Bioinformatic Analyses to Uncover Genes Involved in Trehalose Metabolism in the Polyploid Sugarcane

Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.

Genome-Wide In Silico Analysis and Expression Profiling of Phosphoenolpyruvate Carboxylase Genes in Loquat, Apple, Peach, Strawberry and Pear

Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in Rosaceae species i.e., loquat, apple, peach, strawberry, and pear are yet to be performed. In present study, 27 putative PEPC genes (loquat 4, apple 6, peach 3, strawberry 9, and pear 5) were identified. To further investigate the role of those PEPC genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatic analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of PEPC genes were performed. The result revealed that the PEPcase superfamily domain was conserved in all examined PEPC proteins. Most of the PEPC proteins were predicted to be localized in cytonuclear. Genomic structural and motif analysis showed that the exon and motif number of each PEPC gene ranged dramatically, from 8 to 20, and 7 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of PEPC gene family in Rosacea species. The Ka and Ks values of duplicated genes depicted that PEPC genes have undergone a strong purifying selection. Furthermore, the expression analysis of PEPC genes in root, mature leaf, stem, full-bloom flower, and ripened fruit of loquat, apple, peach, strawberry, and pear was performed. Some genes were differentially expressed in aforementioned plant tissues, signifying their role in plant metabolism. This study provides the first genome-wide identification, characterization, and expression profiling of PEPC gene family in Rosaceae species, and provides the foundation for further functional analysis.

Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.