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Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.

ABSTRACT: 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.

SUBMITTER: de Oliveira LP

PROVIDER: S-EPMC9079074 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.

de Oliveira Lauana Pereira LP Navarro Bruno Viana BV de Jesus Pereira João Pedro JP Lopes Adriana Rios AR Martins Marina C M MCM Riaño-Pachón Diego Mauricio DM Buckeridge Marcos Silveira MS

Scientific reports 20220507 1

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 analyze ...[more]

PMID: 35525890

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Project description:BackgroundSugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes.ResultsTo use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA.ConclusionsThe GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.

Project description:BackgroundBladder cancer (BLCA) is the ninth most common cancer worldwide, with high mortality and recurrence rates. Studies have increasingly reported that molecular diagnosis contributes to the early diagnosis and prognostic assessment of diseases. Thus, this study aims to find new biomarkers for the diagnosis and prognosis of BLCA.MethodsThe microarray datasets GSE147983 and The Cancer Genome Atlas (TCGA)-BLCA mRNA were obtained from the Gene Expression Omnibus (GEO) and TCGA. Differentially expressed genes (DEGs) were screened using the R "Limma" package. The "ClusterProfiler" package was used to conduct Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs. A DEG protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized using Cytoscape. The functional module was reanalyzed using Cytoscape's Molecular Complex Detection ("MCODE") plugin, and key genes related to BLCA were identified via the "cytoHubba" plugin. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and the Tumor Immune Estimation Resource (TIMER) were used to verify the correlation between hub gene expression and immunity. A survival analysis of hub genes was performed using the Kaplan-Meier Plotter online tool.ResultsA total of 355 DEGs were screened out, including 236 upregulated and 119 downregulated DEGs. Some of the GO terms and pathways, such as chromosome separation, cell cycle, and cell senescence, were found to be significantly enriched in the DEGs. The key genes were kinesin family member 11 (KIF11), DLG associated protein 5 (DLGAP5), non-SMC condensin I complex subunit G (NCAPG), cell division cycle 20 (CDC20), cyclin B2 (CCNB2), BUB1 mitotic checkpoint serine (BUB1B), TPX2 microtubule nucleation factor (TPX2), NUF2 component of NDC80 kinetochore complex (NUF2), kinesin family member 2C (KIF2C), and cyclin B1 (CCNB1). Nine of them were immune-related, including KIF11, DLGAP5, NCAPG, CDC20, CCNB2, BUB1B, NUF2, KIF2C, and CCNB1. Survival analysis showed that the overexpression of BUB1B, CCNB1, CDC20, and DLGAP5 significantly reduced overall survival (OS) in patients with BLCA.ConclusionsThis study provided a theoretical basis for elucidating the pathogenesis and evaluating the prognosis of BLCA by screening potential biomarkers of BLCA.

Dataset Information

Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.

Publications

Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.

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