Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment

Abstract

Plant UDP-glucose 6-dehydrogenase (UGDH) is an important enzyme for the formation of hemicellulose and pectin. Previous studies on UGDH have primarily focused on the biosynthesis of cell wall polysaccharides, while few studies have focused on their regulation by exogenous nitrogen. In the present study, four genes encoding PtUGDH proteins were analyzed by bioinformatics methods. And, the expression profiles of PtUGDH genes under different nitrogen treatments were evaluated with qRT-PCR. The results showed that PtUGDHs have conserved NAD coenzyme binding motif GAGYVGG and the catalytic motif GFGGSCFQKDIL. According to the phylogenetic analysis, PtUGDHs were divided into two subgroups. PtUGDH3 and PtUGDH4 were closely related to AtUGDH1 (important for normal development of Arabidopsis cell wall structure). Chromosomal distribution and genome synteny analysis revealed four segmental-duplicated gene pairs on chr4, 8, 10 and 17. Tissue-specific data from PlantGenIE showed that PtUGDH3 and PtUGDH4 were highly expressed in stems. The qRT-PCR detection showed that the expression of PtUGDH3 in the lower stem and PtUGDH2 of upper leaves were significantly increased induced by low ammonium or nitrate condition. This comprehensive analysis of the UGDH family in poplar provides new insights into their regulation by nitrogen, and would increase our understanding of the roles of UGDHs in hemicellulose and pectin biosynthesis in the cell wall and during poplar development.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-021-02697-9.

Keywords: Bioinformatics analysis; Expression traits; Nitrogen treatment; Populus trichocarpa; UDP-glucose 6-dehydrogenase.

Fig. 1

Multiple alignment of P. trichocarpa UGDHs (PtUGDHs). Conserved NAD coenzyme binding motif and catalytic motif are represented by boxes. Blue arrow represents lysine residue (Lys216, Lys335), and green arrow represents proline residue (Pro89, Pro156)

Fig. 2

Phylogenetic analysis of UGDHs from P. trichocarpa, P. tremula × P. tremuloides, P. tomentosa, P. sitchensis, L. kaempferi, E. grandis, O. sativa, N. tabacum, G. max and A. thaliana. The phylogenetic tree was constructed using the neighbor-joining method. UGDHs of P. trichocarpa, P. tremula × P. tremuloides and P. tomentosa are represented by green pentagram, triangle and square, respectively; and of P. sitchensis, L. kaempferi and E. grandis was represented by purple pentagram, triangle and square, respectively. UGDHs of O. sativa, G. max, N. tabacum, and A. thaliana are represented by red pentagram, triangle, square and circles, respectively

Fig. 3

Phylogeny and structure analysis of PtUGDHs in P. trichocarpa. a Phylogenetic tree was generated according to full-length sequences of PtUGDHs using the neighbor-joining method. b Structure of corresponding PtUGDHs. CDSs and the upstream/downstream sequences are represented by yellow and blue lines, respectively. c Motifs in the PtUGDHs sequences predicted by online MEME tool

Fig. 4

Schematic representations for segmental duplications of PtUGDH genes. Gray and red lines indicate all syntenic blocks between each chromosome in the poplar genome and duplicated PtUGDH gene pairs, respectively. The black font at the end of the red line and the scale bar marked on the chromosomes represent the genes name and the length of chromosome (Mb), respectively. Chromosomes numbers were shown at the bottom of each chromosome

Fig. 5

Synteny analysis of UGDHs between P. trichocarpa and A. thaliana, G. max, B. oleracea, and M. truncatula. Gray lines in background and orange lines represent collinear blocks among P. trichocarpa and other plant genomes, as well as UGDH gene pairs, respectively. Red or green lines represent chromosomes which were marked with chromosome number at the top or bottom, and the species names were on the left

Fig. 6

Visual images of tissue-specific expression traits of PtUGDHs. Tissue-specific expression data of roots, internodes, nodes, mature leaves and young leaves derived from PlantGenIE online tool. For each gene, the tissues in the plant with the middle expression level were normalized to 0

Fig. 7

Expression profiles of PtUGDHs in different nitrogen treatments. The expression traits of PtUGDHs in a apical buds, b upper stems, c lower stems, d upper leaves, e lower leaves, f roots under different nitrogen treatments (0.1 mM NH₄Cl, 10 mM NH₄Cl, 0.1 mM NaNO₃, and 10 mM NaNO₃) were detected using qRT-PCR. The 2^−ΔΔCT method was used to calculate the transcriptional level of PtUGDHs, and the relative expression levels were shown using values of log₂ (sample/control) of each PtUGDH under nitrogen treatments. In the heat maps, scale bar was shown at bottom right, and the different color of the cells indicated the expression of the gene in the treated sample up-regulated or down-regulated compared with the control. The significant change of gene expression level is indicated by "*"