of potential effectors of these highly specialised pathogens. Identification of the first host-translocated effectors from mutualistic fungi has revealed that these fungi also manipulate host cells through effectors. The biological activities of some fungal effectors are just beginning to be revealed, while much uncertainty still surrounds the mechanisms of transport into host cells.     

Recent advances in understanding serotonin regulation of cardiovascular function

Serotonin is an important neurohormonal factor that has been implicated in cardiovascular function. It can regulate vascular tone, act directly on cardiomyocytes and stimulate chemosensitive nerves in the heart. Cardiovascular dysfunction is observed when serotonin signaling is altered or when variation in serotonin concentration occurs. Recent studies have provided evidence that, in the absence of peripheral serotonin synthesis, blood serotonin (which is almost exclusively stored in platelets) is markedly reduced, and that this drop leads to heart failure. This implies that the level of circulating serotonin is a key factor in maintaining normal cardiovascular activity. These findings offer new prospects for the use of serotonin in therapies for cardiovascular diseases.     

Information theoretic approaches to understanding circuit function

The analysis of stimulus/response patterns using information theoretic approaches requires the full probability distribution of stimuli and response. Recent progress in using information-based tools to understand circuit function has advanced understanding of neural coding at the single cell and population level. In advances over traditional reverse correlation approaches, the determination of receptive fields using information as a metric has allowed novel insights into stimulus representation and transformation. The application of maximum entropy methods to population codes has opened a rich exploration of the internal structure of these codes, revealing stimulus-driven functional connectivity. We speculate about the prospects and limitations of information as a general tool for dissecting neural circuits and relating their structure and function.     

Thiol-modifying inhibitors for understanding squalene cyclase function.

The function of squalene-hopene cyclase from Alicyclobacillus acidocaldarius was studied by labelling critical cysteine residues of the enzyme, either native or inserted by site-directed mutagenesis, with different thiol-reacting molecules. The access of the substrate to the active centre cavity through a nonpolar channel that contains a narrow constriction harbouring a cysteine residue (C435) was probed by labelling experiments on both a C435S mutant, lacking C435 of the channel constriction, and a C25S/C50S/C455S/C537S mutant, bearing C435 as the only cysteine residue. Labelling experiments with tritiated 3-carboxy-4-nitrophenyl-dithio-1,1',2-trisnorsqualene (CNDT-squalene) showed that the cysteine residue at the channel constriction was covalently modified by the squalene-like inhibitor. Time-dependent inactivation of the C25S/C50S/C455S/C537S mutant by a number of squalene analogues and other agents with thiol-modifying activity suggested that modifying C435 caused the obstruction of the channel constriction thus blocking access of the substrate to the active site. The tryptic fragment comprising C435 of the quadruple mutant labelled with the most effective inhibitor had the expected altered molecular mass, as determined by LC-ESI-MS measurements. The arrangement of the substrate in the active site cavity was studied by using thiol reagents as probes in labelling experiments with the double mutant D376C/C435S in which D376, supposedly the substrate-protonating residue, was substituted by cysteine. The inhibitory effect was evaluated in terms of the reduced ability to cyclize oxidosqualene, as the mutant is unable to catalyse the reaction of squalene to hopene. Among the inhibitors tested, the substrate analogue squalene-maleimide proved to be a very effective time-dependent inhibitor.     

Current understanding of the function of magnesium chelatase

Despite the global significance of chlorophylls and other modified tetrapyrroles, many aspects of their biosynthetic pathways are poorly understood. A key enzyme at the branch point between the haem and chlorophyll pathways, magnesium chelatase, couples the free energy of ATP hydrolysis to the insertion of magnesium into porphyrin, a process that is likely to be mediated through protein conformational changes. Conclusions from recent structural and functional studies of individual subunits are combined to provide a mechanistic outline of the full magnesium chelatase complex. Gathering further information presents a considerable challenge, and recent steps towards this goal will be introduced.     

Bioinformatic strategies for better understanding of immune function

Novartis Foundation sponsored a Symposium which brought together a group of experimental immunologists, theoretical immunologists, and bioinformaticians to discuss the new field of immunoinformatics. The discussion focused on immunological databases, antigen processing and presentation, immunogenomics, host-pathogen interactions, and mathematical modelling of the immune system. A main conclusion of the meeting is the critical role played by immunoinformatics in current immunology research. In particular, immunoinformatics provides a foundation for the emerging fields of systems immunology and immunogenomics.     

Chromosome conformation capture technologies and their impact in understanding genome function

It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencing-based approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the three-dimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.     

L-type voltage-gated calcium channels: understanding function through structure

L-type voltage-gated calcium channels (VGCCs) are multisubunit membrane proteins that regulate calcium influx into excitable cells. Within the last two years there have been four separate reports describing the structure of the skeletal muscle VGCC determined by electron microscopy and single particle analysis methods. There are some discrepancies between the structures, as well as reports for both monomeric and dimeric forms of the channel. This article considers each of the VGCC structures in terms of similarities and differences with an emphasis upon translation of data into a biological context.     

Centrosome biogenesis and function: centrosomics brings new understanding

Centrosomes, which were first described in the late 19th century, are found in most animal cells and undergo duplication once every cell cycle so that their number remains stable, like the genetic material of a cell. However, their function and regulation have remained elusive and controversial. Only recently has some understanding of these fundamental aspects of centrosome function and biogenesis been gained through the concerted application of genomics and proteomics, which we term 'centrosomics'. The identification of new molecules has highlighted the evolutionary conservation of centrosome function and provided a conceptual framework for understanding centrosome behaviour and how it can go awry in human disease.     

Progress and problems in understanding the involvement of calcium in heart function

In this article we have briefly reviewed the role of Ca2+ in the excitation contraction coupling in the myocardium and have indicated that cardiac contraction and relaxation are initiated upon raising and lowering the intracellular concentration of free Ca2+, respectively. Different mechanisms for the entry of Ca2+ through sarcolemma as well as release of Ca2+ from sarcoplasmic reticulum and possibly mitochondria have been outlined for initiating cardiac contraction. Relaxation of the cardiac muscle appears to be intimately dependent upon efflux of Ca2+ through sarcolemma as well as sequestration of Ca2+ by the intracellular storage sites, particularly sarcoplasmic reticulum and possibly mitochondria. The actions of some pharmacological and pathophysiological interventions have been explained on the basis of changes in subcellular Ca2+ movements in myocardium. Quinidine, which produced an initial positive inotropic action on rat heart was also found to increase sarcolemmal Ca2+-ATPase activity without any changes in the Na+-K+ ATPase. Other antiarrhythmic agents, procainamide and lidocaine, also increased sarcolemmal Ca2+-ATPase activity without affecting the Na+-K+ ATPase. On the other hand, both Ca2+-ATPase and Na+-K+ ATPase activities were increased in heart sarcolemma obtained from cardiomyopathic hamsters. In this model the increased Ca2+-ATPase activity may promote the occurrence of intracellular Ca2+ overload in the cardiac cell whereas the increased Na+-K+ ATPase activity may increase Ca2+ efflux through Na+-Ca2+ exchange systems as an adaptive mechanism. It has been suggested that some caution should be exercised while interpreting the data from in vitro experiments in terms of functional changes in the myocardium. Furthermore, it has been proposed that the pathophysiology and pharmacology of Ca2+ movements at different membrane sites be understood fully in normal and diseased myocardium in order to improve the therapy of heart disease.     

Ecological genomics: understanding gene and genome function in the natural environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future.     

Toward an understanding of structure and function of ion channels

The second half of the 1980s is certain to be considered a turning point in the study of ion channels. Within the last few years, monumental advances in the application of molecular biology, single-channel recording, and direct molecular characterization have been brought to bear on the problem of relating the molecular structure of the ion channel proteins to their function in the cell membrane. Structure-function relationships can now be studied at a level of detail that was unimagined a decade ago. Recently, advances made with the techniques of molecular biology appear to have dominated the literature in this field; however, innovative strategies of structural characterization and electrical measurements of functioning channels in native and artificial membranes continue to break new ground. This paper is a selective review of current progress in understanding structure-function relationships in ion channels. The relative usefulness of determining amino acid sequences of channel proteins together with the resulting deductions about 3-dimensional structure and function will be evaluated with respect to the potential importance of studying the channel molecules more directly by biochemical, immunological, and electrophysiological methods. A full understanding of the details of channel structure and its relationship to function may be realized in the near future as a result of the interdisciplinary application of biophysical, biochemical, and molecular biological techniques.