A survey of sRNA families in α-proteobacteria

We have performed a computational comparative analysis of six small non-coding RNA (sRNA) families in α-proteobacteria. Members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont S. meliloti by a combined bioinformatics screen followed by experimental verification. Consensus secondary structures inferred from covariance models for each sRNA family evidenced in some cases conserved motifs putatively relevant to the function of trans-encoded base-pairing sRNAs i.e., Hfq-binding signatures and exposed anti Shine-Dalgarno sequences. Two particular family models, namely αr15 and αr35, shared own sub-structural modules with the Rfam model suhB (RF00519) and the uncharacterized sRNA family αr35b, respectively. A third sRNA family, termed αr45, has homology to the cis-acting regulatory element speF (RF00518). However, new experimental data further confirmed that the S. meliloti αr45 representative is an Hfq-binding sRNA processed from or expressed independently of speF, thus refining the Rfam speF model annotation. All the six families have members in phylogenetically related plant-interacting bacteria and animal pathogens of the order of the Rhizobiales, some occurring with high levels of paralogy in individual genomes. In silico and experimental evidences predict differential regulation of paralogous sRNAs in S. meliloti 1021. The distribution patterns of these sRNA families suggest major contributions of vertical inheritance and extensive ancestral duplication events to the evolution of sRNAs in plant-interacting bacteria.     

Role of Sphingomonas sp. strain Fr1 PhyR-NepR-σEcfG cascade in general stress response and identification of a negative regulator of PhyR

The general stress response in Alphaproteobacteria was recently described to depend on the alternative sigma factor σ(EcfG), whose activity is regulated by its anti-sigma factor NepR. The response regulator PhyR, in turn, regulates NepR activity in a partner-switching mechanism according to which phosphorylation of PhyR triggers sequestration of NepR by the sigma factor-like effector domain of PhyR. Although genes encoding predicted histidine kinases can often be found associated with phyR, little is known about their role in modulation of PhyR phosphorylation status. We demonstrate here that the PhyR-NepR-σ(EcfG) cascade is important for multiple stress resistance and competitiveness in the phyllosphere in a naturally abundant plant epiphyte, Sphingomonas sp. strain Fr1, and provide evidence that the partner switching mechanism is conserved. We furthermore identify a gene, designated phyP, encoding a predicted histidine kinase at the phyR locus as essential. Genetic epistasis experiments suggest that PhyP acts upstream of PhyR, keeping PhyR in an unphosphorylated, inactive state in nonstress conditions, strictly depending on the predicted phosphorylatable site of PhyP, His-341. In vitro experiments show that Escherichia coli inner membrane fractions containing PhyP disrupt the PhyR-P/NepR complex. Together with the fact that PhyP lacks an obvious ATPase domain, these results are in agreement with PhyP functioning as a phosphatase of PhyR, rather than a kinase.     

Mechanical response and conformational amplification in α-helical coiled coils

α-Helical coiled coils (CCs) are ubiquitous tertiary structural domains that are often found in mechanoproteins. CCs have mechanical rigidity and are often involved in force transmission between protein domains. Although crystal structures of CCs are available, information about their conformational flexibility is limited. The role of hydrophobic interactions in determining the CC conformation is not clear. In this work we examined the mechanical responses of typical CCs and constructed a coarse-grained mechanical model to describe the conformation of the protein. The model treats α-helices as elastic rods. Hydrophobic bonds arranged in a repeated pattern determine the CC structure. The model is compared with molecular-dynamics simulations of CCs under force. We also estimate the effective bending and twisting persistence length of the CC. The model allows us to examine unconventional responses of the CC, including significant conformational amplification upon binding of a small molecule. We find that the CC does not behave as a simple elastic rod and shows complex nonlinear responses. These results are significant for understanding the role of CC structures in chemoreceptors, motor proteins, and mechanotransduction in general.     

The α-proteobacteria: the Darwin finches of the bacterial world

The α-proteobacteria represent one of the most diverse bacterial subdivisions, displaying extreme variations in lifestyle, geographical distribution and genome size. Species for which genome data are available have been classified into a species tree based on a conserved set of vertically inherited core genes. By mapping the variation in gene content onto the species tree, genomic changes can be associated with adaptations to specific growth niches. Genes for adaptive traits are mostly located in ‘plasticity zones’ in the bacterial genome, which also contain mobile elements and are highly variable across strains. By physically separating genes for information processing from genes involved in interactions with the surrounding environment, the rate of evolutionary change can be substantially enhanced for genes underlying adaptation to new growth habitats, possibly explaining the ecological success of the α-proteo-bacterial subdivision.     

Genotypic variability in physiological,biomass and yield response to drought stress?in pigeonpea

Three pigeonpea (Cajanus cajan L. Millsp.) genotypes- GT-1, AKP-1 and PRG-158 with varying crop duration, growth habit and flowering pattern were evaluated for variability in their response for drought stress. Drought stress was imposed at initiation of flowering and the observations on biomass and seed yield parameters were recorded at harvest. The magnitude of response of individual component to drought stress was found to be genotype specific. Drought stress significantly decreased photosynthetic rate (P_N), transpiration rate (Tr) and relative water content (RWC) in all the genotypes, however the magnitude of reduction differed with genotype. With drought stress, the reduction of P_N was highest in GT-1 while reduction in Tr was highest in PRG-158. The genotype AKP-1, accumulated significantly higher concentrations of osmotic solutes especially proline under water deficit stress, this facilitated it to maintain higher relative water content (RWC) and lower malondialdehyde (MDA) content as compared to other genotypes. Drought stress also impacted biomass production and their partitioning to vegetative and reproductive components at harvest. There was significant variability between the genotypes for seed yield under drought stress while it was non-significant under well-watered condition. Drought stress enhanced flower drop and decreased flower to pod conversion resulting in reduced pod number and seed number in PRG-158 and GT-1. The genotype AKP-1 recorded superior performance for seed yield under stress environment due to its ability in maintaining pod and seed number as well as improved test weight (100 seed weight). Under drought stress, significant positive association of seed yield with proline, seed number, pod number and test weight clearly indicating their role in drought tolerance.     

HDAC6 regulates aggresome-autophagy degradation pathway of α-synuclein in response to MPP+-induced stress

Increasing evidence suggests that the ubiquitin-binding histone deacetylase-6 (HDAC6) plays an important role in the clearance of misfolded proteins by autophagy. In this study, we treated PC-12 cells over-expressing human mutant (A53T) α-synuclein (α-syn) and SH-SY5Y cells with MPP(+). It was found that HDAC6 expression significantly increased and mainly colocalized with α-syn in the perinuclear region to form aggresome-like bodies. HDAC6 deficiency blocked the formation of aggresome-like bodies and interfered with the autophagy in response to MPP(+)-induced stress. Moreover, misfolded α-syn accumulated into the nuclei, resulting in its reduced clearance, and finally, the number of apoptotic cells significantly increased. Taken together, HDAC6 participated in the degradation of MPP(+)-induced misfolded α-syn aggregates by regulating the aggresome-autophagy pathway. Understanding the mechanism may disclose potential therapeutic targets for synucleinopathies such as Parkinson's disease.     

Bystander cell death and stress response is inhibited by the radical scavenger α(1)-microglobulin in irradiated cell cultures

Alpha-particle irradiation of cells damages not only the irradiated cells but also nontargeted bystander cells. It has been proposed that the bystander effect is caused by oxidants and free radicals generated by the radiation. Recent studies have shown that α(1)-microglobulin protects against cell damage caused by oxidants and free radicals. Using a novel experimental system that allows irradiation of 0.02% of a human hepatoma monolayer, leaving 99.98% as bystander cells, we investigated the influence of oxidative stress and the cell-protective effects of α(1)-microglobulin during α-particle irradiation. The results showed an increase in cell death in both irradiated cells and bystander cells. A significant increase in apoptosis, oxidation markers and expression of the stress response genes heme oxygenase 1, superoxide dismutase, catalase, glutathione peroxidase 1, p21 and p53 were observed. Addition of α(1)-microglobulin reduced the amount of dead cells and inhibited apoptosis, formation of oxidation markers, and up-regulation of stress response genes. The results emphasize the role of oxidative stress in promoting bystander effects. Furthermore, the results suggest that α(1)-microglobulin protects nonirradiated cells by eliminating oxidants and free radicals generated by radiation and imply that α(1)-microglobulin can be used in radiation therapy of tumors to minimize damage to surrounding tissues.     

Similarities and differences in the effect of cocaine on α-adrenergic and muscarinic response

Similarities and differences in the effect of cocaine on [alpha]-adrenergic and muscarinic receptors were shown in three experimental models. The postsynaptic stimulating effect of cocaine, mediated by [alpha]-adrenergic receptors was revealed in uninnervated chick amnion and innervated rat vas deferens. In vas deferens cocaine caused an increase of the amount of active [alpha]-adrenergic receptors, the appearance of an additional receptor pool, and change in the dimerization level. Cocaine acted as an antagonist on muscarinic receptors of the chick amnion. The inhibition by cocaine of muscarinic receptors in the rat brain cortex membranes led to a decrease in the number of receptors and their partial monomerization. Thus, cocaine influences both the [alpha]-adrenergic and the muscarinic response at the receptor level. Experiments on various objects have shown that cocaine activates the [alpha]-adrenergic response and inhibits the muscarinic one.     

Rad3 and Sty1 function in Schizosaccharomyces pombe: an integrated response to DNA damage and environmental stress?

In Schizosaccharomyces pombe , the Ataxia Telangiectasia-mutated (Atm)/Atm and Rad 3 Related (Atr) homologue Rad3 is an essential regulator of the response to DNA damage and stalled replication forks. Rad3 activates the downstream kinases Chk1 and Cds1. These kinases in turn inhibit cell cycle progression by mediating Cdc2 phosphorylation. Studies in both yeast and mammalian cells suggest additional roles for Rad3 in regulating cellular responses to environmental stress. In S. pombe , cellular responses to various environmental stresses are regulated primarily through the stress-activated MAP kinase p38 homologue Sty1. An important function of Sty1 is to drive cells rapidly through mitosis by facilitating the accumulation of Cdc25. Interestingly, Sty1 is activated simultaneously with Rad3 following exposure to UV radiation or ionizing radiation (IR). Similarly, exposure to environmental stresses induces the expression of rad3 ⁺, cds1 ⁺ and other checkpoint regulator genes. It is currently unclear how the pathways regulated by Sty1 and Rad3 and their opposing effects on mitosis are integrated. Recent studies suggest that Sty1 and Rad3 function together to regulate the expression of several stress response genes following exposure to IR. In this review, we discuss current knowledge on the interaction of Rad3/Atm and Sty1/p38 in regulating cellular responses to environmental stress and DNA damage.     

Nitric oxide production in tobacco leaf cells: a generalized stress response?

The function of nitric oxide (NO), a gaseous free radical emitted by many plants, is incompletely understood. In the present study the hypothesis that NO generation, like that of the reactive oxygen species, occurs as a general response to different environmental cues was tested. Leaf peels and mesophyll cell suspensions of Nicotiana tabacum cv. Xanthi were loaded with the NO‐specific fluorophore, diaminofluorescein, and subjected to an abiotic stressor. Light stress and mechanical injury had no apparent effect on NO production. In contrast, high temperatures, hyperosmotic stress, salinity and epi‐illumination in a microscope all led to rapid surges in NO‐induced fluorescence. The fluorescence originated from cells of the palisade mesophyll and across all epidermal cell types, including guard cells, subsidiary cells, and long and short trichomes. Fluorescence was evident first in the plastids, then in the nucleus and finally throughout the cytosol. Nicotiana plumbaginifolia cell suspensions expressing the calcium reporter aequorin provided evidence that, under hyperosmotic stress, NO participates in the elevation of free Ca²⁺ in the cytoplasm. The physiological significance of NO production in response to abiotic stressors is discussed.     

Biochemical changes involved in stress response and ripening behaviour of γ-irradiated mango fruit

The stress response of ripening mango fruits treated in the pre-climacteric phase with radiation doses of 0.75, 1.25 and 1.75 kGy was investigated. L-Phenylalanine ammonialyase, polyphenol oxidase, peroxidase and catalase activities were determined and significant differences were observed. Differences in the patterns of total phenolics, flavanols and proteins were also observed. Malic enzyme activity was used as an indicator of the ripening stage (climacteric rise, climacteric peak and post-climacteric phase) as well as a measure of the effect of γ-irradiation on fruit ripening. It seems that radiation treatment causes a stress condition in the fruit which, depending on the dose, may lead to browning of the tissue or necrotic decay.