Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues

Subtilisin-like serine proteases (subtilases) are a very diverse family of serine proteases with low sequence homology, often limited to regions surrounding the three catalytic residues. Starting with different Hidden Markov Models (HMM), based on sequence alignments around the catalytic residues of the S8 family (subtilisins) and S53 family (sedolisins), we iteratively searched all ORFs in the complete genomes of 313 eubacteria and archaea. In 164 genomes we identified a total of 567 ORFs with one or more of the conserved regions with a catalytic residue. The large majority of these contained all three regions around the "classical" catalytic residues of the S8 family (Asp-His-Ser), while 63 proteins were identified as S53 (sedolisin) family members (Glu-Asp-Ser). More than 30 proteins were found to belong to two novel subsets with other evolutionary variations in catalytic residues, and new HMMs were generated to search for them. In one subset the catalytic Asp is replaced by an equivalent Glu (i.e. Glu-His-Ser family). The other subset resembles sedolisins, but the conserved catalytic Asp is not located on the same helix as the nucleophile Glu, but rather on a beta-sheet strand in a topologically similar position, as suggested by homology modeling. The Prokaryotic Subtilase Database (www.cmbi.ru.nl/subtilases) provides access to all information on the identified subtilases, the conserved sequence regions, the proposed family subdivision, and the appropriate HMMs to search for them. Over 100 proteins were predicted to be subtilases for the first time by our improved searching methods, thereby improving genome annotation.     

Unnoticed spread of class 1 integrons in gram-positive clinical strains isolated in Guangzhou, China

A total of 46 gram-positive bacteria isolated from clinical specimens collected in China were subjected to PCR analysis with the intI1-specific primers, and the intI1-positive strains were further analyzed for their resistance gene cassette. All isolates possessed the class 1 integron in their genomes and the array of gene cassettes was dhfrXII-orfF-aadA2, which is very similar to other organisms except in one isolate carrying an additional copy of the class 1 integron containing the aadA2 gene cassette. Altogether, the results indicate that the class 1 integron is widespread in gram-positive clinical strains isolated in Guangzhou, China.     

Interaction of protamine with gram‐negative bacteria membranes: possible alternative mechanisms of internalization in Escherichia coli,Salmonella typhimurium and Pseudomonas aeruginosa

This study was concerned with the interaction between the cationic antimicrobial peptide, protamine (Ptm) and the cytoplasmic membranes of the gram‐negative bacteria Escherichia coli, Salmonella typhimurium and Pseudomonas aeruginosa. The objective of the study was to explain the observed paradox of internalization without permanent disruption of the cell envelope. We carried out Monte Carlo computer simulation of Ptm in an aqueous environment in the presence of ~100 mM NaCl and model membranes consisting of either (65:35) or (75:25) PE:PG molar ratios. The (75:25) model, representative of the gram‐negative cytoplasmic membrane, showed that the Ptm center of mass remained at least 7 nm from the membrane surface leading to the prediction that Ptm would not internalize via disruption of the inner membrane. By using immunoelectron microscopy of Ptm‐treated cells, we showed that Ptm internalization to the cytoplasm took place rapidly in the presence or absence of the outer envelope. Ultrastructural examination revealed no obvious morphological changes to cells that were treated with subinhibitory or bactericidal levels of Ptm. Reconstituted phospholipid bilayers were constructed and were unperturbed by Ptm treatment over a wide range of concentrations and applied transmembrane voltages. We conclude that in the cases of the cell envelopes of E. coli, S. typhimurium and P. aeruginosa, Ptm internalized by means independent of the phospholipid bilayer, most likely mediated by one or more membrane proteins such as cation‐selective barrel‐like proteins. Work is currently underway to test this hypothesis. © 2014 The Authors. Journal of Peptide Science published by John Wiley & Sons, Ltd.     

Copper tolerance in bacteria requires the activation of multiple accessory pathways

Copper is a required micronutrient for bacteria and an essential cofactor for redox-active cuproenzymes. Yet, excess copper is extremely toxic, and is exploited as a bacteriocide in medical and biotechnological applications and also by the mammalian immune system. To evade copper toxicity, bacteria not only control intracellular copper homeostasis, but they must also repair the damage caused by excess copper. In this review, we summarize the bacterial cell-wide response to copper toxicity in Enterobacteria. Tapping into the abundant research data on two key organisms, Escherichia coli and Salmonella enterica, we show that copper resistance requires both the direct copper homeostatic response and also the indirect accessory pathways that deal with copper-induced damage. Since patterns of copper response are conserved through the Proteobacteria, we propose a cell-wide view of copper detoxification and copper tolerance that can be used to identify novel targets for copper-based antibacterial therapeutics.     

氧化型革兰氏阴性杆菌一管多用鉴定培养基的研制和应用

研制出一种一管多用鉴定培养基。在一支单管培养基上,可根据高层是否产气,斜面有无荧光,高层、斜面与凝固水附近的颜色变化五个特征,结合氧化酶试验与鞭毛染色结果,同步将临床常见的氧化型革兰氏阴性杆菌鉴定到属或种,具有广泛的实用性。     

Endophytic Pseudomonas fluorescens Endo2 and Endo35 induce resistance in black gram (Vigna mungo L. Hepper) to the pathogen Macrophomina phaseolina

Abstract

The effect of endophytic Pseudomonas fluorescens isolates Endo2 and Endo35 on induced systemic disease protection against dry root rot of black gram (Vigna mungo L. Hepper) caused by Macrophomina phaseolina was investigated under glasshouse conditions. When the bacterized black gram plants were inoculated with dry root rot pathogen, the activities of peroxidase (PO), polyphenol oxidase (PPO), phenylalanine ammonia-lyase (PAL) were stimulated in addition to accumulation of phenolics and lignin. Activity of phenylalanine ammonia-lyase (PAL) reached the maximum 24 h after pathogen challenge inoculation, whereas the activities of PO and PPO reached the maximum at 72 h and 48 h, respectively. Isoform analysis revealed that a unique PPO3 isozyme was induced in bacterized black gram tissues inoculated with the pathogen. Phenolics were found to accumulate in bacterized black gram tissues challenged with M. phaseolina one day after pathogen challenge. The accumulation of phenolics reached maximum at the third day after pathogen inoculation. Similar observation was found in the lignin content of black gram plants. In untreated control plants, the accumulation of defence enzymes and chemicals started at the first day and drastically decreased 3 days after pathogen inoculation. These results suggest that induction of defense enzymes involved in phenylpropanoid pathway and accumulation of phenolics and PR-proteins might have contributed to restricting invasion of Macrophomina phaseolina in black gram roots.     

The crystal structures of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate

The type III secretion system (T3SS) is a protein injection nanomachinery required for virulence by many human pathogenic bacteria including Salmonella and Shigella. An essential component of the T3SS is the tip protein and the Salmonella SipD and the Shigella IpaD tip proteins interact with bile salts, which serve as environmental sensors for these enteric pathogens. SipD and IpaD have long central coiled coils and their N-terminal regions form α-helical hairpins and a short helix α3 that pack against the coiled coil. Using AutoDock, others have predicted that the bile salt deoxycholate binds IpaD in a cleft formed by the α-helical hairpin and its long central coiled coil. NMR chemical shift mapping, however, indicated that the SipD residues most affected by bile salts are located in a disordered region near helix α3. Thus, how bile salts interact with SipD and IpaD is unclear. Here, we report the crystal structures of SipD in complex with the bile salts deoxycholate and chenodeoxycholate. Bile salts bind SipD in a region different from what was predicted for IpaD. In SipD, bile salts bind part of helix α3 and the C-terminus of the long central coiled coil, towards the C-terminus of the protein. We discuss the biological implication of the differences in how bile salts interact with SipD and IpaD.     

Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae

Streptococcus pneumoniae open reading frame SP1492 encodes a surface protein that contains a novel conserved domain similar to the repeated fragments of mucin-binding proteins from lactobacilli and lactococci. To investigate the functional role(s) of this protein and its potential adhesive properties, the surface-exposed region of SP1492 was expressed in Escherichia coli, purified to homogeneity, and partially characterized by biophysical and immunological methods. Circular dichroism and sedimentation measurements confirmed that SP1492 is an all-beta protein that exists in solution as a monomer. The SP1492 protein has been shown to be expressed by S. pneumoniae and was experimentally localized to its surface. The protein functional domain binds to mucins II and III from porcine stomach and to purified submaxillary bovine gland mucin. It appears to be one of the very few unambiguous pneumococcal adhesin molecules known to date. A hypothetical model constructed by ab initio techniques predicts a novel beta-sandwich protein structure.     

The positional specificities of the oxygenation of linoleic acid catalyzed by two forms of lipoxygenase isolated from Bengal gram (Cicer arietinum)

The products generated from linoleic acid by the two forms of Bengal gram lipoxygenase, BGL₁ and BGL₂, were analysed by high-performance liquid chromatography using μ-porasil column with isooctane containing 0.5% ethanol as the solvent system. The l3-hydroperoxyoctadecadienoic acid and its 9-isomer which are known to be produced by soybean lipoxygenase-1 and the potato enzyme respectively were used as standards. The results show that BGL₁ generated almost exclusively the l3-hydroperoxyoctadecadienoic acid while BGL₂ produced both l3-and the 9-isomer in the ratio 21:79. The secondary keto derivatives formed in the BGL₂ reaction were also separated by this technique.     

基于同源基因的病原菌鉴定和分型靶位点的功能基因组学研究

利用病原菌序列差异,对病原菌特定基因和位点进行检测,可以快速发现和鉴别病原菌的分类和特征,对传染病快速诊断和溯源具有基础性意义和重要价值.本文旨在覆盖中国重要传染病的103种病原菌,寻找各分类阶元中特有的同源基因,并从中挑选出适合用于病原菌鉴定、分型的候选基因.利用生物信息学和基因组学方法,对已有全基因组序列的275株病原菌的836415个基因进行比对分析,进一步明确菌株的门、纲、目、科、属各分类阶元中特有的同源基因集合;通过COG功能分类方法,对同源基因集合进行功能注释,并分析在不同分类阶元内的保守基因功能的变化规律.本研究寻找到适合鉴定和分型的不同分类阶元（门、纲、目、科、属）的同源基因集合共19563个（门2891个、纲1016个、目3601个、科10130个、属1925个）.对同源基因功能的分析表明,适合对病原菌进行鉴定的基因在不同分类阶元中,表现的功能存在较大差异.革兰氏阳性和阴性病原菌在不同分类阶元中,同源基因表现出的功能也存在差异.该结果将为对在中国广泛存在的病原菌进行检测所涉及的探针、芯片设计提供理论依据,加快目标探针的筛选工作.同时,研究也是首次将世界范围内的全基因组数据和中国重大传染病涉及的病原菌紧密联系结合,为利用功能基因组学开展区域性、有针对性的病原检测和监测,提供候选基因和位点筛选的新方法.相关结果在细菌的元基因组学研究中也具有一定的应用价值.     

Emerging Technologies for the Electrochemical Detection of Bacteria

Infections are a huge economic liability to the health care system, although real‐time detection can allow early treatment protocols to avoid some of this cost and patient morbidity and mortality. Pseudomonas aeruginosa (PA) is a drug‐resistant gram‐negative bacterium found ubiquitously in clinical settings, accounting for up to 27% of hospital acquired infections. PA secretes a vast array of molecules, ranging from secondary metabolites to quorum sensing molecules, of which many can be exploited to monitor bacterial presence. In addition to electrochemical immunoassays to sense bacteria via antigen–antibody interactions, PA pertains a distinct redox‐active virulence factor called pyocyanin (PYO), allowing a direct electrochemical detection of the bacteria. There has been a surge of publications relating to the electrochemical tracing of PA via a myriad of novel biosensing techniques, materials, and methodologies. In addition to indirect methods, research approaches where PYO has been sensitively detected using surface modified electrodes are reviewed and compared with conventional PA‐sensing methodologies. This review aims at presenting indirect and direct electrochemical methods currently developed using various surface modified electrodes, materials, and electrochemical configurations on their electrocatalytic effects on sensing of PA and in particular PYO.     

Structure‐kinetic relationship of carbapenem antibacterials permeating through E. coli OmpC porin

The emergence of Gram‐negative “superbugs” exhibiting resistance to known antibacterials poses a major public health concern. Low molecular weight Gram‐negative antibacterials are believed to penetrate the outer bacterial membrane (OM) through porin channels. Therefore, intracellular exposure needed to drive antibacterial target occupancy should depend critically on the translocation rates through these proteins and avoidance of efflux pumps. We used electrophysiology to study the structure‐translocation kinetics relationships of a set of carbapenem antibacterials through purified porin OmpC reconstituted in phospholipid bilayers. We also studied the relative susceptibility of OmpC+ and OmpC‐ E. coli to these compounds as an orthogonal test of translocation. Carbapenems exhibit good efficacy in OmpC‐expressing E. coli cells compared with other known antibacterials. Ertapenem, which contains an additional acidic group compared to other analogs, exhibits the fastest entry into OmpC (k_on ≈ 2 × 10⁴ M^?1 s^?1). Zwitterionic compounds with highly polar groups attached to the penem‐2 ring, including panipenem, imipenem and doripenem exhibit faster k_on (>10⁴ M^?1 s^?1), while meropenem and biapenem with fewer exposed polar groups exhibit slower k_on (～5 × 10³ M^?1 s^?1). Tebipenem pivoxil and razupenem exhibit ～13‐fold slower k_on (～1.5 × 10³ M^?1 s^?1) than ertapenem. Overall, our results suggest that (a) OmpC serves as an important route of entry of these antibacterials into E. coli cells; and (b) that the structure‐kinetic relationships of carbapenem translocation are governed by H‐bond acceptor/donor composition (in accordance with our previous findings that the enthalpic cost of transferring water from the constriction zone to bulk solvent increases in the presence of exposed nonpolar groups). Proteins 2014; 82:2998–3012. © 2014 Wiley Periodicals, Inc.     

牛种布鲁氏菌2308不同途径小鼠感染模型的建立与评估

[背景] 布鲁氏菌可经口、皮肤、黏膜和呼吸道感染人和动物。小鼠是布鲁氏菌研究中最常用的模型动物。[目的] 建立牛种布鲁氏菌2308不同途径和剂量感染BALB/c小鼠的模型,为布鲁氏菌小鼠感染试验提供参考。[方法] 用10¹-10⁵ CFU这5个不同感染剂量,分别经注射、口服和点眼方式感染BALB/c小鼠。在感染后不同时间点采集小鼠血清,检测IgG、IgM、IgA抗体含量、脾脏重量及脾脏含菌量,评价布鲁氏菌经不同途径感染BALB/c小鼠的效果。[结果] 10 CFU是注射感染BALB/c小鼠的最小感染剂量;10⁵ CFU是口服感染BALB/c小鼠的最小感染剂量。10¹-10⁵ CFU这5个不同感染剂量经点眼途径均未能成功感染BALB/c小鼠。在10⁵ CFU感染剂量下,口服与注射感染组小鼠每克脾脏平均含菌量分别为10^5.673 CFU/g和10^5.009 CFU/g,无显著差异（P>0.05）,但口服感染组小鼠脾脏平均重量为0.310 g,显著高于注射感染组0.165 g （P<0.01）。在试验期内,注射感染组和口服感染组小鼠体内IgG抗体的滴度均随感染时间延长而持续升高;整体上,口服感染组IgG抗体峰值显著高于注射感染组;2组IgM抗体变化趋势一致;口服感染组有2只小鼠在感染28 d后产生IgA抗体,注射感染组均未检测到IgA抗体。[结论] 建立了牛种布鲁氏菌2308通过不同途径感染BALB/c小鼠的模型。     

Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase

Here we report a high resolution structure of RecU-Holliday junction resolvase from Bacillus stearothermophilus. The functional unit of RecU is a homodimer that contains a "mushroom" like structure with a rigid cap and two highly flexible loops extending outwards. These loops appear to be highly flexible/dynamic, and presumably are directly involved in DNA binding and holding it for catalysis. Structural modifications of both the protein and DNA upon their interaction are essential for catalysis. An Mg2+ ion is present in each of the two active sites in this homodimeric enzyme, and two water molecules are coordinated with each Mg2+ ion. Our data are consistent with one of these water molecules acting as a nucleophile and the other as a general acid. The identities of the general base and general acid involved in catalysis and the Lewis acid that stabilizes the pentacovalent transition state phosphate ion are proposed. A model for the RecU-Holliday junction DNA complex is also proposed and discussed in the context of DNA binding and cleavage.     

Soil warming alters microbial substrate use in alpine soils

Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C‐rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007–2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO₂ enrichment experiment using depleted ¹³CO₂ (δ¹³C = ?30‰, 2001–2009). We traced this depleted ¹³C label in phospholipid fatty acids (PLFA) of the organic layer (0–5 cm soil depth) and in C mineralized from root‐free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 (‘old’), from 2001 to 2009 (‘new’) or in 2010 (‘recent’). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root‐free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem.     

Genetic differentiation of <Emphasis Type="Italic">Vigna</Emphasis> species by RAPD,URP and SSR markers

Seventy genotypes belonging to 7 wild and cultivated Vigna species were genetically differentiated using randomly amplified polymorphic DNA (RAPD), universal rice primer (URP) and simple sequence repeat (SSR) markers. We identified RAPD marker, OPG13 which produced a species-specific fingerprint profile. This primer characterized all the Vigna species uniquely suggesting an insight for their co-evolution, domestication and interspecific relationship. The cluster analysis of combined data set of all the markers resulted in five major groups. Most of the genotypes belonging to cultivated species formed a specific group whereas all the wild species formed a separate cluster using unweighted paired group method with arithmetic averages and principle component analysis. The Mantel matrix correspondence test resulted in a high matrix correlation with best fit (r = 0.95) from combined marker data. Comparison of three-marker systems showed that SSR marker was more efficient in detecting genetic variability among all the Vigna species. The narrow genetic base of the V. radiata cultivars obtained in the present study emphasized that large germplasm collection should be used in Vigna improvement programme.     

Bioremediation of sago industry effluent and its impact on seed germination (green gram and maize)

In this study, we attempted two investigational systems: one is treatment of sago industry effluent by aerobic bacterial consortium and the other is impact of treated and untreated effluent on seed germination. For the treatment system, the starch degrading bacteria were isolated from sago industry effluent and effluent contaminated soil. The genera, Alcaligenes, Bacillus and Corynebacterium were found efficient in starch degradation. The selected isolates were tested for their efficiency on the degradation of starch both in Mineral Salts Medium (MSM) and in sago industry effluent. About 85% of the starch was degraded in MSM by a bacterial consortium composed of Alcaligenes, Bacillus and Corynebacterium, whereas in effluent the degradation of starch was only 63%. The physico-chemical properties such as electrical conductivity, total solids, suspended solids, dissolved solids, BOD, COD, nitrogen and phosphate were found decreased in effluent after 72 h. The pH of the effluent was relatively increased from 3 to 6.7. The study of seed germination (maize and green gram) was carried out at 25, 50, 75 and 100% concentrations of treated and untreated effluent using soil sowing method. Shoot length, root length, fresh weight, dry weight and chlorophyll content showed an increase when treated effluent was tested whereas a decrease of growth was noticed in untreated effluent tested seedlings. The results revealed that effluent treated by aerobic microorganisms has no negative impact on the seed germination and can be effectively used for irrigation.