Genome-Wide Identification and Analysis of Gene Family of Carbohydrate-Binding Modules in Ustilago crameri

Abstract

Ustilago crameri is a pathogenic basidiomycete fungus that causes foxtail millet kernel smut (FMKS), a devastating grain disease in most foxtail millet growing regions of the world. Carbohydrate-Binding Modules (CBMs) are one of the important families of carbohydrate-active enzymes (CAZymes) in fungi and play a crucial role in fungal growth and development, as well as in pathogen infection. However, there is little information about the CBM family in U. crameri. Here, 11 CBM members were identified based on complete sequence analysis and functional annotation of the genome of U. crameri. According to phylogenetic analysis, they were divided into six groups. Gene structure and sequence composition analysis showed that these 11 UcCBM genes exhibit differences in gene structure and protein motifs. Furthermore, several cis-regulatory elements involved in plant hormones were detected in the promoter regions of these UcCBM genes. Gene ontology (GO) enrichment and protein-protein interaction (PPI) analysis showed that UcCBM proteins were involved in carbohydrate metabolism, and multiple partner protein interactions with UcCBM were also detected. The expression of UcCBM genes during U. crameri infection is further clarified, and the results indicate that several UcCBM genes were induced by U. crameri infection. These results provide valuable information for elucidating the features of U. crameri CBMs' family proteins and lay a crucial foundation for further research into their roles in interactions between U. crameri and foxtail millet.

Keywords: CBM; Ustilago crameri; foxtail millet; pathogenicity.

Figure 1

A phylogenetic tree of the UcCBM proteins and their homologous proteins in other smut fungi, including Sporisorium scitamineum, U. maydis, and U. hordei. The phylogenetic tree was constructed with MEGA7 software using the Neighbor-Joining (NJ) method. Different groups are represented by branches and frames of different colors.

Figure 2

Motif distribution, conserved domain, and gene structure analysis of UcCBMs. (A) Phylogenetic trees and conserved motifs of 11 UcCBMs. (B) nserved motif sequence logo of UcCBM proteins. (C) Domain analysis of UcCBMs. (D) Exon–intron structures of UcCBMs.

Figure 3

Cis-acting elements of UcCBM family members in U. crameri. The 2000 bp promoter sequences of U. crameri UcCBM genes contain a variety of cis-acting elements, including hormone responsive elements, drought, low-temperature, and other response elements, as well as an MYBHv1 binding site.

Figure 4

Three-dimensional (3D) modeling of the UcCBM proteins that were predicted, displayed at a confidence level > 0.7.

Figure 5

Gene Ontology enrichment analysis of UcCBM genes.

Figure 6

Expression of UcCBM gene in U. crameri at different inoculation time points.

Figure 7

Protein–protein interaction network of UcCBM family proteins, constructed based on smut fungi U. hordei genome. UHOR_06976: UcCBM1; UHOR_02432: UcCBM3; UHOR_02718: UcCBM2; UHOR_00509: UcCBM4 or UcCBM6; UHOR_00973: UcCBM5; UHOR_02067: UcCBM7; UHOR_04077: UcCBM8; UHOR_06273: UcCBM9; UHOR_03469: UcCBM10; UHOR_03282: UcCBM11.