Cation/proton antiporter complements of bacteria: why so large and diverse?

Most bacterial genomes have five to nine distinct genes predicted to encode transporters that exchange cytoplasmic Na⁺ and/or K⁺ for H⁺ from outside the cell, i.e. monovalent cation/proton antiporters. By contrast, pathogens that live primarily inside host cells usually possess zero to one such antiporter while other stress-exposed bacteria exhibit even higher numbers. The monovalent cation/proton antiporters encoded by these diverse genes fall into at least eight different transporter protein families based on sequence similarity. They enable bacteria to meet challenges of high or fluctuating pH, salt, temperature or osmolarity, but we lack explanations for why so many antiporters are needed and for the value added by specific antiporter types in specific settings. In this issue of Molecular Microbiology, analyses of the pH dependence of cytoplasmic [Na⁺], [K⁺], pH and transmembrane electrical potential in the 'poly extremophile' Natranaerobius thermophilus are the context for assessment of the catalytic properties of 12 predicted monovalent cation/proton antiporters in the genome of this thermophilic haloalkaliphile. The results provide a profile of adaptations of the poly extremophilic anaerobe, including a proposed role of cytoplasmic buffering capacity. They also provide new perspectives on two large monovalent cation/proton antiporter families, the NhaC and the cation/proton antiporter-3 antiporter families.     

Transdifferentiation: why and how?

Cell therapy is based on the replacement of damaged cells in order to restore injured tissues. The first consideration is that an abundant source of cells is needed; second, these cells should be immunologically compatible with the guest and third, there should be no real threat of these cells undergoing malignant transformation in the future. Given these requirements, already differentiated adult cells or adult stem cells obtained from the body of the patient appear to be the ideal candidates to meet all of these demands. The utilization of somatic cells also avoids numerous ethical and political drawbacks and concerns. Transdifferentiation is the phenomenon by which an adult differentiated cell switches to another differentiated cell. This paper reviews the importance of transdifferentiation, discussing the cells that are suitable for this process and the methods currently employed to induce the change in cell type.     

An ecological map of Europe: why and how?

After a recall of the recent emergence of the great ecological problems on the scale of the European continent and of the privileged use of vegetation maps as an ecological tool, a cartographic synthesis of the main plant formations in Europe is submitted on the basis of a hierarchized and numerized nomenclature of the vegetation units. Examples of connections between vegetation and ecology, as suggested or facilitated by this map, are given: use of the monthly ombrothermic diagrams as a privileged tool, thermic limits of the boreal zone, indicative value of the Mediterranean xerothermic area, predictive models of the geographical shifts of the great ecosystems according to the expected climate changes.     

Physiology of tmRNA: what gets tagged and why?

Transfer-messenger RNA (tmRNA) enters stalled translational complexes and, with small protein B (SmpB), mediates peptide tagging of the nascent protein and release of the stalled ribosome. Recent studies clarify how the tmRNA system is targeted to ribosomes and suggest that tmRNA-tagging is used for both quality control and specific regulation of cellular physiology.     

Brain donation: who and why?

Understanding what influences people to donate, or not donate, body organs and tissues is very important for the future of transplant surgery and medical research (Garrick in J Clin Neurosci 13:524–528, 2006). A previous web-based motivation survey coordinated by the New South Wales Tissue Resource Centre found that most people who participated in brain donation were young, female, educated Australians, not affiliated with any particular religion, and with a higher prevalence of medical illness than the general Australian population. It discussed the main motivating factors for brain donation to be “the benefits of the research to medicine and science”. This study has been replicated in a paper-based version to capture a broader cross-section of the general population, to find out who they are and what motivates them to donate. All consented and registered brain donors (n = 1,323) were sent a questionnaire via the post and recipients were given 3 months to complete the questionnaire and return it in a reply paid envelope. Results were entered into the original web-based survey and analyzed using SPSS version 10. Six hundred and fifty-eight questionnaires were returned completed, a response rate of 53%. The results show that people from all age groups are interested in brain donation. The over 65’s are the largest of the groups (30.7%). The majority of the participants were female (60.6%), married (49.2%) with children (65.8%), employed (52.9%) and have a tertiary education (73.3%). They were either non-religious (48.2%) or Christian (41.6%) and were mostly Australian (65.4%). Most (81%) had pledged to donate other organs and tissues for transplantation. The most commonly cited reasons for the donation were to benefit science (27.6%), to benefit medicine (23.9%), a family illness (17.5%) and to benefit the community (16.6%). This study demonstrates that people across all age groups are interested in brain donation. Recruitment of new brain donors could target the over 65 female Australians, who are not religious or Christian and who have also donated other organs and tissues for transplant purposes. It also indicates the need to make donation for research part of the national transplant donation program.     

Connecting ORC and heterochromatin: why?

Considerable evidence connects heterochromatin or silenced chromatin with the Origin Recognition Complex (ORC) which is needed for initiation of DNA replication. In this review we consider biological forces that might be served by this connection. The prevailing view in the literature is that ORC recruits heterochromatin. This seems paradoxical because a replication initiator, ORC, would be recruiting factors which seem to oppose replication by forming inaccessible chromatin structures. Here we suggest a different view, that heterochromatin recruits ORC to facilitate replication of hard-to-replicate heterochromatic regions. We consider how existing data can be reconciled with this viewpoint, and we consider the biological predictions that arise from this perspective     

How to measure and analyze tryptophan fluorescence in membranes properly, and why bother?

Tryptophan fluorescence is a powerful tool for studying protein structure and function, especially membrane-active proteins and peptides. It is arguably the most frequently used tool for examining the interactions of proteins and peptides with vesicular unilamellar model membranes. However, high light scattering associated with vesicular membrane systems presents special challenges. Because of their reduced light scattering compared to large unilamellar vesicles (LUV), small unilamellar vesicles (SUV) produced by sonication are widely used membrane models. Unfortunately, SUV, unlike LUV, are metastable and consequently unsuitable for equilibrium thermodynamic measurements. We present simple and easily implemented experimental procedures for the accurate determination of tryptophan (Trp) fluorescence in either LUV or SUV. Specifically, we show that Trp spectra can be obtained in the presence of up to 6 mM LUV that are virtually identical to spectra obtained in buffer alone, which obviates the use of SUV. We show how the widths and peak positions of such spectra can be used to evaluate the heterogeneity of the membrane conformation and penetration of peptides. Finally, we show how to use a reference fluorophore for the correction of intensity measurements so that the energetics of peptide partitioning into membranes can be accurately determined.     

Abundant proton pumping in Plasmodium,but why?

Intraerythrocytic Plasmodium parasites depend on glycolysis for energy production. The stoichiometric amounts of lactate and protons produced are efficiently removed by a lactate:H(+) symporter. However, inhibition of recently identified plasma-membrane proton pumps result in acidification, suggesting additional mechanism(s) for proton generation. This article attempts to integrate the knowledge on the metabolic generation of protons and their disposal in the regulation of parasite cytosolic pH, and suggests additional roles for the various proton pumps that act in the parasite membrane.     

Order parameters of unsaturated phospholipids in membranes and the effect of cholesterol: a 1H–13C solid-state NMR study at natural abundance

Most biological phospholipids contain at least one unsaturated alkyl chain. However, few order parameters of unsaturated lipids have been determined because of the difficulty associated with isotopic labeling of a double bond. Dipolar recoupling on axis with scaling and shape preservation (DROSS) is a solid-state nuclear magnetic resonance technique optimized for measuring ¹H–¹³C dipolar couplings and order parameters in lipid membranes in the fluid phase. It has been used to determine the order profile of 1,2-dimyristoyl-sn-glycero-3-phosphocholine hydrated membranes. Here, we show an application for the measurement of local order parameters in multilamellar vesicles containing unsaturated lipids. Taking advantage of the very good ¹³C chemical shift dispersion, one can easily follow the segmental order along the acyl chains and, particularly, around the double bonds where we have been able to determine the previously misassigned order parameters of each acyl chain of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We have followed the variation of such order profiles with temperature, unsaturation content and cholesterol addition. We have found that the phase formed by DOPC with 30% cholesterol is analogous to the liquid-ordered (l_o) phase. Because these experiments do not require isotopic enrichment, this technique can, in principle, be applied to natural lipids and biomembranes.Electronic Supplementary Material Supplementary material is available for this article at .     

Continuous endocytic recycling of tight junction proteins: how and why?

Tight junctions consist of many proteins, including transmembrane and associated cytoplasmic proteins, which act to provide a barrier regulating transport across epithelial and endothelial tissues. These junctions are dynamic structures that are able to maintain barrier function during tissue remodelling and rapidly alter it in response to extracellular signals. Individual components of tight junctions also show dynamic behaviour, including migration within the junction and exchange in and out of the junctions. In addition, it is becoming clear that some tight junction proteins undergo continuous endocytosis and recycling back to the plasma membrane. Regulation of endocytic trafficking of junctional proteins may provide a way of rapidly remodelling junctions and will be the focus of this chapter.     

Cell-cycle-specific Golgi fragmentation: how and why?

The Golgi membranes, in the form of stacks of cisternae, are contained in the pericentriolar region of mammalian cells. During mitosis, these membranes are fragmented and dispersed throughout the cell. Recent studies are revealing the significance of pericentriolar position of the Golgi apparatus and mechanism by which these membranes are fragmented during mitosis.     

Anomalous effect of uncouplers on respiratory chain-linked transhydrogenation in Escherichia coli membranes: evidence for a localized proton pathway?

Energization of the pyridine nucleotide transhydrogenase in everted membrane vesicles from Escherichia coli JM83 was compared with the process in vesicles of the same strain transformed with the plasmid pDC21 overexpressing this enzyme. Proton translocation was assayed by the quenching of the fluorescence of the probe quinacrine. Agents able to discharge transmembrane proton gradients such as nigericin and the uncouplers 3,3',4',5-tetrachlorosalicylanilide and carbonyl cyanide m-chlorophenylhydrazone inhibited ATP-dependent transhydrogenation of NADP by NADH and discharged transmembrane proton gradients generated by transhydrogenation of AcNAD by NADPH, by oxidation of NADH, and by hydrolysis of ATP. This was observed in everted membrane vesicles of both strains JM83 and JM83pDC21. These strains differed significantly in the response of the NADH oxidation-dependent transhydrogenase. This reaction was inhibited by nigericin and uncouplers in membrane vesicles of JM83 but there was little inhibition or the reaction was stimulated in JM83pDC21, in spite of the discharge of the NADH oxidation-generated proton gradient measured by quinacrine fluorescence in the latter strain. It is proposed that the transhydrogenase is energized by direct or local (nonbulk phase) proton translocation in membranes of this strain. Uncouplers might facilitate these routes but would not discharge them. The generality of these observations was shown using other strains. NADH oxidase activity was severalfold lower in membrane vesicles of JM83pDC21 compared with JM83. The levels of ubiquinone and cytochromes, and the activities of NADH dehydrogenases I and II, and of cytochrome oxidase, were similar in the two strains. It is concluded that the NADH oxidase activity of JM83pDC21 is low because of the reduced rate of collision between electron-transferring complexes of the respiratory chain due to the large amount of transhydrogenase protein in the membranes of this strain. The large amount of transhydrogenase favors direct, nonbulk phase proton transfer. Transhydrogenase activity was stimulated by Ca2+, Mg2+, or Mn2+.     

Apoptosis in the heart: when and why?

Since mammalian cardiac myocytes essentially rely on aerobic energy metabolism, it has been assumed that cardiocytes die in a catastrophic breakdown of cellular homeostasis (i.e. necrosis), if oxygen supply remains below a critical limit. Recent observations, however, indicate that a process of gene-directed cellular suicide (i.e. apoptosis) is activated in terminally differentiated cardiocytes of the adult mammalian heart by ischemia and reperfusion, and by cardiac overload as well. Apoptosis or programmed cell death is an actively regulated process of cellular self destruction, which requires energy and de novo gene expression, and which is directed by an inborn genetic program. The final result of this program is the fragmentation of nuclear DNA into typical nucleosomal ladders, while the functional integrity of the cell membrane and of other cellular organelles is still maintained. The critical step in this regulated apoptotic DNA fragmentation is the proteolytic inactivation of poly-[ADPribose]-polymerase (PARP) by a group of cysteine proteases with some structural homologies to interleukin-1-converting enzyme (ICE-related proteases [IRPs] such as apopain, yama and others). PARP catalyzes the ADP-ribosylation of nuclear proteins at the sites of spontaneous DNA strand breaks and thereby facilitates the repair of this DNA damage. IRP-mediated destruction of PARP, the supervisor of the genome, can be induced by activation of membrane receptors (e.g. FAS or APOI) and other signals, and is inhibited by activation of anti-death genes (e.g. bcl-2). Overload-triggered myocyte apoptosis appears to contribute to the transition to cardiac failure, which can be prevented by therapeutic hemodynamic unloading. In myocardial ischemia, the activation of the apoptotic program in cardiocytes does not exclude their final destiny to catastrophic necrosis with release of cytosolic enzymes, but might be considered as an adaptive process in hypoperfused ventricular zones, sacrificing some jeopardized myocytes to regulated apoptosis, which may by less arrhythmogenic than necrosis with the primary disturbance of membrane function.     

Evolving endosomes: how many varieties and why?

The cell biologist's insight into endosomal diversity, in terms of both form and function, has increased dramatically in the past few years. This understanding has been promoted by the availability of powerful new techniques that allow imaging of both cargo and machinery in the endocytic process in real time, and by our ability to inhibit components of this machinery by RNA interference. The emerging picture from these studies is of a highly complex, dynamic and adaptable endosomal system that interacts at various points with the secretory system of the cell.     

Cell-death alternative model organisms: why and which?

Classical model organisms have helped greatly in our understanding of cell death but, at the same time, might have constrained it. The use of other, non-classical model organisms from all biological kingdoms could reveal undetected molecular pathways and better-defined morphological types of cell death. Here we discuss what is known and what might be learned from these alternative model systems.     

High-resolution MRI: in vivo histology?

For centuries scientists have been fascinated with the question of how the brain works. Investigators have looked at both where different functions are localized and how the anatomical microstructure varies across the brain surface. Here we discuss how advances in magnetic resonance imaging (MRI) have allowed in vivo visualization of the fine structure of the brain that was previously only visible in post-mortem brains. We present data showing the correspondence between definitions of the primary visual cortex defined anatomically using very high-resolution MRI and functionally using functional MRI. We consider how this technology can be applied to allow the investigation of brains that differ from normal, and what this ever-evolving technology may be able to reveal about in vivo brain structure in the next few years.