The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins

Probabilities of disorder for FlgM proteins of 39 species whose optimal growth temperature ranges from 273 K (0°C) to 368 K (95°C) were predicted by a newly developed method called Sequence-based Prediction with Integrated NEural networks for Disorder (SPINE-D). We showed that the temperature-dependent behavior of FlgM proteins could be separated into two subgroups according to their sequence lengths. Only shorter sequences evolved to adapt to high temperatures (>318 K or 45°C). Their ability to adapt to high temperatures was achieved through a transition from a fully disordered state with little secondary structure to a semidisordered state with high predicted helical probability at the N-terminal region. The predicted results are consistent with available experimental data. An analysis of all orthologous protein families in 39 species suggests that such a transition from a fully disordered state to semidisordered and/or ordered states is one of the strategies employed by nature for adaptation to high temperatures.     

The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins

Probabilities of disorder for FlgM proteins of 39 species whose optimal growth temperature ranges from 273 K (0°C) to 368 K (95°C) were predicted by a newly developed method called Sequence-based Prediction with Integrated NEural networks for Disorder (SPINE-D). We showed that the temperature-dependent behavior of FlgM proteins could be separated into two subgroups according to their sequence lengths. Only shorter sequences evolved to adapt to high temperatures (>318 K or 45°C). Their ability to adapt to high temperatures was achieved through a transition from a fully disordered state with little secondary structure to a semidisordered state with high predicted helical probability at the N-terminal region. The predicted results are consistent with available experimental data. An analysis of all orthologous protein families in 39 species suggests that such a transition from a fully disordered state to semidisordered and/or ordered states is one of the strategies employed by nature for adaptation to high temperatures.     

A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation

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The Role of Geography in Human Adaptation

Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme F_ST values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.     

The Role of Visual Processing Speed in Reading Speed Development

A steady increase in reading speed is the hallmark of normal reading acquisition. However, little is known of the influence of visual attention capacity on children''s reading speed. The number of distinct visual elements that can be simultaneously processed at a glance (dubbed the visual attention span), predicts single-word reading speed in both normal reading and dyslexic children. However, the exact processes that account for the relationship between the visual attention span and reading speed remain to be specified. We used the Theory of Visual Attention to estimate visual processing speed and visual short-term memory capacity from a multiple letter report task in eight and nine year old children. The visual attention span and text reading speed were also assessed. Results showed that visual processing speed and visual short term memory capacity predicted the visual attention span. Furthermore, visual processing speed predicted reading speed, but visual short term memory capacity did not. Finally, the visual attention span mediated the effect of visual processing speed on reading speed. These results suggest that visual attention capacity could constrain reading speed in elementary school children.     

Bacterial Adaptation through Loss of Function

The metabolic capabilities and regulatory networks of bacteria have been optimized by evolution in response to selective pressures present in each species'' native ecological niche. In a new environment, however, the same bacteria may grow poorly due to regulatory constraints or biochemical deficiencies. Adaptation to such conditions can proceed through the acquisition of new cellular functionality due to gain of function mutations or via modulation of cellular networks. Using selection experiments on transposon-mutagenized libraries of bacteria, we illustrate that even under conditions of extreme nutrient limitation, substantial adaptation can be achieved solely through loss of function mutations, which rewire the metabolism of the cell without gain of enzymatic or sensory function. A systematic analysis of similar experiments under more than 100 conditions reveals that adaptive loss of function mutations exist for many environmental challenges. Drawing on a wealth of examples from published articles, we detail the range of mechanisms through which loss-of-function mutations can generate such beneficial regulatory changes, without the need for rare, specific mutations to fine-tune enzymatic activities or network connections. The high rate at which loss-of-function mutations occur suggests that null mutations play an underappreciated role in the early stages of adaption of bacterial populations to new environments.     

Recombinational Rearrangements in Bacterial Genome and Bacterial Adaptation to the Environment

The rearrangement of bacterial chromosomes induced by intragenomic recombination is considered. The role of stochastic and programmed genome rearrangements in bacterial adaptation to the environment and in cell differentiation is discussed.     

综述: 线粒体自噬在低氧适应中的作用

低氧是一种典型的应激环境,细胞在低氧条件下能量和氧化代谢发生改变,其中线粒体产生的大量活性氧严重威胁细胞的存活．线粒体自噬是近年来被发现的细胞适应低氧的一种适应性代谢反应．细胞在低氧条件下能通过上调低氧诱导因 子1(HIF-1),激活BNIP3/BNIP3L及Beclin-1介导的通路诱导线粒体自噬,最终减少ROS的产生,促进细胞的存活,使机体产生低氧适应．综述了线粒体自噬在低氧适应中的作用及其机制．     

The Role of Functional Amyloids in Bacterial Virulence

Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets.     

Bacterial Thermotaxis by Speed Modulation

Naturally occurring gradients often extend over relatively long distances such that their steepness is too small for bacteria to detect. We studied the bacterial behavior in such thermal gradients. We find that bacteria migrate along shallow thermal gradients due to a change in their swimming speed resulting from the effect of temperature on the intracellular pH, which also depends on the chemical environment. When nutrients are scarce in the environment the bacteria''s intracellular pH decreases with temperature. As a result, the swimming speed of the bacteria decreases with temperature, which causes them to slowly drift toward the warm end of the thermal gradient. However, when serine is added to the medium at concentrations >300 μM, the intracellular pH increases causing the swimming speed to increase continuously with temperature, and the bacteria to drift toward the cold end of the temperature gradient. This directional migration is not a result of bacterial thermotaxis in the classical sense, because the steepness of the gradients applied is below the sensing threshold of bacteria. Nevertheless, our results show that the directional switch requires the presence of the bacterial sensing receptors. This seems to be due to the involvement of the receptors in regulating the intracellular pH.     

The Role of ACT-Like Subdomain in Bacterial Threonine Dehydratases

In bacteria, threonine dehydratases could convert L-threonine to 2-ketobutyrate. Some threonine dehydratases contain only a catalytic domain, while others contain an N-terminal catalytic domain and a C-terminal regulatory domain composed of one or two ACT-like subdomains. However, the role of the ACT-like subdomain in threonine dehydratases is not clear. Here, nine different bacterial threonine dehydratases were studied. Three of the nine contain no ACT-like subdomain, four of them contain a single ACT-like subdomain, and two of them contain two ACT-like subdomains. The nine genes encoding these threonine dehydratases were individually overexpressed in E. coli BL21(DE3), and the enzymes were purified to homogeneity. Activities of the purified enzymes were analyzed after incubation at different temperatures and different pHs. The results showed that threonine dehydratases with a single ACT-like subdomain are more stable at higher temperatures and a broad range of pH than those without ACT-like subdomain or with two ACT-like subdomains. Furthermore, the specific activity of threonine dehydratases increases with the increase of the number of ACT-like subdomains they contain. The results suggest that the ACT-like subdomain plays an important role in bacterial threonine dehydratases.     

线粒体自噬在缺氧条件下适应机制的研究进展

由于线粒体能敏感地感受机体内氧浓度的变化,缺氧时会影响线粒体氧化磷酸化过程中电子传递链的正常功能,抑制ATP生成,产生大量活性氧(ROS)。ROS蓄积导致氧化损伤细胞内脂质、DNA和蛋白质等大分子物质,线粒体肿胀,通透性转换孔开放,释放细胞色素C等促凋亡因子,最终严重影响细胞的存活。因此这些功能异常或受损线粒体是缺氧应激状态下细胞是否存活的危险因素,及时清除这些线粒体,对维持线粒体质量、数量及细胞稳态具有重要意义。线粒体自噬是近年来发现的细胞适应缺氧的一种防御性代谢过程,它通过自噬途径选择性清除损伤、衰老和过量产生ROS的线粒体,促进线粒体更新和循环利用,确保细胞内线粒体功能稳定,保护缺氧应激下细胞的正常生长发挥重要的调节作用。本文就线粒体自噬在缺氧条件下发生过程、参与相关蛋白及调节机制等方面研究进行了综述。     

State-stabilizing Interactions in Bacterial Mechanosensitive Channel Gating and Adaptation

We outline several principles that we believe define the gating of two bacterial mechanosensitive channels, MscL and MscS. Serving as turgor regulators in bacteria and other walled cells, these molecules are tangible models for studying conformational transitions in membrane proteins driven directly by membrane tension. MscL, a compact pentamer, reversibly opens a gigantic 30-Å pore at near-lytic tensions. MscS, a heptameric complex, exhibits transient activation of a smaller pore at moderate tensions, thereby entering a tension-insensitive inactivated state. By comparing the structures and predicted transitions in these channels, we concluded that opening is commonly achieved through tilting and outward motion of the pore-lining helices, which is kinetically limited by hydration of the pore. The intricate adaptive behavior in MscS appears to depend on specific interhelical associations and the flexibility of the pore-lining helices. We discuss physical factors that may direct the transitions and stabilize main functional states in these channels.Osmotic forces are strong, which necessitated development of osmoregulation along with the first semipermeable membrane delineating the early cell. A simple estimation shows that a 1-μm cell behaving as an ideal osmometer would sustain a downshock no stronger than 20 mm, after which membrane tension would exceed the lytic limit of 10–12 dynes/cm. Thus, a cell without a reinforcing envelope or protective valves is very vulnerable. Free-living and enteric microorganisms cycling through the soil and experiencing drastic environmental changes developed robust mechanisms to maintain volume and integrity (1). The mechanosensitive channels MscS and MscL (mechanosensitive channels of small and large conductance, respectively) have been identified as primary osmolyte release valves limiting the turgor pressure under acute osmotic shock (2–4).Without mscS and mscL genes, Escherichia coli survives a 300 mosm osmotic downshock (2), its resistance attributed to the peptidoglycan layer partially restraining swelling. However, expression of either MscS or MscL allows cells to withstand a 700–800 mosm downshock through release of small osmolytes (2). Purification and reconstitution proved that MscL and MscS respond directly to tension in the lipid bilayer (5–7). Both channels reside in the inner (cytoplasmic) membrane (8), with MscL localized at the cell poles, bearing high curvature (9).As primary components of the turgor regulation system, E. coli MscS and MscL became convenient models for studies of tension-driven conformational transitions in membrane proteins (10). The crystal structures of closed-state Mycobacterium tuberculosis MscL (11) and E. coli MscS in two distinct conformations (12, 13) provided invaluable initial points to explore their gating mechanisms, in which computational methods play increasingly important roles.     

Functional Adaptation in Female Rats: The Role of Estrogen Signaling

Background

Sex steroids have direct effects on the skeleton. Estrogen acts on the skeleton via the classical genomic estrogen receptors alpha and beta (ERα and ERβ), a membrane ER, and the non-genomic G-protein coupled estrogen receptor (GPER). GPER is distributed throughout the nervous system, but little is known about its effects on bone. In male rats, adaptation to loading is neuronally regulated, but this has not been studied in females.

Methodology/Principal Findings

We used the rat ulna end-loading model to induce an adaptive modeling response in ovariectomized (OVX) female Sprague-Dawley rats. Rats were treated with a placebo, estrogen (17β-estradiol), or G-1, a GPER-specific agonist. Fourteen days after OVX, rats underwent unilateral cyclic loading of the right ulna; half of the rats in each group had brachial plexus anesthesia (BPA) of the loaded limb before loading. Ten days after loading, serum estrogen concentrations, dorsal root ganglion (DRG) gene expression of ERα, ERβ, GPER, CGRPα, TRPV1, TRPV4 and TRPA1, and load-induced skeletal responses were quantified. We hypothesized that estrogen and G-1 treatment would influence skeletal responses to cyclic loading through a neuronal mechanism. We found that estrogen suppresses periosteal bone formation in female rats. This physiological effect is not GPER-mediated. We also found that absolute mechanosensitivity in female rats was decreased, when compared with male rats. Blocking of adaptive bone formation by BPA in Placebo OVX females was reduced.

Conclusions

Estrogen acts to decrease periosteal bone formation in female rats in vivo. This effect is not GPER-mediated. Gender differences in absolute bone mechanosensitivity exist in young Sprague-Dawley rats with reduced mechanosensitivity in females, although underlying bone formation rate associated with growth likely influences this observation. In contrast to female and male rats, central neuronal signals had a diminished effect on adaptive bone formation in estrogen-deficient female rats.