Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining

Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A. nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus

Avaliação do potencial biotecnológico de microorganismos associados ao inseto-praga diabrotica speciosa na produção de polímeros biobaseados e biodegradáveis

Technological development and market pressure turned polymers into widely used structural materials for several different applications, being manufactured by a wide range of monomers. However, traditional polymers usually show some drawbacks regarding environmental aspects, as most used polymers are produced with nonrenewable feedstock and generate huge amounts of non-biodegradable residues. Therefore it is imperative the sustainable development of new bio-based and biodegradable polymeric materials. The use of microorganisms for obtaining biopolymers is a very promising reality. However, in order to achieve viable production in industrial scale it is necessary to overcome economic barriers, by using microbes with good assimilation of low-cost substrates and high biopolymer yields. As such, the objective of this work was the isolation and identification of bacteria associated with the insect Diabrotica speciosa, as well as the evaluation microbial capacity of biopolymer production. The insect presented great microbial diversity, identified as an underexplored niche with tremendous biotechnological potential for the investigation of novel species and/or strains. In an attempt to find bacterial isolates effective on the production of two classes of biopolymers, polyhydroxyalkanoates (PHA) and exopolysaccharides (EPS), it was obtained 73 strains of bacteria associated with Diabrotica speciosa. These bacteria were identified at genus level by genetic techniques using 16S rDNA sequencing and by proteomic techniques using MALDI-TOF MS. Both characterization methods yielded 100% convergence on results. It was found 17 different bacterial genera, which were submitted to qualitative screening assays in order to identify strains producing PHA using Nile Red dye method, as well as for EPS by using the bacterial spot test. Promising strains on both assays were selected for further quantitative studies and structural characterization of the obtained biopolymers. Quantitative analyses for PHA production corroborated satisfactorily with qualitative results, especially to bacteria from genera Aurantimonas and Delftia which demonstrated high PHA production capacity with 50 and 90% polymer yield on dry mass, both strains being strains able to use substrates such as glucose, acetate and glycerol. GC-MS analyses indicated that Aurantimonas sp. produced mostly a homopolymer of polyhydroxybutyrate (PHB), while Delftia sp. was able to produce a copolymer having butyrate and valerate (PHBV), with up to 10% (w/w) of valerate. Regarding EPS production, the screening showed that the isolates were able to produce polymers in variable amounts, with vast and complex structural variations. Strains from genera Acidovorax, Aurantimonas and Luteibacter were further selected for quantitative analysis of EPS production and analytical characterization of the obtained biopolymer. After analyses using NMR, MALDI-TOF, SEC-UV-ELSD and GC-MS, bacteria from genus Luteibacter produced a highly complex polymer rich in mannose, glucose, fucose and xylose; genus Acidovorax produced a glucomannan-type EPS with a high degree of branching; and genus Aurantimonas was able to produce up to 2 g.L-1 of a water insoluble EPS. In face of these results, it was possible to conclude that D. speciosa microbiota showed to be extremely rich in bacterial species viable for exploratory studies with biotechnological context of biopolymer production. Investigated strains showed promising characteristics to be further evaluated in larger scale (fermenters), especially the bacteria Aurantimonas sp., able to produce PHBV and EPS.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)O desenvolvimento tecnológico e a pressão de mercado fizeram com que os polímeros se tornassem materiais estruturais amplamente utilizados em uma grande variedade de aplicações, sendo manufaturados a partir de uma ampla gama de monômeros. Entretanto, estes materiais geralmente apresentam algumas desvantagens do ponto de vista ambiental, pois os polímeros mais utilizados são produzidos com matérias-primas não renováveis e geram grandes volumes de resíduos não biodegradáveis. Assim, torna-se necessário o desenvolvimento sustentável de novos materiais biobaseados e biodegradáveis. O uso de microorganismos para a obtenção deste tipo de polímero é uma realidade bastante promissora. Todavia, para a produção viável em escala industrial é necessário superar barreiras econômicas, através do uso de cepas com boa assimilação de substratos de baixo custo, proporcionando uma alta produtividade. Assim, este trabalho teve por objetivo o isolamento e identificação de bactérias associadas ao inseto Diabrotica speciosa, bem como a avaliação da capacidade microbiana de produção de biopolímeros. O inseto apresentou uma grande diversidade em sua microbiota, mostrando ser este um nicho subexplorado e com enorme potencial para a investigação de novas espécies e/ou isolados. Com o propósito de encontrar isolados eficientes na produção de duas classes de biopolímeros, polihidroxialcanoatos (PHAs) e exopolissacarídeos (EPS), foram obtidos 73 isolados bacterianos do inseto praga Diabrotica speciosa. Todas as cepas foram identificadas em nível de gênero pelo uso de técnicas genéticas, através do sequenciamento de 16S rDNA parcial e por análises proteômicas, avaliando-se o perfil proteico obtido via MALDI-TOF MS. Ambas as técnicas de identificação apresentaram 100% de convergência entre os resultados. Foram encontrados no total 17 gêneros de bactérias, que foram submetidas a ensaios qualitativos de triagem para identificação de isolados produtores de PHAs pelo método do corante vermelho de Nilo, bem como para EPS pelo método do teste de ponto bacteriano. Isolados promissores em ambos os ensaios foram selecionados para estudos quantitativos e caracterização estrutural dos polímeros obtidos. As análises quantitativas para a produção de PHA corroboraram satisfatoriamente com os resultados qualitativos, com destaque para as bactérias do gênero Aurantimonas e Delftia que apresentaram alta capacidade de produção de PHA, com rendimentos de 50 e 90% de polímero em massa seca, respectivamente, sendo ambas as cepas capazes de utilizar substratos como glicose, acetato e glicerol. Análises por GC-MS realizadas após metanólise do polímero indicaram que Aurantimonas sp. produziu majoritariamente homopolímero de polihidroxibutirato (PHB), enquanto Delftia sp. foi capaz de produzir um copolímero contendo monômeros do tipo butirato e valerato (PHBV), contendo até 10% em massa de valerato. Com relação à produção de EPS, a triagem indicou que os isolados se mostraram capazes de produzir polímeros em quantidade variáveis, com uma grande e complexa variação estrutural. Isolados dos gêneros Acidovorax, Aurantimonas e Luteibacter foram selecionados para avaliação quantitativa da produção de EPS e caracterização estrutural do biopolímero. Após análises por NMR, MALDI-TOF, SEC-UV-ELSD e GC-MS, o gênero Luteibacter produziu um polímero altamente complexo contendo manose, glicose, fucose e xilose, o gênero Acidovorax produziu um EPS do tipo glucomanana altamente ramificado;= e o gênero Aurantimonas foi capaz de produzir até 2 g.L-1 de um EPS insolúvel em água. Deste modo, foi possível concluir que a microbiota de D. speciosa se apresentou extremamente rica em isolados microbianos viáveis para estudos exploratórios no contexto biotecnológico de produção de biopolímeros. Os isolados investigados apresentaram características promissoras para serem futuramente avaliadas em escalas maiores (fermentadores), especialmente a bactéria Aurantimonas sp., que foi capaz de produzir tanto PHBV, quanto EPS

Development of methods for the study of dioxins in sugarcane bagasse ash: evaluation of bioremediation potential of microbial strains in aerobic composting

Sugarcane bagasse ash is a byproduct of sugar and alcohol industry with potential for field application. However, the presence of organic contaminants such as dioxins turns necessary the development of strategies for removal of those pollutants, such as bioremediation. Because of the high toxicity of dioxins, it is wise to develop effective and low risk methods for initial evaluation of microbial degradation capacity of those compounds by using less dangerous alternatives such as screening tools to select possible microorganisms as candidates for bioremediation. In such context, this work aimed to apply statistical models to evaluate microbial growth capacity under influence of components of a compost windrow already used for other sugarcane industry residues, and also development of qualitative and quantitative methods to evaluate microbial degradation of the dye RBBR and 1,2,3,4-TCDD, molecules selected as model compounds. The Scott-Knott method grouping multiple means showed good results, indicating microbial growth inhibition of all fungi in culture medium with compost windrow, and microbial growth promotion for Aspergillus strains in sugarcane ash doped medium. Furthermore, quantification of RBBR dye in liquid broth was developed, validated and applied through a dilute-and-shoot technique followed by LC-MS/MS, where it was possible to detect up to 4,8pM of dye, being observed a degradation from 40-99% of dye over 30 days. In a similar way, it was developed and validated a GC-MS method to quantify 1,2,3,4-TCDD in liquid broth after extraction, with detection limits of 10ppb, observing a removal of up to 20% of dioxin after 30 days. Another point evaluated was the identification of RBBR degradation products, where it was observed the presence of four dye metabolites during the course of the experiment, which allowed us to propose a degradation pathway of RBBR dye by Aspergillus flavus.Financiadora de Estudos e ProjetosA cinza do bagaço da cana-de-açúcar é um subproduto da indústria sucroalcooleira que apresenta potencial para aplicação no campo. Porém, a presença de contaminantes orgânicos como dioxinas torna necessário o desenvolvimento de estratégias para a remoção destes poluentes, como a biorremediação. Por serem as dioxinas extremamente tóxicas, é sensato o desenvolvimento de métodos eficazes e de baixo risco para avaliação inicial da capacidade microbiana de degradação destes compostos usando alternativas menos perigosas como ferramentas de triagem e seleção de micro-organismos candidatos à biorremediação. Neste contexto, este trabalho teve como objetivo o uso de modelos estatísticos para avaliação do crescimento microbiano em componentes de uma composteira já utilizada para tratamentos de outros resíduos sucroalcooleiros, bem como o desenvolvimento de métodos analíticos qualitativos e quantitativos de avalição da capacidade microbiana de degradação do corante RBBR e da 1,2,3,4-TCDD, moléculas selecionadas como modelos. O agrupamento de médias por Scott-Knott apresentou bons resultados na avaliação do crescimento microbiano, apontando inibição do crescimento de todos os fungos pela composteira, e promoção de crescimento das cepas de Aspergillus no meio com cinza. Ademais, foi desenvolvido e validado um método para quantificação do corante RBBR direto do meio de cultura líquido usando a técnica dilute-and-shoot seguido por LC-MS/MS, onde foi possível detectar até 4,8pM de corante, sendo observada uma degradação entre 40-99% do corante em 30 dias. Da maneira similar, foi desenvolvido e validado um método por GC-MS para quantificação da 1,2,3,4-TCDD em meio líquido após extração, com limites de detecção de 10ppb, onde foi observada uma remoção de até 20% da dioxina em 30 dias de cultivo. Outro ponto avaliado foi a identificação dos produtos de degradação do RBBR durante o experimento, sendo observada a presença de quatro metabólitos do corante nas amostras, o que nos permitiu propor a rota de degradação do corante por Aspergillus flavus

Green chemistry, sustainable agriculture and processing systems: a Brazilian overview

Abstract There is a pressing need for renewable and optimal use of resources towards sustainable primary production and processing systems worldwide. Current technologies for food and feedstock production are held accountable for several environmental problems, such as for instance soil and water contamination due to the use of hazardous substances, generation of toxic products and even excess of biomass that is considered waste. To minimize or solve these questions in order to produce an adequate quantity of reliable and healthy food, fibers and other products and energy, new paradigms focusing on sustainable agriculture, bio-based industries or biorefineries have emerged over the last decades. Biorefineries integrate sustainable and environmentally friendly concepts of Green Chemistry with intelligent and integrated farming processes, optimizing the agricultural production. Thermochemical and biochemical processes are excellent alternatives for the production of new classes of renewable biofuels and feedstock, showing relatively small impact on greenhouse gas emissions and important pathways to obtain platform chemicals. This review discusses the current and incipient technological developments for using biomass to generate bio-based chemicals over the last decade, focusing on Green Chemistry concepts towards sustainable agriculture and processing models in Brazil.</jats:p

Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining

Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A. nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus.</jats:p

Genome Mining for Unknown-Unknown Natural Products

Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. In this work, we focused on a conserved fungal biosynthetic pathway (ank) that lacks a canonical core enzyme, and used heterologous expression to identify the associate natural product to be a highly modified cyclo-arginine-tyrosine dipeptide (cRY). Biochemical characterization of the ank pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein (HP) and has no sequence homology to nonribosomal peptide synthetase (NPRS) or bacterial cyclodipeptide synthase (CDPS). RCDPS homologs are widely encoded in fungal genomes and we showed other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides. Characterization of a cyclo-Arg-Trp (cRW) RCDPS showed the enzyme is aminoacyl-tRNA dependent, and represents the first report of such CDPS-like enzyme from fungi. Further characterization of the biosynthetic pathway anchored by the cRW synthase led to discovery of new compounds of which the structures would not have been predicted without knowledge of RCDPS function

Genome mining for unknown-unknown natural products.

Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. Here we focused on a conserved fungal biosynthetic pathway that lacks a canonical core enzyme and used heterologous expression to identify the associated natural product, a highly modified cyclo-arginine-tyrosine dipeptide. Biochemical characterization of the pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein and has no sequence homology to non-ribosomal peptide synthetase or bacterial cyclodipeptide synthase. RCDPS homologs are widely encoded in fungal genomes; other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides, and characterization of a cyclo-arginine-tryptophan RCDPS showed that the enzyme is aminoacyl-tRNA dependent. Further characterization of the biosynthetic pathway led to discovery of new compounds whose structures would not have been predicted without knowledge of RCDPS function