Molecular characterization of Paenibacillus antarcticus IPAC21, a bioemulsifier producer isolated from Antarctic soil

Paenibacillus antarcticus IPAC21, an endospore-forming and bioemulsifier-producing strain, was isolated from King George Island, Antarctica. As psychrotolerant/psychrophilic bacteria can be considered promising sources for novel products such as bioactive compounds and other industrially relevant substances/compounds, the IPAC21 genome was sequenced using Illumina Hi-seq, and a search for genes related to the production of bioemulsifiers and other metabolic pathways was performed. The IPAC21 strain has a genome of 5,505,124 bp and a G + C content of 40.5%. Genes related to the biosynthesis of exopolysaccharides, such as the gene that encodes the extracellular enzyme levansucrase responsible for the synthesis of levan, the 2,3-butanediol pathway, PTS sugar transporters, cold-shock proteins, and chaperones were found in its genome. IPAC21 cell-free supernatants obtained after cell growth in trypticase soy broth at different temperatures were evaluated for bioemulsifier production by the emulsification index (EI) using hexadecane, kerosene and diesel. EI values higher than 50% were obtained using the three oil derivatives when IPAC21 was grown at 28°C. The bioemulsifier produced by P. antarcticus IPAC21 was stable at different NaCl concentrations, low temperatures and pH values, suggesting its potential use in lower and moderate temperature processes in the petroleum industry

Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential

The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation

Análise do transcriptoma parcial do fungo Paracoccidioides brasiliensis recuperado após infecção de macrófagos peritoneais murinos

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Medicina, 2006.O fungo patogênico e dimórfico Paracoccidioides brasiliensis é o agente etiológico da paracoccidioidomicose, a micose sistêmica de maior prevalência na América do Sul. O fungo ocorre na natureza na forma de micélio, na temperatura de 26ºC, e na forma de levedura, na temperatura de 37ºC in vitro, sendo esta a forma encontrada nos tecidos de hospedeiros. A transição dimórfica da forma miceliana para a de levedura parece ser essencial para a patogênese, como também observado para outros fungos patogênicos e dimórficos. O projeto "Genoma Funcional e Diferencial do Fungo P. brasiliensis", realizado sob coordenação de nosso laboratório, foi empreendido a partir do seqüenciamento de bibliotecas de cDNA das formas de micélio e levedura cultivadas in vitro. No contexto desse trabalho, foi construída uma biblioteca de cDNA a partir do RNA total de P. brasiliensis obtido após seis horas de co-cultivo com células de macrófagos peritoneais murinos, sem qualquer cultivo adicional do fungo in vitro. A análise do perfil transcricional desse fungo a partir dessa biblioteca de cDNA, denominada PbY-MF, visa melhor compreender o padrão de expressão de genes potencialmente importantes para a adaptação e sobrevivência de P. brasiliensis no modelo de infecção. Nesse sentido, esse trabalho iniciou a caracterização do transcriptoma de P. brasiliensis recuperado de macrófagos, pelo seqüenciamento de cDNAs da biblioteca PbY-MF. A partir da submissão das seqüências ao pipeline de análise, um total de 474 ESTs de qualidade (PHRED ³ 20 e tamanho ³ 100 nt), foram geradas e analisadas. Após agrupamento pelo CAP3, essas ESTs foram agrupadas em 16 contigs e 99 singlets. Análises de similaridades empregando os bancos de dados do projeto transcriptoma de P. brasiliensis, GeneBank nr e dbEST, utilizando as ferramentas Blastn e Blastx, foram realizadas. Os resultados dessa análise revelam que 355 ESTs, agrupadas em 4 contigs e 16 singlets, apresentaram similaridades com seqüências já descritas para o fungo P. brasiliensis, sendo a maioria relacionada com genes da maquinaria traducional mitocondrial. Cinco contigs e sete singlets, ainda não descritos em P. brasiliensis, apresentaram similaridades com seqüências de outros organismos, sendo que a maioria também mostrava similaridade com genes mitocondriais que codificam proteínas da cadeia de transporte de elétrons. Das 474 ESTs analisadas no contexto desse trabalho, seis contigs e 63 singlets não apresentaram similaridades com nenhuma seqüência descrita nos bancos de dados empregados nessa análise, correspondendo a genes novos potencialmente específicos de P. brasiliensis. Em adição, nesse trabalho também foi realizada a análise de quatro contigs que apresentam similaridades com o gene de isocitrato liase (icl), o qual codifica uma proteína chave do ciclo do glioxilato, que mostra-se ativado em diferentes modelos de células de mamíferos infectadas por patógenos intracelulares facultativos. Essas contigs foram identificadas no transcriptoma de P. brasiliensis cultivado in vitro. Nesse sentido, foram realizados o seqüenciamento adicional de clones de cDNAs relacionados a essas contigs, análises de similaridade dessas seqüências e experimentos de Southern blot. Os resultados sugerem que três contigs, apresentando similaridade com uma mesma seqüência de isocitrato liase do fungo Coccidioides immitis, representam provavelmente um mesmo transcrito de P. brasiliensis, enquanto a quarta contig apresenta maior similaridade com o gene metilisocitrato liase do fungo Emericella nidulans. _______________________________________________________________________________________ ABSTRACTThe dimorphic fungus Paracoccidioides brasiliensis is the causative agent of paracocidioidomycosis, the most prevalent systemic mycosis in Latin America. Dimorphic transition is triggered by a temperature shift from the environmental 26 ºC, in which the fungus is found as a free-living mycelium, to the 37 ºC of the human host, when it changes to the pathogenic yeast form. The dimorphic transition is believed to play an essential role in pathogenesis, as described for other dimorphic pathogenic fungi. The project "Functional and Differential Genomics of the P. brasiliensis fungus", coordinated by our laboratory, has performed the sequencing of cDNA libraries from in vitro grown yeast and mycelium cells, resulting in 19,718 expressed sequence tags (ESTs) from in vitro cultivated yeast (9,941 ESTs) and mycelium (9,777 ESTs). The CAP3 clusterization software has assembled these raw sequence data into 2,655 contigs and 3,367 singlets. In order to better understand the expression of genes potentially involved in P. brasiliensis adaptation and survival in an infection model, in this work we describe the construction of a cDNA library using as template mRNA extracted from a six-hour co-culture of P. brasiliensis yeast cells and murine peritoneal macrophages, named PbY-MΦ. The sequencing of the PbY-MΦ library generated 474 ESTs that suited inclusion criteria of PHRED ≥ 20 and size greater than 100 nucleotides, which were clustered into 16 contigs and 99 singlets. BLAST-analysis against the P. brasiliensis transcritpome project, nr and dbEST databases, grouped 355 ESTs into four contigs and 16 singlets similar to previously described P. brasiliensis sequences, most of them corresponding to components of the mitochondrial translation apparatus. Five contigs and seven singlets, which were not described in P. brasiliensis, were found to be similar to sequences described in other organisms, with most of them implicated in the mitochondrial electron transport chain. Six contigs and 63 singlets were unique in that they had no homology to known sequences. In addition, we have performed a better characterization of four contigs described in the in vitro transcriptome, which were similar to the isocitrate lyase gene (icl), an enzyme of the glyoxylate cycle. Sequencing, similarity analysis and southern blotting experiments of these contigs suggest that three of them correspond to the isocitrate lyase from Coccidioides immitis, while the fourth is related to a methyl-isocitrate lyase gene from Emericella nidulans