Identification and characterization of lineage-specific genes in Populus trichocarpa

Species- or lineage-specific genes can facilitate studying the unique characteristics of biological processes. Updated genome sequences in Populus trichocarpa were screened against thirty newly sequenced or resequenced plant genomes to identify a set of species-specific genes (PtSS). Forty PtSS genes have been isolated with no similarity to any sequence outside the P. trichocarpa genome, therefore have no annotated functions. Protein motif, intron/exon features, subcellular localization and gene expression were analyzed in these PtSS genes. Results reflect their basic genic characters, expression analysis and primary function exploration might provide insight to their possible involvements in lineage specific biological process in woody plants.     

Responses of Populus trichocarpa galactinol synthase genes to abiotic stresses

Galactinol synthase (GolS; EC 2.4.1.123) is a member of the glycosyltransferase eight family that catalyzes the first step in the biosynthesis pathway of the raffinose family of oligosaccharides (RFOs). The accumulation of RFOs in response to abiotic stress indicates a role for RFOs in stress adaptation. To obtain information on the roles of RFOs in abiotic stress adaptation in trees, we investigated the expression patterns of nine Populus trichocarpa GolS (PtrGolS) genes with special reference to stress responses. PtrGolS genes were differentially expressed in different organs, and the expressions of PtrGolS4 and PtrGolS6 were relatively high in all tested organs. The expression levels of all PtrGolS genes, except PtrGolS9, changed in response to abiotic stress in gene- and stress-type-specific manners. Moreover, short- and long-term stress treatments revealed that induction of PtrGolS by salt stress is obvious only in the early period of treatment (within 24 h), whereas water-deficit stress treatments continued to upregulate PtrGolS gene expression after two days of treatment, in addition to induction within 24 h of treatment. Consistent with these expression patterns, the galactinol content in leaves increased after four days of drought stress, but not under salt stress. Our findings suggest divergent roles for PtrGolS genes in abiotic stress responses in poplars.     

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

Fructokinase (FRK) is the main fructose phosphorylase and plays an important role in catalyzing the irreversible reaction of free fructose phosphorylation. In order to study the regulatory effect of different forms and concentrations of nitrogen on PtFRK genes in Populus trichocarpa, seven genes encoding the hypothetical FRK proteins were identified in Populus trichocarpa genome by bioinformatics method. Phylogenetic analysis revealed that PtFRK family genes can be divided into two subgroups: SI (PtFRK 1, 3, 4, 6) and SII (PtFRK 2, 5, 7). The tissue-specific expression data obtained from PopGenIE indicate that PtFRK2, 3, 4 and 5 are expressed highly in the stem. Quantitative real-time RT-PCR illustrate that PtFRK1-7 showed different expression patterns in different tissues under different concentrations and morphological nitrogen application. Under high nitrate treatment, the expression levels of PtFRK1, 2, 3 and 6 in stem increased significantly, while under low nitrate treatment, only the expression of PtFRK1, 4 in the upper stem and the expression of PtFRK3, 5 in the lower stem increased significantly. In contrast, ammonium tends to inhibit the expression of PtFRKs in lower stems, the expression levels of PtFRK2, 3, 4 and 5 are significantly reduced under ammonium treatment. However, high ammonium had significant effects on PtFRK6 in the apical bud and upper leaves, which were 6 and 8 times of the control, respectively. These results laid the foundation for the study of the PtFRK gene family of poplar and provided a theoretical basis for the molecular mechanism of nitrogen regulating cell wall development.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01055-6.     

Structure, inheritance, and expression of hybrid poplar (Populus trichocarpa x Populus deltoides) phenylalanine ammonia-lyase genes.

A heterologous probe encoding phenylalanine ammonia-lyase (PAL) was used to identify PAL clones in cDNA libraries made with RNA from young leaf tissue of two Populus deltoides x P. trichocarpa F1 hybrid clones. Sequence analysis of a 2.4-kb cDNA confirmed its identity as a full-length PAl clone. The predicted amino acid sequence is conserved in comparison with that of PAL genes from several other plants. Southern blot analysis of popular genomic DNA from parental and hybrid individuals, restriction site polymorphism in PAL cDNA clones, and sequence heterogeneity in the 3' ends of several cDNA clones suggested that PAL is encoded by at least two genes that can be distinguished by HindIII restriction site polymorphisms. Clones containing each type of PAL gene were isolated from a poplar genomic library. Analysis of the segregation of PAL-specific HindIII restriction fragment-length polymorphisms demonstrated the existence of two independently segregating PAL loci, one of which was mapped to a linkage group of the poplar genetic map. Developmentally regulated PAL expression in poplar was analyzed using RNA blots. Highest expression was observed in young stems, apical buds, and young leaves. Expression was lower in older stems and undetectable in mature leaves. Cellular localization of PAL expression by in situ hybridization showed very high levels of expression in subepidermal cells of leaves early during leaf development. In stems and petioles, expression was associated with subepidermal cells and vascular tissues.     

Identification and expression pattern analysis of PtCarA and PtCarB genes in Populus trichocarpa under different nitrogen treatments

• Carbamoyl phosphate synthetase (CPS) catalyses the synthesis of ammonia carbamoyl phosphate (CP), which plays a key role in the biosynthesis of arginine and pyrimidine nucleotides. There are two subunits of the CPS enzyme in Populus trichocarpa, CarA (small subunit) and CarB (large subunit). Only when they coexist can CPS catalyse synthesis of CP. However, it is not clear how CPS responds to nitrogen (N) to affect arginine and pyrimidine nucleotide biosynthesis.
• In this study, bioinformatics methods were used to analyse the expression patterns of genes encoding CarA and CarB, and qRT-PCR and RNA-seq were used to investigate their molecular responses under different N concentrations.
• Phylogenetic analysis revealed that the phylogenetic trees of CarA and CarB had similar topologies. qRT-PCR showed that the PtCarA and PtCarB genes were regulated by N, while their N-regulated patterns differed in different tissues. The expression patterns of PtCarA and PtCarB show a significant positive correlation according to qRT-PCR and RNA-seq. The analysis of promoter cis-acting elements showed that the promoter regions of PtCarA1, PtCarA2 and PtCarB contained some identical cis-acting elements. According to analysis of the phylogenetic tree, expression patterns and promoter elements, we speculate that there might be coevolution among PtCarA1, PtCarA2 and PtCarB.
• This study provides valuable information for further understanding the function of CPS in poplar, especially for N response, and provides new ideas for studying the evolution of gene families related to heteromultimers.

     

Molecular Characterization of Quinate and Shikimate Metabolism in Populus trichocarpa

The shikimate pathway leads to the biosynthesis of aromatic amino acids essential for protein biosynthesis and the production of a wide array of plant secondary metabolites. Among them, quinate is an astringent feeding deterrent that can be formed in a single step reaction from 3-dehydroquinate catalyzed by quinate dehydrogenase (QDH). 3-Dehydroquinate is also the substrate for shikimate biosynthesis through the sequential actions of dehydroquinate dehydratase (DQD) and shikimate dehydrogenase (SDH) contained in a single protein in plants. The reaction mechanism of QDH resembles that of SDH. The poplar genome encodes five DQD/SDH-like genes (Poptr1 to Poptr5), which have diverged into two distinct groups based on sequence analysis and protein structure prediction. In vitro biochemical assays proved that Poptr1 and -5 are true DQD/SDHs, whereas Poptr2 and -3 instead have QDH activity with only residual DQD/SDH activity. Poplar DQD/SDHs have distinct expression profiles suggesting separate roles in protein and lignin biosynthesis. Also, the QDH genes are differentially expressed. In summary, quinate (secondary metabolism) and shikimate (primary metabolism) metabolic activities are encoded by distinct members of the same gene family, each having different physiological functions.     

杨树基因组AMT转运蛋白的生物信息学特性

本研究中,通过隐马尔科夫模型(HMM)和杨树蛋白质库搜索,共找到17个杨树铵转运体蛋白(PtAMTs).利用生物信息学方法,我们对杨树家族17条AMT蛋白序列的系统发生和AMT基因组定位进行分析,然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析,同时还分析了杨树与拟南芥、水稻、番茄、百脉根和欧洲油菜的AMT基因家族之间的联系.二级结构预测结果发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异;α-螺旋和无规则卷曲为主要二级结构组成部分.同源性比对分析表明,PtAMT基因家族主要分为2个亚家族,AMT1 (11个成员)和AMT2 (6个成员),基因结果分析表明AMT2亚家族成员不含内含子.杨树AMT蛋白的亚细胞定位分析表明PtAMT主要定位于膜结构上.电子表达图谱分析结果表明:只有XP_002309151和 XP_002334025基因有对应的EST序列,并有相应的电子表达谱,并主要在花蕾表达.     

Potassium,calcium and magnesium antagonism in clones of Populus trichocarpa

Two clones of Populus trichocarpa varying in growth rate were grown in nutrient solutions with a range of K supply. In the leaves an antagonism between the levels of K and Ca+Mg was found, this was most extreme in the older leaves. Analysis of the contents of these elements in leaf vacuoles and cytoplasm suggests that in the vacuoles the total contents of K+Ca+Mg are controlled to maintain ionic and osmotic balance. At low K supply, the K deficit in the cytoplasm is not balance by accumulation of Ca and Mg, and it is suggested that other organic osmotica may accumulate. The regulation of K+Mg+Ca supplied to the leaves seems to be regulated by the roots and is not simple competition of ions for uptake sites at the plasmalemma.