Wide Screening of Phage-Displayed Libraries Identifies Immune Targets in Planta

Microbe-Associated Molecular Patterns and virulence effectors are recognized by plants as a first step to mount a defence response against potential pathogens. This recognition involves a large family of extracellular membrane receptors and other immune proteins located in different sub-cellular compartments. We have used phage-display technology to express and select for Arabidopsis proteins able to bind bacterial pathogens. To rapidly identify microbe-bound phage, we developed a monitoring method based on microarrays. This combined strategy allowed for a genome-wide screening of plant proteins involved in pathogen perception. Two phage libraries for high-throughput selection were constructed from cDNA of plants infected with Pseudomonas aeruginosa PA14, or from combined samples of the virulent isolate DC3000 of Pseudomonas syringae pv. tomato and its avirulent variant avrRpt2. These three pathosystems represent different degrees in the specificity of plant-microbe interactions. Libraries cover up to 26107 different plant transcripts that can be displayed as functional proteins on the surface of T7 bacteriophage. A number of these were selected in a bio-panning assay for binding to Pseudomonas cells. Among the selected clones we isolated the ethylene response factor ATERF-1, which was able to bind the three bacterial strains in competition assays. ATERF-1 was rapidly exported from the nucleus upon infiltration of either alive or heat-killed Pseudomonas. Moreover, aterf-1 mutants exhibited enhanced susceptibility to infection. These findings suggest that ATERF-1 contains a microbe-recognition domain with a role in plant defence. To identify other putative pathogen-binding proteins on a genome-wide scale, the copy number of selected-vs.-total clones was compared by hybridizing phage cDNAs with Arabidopsis microarrays. Microarray analysis revealed a set of 472 candidates with significant fold change. Within this set defence-related genes, including well-known targets of bacterial effectors, are over-represented. Other genes non-previously related to defence can be associated through this study with general or strain-specific recognition of Pseudomonas.

A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

Electrochemical and electron transfer investigations of copper proteins

A study of the pH and temperature dependence of the redox potentials of azurins from five species of bacteria has been performed. The variations in the potentials with pH have been interpreted in terms of electrostatic interactions between the copper site and titrating histidine residues, including the effects of substitutions in the amino acid sequences of the proteins on the electrostatic interactions. A comparison of the observed pH dependences with predictions based on histidine pK_a values known for Pseudomonas aeruginosa (Pae), Alcaligenes denitrificans (Ade), and Alcaligenes faecalis (Afa) azurins indicates that the Pae and Ade redox potentials exhibit pH dependences in line with electrostatic arguments, while Afa azurin exhibits more complex behavior. Redox enthalpies and entropies for four of the azurins at low and high pH values have also been obtained. Based on these results in conjuction with the variable pH experiments, it appears that Bordetella bronchiseptica azurin may undergo a more substantial conformational change with pH than has been observed for other species of azurin.

The temperature dependence of the redox potential of bovine erythrocyte superoxide dismutase (SOD) has been determined at pH 7.0, with potassium ferricyanide as the mediator. The following thermodynamic parameters have been obtained (T = 25°C): E°' = 403±5 mV vs. NHE, ΔG°' = -9.31 kcal/mol, ΔH°' = -21.4 kcal/mol, ΔS°' = -40.7 eu, ΔS°'_(rc) = -25.1 eu. It is apparent from these results that ΔH°', rather than ΔS°', is the dominant factor in establishing the high redox potential of SOD. The large negative enthalpy of reduction may also reflect the factors which give SOD its high specificity toward reduction and oxidation by superoxide.

Avaliação de uma resina polimérica contendo nanopartículas de prata

Neste trabalho foi testada a eficiência antimicrobiana de um nanocompósito de prata preparado a partir da modificação da resina comercial Lewatit VPOC1800 (contendo grupos sulfônicos) para três espécies de bactérias (Staphylococcus aureus, Pseudomonas aeruginosa e Escherichia coli.) cuja estrutura e composição das camadas externas da parede celular são distintas. Em termos da susceptibilidade aos biocidas essa diferença pode significar um fator importante de estudo. A avaliação da atividade biocida foi feita através de experimento que estimou a zona de inibição proporcionada pela atividade da resina sobre as bactérias estudadas. A resina mostrou eficiência biocida que aparentemente não é afetada pelas diferenças morfológicas das bactérias estudadas. Uma série de teste em batelada foi realizado com o intuito de se verificar a massa da resina e o tempo de contato ideal com a solução a ser descontaminada, chegando aos valores de 0,2g e 1minuto. As diferentes concentrações bacterianas utilizadas no estudo não influenciaram na atividade antimicrobiana da resina. Um estudo em coluna foi realizado para se averiguar o ponto de saturação do compósito, observando-se que a curva de ruptura da resina segue um tendência exponencial crescente igual a todas as espécies estudas, atingindo a saturação em aproximadamente 2250 mL

Estudo do crescimento bacteriano e da aplicação de procedimentos de limpeza e desinfecção no aço inoxidável 304L

Técnicas de limpeza química ou mecânica são comumente empregadas para evitar a formação de biofilmes e problemas associados com a colonização de superfícies por micro-organismos. Neste trabalho, amostras de aço inox 304L foram submetidas a ensaios acelerados de crescimento de biofilme, o qual foi posteriormente removido por tratamentos de limpeza e desinfecção (choque térmico com água a 70C por 1h, limpeza com ácido fosfórico 20 % v/v por 30min e desinfecção com peróxido de hidrogênio 0,17 % v/v por 1h). Com o objetivo de verificar a influência destes tratamentos na remoção do biofilme, este foi caracterizado (por quantificação microbiana e análises de espectroscopia de impedância eletroquímica - EIE), antes e após a aplicação dos tratamentos. Dois casos foram estudados. No primeiro caso, simularam-se condições presentes em tubulações de ambientes hospitalares e sistemas de distribuição de água quente. O micro-organismo utilizado foi a bactéria Serratia marcences. O processo de formação de biofilme e posterior limpeza e desinfecção foi realizado de modo contínuo durante 15 semanas. Os resultados de quantificação microbiana e de EIE mostraram que desde a primeira semana de exposição e ao longo dos ensaios, formou-se um biofilme aderente à superfície do aço e que o emprego dos tratamentos de limpeza e desinfecção não foi eficaz na remoção do biofilme. Em um segundo caso, simularam-se condições presentes em tubulações da indústria de água mineral, empregando-se a bactéria Pseudomonas aeruginosa. Neste caso, as técnicas de limpeza e desinfecção foram aplicadas individualmente e em conjunto. A aplicação de choque térmico, assim como da limpeza ácida, sobre um biofilme com 72 h de formação foi capaz de eliminar as bactérias viáveis, presentes na superfície do aço. Entretanto, a desinfecção com peróxido de hidrogênio não foi capaz de eliminá-las. Nas duas condições, porém, as análises de EIE do sistema aço/biofilme mostraram que o mesmo não foi completamente removido da superfície do metal. Correlacionando os dois casos, pode-se inferir que a superfície do aço inox 304L é rapidamente colonizada pelas duas espécies microbianas e que as técnicas de limpeza e desinfecção são capazes de reduzir e até eliminar as células viáveis, embora não removam completamente o biofilme da superfície. Por outro lado, é importante ressaltar que fatores como a arquitetura, espessura e porosidade do biofilme, e propriedades intrínsecas da superfície, são fatores que afetam os valores de impedância medidos, sendo necessário considerá-los na análise, tanto da formação do biofilme, quanto dos efeitos dos procedimentos de limpeza e desinfecção

Achromobacter xylosoxidans na fibrose cística: infecção crônica e disseminação clonal

A mortalidade na Fibrose Cística (FC) é decorrente de infecções pulmonares causadas comumente por: Pseudomonas aeruginosa, Staphylococcus aureus e espécies do Complexo Burkholderia cepacia (CBc). Mais recentemente, tem sido observada a emergência de BGN-NF raros, como Achromobacter xylosoxidans, porém, sua prevalência, potencial de transmissão e significado clínico são desconhecidos. O objetivo deste trabalho foi verificar a ocorrência de colonização crônica por A. xylosoxidans e avaliar a possibilidade de transmissão cruzada entre os pacientes acompanhados em dois centros de referência na cidade do Rio de Janeiro. Foram incluídos 39 pacientes com FC, com pelo menos uma cultura positiva para o gênero Achromobacter spp., em um total de 897 analisadas, do período de janeiro de 2003 a dezembro de 2008. A frequência de isolamento de Achromobacter spp. nas culturas analisadas foi de 14,5% (130 em 897 culturas). A maioria (n=122; 93,8%) foi identificada como A. xylosoxidans por testes fenotípicos e pelo sequenciamento do gene rrs que codifica o 16S rRNA. A análise do polimorfismo genético dos isolados de A. xylosoxidans pela técnica de PFGE, mostrou 22 grupos clonais. Destes, sete foram compartilhados entre pacientes distintos sugerindo transmissão cruzada. Apenas o clone G foi amplamente disseminado entre 56,4% dos pacientes estudados, sugerindo a possibilidade de um surto. Os 15 clones restantes constituíram-se em clones exclusivos por pacientes. Os cinco pacientes colonizados cronicamente por A. xylosoxidans mostraram a prevalência de clones únicos. Até o momento, este é o primeiro caso da ocorrência de surto por A. xylosoxidans em pacientes com Fibrose Cística. A. xylosoxidans é um microrganismo que vem se destacando em frequência e como um possível patógeno pulmonar nesses pacientes. Entretanto, até o momento os dados são insuficientes para avaliar a sua contribuição para a evolução da doença pulmonar. Estudos que busquem elucidar as características de A. xylosoxidans que o permitem colonizar persistentemente o pulmão dos pacientes com FC, bem como seu potencial de virulência, são necessários.

Studies on fish epidemics from Assam

Investigations conducted since July 1988 on ulcerative fish epidemics in Assam, India, indicated that mainly four species of fishes belonging to the genera Puntius, Channa, Macrognathus and Mystus were widely affected by the disease. Results indicated that outbreak of the disease may not be due to organic pollution of water or radioactive and heavy-metallic contamination. Bacterial culture revealed colonies of Escherichia coli and Pseudomonas aeruginosa in the surface muscular lesions and gill tissues while preliminary electron microscopic studies indicated the presence of viruses in the muscles and gills of diseased fishes.

噬菌蛭弧菌的分离及初步鉴定

采用双层平板法,以滤膜过滤的方法来收集噬菌蛭弧菌,以嗜水气单胞菌(Aeromonas hudrophila)、荧光假单胞菌(Pseudomonas fluorescent)和绿脓杆菌(Pseudomonas aeruginosa)为宿主菌,进行噬菌蛭弧菌的分离研究;并在此基础上,通过接触酶检测和寄生性确认对噬菌蛭弧菌(Bdellovibrio bacteriovorus)进行了初步的鉴定。结果表明未使用滤膜过滤,采用自来水琼脂双层平板法分离噬菌蛭弧菌的效果较好;并经过接触酶和寄生性检测初步鉴定此BD-SP

Establishment and characterization of dual-species biofilms formed between a 3,5-dinitrobenzoic-degrading strain and bacteria with high biofilm-forming capabilities

In this study, the possibility of establishing a dual-species biofilm from a bacterium with a high biofilm-forming capability and a 3,5-dinitrobenzoic acid (3,5-DNBA)-degrading bacterium, Comamonas testosteroni A3, was investigated. Our results showed that the combinations of strain A3 with each of five strains with a high biofilm-forming capability (Pseudomonas sp. M8, Pseudomonas putida M9, Bacillus cereus M19, Pseudomonas plecoglossicida M21 and Aeromonas hydrophila M22) presented different levels of enhancement regarding biofilm-forming capability. Among these culture combinations, the 24-h dual-species biofilms established by C. testosteroni A3 with P. putida M9 and A. hydrophila M22 showed the strongest resistance to 3,5-DNBA shock loading, as demonstrated by six successive replacements with DMM2 synthetic wastewater. The degradation rates of 3,5-DNBA by these two culture combinations reached 63.3-91.6% and 70.7-89.4%, respectively, within 6 h of every replacement. Using the gfp-tagged strain M22 and confocal laser scanning microscopy, the immobilization of A3 cells in the dual-species biofilm was confirmed. We thus demonstrated that, during wastewater treatment processes, it is possible to immobilize degrader bacteria with bacteria with a high biofilm-forming capability and to enable them to develop into the mixed microbial flora. This may be a simple and economical method that represents a novel strategy for effective bioaugmentation.

污灌和农药对农田土壤假单胞菌种群的影响

随着环境污染问题的日益严重，微生物修复起到越来越重要的作用。假单胞菌是土壤微生物中最重要、研究最多的细菌之一，能降解简单和复杂的有机物，它们因此而广泛的存在于土壤和水体。但有关于石油、重金属及农药污染物对农田土壤假单胞菌多样性及种群结构的影响却缺乏全面和系统的认识。 本论文首次采用传统微生物培养方法与PCR-DGGE等现代微生物分子生态学研究方法相结合的手段，系统评价了长期含石油和重金属污水灌溉对中国最大的石油、重金属污灌区——沈抚、张士灌区农田土壤中的假单胞菌多样性及其种群结构的影响。同时，本论文也研究了乙草胺、甲胺磷对黑土假单胞菌多样性及种群结构的影响。得出以下结果： 石油污灌区土壤中总的假单胞菌多样性显著高于重金属污灌区；石油污灌区旱田土壤假单胞菌多样性接近于对照清洁土壤,同时低于相似污染程度的石油污灌区水田土壤。进一步测序发现，Pseudomonas mendocina、Pseudomonas stutzeri、Pseudomonas aeruginosa是所分析石油和重金属污灌区土壤中的优势类群，说明在长期污染胁迫下这3种假单胞菌分别得到了不同程度的富集。DGGE 结果显示石油和重金属污染土壤样品的可培养假单胞菌多样性没有显著差异，但均低于对照清洁土壤样品。对各个土壤样品可培养假单胞菌菌株进行REP-PCR基因分型，结果表明这些假单胞菌之间有显著的遗传差异。进一步测序表明，土壤样品中可培养假单胞菌优势类群中含有Pseudomonas. fluorescens 和Pseudomonas. Putida两种。 黑土农田土壤中使用乙草胺会严重降低总的及可培养假单胞菌群落的多样性，而且在5周内不能恢复。而甲胺磷处理土壤与对照相比则差异不显著，并且经过一段时间的适应，土壤中的总的及可培养假单胞菌种群不仅得到恢复而且超过对照。对各处理土壤总的及可培养假单胞菌DGGE谱带类型聚类分析，发现乙草胺、甲胺磷处理土壤样品均各自聚为一簇，说明农药污染类型是影响土壤中假单胞菌种群结构的重要因素。

一株嗜杂醇油细菌的分离、鉴定和特性研究

为结合一般白酒存在的杂醇油含量偏高或超标问题，作者试图寻找能嗜高醇类(含杂醇油)的有效菌株加以开发利用。本文研究了一株从富集分离、定向诱导得到的嗜异戊醇的W-2菌，该菌能以异戊醇或其它某些多碳醇作为唯一的碳源和能源进行生长。该菌在PH8.5的环境条件下，异戊醇的利用率可高达84.4%。此外，该菌还能广泛利用糖类、醇、有机酸、酯、盐等有机物作为唯一的碳源和能源。一般不利用—碳化合物。该菌具单极生鞭毛，呈杆状，适宜生长温度范围4℃—43℃。最适生长温度36℃，在PH4.0—11.0均能生长，最适生长PH为8.5—9.0，在培养基产生蓝绿色色素。W-2菌经形态，生理生化鉴定为假单胞菌属中的铜绿假单胞菌的一个变种。初步定名为Pseudomonas aeruginosa W-2。本文最后讨论了该菌的开发应用前景。

Biosorption of uranium by chemically modified Rhodotorula glutinis

The present paper reports the biosorption of uranium onto chemically modified yeast cells, Rhodotorula glutinis, in order to study the role played by various functional groups in the cell wall. Esterification of the carboxyl groups and methylation of the amino groups present in the cells were carried out by methanol and formaldehyde treatment, respectively. The uranium sorption capacity increased 31% for the methanol-treated biomass and 11% for the formaldehyde-treated biomass at an initial uranium concentration of 140 mg/L The enhancement of uranium sorption capacity was investigated by Fourier transform infrared (FTIR) spectroscopy analysis, with amino and carboxyl groups were determined to be the important functional groups involved in uranium binding. The biosorption isotherms of uranium onto the raw and chemically modified biomass were also investigated with varying uranium concentrations. Langmuir and Freundlich models were well able to explain the sorption equilibrium data with satisfactory correlation coefficients higher than 0.9. (C) 2010 Elsevier Ltd. All rights reserved.

Investigation of EscA as a chaperone for the Edwardsiella tarda type III secretion system putative translocon component EseC

Edwardsiella tarda is an important Gram-negative enteric pathogen affecting both animals and humans. It possesses a type III secretion system (T3SS) essential for pathogenesis. EseB, EseC and EseD have been shown to form a translocon complex after secretion, while EscC functions as a T3SS chaperone for EseB and EseD. In this paper we identify EscA, a protein required for accumulation and proper secretion of another translocon component, EseC. The escA gene is located upstream of eseC and the EscA protein has the characteristics of T3SS chaperones. Cell fractionation experiments indicated that EscA is located in the cytoplasm and on the cytoplasmic membrane. Mutation with in-frame deletion of escA greatly decreased the secretion of EseC, while complementation of escA restored the wild-type secretion phenotype. The stabilization and accumulation of EseC in the cytoplasm were also affected in the absence of EscA. Mutation of escA did not affect the transcription of eseC but reduced the accumulation level of EseC as measured by using an EseC-LacZ fusion protein in Ed. tarda. Co-purification and co-immunoprecipitation studies demonstrated a specific interaction between EscA and EseC. Further analysis showed that residues 31-137 of EseC are required for EseC-EscA interaction, Mutation of EseC residues 31-137 reduced the secretion and accumulation of EseC in Ed. tarda. Finally, infection experiments showed that mutations of EscA and residues 31-137 of EseC increased the LD50 by approximately 10-fold in blue gourami fish. These results indicated that EscA functions as a specific chaperone for EseC and contributes to the virulence of Ed. tarda.

Attenuation of Edwardsiella tarda Virulence by Small Peptides That Interfere with LuxS/Autoinducer Type 2 Quorum Sensing

Edwardsiella tarda is a gram-negative pathogen with a broad host range that includes humans, animals, and fish. Recent studies have shown that the LuxS/autoinducer type 2 (AI-2) quorum sensing system is involved in the virulence of E. tarda. In the present study, it was found that the E. tarda LuxS mutants bearing deletions of the catalytic site (C site) and the tyrosine kinase phosphorylation site, respectively, are functionally inactive and that these dysfunctional mutants can interfere with the activity of the wild-type LuxS. Two small peptides, 5411 and 5906, which share sequence identities with the C site of LuxS, were identified. 5411 and 5906 proved to be inhibitors of AI-2 activity and could vitiate the infectivity of the pathogenic E. tarda strain TX1. The inhibitory effect of 5411 and 5906 on AI-2 activity is exerted on LuxS, with which these peptides specifically interact. The expression of 5411 and 5906 in TX1 has multiple effects (altering biofilm production and the expression of certain virulence-associated genes), which are similar to those caused by interruption of luxS expression. Further study found that it is very likely that 5411 and 5906 can be released from the strains expressing them and, should TX1 be in the vicinity, captured by TX1. Based on this observation, a constitutive 5411 producer (Pseudomonas sp. strain FP3/pT5411) was constructed in the form of a fish commensal isolate that expresses 5411 from a plasmid source. The presence of FP3/pT5411 in fish attenuates the virulence of TX1. Finally, it was demonstrated that fish expressing 5411 directly from tissues exhibit enhanced resistance against TX1 infection.