Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4

Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project “Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens” awarded through the 2010 DOE-JGI’s Community Sequencing Program.     

Investigation of C-5 alkynyl (alkynyloxy or hydroxymethyl) and/or N-3 propynyl substituted pyrimidine nucleoside analogs as a new class of antimicrobial agents

The resurgence of mycobacterial infections and the emergence of drug-resistant strains urgently require a new class of agents that are distinct than current therapies. A group of 5-ethynyl (6–10), 5-(2-propynyloxy) (16, 18, 20, 22, 24), 5-(2-propynyloxy)-3-N-(2-propynyl) (17, 19, 21, 23, 25) and 5-hydroxymethyl-3-N-(2-propynyl) (30–33) derivatives of pyrimidine nucleosides were synthesized and evaluated against mycobacteria [Mycobacterium tuberculosis (Mtb), Mycobacterium bovis (BCG) and Mycobacterium avium], gram-positive bacteria (Staphylococcus aureus and Enterococcus faecalis) and gram-negative bacteria (Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa) alone and in combination with existing drugs in in vitro assays. Although several compounds exhibited marked inhibitory activity at a higher concentration against Mtb, M. bovis, S. aureus and E. faecalis, they displayed unexpected synergistic and additive interactions at their lower concentrations with antitubercular drugs isoniazid and rifampicin, and antibacterial drug gentamicin. The active analogues were also found to inhibit intracellular Mtb in a human monocytic cell line infected with H37Ra. Oral administration of 5-hydroxymethyl-3-N-(2-propynyl)-3′-azido-2′,3′-dideoxyuridine (32) and 5-hydroxymethyl-3-N-(2-propynyl)-2′,3′-dideoxyuridine (33) at a dose of 100 mg/kg for two weeks showed promising in vivo effects in mice infected with Mtb (H37Ra). No in vitro cytotoxicity of the test compounds was observed up to the highest concentration tested (CC50 > 300 μg/mL).     

A prevalence survey for zoonotic enteric bacteria in a research monkey colony with specific emphasis on the occurrence of enteric Yersinia

Transmissible pathogenic and opportunistic zoonotic enteric bacteria comprise a recognized occupational health threat to exposed humans from non-human primates (NHPs). In an effort to evaluate the occurrence of selected enteric organisms with zoonotic and biohazard potential in a research colony setting, we performed a prevalence study examining 61 juvenile and young adult rhesus macaques participating in a transplant immunology project. Primary emphasis was directed specifically to detection of pathogenic enteric Yersinia, less well-documented and reported NHP pathogens possessing recognized significant human disease potential. NHPs were surveyed by rectal culture during routine health monitoring on three separate occasions, and samples incubated using appropriate media and specific selective culture methods. Enteric organisms potentially transmissible to humans were subcultured and identified to genus and species. Significant human pathogens of the Salmonella/Shigella, Campylobacter, and enteric Yersinia groups were not isolated throughout the survey, suggesting prevalence of these organisms may generally be quite low.     

LPS的胞内受体Caspase-11的研究进展

以往的研究认为,TLR4是内毒素(LPS)的胞膜受体.新近的研究发现含半胱氨酸的天冬氨酸蛋白水解酶11(Caspase-11,Casp11)可能在胞内LPS的识别中发挥关键作用.Caspase-11与胞内LPS结合后被激活.活化的Casp-11一方面剪切下游gasdermin D分子进而介导细胞焦亡(pyroptosis),另一方面激活NLRP3/ASC-Casp-1通路,使细胞分泌促炎因子IL-1β和IL-18等.Casp-11还能通过促进吞噬体和溶酶体融合,增强细胞对革兰氏阴性菌的杀灭.在严重内毒素血症过程中,由于Casp-11过度活化,大量细胞发生焦亡,致使大量胞内促炎介质被释放到胞外,导致机体出现难以调控的炎症反应,最终发展成内毒素休克.Casp-11是内毒素休克发生的关键分子.本文对Casp-11在LPS的识别、活化及效应方面的最新进展进行综述.     

革兰氏阴性菌脂蛋白Lol系统转运蛋白的功能及表面展示分泌机制

细菌脂蛋白是细胞膜的重要组成成分,在革兰氏阴性菌的生理及致病性中扮演着重要的角色。革兰氏阴性菌中已知负责胞内脂蛋白转运的是Lol(Localization of lipoprotein)系统。该系统识别成熟脂蛋白的分泌信号,将外膜脂蛋白转运并定位于细胞外膜内侧。近年来的研究发现,跨细胞外膜进行表面展示的脂蛋白实际上在革兰氏阴性菌中广泛存在,其分泌机制开始成为研究热点。为了对革兰氏阴性菌中脂蛋白分泌机制的研究现状有一个系统全面的了解,本文概述了脂蛋白转运过程中Lol系统5个转运蛋白的功能与保守性、不同细菌中脂蛋白分泌信号的差异以及表面展示脂蛋白可能的分泌机制。     

Estimation of abundance dynamics of gram-negative bacteria in soil

Bacterial succession in soil was studied for two variants of initiation (moistening and moistening with addition of glucose). To determine the numbers of viable gram-negative bacteria, the modified nalidixic acid method was applied. The numbers of gram-negative bacteria revealed by this method were 2 to 3.5 times higher than those determined by the traditional method. In a developing community, the highest total bacterial numbers were observed on day 7; afterwards their numbers decreased and stabilized at a level exceeding four-to fivefold the initial one. In both experimental variants, the highest numbers of viable gram-negative bacteria were revealed on day 15 (75–85% of the total bacterial numbers). Morphology of these bacteria suggests their classification as cytophagas (chitinophagas) utilizing chitin from the dead fungal mycelium.     

Accumulation of Peptidoglycan O-Acetylation Leads to Altered Cell Wall Biochemistry and Negatively Impacts Pathogenesis Factors of Campylobacter jejuni

Campylobacter jejuni is a leading cause of bacterial gastroenteritis in the developed world. Despite its prevalence, its mechanisms of pathogenesis are poorly understood. Peptidoglycan (PG) is important for helical shape, colonization, and host-pathogen interactions in C. jejuni. Therefore, changes in PG greatly impact the physiology of this organism. O-acetylation of peptidoglycan (OAP) is a bacterial phenomenon proposed to be important for proper cell growth, characterized by acetylation of the C6 hydroxyl group of N-acetylmuramic acid in the PG glycan backbone. The OAP gene cluster consists of a PG O-acetyltransferase A (patA) for translocation of acetate into the periplasm, a PG O-acetyltransferase B (patB) for O-acetylation, and an O-acetylpeptidoglycan esterase (ape1) for de-O-acetylation. In this study, reduced OAP in ΔpatA and ΔpatB had minimal impact on C. jejuni growth and fitness under the conditions tested. However, accumulation of OAP in Δape1 resulted in marked differences in PG biochemistry, including O-acetylation, anhydromuropeptide levels, and changes not expected to result directly from Ape1 activity. This suggests that OAP may be a form of substrate level regulation in PG biosynthesis. Ape1 acetylesterase activity was confirmed in vitro using p-nitrophenyl acetate and O-acetylated PG as substrates. In addition, Δape1 exhibited defects in pathogenesis-associated phenotypes, including cell shape, motility, biofilm formation, cell surface hydrophobicity, and sodium deoxycholate sensitivity. Δape1 was also impaired for chick colonization and adhesion, invasion, intracellular survival, and induction of IL-8 production in INT407 cells in vitro. The importance of Ape1 in C. jejuni biology makes it a good candidate as an antimicrobial target.     

Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts

We have investigated the specificity of six different lysozymes for peptidoglycan substrates obtained by extraction of a number of gram-negative bacteria and Micrococcus lysodeikticus with chloroform/Tris-HCl buffer (chloroform/buffer). The lysozymes included two that are commercially available (hen egg white lysozyme or HEWL, and mutanolysin from Streptomyces globisporus or M1L), and four that were chromatographically purified (bacteriophage lambda lysozyme or LaL, bacteriophage T4 lysozyme or T4L, goose egg white lysozyme or GEWL, and cauliflower lysozyme or CFL). HEWL was much more effective on M. lysodeikticus than on any of the gram-negative cell walls, while the opposite was found for LaL. Also the gram-negative cell walls showed remarkable differences in susceptibility to the different lysozymes, even for closely related species like Escherichia coli and Salmonella Typhimurium. These differences could not be due to the presence of lysozyme inhibitors such as Ivy from E. coli in the cell wall substrates because we showed that chloroform extraction effectively removed this inhibitor. Interestingly, we found strong inhibitory activity to HEWL in the chloroform/buffer extracts of Salmonella Typhimurium, and to LaL in the extracts of Pseudomonas aeruginosa, suggesting that other lysozyme inhibitors than Ivy exist and are probably widespread in gram-negative bacteria.