Expansion and Functional Divergence of Inositol Polyphosphate 5-Phosphatases in Angiosperms

Abstract

Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5` position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. Here, we report a comprehensive molecular evolutionary analysis of the 5PTase gene family and define four groups. These four groups are different from former classifications, which were based on in vitro substrate specificity. Most orthologous groups appear to be conserved as single or low-copy genes in all lineages in Groups II-IV, whereas 5PTase genes in Group I underwent several duplication events in angiosperm, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for 5PTase duplications in angiosperm. Plant 5PTases have more members than that of animals, and most plant 5PTase genes appear to have evolved under strong purifying selection. The paralogs have diverged in substrate specificity and expression pattern, showing evidence of selection pressure. Meanwhile, the increase in 5PTases and divergences in sequence, expression, and substrate might have contributed to the divergent functions of 5PTase genes, allowing the angiosperms to successfully adapt to a great number of ecological niches.

Keywords: gene duplication; gene fate; inositol polyphosphate 5-phosphatase; phosphatidylinositol signaling.

Figure 1

The phosphoinositide metabolic pathway in plants. The free hydroxyl groups of the phosphatidylinositols (PtdIns) can be phosphorylated at positions 3, 4, and/or 5 by distinct kinases (black arrows) to generate various phosphoinositides. Phospholipase C (PLC) can convert substrate PtdIns(4,5)P₂ into the second messenger Ins(1,4,5)P₃. The action of inositol polyphosphate 5-phosphatases (red arrows) modulates the signaling functions of these molecules.

Figure 2

Phylogenetic relationships of species that were used in this study. The species tree was constructed based on the phylogeny of conserved nuclear genes [56,57,58]. The total number of 5PTase proteins found in the genome of each species is indicated.

Figure 3

Phylogeny of representative 5PTase genes from plants, animals, and fungi. Tree topology generated via maximum-likelihood (ML) using MAFFT (MSA tool that uses Fast Fourier Transforms) alignment is shown here. The protein sequences containing the conserved 5PTase domain were used for the alignment. At, Arabidopsis; Os, rice; Pp, Physcomitrella patens; Cre, Chlamydomonas reinhardtii; Hs, Homo sapiens; Dr, Danio rerio; Ce, Caenorhabditis elegans; Sc, Saccharomyces cerevisiae.

Figure 4

Phylogenetic relationships, exon/intron structure, and domain organization of 5PTase genes in Arabidopsis, rice, soybean (A), and humans (B). The motif architecture is demonstrated as colored boxes. IPPC: inositol polyphosphate phosphatase catalytic domain; WD40: WD40/beta-transducin repeats domain; PPR_3: pentatricopeptide repeat domain; DYW: DYW_deaminase domain. The yellow boxes represent exons, the black lines represent introns, and the gray boxes refer to untranslated regions (UTRs).

Figure 5

Phylogenetic analysis of plant 5PTase genes. The tree topology of 5PTase protein sequences was constructed by Maximum Likelihood (ML) using the Jones, Taylor, and Thorton model among Arabidospis, rice, moss, Medicago truncatula, soybean, Lotus japonicas, and Chalamydomonas reinhardtii. The 5PTase protein sequences were aligned using MAFFT (MSA tool that uses Fast Fourier Transforms). The red stars represent major duplication events.

Figure 6

Collinearity analysis of duplicated 5PTase gene pairs. At, Arabidopsis thaliana; Os, Oryza sativa. The syntenic paralogous genes are connected by lines.

Figure 7

Developmental expression patterns of 5PTase family genes in Arabidopsis and rice. Expression profiles of (A) At5PTases and (B) Os5PTase in different developmental stages obtained from microarray data reported in the Genevestigator. Results are shown as heat maps in blue/white/red (low to high) that reflect the percentage of expression.

Figure 8

Functionally characterized 5PTase genes from Arabidopsis. (A) Substrate specificity and protein localization of At5PTases. FRA3, 5PTase9, 5PTase12, and 5PTase14 were localized in the nucleus; 5PTase2, 5PTase6, 5PTase7, and 5PTase8 were localized in the cytoplasm; 5PTase1 was localized in chloroplasts; 5PTase13 was localized in the nucleus and cytoplasm; 5PTase11 was localized in the cytoplasm and plasma membrane; and 5PTase4 was localized in the nucleus, cytoplasm, and plasma membrane. Different localizations were displayed with different colors. 5PTase 1, 5PTase 2, 5PTase 6, 5PTase 12, and 5PTase 13 belong to Type I 5PTases and purple lines are used to connect them with the 5-phosphatase substrates. 5PTase 4, 5PTase 7, 5PTase 8, 5PTase 9, 5PTase 11, 5PTase14, and FRA3 belong to Type II 5PTases and black lines are used to connect them with 5-phosphatase substrates [2]. (B) 5PTases are crucial for multiple processes of plant growth, including seed germination [35], vascular patterning [36,37], root hair initiation [35], and salt stress [40,41].