Coordinated regulation of anthranilate metabolism and bacterial virulence by the GntR family regulator MpaR in Pseudomonas aeruginosa

The GntR family regulators are widely distributed in bacteria and play critical roles in metabolic processes and bacterial pathogenicity. In this study, we describe a GntR family protein encoded by PA4132 that we named MpaR (M vfR-mediated P QS and a nthranilate r egulator) for its regulation of Pseudomonas quinolone signal (PQS) production and anthranilate metabolism in Pseudomonas aeruginosa. The deletion of mpaR increased biofilm formation and reduced pyocyanin production. RNA sequencing analysis revealed that the mRNA levels of antABC encoding enzymes for the synthesis of catechol from anthranilate, a precursor of the PQS, were most affected by mpaR deletion. Data showed that MpaR directly activates the expression of mvfR, a master regulator of pqs system, and subsequently promotes PQS production. Accordingly, deletion of mpaR activates the expression of antABC genes, and thus, increases catechol production. We also demonstrated that MpaR represses the rhl quorum-sensing (QS) system, which has been shown to control antABC activity. These results suggested that MpaR function is integrated into the QS regulatory network. Moreover, mutation of mpaR promotes bacterial survival in a mouse model of acute pneumonia infection. Collectively, this study identified a novel regulator of pqs system, which coordinately controls anthranilate metabolism and bacterial virulence in P. aeruginosa.     

Misannotations of the genes encoding sugar N‐formyltransferases

Tens of thousands of bacterial genome sequences are now known due to the development of rapid and inexpensive sequencing technologies. An important key in utilizing these vast amounts of data in a biologically meaningful way is to infer the function of the proteins encoded in the genomes via bioinformatics techniques. Whereas these approaches are absolutely critical to the annotation of gene function, there are still issues of misidentifications, which must be experimentally corrected. For example, many of the bacterial DNA sequences encoding sugar N‐formyltransferases have been annotated as l ‐methionyl‐tRNA transferases in the databases. These mistakes may be due in part to the fact that until recently the structures and functions of these enzymes were not well known. Herein we describe the misannotation of two genes, WP_088211966.1 and WP_096244125.1, from Shewanella spp. and Pseudomonas congelans, respectively. Although the proteins encoded by these genes were originally suggested to function as l ‐methionyl‐tRNA transferases, we demonstrate that they actually catalyze the conversion of dTDP‐4‐amino‐4,6‐dideoxy‐d ‐glucose to dTDP‐4‐formamido‐4,6‐dideoxy‐d ‐glucose utilizing N¹⁰‐formyltetrahydrofolate as the carbon source. For this analysis, the genes encoding these enzymes were cloned and the corresponding proteins purified. X‐ray structures of the two proteins were determined to high resolution and kinetic analyses were conducted. Both enzymes display classical Michaelis–Menten kinetics and adopt the characteristic three‐dimensional structural fold previously observed for other sugar N‐formyltransferases. The results presented herein will aid in the future annotation of these fascinating enzymes.     

鸡肠道微生物演替与早期定植的研究进展

鸡肠道中寄生着数量庞大且复杂多样的微生物,对宿主的生长发育和健康十分重要,既影响着饲料消化、营养物质吸收,又参与了宿主肠道形态和免疫系统的调控。深入了解鸡肠道微生物区系的时空变化及早期定植特点,将有助于提出新的肠道微生态干预策略,应用于生产。就鸡肠道微生物组成和演替、早期微生物区系建立及调控等方面进行综述,并总结了一些最新研究进展。     

乙醇对瘤胃液接种稻秸的体外发酵产物及细菌群落结构的影响

旨在研究乙醇对山羊瘤胃液与水稻秸秆厌氧共培养的影响。利用频繁传代的体外发酵技术和高通量测序方法,分析了短链脂肪酸(SCFA)产量和细菌群落的变化。结果表明,经体外培养传代8次的稻秸发酵液的总短链脂肪酸产量显著高于瘤胃液(P<0.01);与未添加乙醇的稻秸发酵液相比,添加乙醇显著提高了乙酸、戊酸和己酸的比例,降低了丙酸和丁酸的比例(P<0.01),总SCFA产量及异丁酸和异戊酸比例无显著差异。与瘤胃液相比,稻秸发酵液的拟杆菌门(Bacteroidetes)相对丰度下降,厚壁菌门(Firmicutes)相对丰度升高(P<0.05),且添加乙醇显著提高了厚壁菌门和放线菌门(Actinobacteria)的相对丰度(P<0.05);添加乙醇使双歧杆菌属(Bifidobacterium)、未定性的毛螺菌属(unidentified Lachnospiraceae)、产琥珀酸菌属(Succiniclasticum)、脱硫弧菌属(Desulfovibrio)和未定性的梭菌属(unidentified Clostridiales)的相对丰度显著升高(P<0.05)。乙醇使稻秸发酵液的显著性差异物种(Biomarker)增加;稻秸发酵液与瘤胃液亲缘关系较近,而添加乙醇显著改变了细菌区系;短链脂肪酸比例在稻秸发酵液细菌群落多样性中具有重要作用。研究表明,体外频繁传代和添加乙醇可以提高稻秸发酵液的乙酸、戊酸和己酸产量,乙醇改变了稻秸发酵液的细菌群落结构。     

Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest

Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus‐growing ants. However, little is known regarding the diversity of cuticular bacteria in other ant host species, as well as the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plants, Camponotus femoratus and Crematogaster levior. Our results show that (a) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, (b) 5.2% and 2.0% of operational taxonomic units (OTUs) are respectively specific to Ca. femoratus and Cr. levior, probably representing their respective core cuticular bacterial community, and (c) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species‐specific, suggesting that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest the environment is the dominant source of bacteria found on the cuticle of ants.     

病原菌调节宿主细胞泛素化途径的研究进展

泛素化是真核生物特有的蛋白质翻译后修饰,广泛地参与宿主细胞各种信号通路和生理过程.病原菌常通过分泌毒性效应蛋白,对泛素和泛素结合酶进行独特的共价修饰,或者利用泛素连接酶和去泛素化酶的酶学活性,调节宿主泛素化过程,从而干扰宿主细胞的信号转导,促进细菌的感染和生存.本文概述了病原菌效应蛋白调节宿主泛素化途径的主要研究进展和最新发现.     

Komagataeibacter rhaeticus 3-15全基因组及葡萄糖脱氢酶基因缺失体的构建

细菌纤维素(BC)是一种新型的可再生、可降解的生物高分子材料。为了最大程度的发挥BC生产菌株K.rhaeticus 315的生产能力,本文首先对K.rhaeticus 315进行全基因组测序,通过功能基因的注释、分析碳源代谢流向。结果显示,该菌株碳代谢特征之一是缺乏磷酸果糖激酶的编码基因,不能通过EMP途径代谢糖类碳源,而是主要通过PPP途径和TCA途径代谢碳源,维持菌体生长和BC合成。由于葡萄糖脱氢酶的存在,该菌株在合成BC的同时生成大量副产物—葡萄糖酸。为此,本文通过敲除葡萄糖酸合成酶相关基因,即葡萄糖脱氢酶基因gcd,构建葡萄糖脱氢酶基因缺失重组株(gcd^-),将葡萄糖酸的生成量降低了77%。     

石灰碳铵熏蒸联合生物有机肥对香蕉枯萎病和细菌群落的影响

以连续种植的香蕉枯萎病高发病蕉园为试验点,通过实时定量PCR和高通量测序等方法,研究了田间条件下石灰碳铵熏蒸联合生物有机肥施用对香蕉枯萎病的防治效果,以及对土壤细菌群落结构和组成的影响。结果表明: 与不熏蒸施用有机肥(OF)相比,香蕉枯萎病发病率在施用有机肥前使用石灰碳铵进行熏蒸处理(LAOF)和施用生物有机肥前使用石灰碳铵进行熏蒸处理(LABF)中分别降低了13.3%和21.7%,病原菌的拷贝数分别降低了22.4%和33.0%。与OF处理相比,石灰碳铵熏蒸联合不同肥料施用均显著降低了细菌的丰富度和多样性,形成了明显不同的群落结构,且熏蒸对群落组成的差异产生了决定性的影响。LABF的细菌丰富度和多样性均低于其他处理,群落组成也与其他处理存在明显差异。与OF处理相比,熏蒸处理(LAOF和LABF)显著增加了土壤中水恒杆菌、布鲁式菌和漯河杆菌属的相对丰度,且在LABF中的相对丰度均高于LAOF,水恒杆菌和布鲁式菌的相对丰度差异显著。在田间条件下,施用生物有机肥之前使用石灰碳铵进行熏蒸处理能够显著降低病原菌数量,改变土壤细菌群落结构,激发土壤有益微生物,从而减少香蕉枯萎病的发生。     

Molecular identification and phylogenetic analysis of fungal pathogens isolated from diseased fish in Xinjiang,China

The outbreaks of fungal diseases in cultured fish have been severe in recent years, which is harmful to the healthy and sustainable development of fish farming. In this study, an investigation was conducted for significant fungal infections of 12 species of fish in four regions in Xinjiang, China, to understand the distribution of local fish fungal pathogens. Twenty-six fungal strains with pathogenicity were isolated, and the challenge experiment showed that eight strains from Changji area had high infection rate to fish eggs. Based on internal transcribed spacer sequence data and molecular analysis, the 26 strains were classified into nine different species of six fungal genera. Phylogenetic analysis showed that all strains were divided into two clades, namely Cluster 1 (contains only the genus Mucor) and Cluster 2 (consists of five small branches), and the distribution of strains from the same region was scattered in two clusters. There is no strict host selectivity for these fungi to infect fish. Mucor sp. are the main fungal pathogen of fish in these four regions, whereas Hypophthalmichthys molitrix and Carassius auratus are two types of fish that were susceptible to pathogen. In addition, the environmental adaptability experiments showed that eight highly pathogenic strains have different adaptability to the environment, and their optimum temperature and pH were 25°C and 7.0, respectively, whereas the concentration of NaCl was negatively correlated with the growth of strains. Therefore, these results indicated that the coinfection of multiple fungal pathogens in a culture region should be considered in the future study.     

健康与凋萎病杨梅树体及根围菌群的差异

凋萎病是制约杨梅产业发展的严重病害。为了有效防控凋萎病,本研究分析了杨梅健康和感染凋萎病树体各部位及根表土和根围土中细菌和真菌群落的丰富度与多样性的差异。结果表明: 与健康树相比,病树根围土、根表土、根、枝干、枝皮和叶片的细菌和真菌丰富度均发生了显著变化,其中,根表土细菌和枝皮内真菌的丰富度和多样性均显著降低,而枝皮内细菌和根表土的真菌丰富度和多样性均显著升高。病树各部位及根表、根围土细菌和真菌的优势菌相对丰度在门、纲和属水平上发生了明显的变化,在病树枝干、根和根表土中的假单胞菌属及根表土、根围土中的镰刀菌属的相对丰度明显降低,病树根表土及根围土中青霉菌属的相对丰度明显增加。与凋萎病菌同属的拟盘多毛孢菌在病树根内显著减少,而在其他位置均大量增殖,其相对丰度与多数相对丰度较高的真菌呈正相关。本研究结果将为开发杨梅凋萎病的生态改良、培育健康树体和生物防治技术提供有效的理论依据。