T4-like coliphage ΦKAZ14 virulent to pathogenic and extended spectrum β-lactamase-producing Escherichia coli of poultry origin

<正>Dear Editor,Bacteriophages(otherwise called phages)are a type of virus that infect bacteria.This viral type has found useful applications in the control of bacterial pathogens in foods and food processing environments.In addition,phages may be useful to prevent colonization and shedding of bacteria into the surrounding environment.     

Community composition and spatial variation of bacteria in the sediments of a eutrophic fresh water urban lake， East Lake， Wuhan， China北大核心CSCD

［Objective］ Sediment bacteria are the important biological factors for remediating of eutrophic environments. To enrich our understanding of the bacteria communities in eutrophic urban lake sediments for better environment protection and pollution control in urban lake eco-systems, we resolved the composition of bacteria communities and their spatial variation in the sediments of a middle-size eutrophic urban lake, East Lake. ［Methods］We used 16S rRNA gene RFLP and sequencing methods to generate the phylogeny information of the bacteria community, used principal coordinates analysis （PCoA） and canonical correspondence analysis （CCA） methods to resolve the relationship between East Lake and other lakes, and the relationship between environmental factors and the bacteria communities. ［Results］ Sediments inhabited 13 phyla and 2 unclassified clusters. PCoA further revealed that the bacteria communities in three sub-lakes of East Lake sediments were closely related to the communities in similar eutropic lake environments, and divergent from the hypereutrophic sub-lake Miao Lake, which was also found to inhabit a relative abundant amount of Thermogymnomonas-type archaea. CCA further revealed that the distribution of bacteria was closely correlated with the carbon, nitrogen and phosphate contents in the sediments. ［Conclusion］The environment factors regulated the bacteria community composition and distribution. The results of this study providereference to the research, protection and pollution control on urban lake eco-systems.     

Key enzymes of the protocatechuate branch of the β-ketoadipate pathway for aromatic degradation in Corynebacterium glutamicum

The β-ketoadipate pathway, a primarily chromo-somally encoded catabolic route that plays a signifi-cant role in the degradation of aromatic compounds, is widely distributed in soil bacteria and fungi[1]. This pathway consists of two parallel branches of which the aromatic rings are cleaved by either protocatechuate 3,4-dioxygenase or catechol 1,2-dioxygenase. The two branches converge at β-ketoadipate enol-lactone in bacteria, and three additional steps complete the con-version of the latter…     

PHYPred:a tool for identifying bacteriophage enzymes and hydrolases

Dear Editor,Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle.Many studies have reported that phages are more specific to bacteria than antibiotics are;thus,phage therapy has many potential applications in human medicine,with the advantage of having few side effects(Keen,2012).Investigating the mechanisms of bacteria-killing phages will therefore aid     

Establishment of an efficient germ-free animal system to support functional microbiome research

正Germ-free animals are indispensable models for human and animal functional microbiome research Germ-free animals are animals that typically have no microorganisms living in or on them. These animals have become irreplaceable research tools for studying the relationships among single bacteria strains, multiple bacteria strains and hosts.     

First Complete Genome Sequence of a Probiotic Enterococcus faecium Strain T-110 and Its Comparative Genome Analysis with Pathogenic and Non-pathogenic Enterococcus faecium Genomes

<正>Enterococci bacteria are important in environmental,food and clinical microbiology.Enterococcus faecium is a nosocomial pathogen that causes bacteremia,endocarditis and other infections.It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12%of nosocomial infections in the USA(Linden and Miller,1999).However,certain strains of E.faecium are not only non-pathogenic but also have beneficial     

Gamma-glutamyl transferases: A structural,mechanistic and physiological perspective

Gamma glutamyl transferases （GGT） are highly conserved enzymes that occur from bacteria to humans. They remove terminal y-glutamyl residue from peptides and amides. GGTs play an important role in the homeostasis of glutathione （a major cellular antioxidant） and in the detoxification of xenobiotics in mammals. They are implicated in diseases like diabetes, inflammation, neurodegenerative diseases and cardiovascular diseases. The physiological role of GGTs in bacteria is still unclear. Nothing is known about the basis for the strong conservation of the enzyme across the living system. The review focuses on the enzyme＇s physiology, chemistry and structural properties of the enzyme with emphasis on the evolutionary relationships. The available data indicate that the members of the GGT family share common structural features but are functionally heterogenous.     

Phage lytic enzymes: a history

There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of ‘bacteria-eaters' or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal flora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well(Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specifi c disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay(Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes–from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.     

Val 70,Phe 72 and the last seven amino acid residues of C—terminal are essential to the function of norepinephrine transporter

The norepinephrine transporter(NET) is a member of the Na^ /Cl^- dependent neurotransmitter transporter family and constitutes the target of several clinically important antidepressants.To delineate the critical amino acid residues and the function of C-terminal in regulating transport activity of NET,here we constructed two site mutants (V70F,F72V;V70I,F72V) and one C-terminal truncated mutant (Δ 611-617).The wild type and mutants of NET were expressed in Xenopus oocytes by injection of their cRNA.We found that all of these mutants lost their transport activity.These results indicate that the amino acid residues of V70 and F72,and the last seven amino acids of C-terminal are essential to the transport activity of NET.     

Carrageenan oligosaccharides and associated carrageenan-degrading bacteria induce intestinal inflammation in germ-free mice

Carrageenans (CGNs) are widely used in foods and pharmaceuticals although their safety remains controversial. To investigate the effects of CGNs and CGN-degrading bacteria in the human colon, we screened for CGN degradation by human fecal microbiota, and for inflammatory response to CGNs and/or CGN-degrading bacteria in germ free mice. Thin-layer chromatography indicated that high molecular weight (MW) CGNs (!100 kDa) remained undegraded in the presence of human fecal microbiota, whereas low MW CGNs, i.e., k-carrageenan oligosaccharides (KCO,～4.5 kDa) were degraded when exposed to seven of eight human fecal samples, although sulfate groups were not removed during degradation.Bacteroides xylanisolvens and Escherichia coli isolates from fecal samples apparently degraded KCO synergistically, with B. xylanisolvens serving as the primary degrader. Combined treatment of KCO with KCO-degrading bacteria led to greater pro-inflammatory effects in the colon and rectum of germ-free mice than either KCO or bacteria alone. Similarly, p-p38-, CD3-, and CD79a-positive immune cells were more abundant in combined treatment group mice than in either single treatment group. Our study shows that KCO-degrading bacteria and the low MW products of KCO can promote proinflammatory effects in mice,and represent two key markers for evaluating CGN safety in foods or medicines.     

Complete genome sequence of a novel bacteriophage infecting Bradyrhizobium diazoefficiens USDA110

正Dear Editor,The nitrogen-fixing symbiotic bacteria, rhizobia are the most important beneficial bacteria in soil, as they form nodules with host legume plants to fix nitrogen to maintain soil fertility and facilitate plant growth. Although these bacteria are critically important to agriculture, bacteriophages of rhizobia (rhizobiophages) are commonly present in soils, rhizosphere,and nodules, which have major influences on the composition and population of rhizobia in soils and affect nodulation and nitrogen fixation. Despite the importance of rhizobiophages,only 23 phage full genomes have been sequenced.     

Genetic diversity of Harpins from Xanthomonas oryzae and their activity to induce hypersensitive response and disease resistance in tobacco

The hrp (hypersensitive response and patho-genicity) gene clusters in Gram-negative phytopatho-genic bacteria determine hypersensitive response (HR) in non-host plants and pathogenicity in host plants of the bacteria[1—3]. An hrp gene cluster usually contains genes coding for the components of the type Ⅲ se-cretion pathway, effectors and the proteins that regu-late the productions and transportations of effectors[4]. Many effectors such as Harpins and Avr proteins are believed secreted by …     

Functional characterization of the NF-κB transcription factor gene REL2 from Anopheles gambiae

The REL2 gene plays an important role in innate immunity against both Gram （＋） and Gram （-） bacteria and malaria parasites in Anopheles gambiae, the main vector of malaria in Africa. Through alternative splicing, REL2 produces two protein products, REL2F （with a Rel-homology domain as well as an inhibitory ankyrin repeat region） and REL2S （without the ankyrin repeats）. In the immune-competent cell line SualB from An. gambiae, REL2 has been shown to be a key regulator for cecropin A （or CEC1）. The high level expression of CEC1 in SualB was postulated to be the result of constitutive activation of REL2F. Here we showed that REL2F is indeed processed, albeit at a low level, in the SualB cell line. The primary cleavage requires residue 678 （an aspartic acid）. Proteolytic cleavage of REL2F can be enhanced by challenge with bacteria Escherichia coli and Bacillus subtilis, but not with fungus Beauveria bassiana. The inducible cleavage can be substantially reduced by RNA interference against PGRP-LC and CASPL1. Over-expression of REL2S or a constitutively active form of REL2F （REL2F380C or REL2F678） in An. gambiae cell line can further increase expression of CEC1 and other antimicrobial peptide genes. Over-expression of these constitutive active proteins in an immune naive cell line, MSQ43, from Anopheles stephensi, results in even more dramatic increased expression of antimicrobial peptides.     

A widespread response of Gram-negative bacterial acyl-homoserine lactone receptors to Gram-positive Streptomyces γ-butyrolactone signaling molecules

Cell-cell communication is critical for bacterial survival in natural habitats, in which miscellaneous regulatory networks are encompassed. However, elucidating the interaction networks of a microbial community has been hindered by the population complexity. This study reveals that γ-butyrolactone(GBL) molecules from Streptomyces species, the major antibiotic producers,can directly bind to the acyl-homoserine lactone(AHL) receptor of Chromobacterium violaceum and influence violacein production controlled by the quorum sensing(QS) system. Subsequently, the widespread responses of more Gram-negative bacterial AHL receptors to Gram-positive Streptomyces signaling molecules are unveiled. Based on the cross-talk between GBL and AHL signaling systems, combinatorial regulatory circuits(CRC) are designed and proved to be workable in Escherichia coli(E. coli). It is significant that the QS systems of Gram-positive and Gram-negative bacteria can be bridged via native Streptomyces signaling molecules. These findings pave a new path for unlocking the comprehensive cell-cell communications in microbial communities and facilitate the exploitation of innovative regulatory elements for synthetic biology.     

Symbiotic bacteria attenuate Drosophila oviposition repellence to alkaline through acidification

Metazoans harbor a wealth of symbionts that are ever-changing the environment by taking up resources and/or excreting metabolites.One such common environmental modification is a change in pH.Conventional wisdom holds that symbionts facilitate the survival and production of their hosts in the wild,but this notion lacks empirical evidence.Here,we report that symbiotic bacteria in the genus Enterococcus attenuate the oviposition avoidance of alkaline environments in Drosophila.We studied the effects of alkalinity on oviposition preference for the first time,and found that flies are robustly disinclined to oviposit on alkali-containing substrates.This innate repulsion to alkaline environments is explained,in part,by the fact that alkalinity compromises the health and lifespan of both offspring and parent Drosophila.Enterococcus dramatically diminished or even completely reversed the ovipositional avoidance of alkalinity in Drosophila.Mechanistically,Enterococcus generate abundant lactate during fermentation,which neutralizes the residual alkali in an egg-laying substrate.In conclusion,Enterococcus protects Drosophila from alkali stress by acidifying the ovipositional substrate,and ultimately improves the fitness of the Drosophila population.Our results demonstrate that symbionts are profound factors in the Drosophila ovipositional decision,and extend our understanding of the intimate interactions between Drosophila and their symbionts.     

Metabolic Engineering of Plant-derived (E)-β-farnesene Synthase Genes for a Novel Type of Aphid-resistant Genetically Modified Crop Plants

Aphids are major agricultural pests that cause significant yield losses of crop plants each year.Excessive dependence on insec-ticides for long-term aphid control is undesirable because of the development of insecticide resistance,the potential negative effects on non-target organisms and environmental pollution.Transgenic crops engineered for resistance to aphids via a non-toxic mode of action could be an efficient alternative strategy.(E)-β-Farnesene (EβF) synthases catalyze the formation of EβF,which for many pest aphids is the main component of the alarm pheromone involved in the chemical communication within these species.EβF can also be synthesized by certain plants but is then normally contaminated with inhibitory compounds.Engineering of crop plants capable of synthesizing and emitting EβF could cause repulsion of aphids and also the attraction of natural enemies that use EβF as a foraging cue,thus minimizing aphid infestation.In this review,the effects of aphids on host plants,plants' defenses against aphid herbivory and the recruitment of natural enemies for aphid control in an agricultural setting are briefly introduced.Furthermore,the plant-derived EβF synthase genes cloned to date along with their potential roles in generating novel aphid resistance via genetically modified approaches are discussed.     

16S rDNA-based phylogeny of non-symbiotic bacteria of Entorno-pathogenic nematodes from infected insect cadavers

Using 16S rDNA gene sequencing technique, three different species of non-symbiotic bacteria of entomopatho-genic nematodes (EPNs) (Steinernema sp.and Heterorhabditis sp.) were isolated and identified from infected insect cadavers(Galleria mellonella larvae) after 48-hour post infections.Sequence similarity analysis revealed that the strains SRK3, SRK4 and SRK5 belong to Ochrobactrum cytisi,Schineria larvae and Ochrobactrum anthropi,respectively.The isolates O.anthropi and S.larvae were found to be associated with Heterorhabditis indica strains BDU-17 and Yer-136,respectively,whereas O.cytisi was associated with Steinernema siamkayai strain BDU-87. Phenotypically, temporal EPN bacteria were fairly related to symbiotic EPN bacteria (Photorhabdus and Xenorhabdus genera). The strains SRK3 and SRK5 were phylogeographically similar to several non-symbionts and contaminated EPN bacteria isolated in Germany(LMG3311T) and China (X-14),while the strain SRK4 was identical to the isolates of S.larvae (L1/57,L1/58, L1/68 and L2/11) from Wohlfahrtia magnifica in Hungary.The result was further confirmed by RNA secondary structure and minimum energy calculations of aligned sequences.This study suggested that the non-symbionts of these nematodes are phylogeographically diverged in some extent due to phase variation.Therefore,these strains are not host-dependent, but environment-specific isolates.