Assembly of the Cereus fernambucensis Genome, Gene Annotation, and Tertiary Structure of Secondary Metabolism Enzymes in Carnegiea gigantea, Lophocereus schottii, Pachycereus pringlei, Pereskia humboldtii, Selenicereus undatus, and Stenocereus thurberi
DOI:
https://doi.org/10.29356/jmcs.v67i3.1969Keywords:
Cactaceae, genome assembly, gene annotation, secondary metabolism, bioactive compoundsAbstract
Abstract. Recently, there is growing interest in obtaining bioactive compounds from species in the family Cactaceae, which has been little analyzed at the genomic and transcriptomic level. We here report the assembly of the genome of Cereus fernambucensis and we analyzed six cactus genomes (Carnegiea gigantea, Lophocereus schottii, Pachycereus pringlei, Pereskia humboldtii, Selenicereus undatus and Stenocereus thurberi), the annotation of putative genes, and the modeling of the three-dimensional structures of their predicted proteins involved in flavonoid metabolism. We identified genes encoding proteins related to plant pathogenesis (PR-10), coding secuences (CDS) of aldehyde reductase and flavonoid reductase, CDS of enzymes involved in the biosynthesis of phenolic compounds, and ABC transporters. The grouping of the enzymes aspartic proteinase-like protein, flavanone 3-hydroxylase (F3H), hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT), and protein serine/threonine- phosphatase was shown to be highly conserved in the genomes of the analyzed cacti. We found divergence of the plant PDR ABC-type transporter family protein (PEN3) in Cereus fernambucensis and the absence in this species of sterol methyltransferase (SMT1). Our three-dimensional modeling of the tertiary structure of F3H from a consensus sequence of cactus species had 88 % identity with that reported in Arabidopsis thaliana. We observed the conservation in several plant species of the 2-oxoglutarate and iron-dependent domain of F3H. This is the first report of an exploration of putative genes encoding enzymes involved in secondary metabolism in cacti species providing information that could be used to improve the production of bioactive compounds in them.
Resumen. Recientemente, ha incrementado el interés en obtener compuestos bioactivos de especies de la familia Cactaceae, que ha sido poco analizada a nivel genómico y transcriptómico. Nosotros reportamos el ensamblaje del genoma Cereus fernambucensis y analizamos además seis genomas de cactus (Carnegiea gigantea, Lophocereus schottii, Pachycereus pringlei, Pereskia humboldtii, Selenicereus undatus y Stenocereus thurberi), la anotación de genes putativos y el modelado de las estructuras tridimensionales de sus proteínas involucradas en el metabolismo de los flavonoides. Se identificaron genes que codifican proteínas relacionadas con la patogénesis vegetal (PR-10), secuencias codificantes (CDS) de aldehído reductasas y flavonoide reductasas, CDS de enzimas implicadas en la biosíntesis de compuestos fenólicos y transportadores ABC. La agrupación de las enzimas similar a la proteinasa aspártica, flavanona 3-hidroxilasa (F3H), hidroxicinamoil-CoA shikimato/quinato hidroxicinamoiltransferasa (HCT) y proteína serina/treonina-fosfatasa demostró estar altamente conservada en los genomas de los cactus analizados. Se encontró divergencia de la proteína (PEN3) de la familia transportadora de tipo ABC PDR en Cereus fernambucensis y la ausencia en esta especie de esterol metiltransferasa (SMT1). Nuestro modelado tridimensional de la estructura terciaria de F3H a partir de una secuencia consenso de especies de cactus tuvo una identidad del 88 % con la reportada en Arabidopsis thaliana. Observamos la conservación en varias especies vegetales del dominio 2-oxoglutarato y dependiente del hierro de F3H. Este es el primer informe de una exploración de genes putativos que codifican enzimas involucradas en el metabolismo secundario en especies de cactus que aporta información que podría usarse para mejorar la producción de compuestos bioactivos.
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