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Nat Prod Rep ; 2019 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-31822877


Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.

Microb Genom ; 5(12)2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30946645


Natural products (NPs), or specialized metabolites, are important for medicine and agriculture alike, and for the fitness of the organisms that produce them. NP genome-mining aims at extracting biosynthetic information from the genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process, the likelihood of identifying truly novel systems by this approach is low. To overcome this limitation, we previously introduced EvoMining, a genome-mining approach that incorporates evolutionary principles. Here, we release and use our latest EvoMining version, which includes novel visualization features and customizable databases, to analyse 42 central metabolic enzyme families (EFs) conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these 42 families are lineage specific, opening the metabolic space related to 'shell' enzymes. These enzymes, which have been overlooked, are EFs with orthologues present in most of the genomes of a taxonomic group, but not in all. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving Archaea and Bacteria adaptive evolution. By defining the origin and fate of enzymes, EvoMining complements traditional genome-mining approaches as an unbiased strategy and opens the door to gaining insights into the evolution of NP biosynthesis. We anticipate that EvoMining will be broadly used for evolutionary studies, and for generating predictions of unprecedented chemical scaffolds and new antibiotics. This article contains data hosted by Microreact.

Genome Biol Evol ; 11(1): 319-334, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30534962


Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium, and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. These data were used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.

Caulobacter/genética , Cianobactérias/genética , Cycadopsida/microbiologia , Fixação de Nitrogênio , Raízes de Plantas/microbiologia , Evolução Biológica , Caulobacter/isolamento & purificação , Caulobacter/metabolismo , Cianobactérias/isolamento & purificação , Cianobactérias/metabolismo , Endófitos , Família Multigênica , Simbiose
J Nat Prod ; 80(7): 1955-1963, 2017 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-28704049


2,4-Diacetylphloroglucinol (DAPG) (1) is a phenolic polyketide produced by some plant-associated Pseudomonas species, with many biological activities and ecological functions. Here, we aimed at reconstructing the natural history of DAPG using phylogenomics focused at its biosynthetic gene cluster or phl genes. In addition to around 1500 publically available genomes, we obtained and analyzed the sequences of nine novel Pseudomonas endophytes isolated from the antidiabetic medicinal plant Piper auritum. We found that 29 organisms belonging to six Pseudomonas species contain the phl genes at different frequencies depending on the species. The evolution of the phl genes was then reconstructed, leading to at least two clades postulated to correlate with the known chemical diversity surrounding DAPG biosynthesis. Moreover, two of the newly obtained Pseudomonas endophytes with high antiglycation activity were shown to exert their inhibitory activity against the formation of advanced glycation end-products via DAPG and related congeners. Its isomer, 5-hydroxyferulic acid (2), detected during bioactivity-guided fractionation, together with other DAPG congeners, were found to enhance the detected inhibitory activity. This report provides evidence of a link between the evolution and chemical diversity of DAPG and congeners.

Endófitos/química , Floroglucinol/análogos & derivados , Piper/microbiologia , Plantas Medicinais/microbiologia , Policetídeos/isolamento & purificação , Policetídeos/farmacologia , Pseudomonas/química , Ácidos Cumáricos/química , Ácidos Cumáricos/isolamento & purificação , México , Estrutura Molecular , Família Multigênica , Floroglucinol/química , Floroglucinol/isolamento & purificação , Floroglucinol/farmacologia , Piper/genética , Componentes Aéreos da Planta/química , Plantas Medicinais/genética , Policetídeos/química , Estereoisomerismo
Invert Neurosci ; 11(2): 113-6, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21573754


We investigated whether the Gonadotropin-releasing hormone affects the spontaneous muscular contraction in the earthworm Eisenia foetida. In addition, we investigated the presence of Gonadotropin-releasing hormone receptor in ventral nerve cord by immunohistochemistry and polymerase chain reaction. Gonadotropin-releasing hormone induced a significant increase on both amplitude and muscular tone and decrease in the frequency of spontaneous muscular contraction. We found the presence of immunoreactive material to Gonadotropin-releasing hormone receptor in the ventral nerve cord, likewise the Gonadotropin-releasing hormone receptor mRNA expression. In conclusion, the Gonadotropin-releasing hormone modifies the spontaneous muscular contraction in E. foetida and these effects can be due to the activation of the Gonadotropin-releasing hormone receptor.

Hormônio Liberador de Gonadotropina , Contração Muscular/fisiologia , Receptores LHRH , Animais , Hormônio Liberador de Gonadotropina/metabolismo , Imuno-Histoquímica , Rede Nervosa/metabolismo , Oligoquetos/metabolismo , Receptores LHRH/genética , Receptores LHRH/imunologia