Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom

Abstract

Background: Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins function as an important ecophysiological adaptation for inter- and intra-seasonal nitrogen storage and cycling.

Results: We conducted phylogenetic analyses to determine the distribution and evolution of NP-like proteins in plants. These analyses revealed two major clusters of NP-like proteins in plants. Group I proteins were encoded by genes across a wide range of plant taxa while proteins encoded by Group II genes were dominated by species belonging to the order Malpighiales and included the Populus Bark Storage Protein (BSP) and WIN4-like proteins. Additionally, we evaluated the NP-like genes in Populus by examining the transcript abundance of the 13 NP-like genes found in the Populus genome in various tissues of plants exposed to long-day (LD) and short-day (SD) photoperiods. We found that all 13 of the Populus NP-like genes belonging to either Group I or II are expressed in various tissues in both LD and SD conditions. Tests of natural selection and expression evolution analysis of the Populus genes suggests that divergence in gene expression may have occurred recently during the evolution of Populus, which supports the adaptive maintenance models. Lastly, in silico analysis of cis-regulatory elements in the promoters of the 13 NP-like genes in Populus revealed common regulatory elements known to be involved in light regulation, stress/pathogenesis and phytohormone responses.

Conclusion: In Populus, the evolution of the NP-like protein and gene family has been shaped by duplication events and natural selection. Expression data suggest that previously uncharacterized NP-like proteins may function in nutrient sensing and/or signaling. These proteins are members of Group I NP-like proteins, which are widely distributed in many plant taxa. We conclude that NP-like proteins may function in plants, although this function is undefined.

Figure 1

NP-like family in Populus trichocarpa. (A) Phylogenetic relationship of 13 NP-like proteins in Populus. Numbers at branches indicate posterior probabilities and bootstrap percentages based on 1000 replicates, respectively. Branches in red indicate significant evidence for experiencing episodic diversifying selection based on the branch-site REL test implemented in HyPhy. (B) Heat map representing the relative transcript expression of NP-like genes in shoot tips, young leaves, mature leaves and bark after 8 weeks long-day (LD) conditions and after 3, 6, 8 and 12 weeks short-day (SD) conditions. The 12 week short-day treatment was combined with low-temperature for the final 4 weeks of SD (i.e. after 8 weeks SD). Values were rescaled within each gene between 0 and 1 with 1 indicating highest relative expression levels.

Figure 2

Intron-exon structure for NP-like genes in Populus trichocarpa. A comparison of gene structure was constructed using the primary NP-like transcripts from Phytozome (http://www.phytozome.net) and the gene structure draw server found at the PIECE database (http://wheat.pw.usda.gov/piece/index.php). NP-like gene subfamilies are indicated by brackets.

Figure 3

Chromosome location of NP-like genes in Populus trichocarpa. Arrows indicate approximate location of genes. Roman numerals indicate chromosome designation and numbers reflect start site location according to Phytozome (http://www.phytozome.net). Colored blocks indicate known syntenic regions within the Populus trichocarpa genome v2.0 and the link for these coordinates can be found in the Methods.

Figure 4

Principal component analysis (PCA) of NP-like gene expression in Populus trichocarpa. PCA illustrating the relationships of NP-like genes in Populus trichocarpa based upon the expression data presented in Figure 1B. The percentage of variation explained by each axis is given in parentheses next along each axis.

Figure 5

Cis-regulatory element distribution in the promoter regions of NP-like genes in Populus trichocarpa. CREs identified by two methods of motif prediction are represented as colored bars and correspond to the CRE name.

Figure 6

Principal component analysis (PCA) of NP-like cis-regulatory element motifs in Populus trichocarpa. PCA based upon the abundance of cis-regulatory element motifs within promoter regions of NP-like genes in Populus trichocarpa. The percentage of variation explained by each axis is given in parentheses next along each axis.

Figure 7

Phylogenetic analyses of NP-like proteins in the plant kingdom. Phylogenetic relationships were constructed using Bayesian and maximum-likelihood methods. Numbers at branches indicate posterior probabilities and bootstrap percentages based on 1000 replicates, respectively. Numbers in parentheses correspond to Phytozome or NCBI sequence identifiers, which can be found in the Additional file 7: Table S4. The five predominant taxonomic families are indicated by the highlighted colors.

Figure 8

Hypothetical origin of the NP-like gene family in Populus trichocarpa. Blue arrows represent whole genome duplication events and orange arrows represent tandem duplication events. Asterisks denote ancestral genes with unknown sequence similarity to present-day genes.