Characterization of the SOS regulon of Caulobacter crescentus

The SOS regulon is a paradigm of bacterial responses to DNA damage. A wide variety of bacterial species possess homologs of lex,4 and recA, the central players in the regulation of the SOS circuit. Nevertheless, the genes actually regulated by the SOS have been determined only experimentally in a few bacterial species. In this work, we describe 37 genes regulated in a LexA-dependent manner in the alphaproteobacterium Caulobacter crescentus. In agreement with previous results, we have found that the direct repeat GTTCN(7)GTTC is the SOS operator of C. crescentus, which was confirmed by site-directed mutagenesis studies of the imuA promoter. Several potential promoter regions containing the SOS operator were identified in the genome, and the expression of the corresponding genes was analyzed for both the wild type and the lex,4 strain, demonstrating that the vast majority of these genes are indeed SOS regulated. Interestingly, many of these genes encode proteins with unknown functions, revealing the potential of this approach for the discovery of novel genes involved in cellular responses to DNA damage in prokaryotes, and illustrating the diversity of SOS-regulated genes among different bacterial species.

Regulation of Catalase-Peroxidase KatG Is OxyR Dependent and Fur Independent in Caulobacter crescentus

Most organisms that grow in the presence of oxygen possess catalases and/or peroxidases, which are necessary for scavenging the H(2)O(2) produced by aerobic metabolism. In this work we investigate the pathways that regulate the Caulobacter crescentus katG gene, encoding the only enzyme with catalase-peroxidase function in this bacterium. The transcriptional start site of the katG gene was determined, showing a short 5` untranslated region. The katG regulatory region was mapped by serial deletions, and the results indicate that there is a single promoter, which is responsible for induction at stationary phase. An oxyR mutant strain was constructed; it showed decreased katG expression, and no KatG protein or catalase-peroxidase activity was detected in stationary-phase cell extracts, implying that OxyR is the main positive regulator of the C. crescentus katG gene. Purified OxyR protein bound to the katG regulatory region between nucleotides -42 and -91 from the transcription start site, as determined by a DNase I footprinting assay, and a canonical OxyR binding site was found in this region. Moreover, OxyR binding was shown to be redox dependent, given that only oxidized proteins bound adjacent to the -35 sequence of the promoter and the katG P1 promoter was activated by OxyR in an H(2)O(2)-dependent manner. On the other hand, this work showed that the iron-responsive regulator Fur does not regulate C. crescentus katG, since a fur mutant strain presented wild-type levels of katG transcription and catalase-peroxidase production and activity, and the purified Fur protein was not able to bind to the katG regulatory region.

SpdR, a Response Regulator Required for Stationary-Phase Induction of Caulobacter crescentus cspD

The cold shock protein (CSP) family includes small polypeptides that are induced upon temperature downshift and stationary phase. The genome of the alphaproteobacterium Caulobacter crescentus encodes four CSPs, with two being induced by cold shock and two at the onset of stationary phase. In order to identify the environmental signals and cell factors that are involved in cspD expression at stationary phase, we have analyzed cspD transcription during growth under several nutrient conditions. The results showed that expression of cspD was affected by the medium composition and was inversely proportional to the growth rate. The maximum levels of expression were decreased in a spoT mutant, indicating that ppGpp may be involved in the signalization for carbon starvation induction of cspD. A Tn5 mutant library was screened for mutants with reduced cspD expression, and 10 clones that showed at least a 50% reduction in expression were identified. Among these, a strain with a transposon insertion into a response regulator of a two-component system showed no induction of cspD at stationary phase. This protein (SpdR) was able to acquire a phosphate group from its cognate histidine kinase, and gel mobility shift assay and DNase I footprinting experiments showed that it binds to an inverted repeat sequence of the cspD regulatory region. A mutated SpdR with a substitution of the conserved aspartyl residue that is the probable phosphorylation site is unable to bind to the cspD regulatory region and to complement the spdR mutant phenotype.

Sugarcane Phosphoribosyl Pyrophosphate Synthetase: Molecular Characterization of a Phosphate-independent PRS

Phosphoribosyl pyrophosphate synthetase (PRS-EC:2.7.6.1) is an important enzyme present in several metabolic pathways, thus forming a complex family of isoenzymes. However, plant PRS enzymes have not been extensively investigated. In this study, a sugarcane prs gene has been characterized from the Sugar Cane Expressed Sequence Tag Genome Project. This gene contains a 984-bp open reading frame encoding a 328-amino acid protein. The predicted amino acid sequence has 77% and 78% amino acid sequence identity to Arabidopsis thaliana and Spinacia oleracea PRS4, respectively. The assignment of sugarcane PRS as a phosphate-independent PRS isoenzyme (Class II PRS) is verified following enzyme assay and phylogenetic reconstruction of PRS homologues. To gain further insight into the structural framework of the phosphate independence of sugarcane PRS, a molecular model is described. This model reveals the formation of two conserved domains elucidating the structural features involved in sugarcane PRS phosphate independence. The recombinant PRS retains secondary structure elements and a quaternary arrangement consistent with known PRS homologues, based on circular dichroism measurements.

The defensive functions of plant inhibitors are not restricted to insect enzyme inhibition

Three plant proteinase inhibitors BbKI (kallikrein inhibitor) and BbCI (cruzipain inhibitor) from Bauhinia bouhinioides, and a BrTI (trypsin inhibitor) from B. rufa, were examined for other effects in Callosobruchus maculatus development; of these only BrTI affected bruchid emergence. BrTI and BbKI share 81% identities in their primary sequences and the major differences between them are the regions comprising the RGD and RGE motifs in BrTI. These sequences were shown to be essential for BrTI insecticidal activity, since a modified BbKI [that is a recombinant form (BbKIm) with some amino acid residues replaced by those found in BrTI sequence] also strongly inhibited insect development. By using synthetic peptides related to the BrTI sequence, YLEAPVARGDGGLA-NH(2) (RGE) and IVYYPDRGETGL-NH(2) (RGE), it was found that the peptide with an RGE sequence was able to block normal development of C. maculatus larvae (ED(50) 0.16% and LD(50) 0.09%), this being even more effective than the native protein. (C) 2009 Elsevier Ltd. All rights reserved.

A two-component system, an anti-sigma factor and two paralogous ECF sigma factors are involved in the control of general stress response in Caulobacter crescentus

The extracytoplasmic function sigma factor sigma(T) is the master regulator of general stress response in Caulobacter crescentus and controls the expression of its paralogue sigma(U). In this work we showed that PhyR and NepR act, respectively, as positive and negative regulators of sigma(T) expression and function. Biochemical data also demonstrated that NepR directly binds sigma(T) and the phosphorylated form of PhyR. We also described the essential role of the histidine kinase gene CC3474, here denominated phyK, for expression of sigma(T)-dependent genes and for resistance to stress conditions. Additionally, in vivo evidence of PhyK-dependent phosphorylation of PhyR is presented. This study also identified a conserved cysteine residue (C95) located in the periplasmic portion of PhyK that is crucial for the function of the protein. Furthermore, we showed that PhyK, PhyR and sigma(T) regulate the same set of genes and that sigma(T) apparently directly controls most of its regulon. In contrast, sigma(U) seems to have a very modest contribution to the expression of a subset of sigma(T)-dependent genes. In conclusion, this report describes the molecular mechanism involved in the control of general stress response in C. crescentus.

Synthesis of the C7-C24 fragment of (-)-Macrolactin F

An enantioselective and convergent synthesis of the C7-C24 fragment of Macrolactin F was achieved from four main fragments. A hydrotelluration/transmetalation sequence was used to install the E,Z diene present in the molecule, while a hydrozirconation/transmetalation sequence was used to connect two advanced intermediates. (C) 2008 Elsevier Ltd. All rights reserved.

Characterization and Identification of Proteolytic Bacteria From the Gut of the Velvetbean Caterpillar (Lepidoptera: Noctuidae)

The characterization and identification of proteolytic bacteria from the gut of the velvetbean caterpillar (Anticarsia gemmatalis) were the objectives of this study. Twelve aerobic and anaerobic isolates of proteolytic bacteria were obtained from the caterpillar gut in calcium caseinate agar. The number of colony forming units (CFUs) of proteolytic bacteria was higher when the bacteria were extracted from caterpillars reared on artificial diet rather than on soybean leaves (1.73 +/- 0.35 X 10(3) and 0.55 +/- 0.22 X 10(3) CFU/mg gut, respectively). The isolated bacteria were divided into five distinct groups, according to their polymerase chain reaction restriction fragment-length polymorphism profiles. After molecular analysis, biochemical tests and fatty acid profile determination, the bacteria were identified as Bacillus subtilis, Bacillus cereus, Enterococcus gallinarum, Enterococcus mundtii, and Staphylococcus xylosus. Bacterial proteolytic activity was assessed through in vitro colorimetric assays for (general) proteases, serine proteases, and cysteine proteases. The isolated bacteria were able of hydrolyzing all tested substrates, except Staphylococcus xylosus, which did not exhibit serine protease activity. This study provides support for the hypothesis that gut proteases from velvetbean caterpillar are not exclusively secreted by the insect cells but also by their symbiotic gut bacteria. The proteolytic activity from gut symbionts of the velvetbean caterpillar is suggestive of their potential role minimizing the potentially harmful consequences of protease inhibitors from some of this insect host plants, such as soybean, with implications for the management of this insect pest species.

Structure and Applications of a Rhamnolipid Surfactant Produced in Soybean Oil Waste

Soybean oil soapstock was utilized as an alternative carbon source for the production of rhamnolipids by Pseudomonas aeruginosa LBI strain. The chemical composition and properties of the rhamnolipid mixture obtained were determined to define its potential applications. The chemical characterization of the rhamnolipid has revealed the presence of ten different homologues. The monorhamnolipid RhaC(10)C(10) and the dirhamnolipid Rha(2)C(10)C(10) were the main components of the mixture that showed predominance of 44% and 29%, respectively, after 144-h of cultivation. The biosurfactant was able to form stable emulsions with several hydrocarbons and showed excellent emulsification for soybean oil and chicken fat (100%). The rhamnolipid removed 67% of crude oil present in sand samples and presented antimicrobial activity against Bacillus cereus and Mucor miehei at 64 mu g/mL and inhibition of Neurospora crassa, Staphylococcus aureus, and Micrococcus luteus at 256 mu g/mL. The results demonstrated that the rhamnolipid produced in soybean oil soapstock can be useful in environmental and food industry applications.

Microbial diversity associated with algae, ascidians and sponges from the north coast of Sao Paulo state, Brazil

Little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. The aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. Data derived from ARDRA and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. Microbial strains identified up to the genus level revealed 144 distinct ribotypes out of 256 fungal strains and 158 distinct ribotypes out of 181 bacterial strains. Filamentous fungi were distributed among 24 different genera belonging to Ascomycota, Zygomycota and Basidiomycota, some of which had never been reported in the literature as marine invertebrate-inhabiting fungi (Pestalotiopsis, Xylaria, Botrysphaeria and Cunnninghamella). Bacterial isolates were affiliated to 41 different genera, being Bacillus, Ruegeria, Micrococcus, Pseudovibrio and Staphylococcus the most abundant ones. Results revealed an unexpected high microbial diversity associated to the macroorganisms which have been collected and suggested the selection of certain microbial taxonomic groups according to the host. The combined data gathered from this investigation contribute to broaden the knowledge of microbial diversity associated to marine macroorganisms, including as a promising source for the discovery of new natural products. (C) 2009 Elsevier GmbH. All rights reserved.

Koncentrisk hämning och stimulans av bakterietillväxt i agarkulturer

The aim of this study is to elucidate factors that effect growth of Sarcina lutea and Bacillus subtilis, exposed to the growth inhibitor SDS (Sodiumdodecylsulfat). Agar diffusion experiments revealed repeated, concentric zones of inhibition and stimulation upon exposure to Sodiumdodecylsulphate or to Amoxicillin. Temperature, nutrient concentration and inhibitor concentration were controlled. Formation of successively repeated zones of inhibition, stimulation, inhibition and stimulation is discussed: •The extension of the primary inhibition zone is due to the concentration of applied Sodium dodecyl sulphate.•Immediately outside the primary inhibition zone the bacteria have access to diffusing nutrients that have not been consumed in the primary inhabitation zone.•In zones of dense bacterial growth the bacteria may produce inhibiting substances, affecting growth of bacteria in adjacent zones.•In zones of dense bacterial growth the nutrients will soon become depleted, thus affecting bacteria in adjacent zones.

Estudo sobre a biodegradação do herbicida trufluralina por bactérias isoladas de solo agrícola e proposta metodológica para o ensino de biodegradação

Trifluralina (a, a, a,trifluoro-2,6-dinitro-N, N-dipropil-p-toluidina) (TFL) é um herbicida pré-emergente, incorporado ao solo que tem sido usado na agricultura desde a década de sessenta; ele é moderadamente persistente em vários tipos de solos do Brasil. O objetivo deste estudo foi isolar - de um solo agrícola contaminado por quatro décadas - e caracterizar bactérias resistentes a TFL, determinar suas habilidades em degradar a TFL, investigar a presença de gens degardadores que possam estar envolvidos na degradação da TFL e propor um método de ensino teórico prático sobre a biodegradação, para cursos de graduação. Oito bactérias foram isoladas, pela técnica de subculturas repetidas em meio contendo TFL como única fonte de carbono, e identificadas, pelo método bioquímico e seqüenciamento do rDNA 16S como Klebsiella oxytoca, Herbaspirillum seropedicae, 3 strains of Bacillus simplex, 2 de Pseudomonas montelli e uma outra Pseudomonas sp. Uma terceira bactéria (iaolado #9), não identificada, que crescia ao redor de cristais de TFL em meio sólido, foi isolada; esta é uma técnica nova que poderá ser útil no isolamento de bactérias que são resistentes a outros compostos pouco solúveis em água. Todas as bactérias isoladas foram submetidas ao teste de biodegradação, em um meio contendo sais minerais, 0,1% succinato, 0,1 % de extrato de leveduras e 50 mg. L-1 de TFL Cinco bactérias reduziram a concentração de TFL no meio, após trinta dias de incubação: Klebsiella oxytoca (24,6 %), Herbaspirillum seropedicae (16,4 %), Bacillus simplex 2 (25.0 %), Bacillus simplex 3 (16.0 %) e isolado 9 (21.0 %). Uma bactéria conhecida como degradadora da TFL, Brevundimonas diminuta (NCIMB 10329) degradou a TFL, neste meio, de maneira semelhantes ao das bactérias isoladas. Os DNAs extraídos das quatro bactérias identificadas degradadoras da TFL, foram sondados para os gens catbólicos ndoB, todC, xylX, catA e xylE, os quais codificam as enzimas naftaleno 1,2-dioxigenase, toluene dioxigenase, toluate 1,2-dioxigenase, catecol 1,2-dioxigenase e catecol 2,3-dioxigenase, respectivamente. Técnicas de PCR e hibridização demonstraram que os DNAs de todas estas quatro bactérias foram fortemente hibridizadas para o gen ndoB, contudo, usando a técnica de ¨zonas claras¨, observou-se que nenhuma delas degradou naftaleno. Estes resultados indicam a presença de gens dioxigenases, nestas bactérias degradadoras da TFL, que poderiam estar transformando a TFL como substrato principal, ou como cometabolismo. O conhecimento sobre processos de biodegradação é necessário para os graduados dos cursos de agronomia, química, biologia, tecnologia de alimentos, etc. Neste trabalho, também, propomos o estudo teórico e prático da compostagem o qual estimula o interesse dos estudantes em aprender sobre o metabolismo envolvido neste, e em outros, processos biotecnológicos.

Biorremediação de antraceno, fenantreno e pireno em um argissolo

O antraceno, o fenantreno e o pireno são hidrocarbonetos aromáticos policíclicos (HAPs) que podem ser carcinogênicos e que não são degradados pela maioria dos microrganismos do solo. A biorremediação é uma estratégia para eliminação dos HAPs, que pode demandar a inoculação de microrganismos degradadores e a modificação das condições químicas e físicas do solo. O objetivo do presente estudo foi isolar, identificar e caracterizar microrganismos degradadores e mineralizadores de antraceno, fenantreno e pireno em meio mineral e no solo, assim como avaliar a influência do pH e da disponibilidade de água, N, P, Fe e S na biorremediação de um solo contaminado com antraceno. Seis amostras de solo de landfarming foram inoculadas individualmente a um solo contaminado em laboratório com antraceno. Após 176 dias, o solo com maior produção de C-CO2 foi utilizado para o enriquecimento em meio mineral mais antraceno. Os microrganismos foram isolados e identificados pelo seqüenciamento do gene do RNAr. A capacidade dos microrganismos em degradar os 3 HAPs no meio mineral e no solo foi avaliada por cromatografia gasosa. A mineralização de diferentes concentrações de antraceno, fenantreno e pireno no solo foi avaliada por respirometria, assim como o efeito de diferentes doses de N, P, S e Fe, de diferentes pH e umidades do solo na mineralização do antraceno. Isolou-se do solo de landfarming um consórcio microbiano composto por 6 bactérias, identificadas como Mycobacterium fortuitum, Bacillus cereus, Microbacterium sp., Gordonia polyisoprenivorans, Microbacteriaceae bacterium e Naphthaleneutilizing bacterium, e um fungo, Fusarium oxysporum. O consórcio microbiano degradou respectivamente 48, 67 e 22% do antraceno, fenantreno e pireno do meio mineral. No solo o consórcio degradou, em média, mais de 92% e mineralizou mais de 78% das diferentes concentrações destes 3 HAPs em 70 dias. As maiores mineralizações do antraceno ocorreram nos solos com as maiores umidades gravimétricas (12,5%) e pH (7,5). A adição de 100 kg ha-1 ou mais de nitrogênio no solo e a conseqüente redução da relação C:N para valores inferiores a 67:1 diminuíram a mineralização do antraceno no solo. O aumento da disponibilidade do fósforo, do ferro e do enxofre e a presença de amplas relações C:P (1076:1 a 50:1) e C:N:P (1076:16:1 a 50:1,3:1) no solo não influenciaram a mineralização do antraceno. Conclui-se que a seleção e a inoculação ao solo de microrganismos degradadores de HAPs, associado a modificação das condições ambientais, pode conduzir a um eficiente processo de biorremediação, onde a grande maioria dos HAPs é mineralizada em curto período de tempo.

Produção de hidrolisados protéícos de penas de frango utilizando bactérias queratinolíticas.

Com o crescimento populacional, a indústria avícola tem se desenvolvido rapidamente, devido à demanda de alimentos. O seu produto possui grande aceitação no mercado mundial, em função do seu valor nutricional e por não existirem restrições culturais. Entretanto, este alimento gera grande quantidade de resíduos, dentre eles, as penas. Elas são compostas principalmente por queratina, substância de difícil degradação. Neste trabalho foram utilizadas duas bactérias queratinolíticas de resíduos da indústria avícola, para se avaliar a capacidade de degradação das mesmas. Foram produzidos hidrolisados de penas por proteólise bacteriana com ambos microrganismos: Bacillus cereus (KR16) e Chryseobacterium sp. (KR6). O crescimento das bactérias em diferentes quantidades de penas, e o fator de degradação das penas comprovaram que em até 5 % obteve-se degradação para KR6, enquanto, para a KR16, obteve-se degradação até 1%. A digestibilidade in vitro dos hidrolisados foi avaliada. Observou-se que o hidrolisado da bactéria KR6 apresentou maior digestibilidade, enquanto o de farinha de penas apresentou o menor valor. A composição de aminoácidos dos hidrolisados foi determinada, sendo observadas baixas concentrações de metionina, histidina e lisina. A partir da digestibilidade in vitro e da composição de aminoácidos, foram calculados o escore de aminoácidos corrigidos (PDCAAs), o coeficiente de eficiência protéica (PER) e o valor biológico (BV). O tratamento das penas com KR6 resultou em hidrolisados com os valores mais altos de PDCAAs, PER e BV, sugerindo que este microrganismo produz hidrolisados com propriedades nutricionais superiores aos demais.

Propagação de espécies nativas com potencial ornamental : Kelissa brasiliensis (Baker) Ravenna e Sinningia lineata (Hjelmq.) Chautems

A pesquisa em tecnologia de sementes contribui para a manutenção de bancos de germoplasma. Kelissa brasiliensis (Baker) Ravenna e Sinningia lineata (Hjelmq.) Chautems são espécies nativas com potencial ornamental. Os objetivos deste trabalho foram desenvolver testes para a germinação de sementes, conhecer a qualidade fisiológica de lotes coletados in situ, desenvolver protocolos de propagação vegetativa e conhecer estratégias reprodutivas no ambiente. Avaliaram-se o vigor, bem como o comportamento germinativo das sementes em diferentes substratos, temperaturas e condições de luz. Foram realizados experimentos com propagação vegetativa de S. lineata. O trabalho foi conduzido no Laboratório de Sementes da Fepagro, no Jardim Botânico de Porto Alegre e na Faculdade de Agronomia da UFRGS. Durante as coletas, foi feita a observação dos nichos das espécies. O delineamento experimental foi completamente casualizado com quatro repetições de 10 e 20 sementes para K. brasiliensis e S. lineata, respectivamente; para S. lineata, três tratamentos com 17 repetições foram utilizados no experimento com estaquia, e nove tratamentos com quatro repetições para o teste de divisão dos tubérculos. A comparação das médias foi realizada através do teste de Duncan (P<0,05). A temperatura mais adequada para a germinação de sementes de K. brasiliensis foi 10ºC, o que explica a sua restrita distribuição ao bioma Pampa; a combinação 24h/25ºC levou a uma liberação maior de lixiviados na condutividade elétrica; o envelhecimento acelerado (72 h em 41ºC e 100% de umidade) não provocou redução significativa no percentual de germinação das sementes de K. brasiliensis. Já as sementes de S. lineata não germinaram após serem expostas ao estresse. A temperatura mais adequada para o teste de germinação de sementes de S. lineata foi 20ºC; para ambas espécies, o substrato papel e a presença de luz foram as condições mais adequadas para a germinação. S. lineata demonstrou ser facilmente propagada por sementes e via assexuada, o que revelou a rusticidade característica das espécies rupícolas.