When Rab GTPases meet innate immune signaling pathways

Ras-related protein in brain (Rab) GTPases, the subfamily of small GTP-binding proteins superfamily, play a vital role in regulating and controlling vesicles' transport between different membrane-bound organelles. As the first-line defense against invading pathogens, the host's innate immune system recognizes various pathogen-associated molecular patterns through a series of membrane-bound or cytoplasmic pathogen recognition receptors to activate the downstream signaling pathway and induce the type I interferons (IFN-I). Numerous studies have demonstrated that Rab GTPases participate in innate immunity by regulating transmembrane signals' transduction and the transport, adhesion, anchoring, and fusion of vesicles. However, the underlying mechanism of Rab GTPases regulating innate immunity is not entirely understood. A comprehensive understanding of the interplay between the Rab GTPases and innate immunity will help develop novel therapeutics against microbial infections and chronic inflammations.     

The mediator of cellular immunity. IV. Cooperation between lymphocytes and mononuclear phagocytes

Acquired resistance to an intravenous infection with Listeria monocytogenes involves the interaction of two cell types: specifically committed lymphocytes and monocyte-derived macrophages. This interaction was revealed in experiments using the polyfunctional alkylating agent, cyclophosphamide. Cyclophosphamide is toxic for both lymphocytes and blood monocyte antecedents. Rats treated with cyclophosphamide were immunized adoptively with cells obtained from the thoracic duct lymph of Listeria-immune donors. But such animals benefited from a lymphocyte injection only while they could assemble monocyte-derived macrophages in an inflammatory exudate. The results imply that blood monocytes provide an essential element to the host's defense mechanism against intracellular bacterial parasites, and that monocyte-derived macrophages are the instruments through which cellular resistance to infection is expressed.     

Local parasite pressures and host genotype modulate epigenetic diversity in a mixed‐mating fish

Parasite‐mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of long‐term self‐fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host's ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MS‐AFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a predomintanly self‐fertilizing fish, to analyze the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.     

The mammalian complement system as an epitome of host–pathogen genetic conflicts

The complement system is an innate immunity effector mechanism; its action is antagonized by a wide array of pathogens and complement evasion determines the virulence of several infections. We investigated the evolutionary history of the complement system and of bacterial‐encoded complement‐interacting proteins. Complement components targeted by several pathogens evolved under strong selective pressure in primates, with selection acting on residues at the contact interface with microbial/viral proteins. Positively selected sites in CFH and C4BPA account for the human specificity of gonococcal infection. Bacterial interactors, evolved adaptively as well, with selected sites located at interaction surfaces with primate complement proteins. These results epitomize the expectation under a genetic conflict scenario whereby the host's and the pathogen's genes evolve within binding avoidance‐binding seeking dynamics. In silico mutagenesis and protein–protein docking analyses supported this by showing that positively selected sites, both in the host's and in the pathogen's interacting partner, modulate binding.     

生物被膜：益生菌肠道定植的新策略

益生菌可改善机体微生态平衡,在促进营养吸收、控制肠道感染和调节免疫功能等方面具有特殊的功效,但存在胃肠道环境难定植、口服生物利用度低等问题。生物被膜是多个细菌黏附于非生物或生物表面,分泌胞外聚合物(extracellular polymeric substances),并将自身包裹其中形成的一种有组织的细菌集团,包含胞外多糖(exopolysaccharides,EPS)、蛋白质、胞外DNA(extracellular deoxyribonucleic acid, eDNA)和脂质等多种组成成分,是一个具有三维立体空间结构的聚集体。被膜状态的益生菌较浮游菌在抗逆性、对抗病原菌和调节免疫功能等方面具有明显优势,这些特点为新型益生菌的开发提供了新的研究思路。本文阐述了被膜状态益生菌的优势,重点介绍了促进益生菌生物被膜形成的活性物及其形成机制,简述了益生菌生物被膜的安全性问题。当前,益生菌生物被膜的研究尚处于起步阶段,希望本文能为该领域未来的研究提供参考。     

A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs

The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 kDa) were purified and found to be inactive separately, but together degraded several different glc-HMC modified DNAs (T4, T2 and T6). The GMR enzyme is able to degrade both alpha-glucosy-HMC T4 DNA and beta-glucosyl-HMC T4 DNA, whereas no activity was observed against non-modified DNAs including unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme activity requires NTP, favors UTP, is stimulated by calcium, and initially produces 4 kb DNA fragments that are further degraded to low molecular mass products. The enzyme is inhibited by the T4 phage internal protein I* (IPI*) to which it was found to bind. Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs. IPI* thus represents a third generation bacteriophage defense against restriction nucleases of the Gmr type.     

Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition

Bacterial restriction endonuclease EcoRII requires two recognition sites to cleave DNA. Proteolysis of EcoRII revealed the existence of two stable domains, EcoRII-N and EcoRII-C. Reduction of the enzyme to its C-terminal domain, EcoRII-C, unleashed the enzyme activity; this truncated form no longer needed two recognition sites and cleaved DNA much more efficiently than EcoRII wild-type. The crystal structure of EcoRII showed that probably the N-terminal domain sterically occludes the catalytic site, thus apparently controlling the cleavage activity. Based on these data, EcoRII was the first restriction endonuclease for which an autoinhibition mechanism as regulatory strategy was proposed. In this study, we probed this assumption and searched for the inhibitory element that mediates autoinhibition. Here we show that repression of EcoRII-C is achieved by addition of the inhibitory domain EcoRII-N or by single soluble peptides thereof in trans . Moreover, we perturbed contacts between the N- and the C-terminal domain of EcoRII by site-directed mutagenesis and proved that β-strand B1 and α-helix H2 are essential for autoinhibition; deletion of either secondary structural element completely relieved EcoRII autoinhibition. This potent regulation principle that keeps EcoRII enzyme activity controlled might protect bacteria against suicidal restriction of rare unmodified recognition sites in the cellular genome.     

Common and contrasting themes in host cell-targeted effectors from bacterial,fungal, oomycete and nematode plant symbionts described using the Gene Ontology

A wide diversity of plant-associated symbionts, including microbes, produce proteins that can enter host cells, or are injected into host cells in order to modify the physiology of the host to promote colonization. These molecules, termed effectors, commonly target the host defense signaling pathways in order to suppress the defense response. Others target the gene expression machinery or trigger specific modifications to host morphology or physiology that promote the nutrition and proliferation of the symbiont. When recognized by the host's surveillance machinery, which includes cognate resistance (R) gene products, defense responses are engaged to restrict pathogen proliferation. Effectors from diverse symbionts may be delivered into plant cells via varied mechanisms, including whole organism cellular entry (viruses, some bacteria and fungi), type III and IV secretion (in bacteria), physical injection (nematodes and insects) and protein translocation signal sequences (oomycetes and fungi). This mini-review will summarize both similarities and differences in effectors and effector delivery systems found in diverse plant-associated symbionts as well as how these are described with Plant-Associated Microbe Gene Ontology (PAMGO) terms.     

An update on the diversity of Wolbachia in Spalangia spp. (Hymenoptera: Pteromalidae)

Results from 13 additional host populations improves resolution on the diversity of Wolbachia bacteria in Spalangia spp. (Hymenoptera: Pteromalidae). These bacteria are of interest because they can profoundly affect their host's reproduction. Manipulating Wolbachia infections may provide a method to improve the efficacy of biocontrol agents including Spalangia spp.     

Polymorphism of attack and defense

Coevolution of attack and defense occurs in host-parasite systems and various forms of genomic conflict. Attackers benefit when their specific molecules allow entry past host defenses. Defenders gain when their matching biochemical specificities aid recognition. Selection continually favors new attack specificities that avoid matching defense and, in turn, new defense specificities that match novel attackers. The introduction of novel specificities strongly influences the spatial and temporal dynamics of conflict. Lack of reciprocally matching diversity in a particular system suggests biochemical constraints that prevent diversification. New work on cytoplasmic male sterility, B chromosomes and meiotic drive suggests that varying biochemical constraints on recognition cause varying patterns of diversity and spatiotemporal dynamics     

The biology of bacterial peptidoglycans and their impact on host immunity and physiology

Peptidoglycans (PGN) are a constituent of the bacterial cell wall, and are shed as bacteria divide. The presence of PGN is therefore a marker of bacterial activity that has been exploited by both plants and animals to induce defence mechanisms. Pattern recognition receptors that recognize PGN are extremely well conserved throughout evolution and shown to play important and diverse role in the development, homeostasis and activation of the immune system. In addition, PGN can be detected beyond mucosal surfaces, and their receptor can be expressed in tissues and cells that are far from the niches where bacteria reside. Thus, PGN affects not only the host's immunity, but also more generally the host's physiology. In this review, we discuss the biochemistry and biology of PGN, and their intriguing effects on the development of the immune system and the host physiology.     

Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy

Bacterial type I restriction/modification systems are capable of performing multiple actions in response to the methylation pattern on their DNA recognition sequences. The enzymes making up these systems serve to protect the bacterial cells against viral infection by binding to their recognition sequences on the invading DNA and degrading it after extensive ATP-driven translocation. DNA cleavage has been thought to occur as the result of a collision between two translocating enzyme complexes. Using atomic force microscopy (AFM), we show here that EcoKI dimerizes rapidly when bound to a plasmid containing two recognition sites for the enzyme. Dimerization proceeds in the absence of ATP and is also seen with an EcoKI mutant (K477R) that is unable to translocate DNA. Only monomers are seen when the enzyme complex binds to a plasmid containing a single recognition site. Based on our results, we propose that the binding of EcoKI to specific DNA target sequences is accompanied by a conformational change that leads rapidly to dimerization. This event is followed by ATP-dependent translocation and cleavage of the DNA.     

Egg puncture allows shiny cowbirds to assess host egg development and suitability for parasitism

Parasitic cowbirds and cuckoos generally reduce the clutch size of the hosts they parasitize by removing or destroying some of their eggs. Shiny cowbirds (Molothrus bonariensis) puncture their hosts'' eggs both when parasitizing the nests and also when they do not parasitize them. We propose that, by puncturing the host''s eggs, shiny cowbirds gain an informational benefit. They assess the degree of development of the host''s embryos and so avoid laying in nests that would not provide enough incubation time for the parasitic eggs to hatch. Two predictions follow: (i) punctures should occur in advance or immediately before parasitic events, and (ii) the occurrence of parasitism should depend on the degree of development of the host''s embryos when punctures occurred, i.e. on the stage of incubation. Both predictions are supported by our data of shiny cowbirds parasitizing yellow-winged blackbirds (Agelaius thilius). Egg punctures are not used to reset the host''s nesting attempt when shiny cowbirds do not parasitize the nests. We discuss the potential mechanisms implicated in egg development assessment and propose a critical experiment to test this hypothesis.     

Impact of H216 on the DNA Binding and Catalytic Activities of the HIV Restriction Factor APOBEC3G

APOBEC3G has an important role in human defense against retroviral pathogens, including HIV-1. Its single-stranded DNA cytosine deaminase activity, located in its C-terminal domain (A3Gctd), can mutate viral cDNA and restrict infectivity. We used time-resolved nuclear magnetic resonance (NMR) spectroscopy to determine kinetic parameters of A3Gctd''s deamination reactions within a 5′-CCC hot spot sequence. A3Gctd exhibited a 45-fold preference for 5′-CCC substrate over 5′-CCU substrate, which explains why A3G displays almost no processivity within a 5′-CCC motif. In addition, A3Gctd''s shortest substrate sequence was found to be a pentanucleotide containing 5′-CCC flanked on both sides by a single nucleotide. A3Gctd as well as full-length A3G showed peak deamination velocities at pH 5.5. We found that H216 is responsible for this pH dependence, suggesting that protonation of H216 could play a key role in substrate binding. Protonation of H216 appeared important for HIV-1 restriction activity as well, since substitutions of H216 resulted in lower restriction in vivo.     

Role of the penetration‐resistance genes PEN1, PEN2 and PEN3 in the hypersensitive response and race‐specific resistance in Arabidopsis thaliana

Plants are highly capable of recognizing and defending themselves against invading microbes. Adapted plant pathogens secrete effector molecules to suppress the host's immune system. These molecules may be recognized by host‐encoded resistance proteins, which then trigger defense in the form of the hypersensitive response (HR) leading to programmed cell death of the host tissue at the infection site. The three proteins PEN1, PEN2 and PEN3 have been found to act as central components in cell wall‐based defense against the non‐adapted powdery mildew Blumeria graminis fsp. hordei (Bgh). We found that loss of function mutations in any of the three PEN genes cause decreased hypersensitive cell death triggered by recognition of effectors from oomycete and bacterial pathogens in Arabidopsis. There were considerable additive effects of the mutations. The HR induced by recognition of AvrRpm1 was almost completely abolished in the pen2 pen3 and pen1 pen3 double mutants and the loss of cell death could be linked to indole glucosinolate breakdown products. However, the loss of the HR in pen double mutants did not affect the plants' ability to restrict bacterial growth, whereas resistance to avirulent isolates of the oomycete Hyaloperonospora arabidopsidis was strongly compromised. In contrast, the double and triple mutants demonstrated varying degrees of run‐away cell death in response to Bgh. Taken together, our results indicate that the three genes PEN1, PEN2 and PEN3 extend in functionality beyond their previously recognized functions in cell wall‐based defense against non‐host pathogens.     

Self or nonself? That is the question: sensing of cytomegalovirus infection by innate immune receptors

Cytomegaloviruses (CMV) are ubiquitous, opportunistic DNA viruses that have mastered the art of immune evasion through their ability to mimic host proteins or to inhibit antiviral responses. The study of the host response against CMV infection has illuminated many facets of the complex interaction between host and pathogen. Here, we review evidence derived from the animal models and human studies that supports the central role played by innate immune receptors in the recognition of virus infection and their participation in the many layers of defense.     

Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme

Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25–27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recognition site was suggested to influence the site of DNA cleavage by the enzyme. In this investigation, we demonstrate that the cleavage site of the R.EcoP15I restriction enzyme does not depend on the sequence context of the recognition site. Strikingly, this study demonstrates that the enzyme can cleave linear DNA having either recognition sites in the same orientation or a single recognition site. Cleavage occurs predominantly at a site proximal to the DNA end in the case of multiple site substrates. Such cleavage can be abolished by the binding of Lac repressor downstream (3′ side) but not upstream (5′ side) of the recognition site. Binding of HU protein has also been observed to interfere with R.EcoP15I cleavage activity. In accordance with a mechanism requiring two enzyme molecules cooperating to elicit double-strand break on DNA, our results convincingly demonstrate that the enzyme translocates on DNA in a 5′ to 3′ direction from its recognition site and indicate a switch in the direction of enzyme motion at the DNA ends. This study demonstrates a new facet in the mode of action of these restriction enzymes.     

Modification profiles of bacterial genomes

DNAs were prepared from twenty-six bacterial species and digested with a variety of restriction endonucleases to determine what modifications the DNAs carry. Several general conclusions could be made: 1) First, in no instance was the DNA of a restriction enzyme. 2) The specificity of the DNA modification was the same as that of its restriction counterpart; there were no cases of the DNAs being modified against a less specific class of restriction enzymes. 3) In most (but not all) cases, the resistance of a bacterium's DNA to its own restriction enzyme could be generalized to include resistance to all other restriction enzymes with the same specificity (isoschizomers). 4) DNA modified within the central tetramer of a recognition sequence is usually protected against cleavage by all related hexameric enzymes possessing that central tetramer. Only three families of DNA presented in this study disobey this rule. 5) Finally, a significant number of cases emerge where bacterial DNA carries a modification but no corresponding restriction endonuclease activity.