Genome-wide identification of BXL genes in Populus trichocarpa and their expression under different nitrogen treatments

Abstract

β-d-xylosidase (BXL) hydrolyzes xylobiose and xylo-oligosaccharides into xylose monomers, and is a rate-limiting enzyme in the degradation of hemicellulose in the cell wall. In this study, ten genes encoding putative BXL proteins were identified in the Populus trichocarpa genome by bioinformatics methods. In the phylogenetic analysis, the PtBXLs formed two subfamilies. PtBXL8 and PtBXL9 were closely related to AtBXL1, an important enzyme in the normal development of the Arabidopsis cell wall structure. Chromosomal distribution and genome synteny analyses revealed two tandem-duplicated gene pairs PtBXL3/4 and PtBXL6/7 on chromosomes II and V, respectively, and six segmental-duplicated gene pairs on chromosomes II, V, VIII, X, and XIV among the PtBXL gene family. Tissue-specific expression data from PlantGenIE indicated that PtBXL2, 4, 5, and 10 were highly expressed in stems. Quantitative real-time RT-PCR analyses revealed that PtBXL4, 5, and 9 were up-regulated in the upper stem in response to the low and high ammonium and nitrate treatments. The influence of nitrogen on the expression of PtBXL4, 5, and 9 genes may affect the formation of the plant secondary cell wall. This comprehensive analysis of the BXL family in poplar provides new insights into their regulation by nitrogen and increases our understanding of the roles of BXLs in hemicellulose metabolism in the secondary cell wall and during plant development.

Keywords: Evolution; Expression pattern; Nitrogen treatment; Populus trichocarpa; β-d-xylosidase.

Fig. 1

Multiple alignment of deduced amino acid sequences of 10 PtBXLs. Boxes indicate conserved WGR and KH motifs; blue arrow represents the presumed catalytic nucleophile (Asp₂₆₇) and the presumed catalytic acid/base (Glu₄₇₁). Green arrow represents alternative catalytic acid/base residue (Glu₄₆₉)

Fig. 2

Phylogenetic analysis of BXL proteins of Populus trichocarpa and Arabidopsis thaliana. The phylogenetic tree was constructed using the neighbor-joining method. Blue diamond represents PtBXLs; green dot represents AtBXLs

Fig. 3

Phylogenetic tree and structure analysis of proteins encoded by 10 PtBXL genes. a Phylogenetic tree based on deduced full-length amino acid sequences of PtBXLs was constructed using the neighbor-joining method. b Structure of corresponding PtBXL genes. Yellow indicates protein-coding sequences (CDSs); blue indicates upstream/downstream sequences; black line indicates introns. c Motifs in the PtBXL amino acid sequences predicted using the MEME tool

Fig. 4

Chromosomal distribution of PtBXL genes. Yellow strips represent chromosomes. Chromosome numbers are shown above the bar chart; BXL genes are on both sides of the chromosome. Scale on the left indicates chromosome length (Mb)

Fig. 5

Schematic representations of segmental duplications of PtBXL genes. Gray lines indicate all syntenic blocks between each chromosome in the poplar genome; thick green lines indicate duplicated BXL gene pairs. Gene names are shown in red font. Chromosome number is indicated at the bottom of each chromosome. Scale bars marked on each chromosome indicates chromosome length (Mb)

Fig. 6

Synteny analysis of BXL genes between poplar and other plants. a Monocotyledonous plant maize. b Dicotyledonous plants Arabidopsis, soybean, barrel medic, and kale. Gray lines in background indicate collinear blocks within poplar and other plant genomes; blue lines indicate syntenic BXL gene pairs. Species names: Zea mays, Arabidopsis thaliana, Glycine max, Medicago truncatula, Brassica oleracea, and Populus trichocarpa. Red or green bars represent chromosomes with number labeled at top or bottom

Fig. 7

Tissue-specific expression profiles of PtBXL genes. Visual images of PtBXL genes in Populus trichocarpa were generated using tissue-specific expression data of mature leaves, young leaves, roots, nodes, and internodes derived from https://PlantGenIE.org

Fig. 8

Expression patterns of PtBXL genes in different tissues under different nitrogen treatments. Expression pattern of PtBXL genes in a apical buds, b upper stems, c lower stems, d upper leaves, e lower leaves, f roots under different nitrogen treatments (low and high ammonium (0.1 mM and 10 mM NH₄Cl) and low and high nitrate (0.1 mM and 10 mM NaNO₃). Transcript levels of PtBXLs were calculated using the 2^−ΔΔCT method. For each PtBXL gene, log₂ (sample/control) values under the different nitrogen treatment conditions were calculated as relative expression levels. Scale bars are shown at bottom right. Colors of cells in the heatmaps indicate up-regulated or down-regulated expression in treated samples compared with controls