Hydrophobic substances induce water stress in microbial cells

Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes – metabolites that protect against osmotic and chaotrope-induced stresses – ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope-induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.     

Male–Male Relationships in Lion-tailed Macaques (<Emphasis Type="Italic">Macaca silenus</Emphasis>) and Bonnet Macaques (<Emphasis Type="Italic">Macaca radiata</Emphasis>)

Socioecology suggests that female distribution in space is determined by the distribution of food resources and the male distribution is influenced by female distribution. Though studies have traditionally focused on females, males have received increasing attention in recent years. We compared male–male relationships in lion-tailed macaques and bonnet macaques. Because bonnet macaques have a high adult male:female sex ratio and are seasonal breeders whereas lion-tailed macaques have a low adult male:female sex ratio and are largely aseasonal breeders, we predicted that bonnet macaque males would be spatially and socially more tolerant of each other and would have less linear dominance relationships than lion-tailed macaques. We recorded male–male and male–female relationships in 1 group of wild macaques of each species via scan sampling and 1–0 sampling. The results revealed that lion-tailed macaque males largely remained at a distance from each other whereas bonnet macaque males remained in close proximity to one another. Lion-tailed macaque males were more agonistic toward each other whereas bonnet macaque males showed more affiliative interactions. The dominance hierarchy among lion-tailed macaque males was more linear than among bonnet macaque males. Our data support the hypothesis that the study of spatial structuring, temporality of interactions, and linearity of social relationships may contribute to a better understanding of macaque social systems.     

New nomenclature for mammalian BSP genes

BSP proteins and their homologs are a family of structurally related proteins characterized by the presence of tandem fibronectin type II domains. In the bovine species, BSP proteins were shown to be involved in sperm capacitation, a posttesticular maturation event necessary for sperm to acquire the ability to fertilize an oocyte. Recently, many new genes from this family have been discovered in numerous mammalian species. However, inconsistency in the nomenclature is creating much confusion. In light of the rapid growth of the BSP superfamily of proteins, we propose a new nomenclature in collaboration with the HUGO Gene Nomenclature Committee.     

mTORC1 Hyperactivity Inhibits Serum Deprivation-Induced Apoptosis via Increased Hexokinase II and GLUT1 Expression,Sustained Mcl-1 Expression,and Glycogen Synthase Kinase 3β Inhibition

The current concept is that Tsc-deficient cells are sensitized to apoptosis due to the inhibition of Akt activity by the negative feedback mechanism induced by the hyperactive mTORC1. Unexpectedly, however, we found that Tsc1/2-deficient cells exhibit increased resistance to serum deprivation-induced apoptosis. mTORC1 hyperactivity contributes to the apoptotic resistance of serum-deprived Tsc1/2-deficient cells in part by increasing the growth factor-independent expression of hexokinase II (HKII) and GLUT1. mTORC1-mediated increase in hypoxia-inducible factor 1α (HIF1α) abundance, which occurs in the absence of serum in normoxic Tsc2-deficient cells, contributes to these changes. Increased HIF1α abundance in these cells is attributed to both an increased level and the sustained translation of HIF1α mRNA. Sustained glycogen synthase kinase 3β inhibition and Mcl-1 expression also contribute to the apoptotic resistance of Tsc2-deficient cells to serum deprivation. The inhibition of mTORC1 activity by either rapamycin or Raptor knockdown cannot resensitize these cells to serum deprivation-induced apoptosis because of elevated Akt activity that is an indirect consequence of mTORC1 inhibition. However, the increased HIF1α abundance and the maintenance of Mcl-1 protein expression in serum-deprived Tsc2^−/− cells are dependent largely on the hyperactive eIF4E in these cells. Consistently, the reduction of eIF4E levels abrogates the resistance of Tsc2^−/− cells to serum deprivation-induced apoptosis.Growth factors are obligatory for the survival of mammalian cells. The evolutionarily conserved kinase Akt has emerged as the predominant and indispensable mediator of the ability of growth factors to promote cell survival in mammalian cells (reviewed in reference 9). Akt promotes cell survival by multiple mechanisms, including key roles in regulating cellular energy metabolism. Akt maintains mitochondrial integrity and inhibits apoptosis at least in part through effects on mitochondrial hexokinases and their functionally coupled facilitated glucose transporters (reviewed in reference 18). One of the most crucial functions of Akt involves the activation of the mammalian target of rapamycin complex 1 (mTORC1), which integrates growth factor signaling with nutritional cues and synchronizes these upstream signals with the downstream stimulation of cell growth and proliferation (reviewed in reference 1). Akt activates mTORC1 in part by inhibiting the heterodimeric tuberous sclerosis complex (Tsc1/Tsc2). Tsc2 (or tuberin) functions as a GTPase-activating protein (GAP) to specifically inhibit the small GTPase Rheb, which activates mTORC1. The formation of a functional heterodimeric complex between Tsc2 and Tsc1 (or hamartin) is required for mTORC1 inhibition. As such, the disruption of the expression or function of either Tsc1 or Tsc2 is sufficient to activate mTORC1. Mammalian cells have evolved a negative feedback mechanism between mTORC1 and Akt to maintain an optimal balance between their activities. When Akt activates mTORC1, it initiates a negative feedback loop that serves to attenuate Akt activity. As such, mTORC1 serves as both an upstream and a downstream effector of Akt signaling. The loss of a functional Tsc1/Tsc2 complex disrupts this delicate balance, resulting in mTORC1 hyperactivity, which greatly reduces Akt activation (reviewed in reference 1). This is relevant to the heritable development of tuberous sclerosis in humans, which is caused by the mutational inactivation of either the TSC1 or TSC2 gene, leading to benign hamartoma formation and growth in a variety of organs (11).It is widely appreciated that low basal Akt activity renders Tsc1/2-deficient cells more sensitive to proapoptotic stimuli (4, 19). Unexpectedly, however, we found that both Tsc1 and Tsc2 null cells exhibit increased apoptotic resistance to growth factor withdrawal despite greatly reduced Akt activity relative to that of their wild-type counterparts. This implies that Tsc1/2 deficiency promotes or unmasks potent antiapoptotic mechanisms that reduce mammalian cell dependence upon growth factors and Akt for survival. Further investigation has uncovered a critical role for mTORC1 in promoting cell survival in the absence of growth factors.Trophic growth factors found in serum play a pivotal role in the cellular uptake and utilization of glucose, and serum withdrawal results in attenuated glucose metabolism. The maintenance of glucose utilization by the overexpression of the rate-limiting glycolytic enzyme hexokinase and its functionally coupled facilitative glucose transporters maintains cell survival in the absence of growth factors (reviewed in reference 18). We found that serum deprivation markedly increased both hexokinase II (HKII) and GLUT1 abundance in Tsc2-deficient cells, and the knockdown of HKII and GLUT1 increased the apoptotic susceptibility of these cells to serum deprivation. The elevated expression of HKII and GLUT1 is mediated by hypoxia-inducible factor 1α (HIF1α) protein, which is markedly induced by mTORC1 in serum-deprived Tsc2^−/− cells.In addition to increased HKII and GLUT1 expression, Tsc2^−/− cells display the sustained inhibition of glycogen synthase kinase 3 (GSK3) activity and stable Mcl-1 abundance following serum withdrawal, which also contribute to their apoptotic resistance under these conditions. Mcl-1 abundance, which normally declines following serum deprivation, is sustained in Tsc2^−/− cells by the constitutive inhibition of GSK3 and the activation of eIF4E.     

A classification scoring schema to validate protein interactors

Hypothetical protein [HP] annotation poses a great challenge especially when the protein is putatively linked or mapped to another protein. With protein interaction networks (PIN) prevailing, many visualizers still remain unsupported to the HP annotation. Through this work, we propose a six-point classification system to validate protein interactions based on diverse features. The HP data-set was used as a training data-set to find putative functional interaction partners to the remaining proteins that are waiting to be interacting. A Total Reliability Score (TRS) was calculated based on the six-point classification which was evaluated using machine learning algorithm on a single node. We found that multilayer perceptron of neural network yielded 81.08% of accuracy in modelling TRS whereas feature selection algorithms confirmed that all classification features are implementable. Furthermore statistical results using variance and co-variance analyses confirmed the usefulness of these classification metrics. It has been evaluated that of all the classification features, subcellular location (sorting signals) makes higher impact in predicting the function of HPs.     

The Shigella dysenteriae serotype 1 proteome,profiled in the host intestinal environment,reveals major metabolic modifications and increased expression of invasive proteins

Shigella dysenteriae serotype 1 (SD1) causes the most severe form of epidemic bacillary dysentery. We present the first comprehensive proteome analysis of this pathogen, profiling proteins from bacteria cultured in vitro and bacterial isolates from the large bowel of infected gnotobiotic piglets (in vivo). Overall, 1061 distinct gene products were identified. Differential display analysis revealed that SD1 cells switched to an anaerobic energy metabolism in vivo. High in vivo abundances of amino acid decarboxylases (GadB and AdiA) which enhance pH homeostasis in the cytoplasm and protein disaggregation chaperones (HdeA, HdeB and ClpB) were indicative of a coordinated bacterial survival response to acid stress. Several type III secretion system effectors were increased in abundance in vivo, including OspF, IpaC and IpaD. These proteins are implicated in invasion of colonocytes and subversion of the host immune response in S. flexneri. These observations likely reflect an adaptive response of SD1 to the hostile host environment. Seven proteins, among them the type III secretion system effectors OspC2 and IpaB, were detected as antigens in Western blots using piglet antisera. The outer membrane protein OmpA, the heat shock protein HtpG and OspC2 represent novel SD1 subunit vaccine candidates and drug targets.     

Transport of angiotensin peptides across the Caco-2 monolayer

The bidirectional transport of the angiotensin peptides--des-Asp-angiotensin I (DAAI), angiotensins III and IV--were studied using human intestinal Caco-2 monolayers. The peptides had low permeability rates but were relatively stable to enzymatic hydrolysis. DAAI was transported by diffusion while angiotensins III and IV were transported by an energy requiring, carrier-mediated process. The physicochemical properties and solution conformations of the peptides were investigated in an attempt to establish structure-transport correlations. Among the three peptides, DAAI was the most hydrophobic, had the highest hydrogen bonding potential and was the only peptide to have a random solution conformation, as determined from circular dichroism, two-dimensional (1)H NMR and molecular modelling. On the other hand, the more hydrophilic angiotensin IV had less hydrogen bonding potential and a solution conformation characterized by a beta turn. These factors may influence the transport characteristics of DAAI and angiotensin IV.