The Predicted Functional Compartmentation of Rice Terpenoid Metabolism by Trans-Prenyltransferase Structural Analysis, Expression and Localization

Abstract

Most terpenoids are derived from the basic terpene skeletons of geranyl pyrophosphate (GPP, C10), farnesyl-PP (FPP, C15) and geranylgeranyl-PP (GGPP, C20). The trans-prenyltransferases (PTs) mediate the sequential head-to-tail condensation of an isopentenyl-PP (C5) with allylic substrates. The in silico structural comparative analyses of rice trans-PTs with 136 plant trans-PT genes allowed twelve rice PTs to be identified as GGPS_LSU (OsGGPS1), homomeric G(G)PS (OsGPS) and GGPS_SSU-II (OsGRP) in Group I; two solanesyl-PP synthase (OsSPS2 and 3) and two polyprenyl-PP synthases (OsSPS1 and 4) in Group II; and five FPSs (OsFPS1, 2, 3, 4 and 5) in Group III. Additionally, several residues in “three floors” for the chain length and several essential domains for enzymatic activities specifically varied in rice, potentiating evolutionarily rice-specific biochemical functions of twelve trans-PTs. Moreover, expression profiling and localization patterns revealed their functional compartmentation in rice. Taken together, we propose the predicted topology-based working model of rice PTs with corresponding terpene metabolites: GPP/GGPPs mainly in plastoglobuli, SPPs in stroma, PPPs in cytosol, mitochondria and chloroplast and FPPs in cytosol. Our findings could be suitably applied to metabolic engineering for producing functional terpene metabolites in rice systems.

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

“…It was found that VvGGPPS (VIT_205s0020g01240) was clustered in the same clade as the other five protein sequences for which the subcellular localization was experimentally demonstrated (Supplementary Figure S7). The target VvGGPPS in this study presented the shortest distance from the rice XP 015647986 and tomato Solyc11g011240 sequences, both of which have been experimentally shown to be in chloroplasts (Zhou et al, 2017;You et al, 2020;Zhou and Pichersky, 2020;Barja et al, 2021). Chloroplasts are a type of plastid.…”

Effect of Developmental Stages on Genes Involved in Middle and Downstream Pathway of Volatile Terpene Biosynthesis in Rose Petals

“…chinensis genome comprised seven complete RcTPTs , indicating that the number of TPTs in R . chinensis is less than those reported in Arabidopsis thaliana (16), tomato (10), Cinnamomum camphora (10), and Oryza sativa (12), and more than or equal to that in Chlamydomonas reinhardtii (4) and Physcomitrella patens (7) ( Table S5 ) [ 25 , 28 , 58 ]. Unlike the TPT gene family in Cinnamomum camphora (Lauraceae) that has segmentally duplicated TPT genes [ 28 ], no such TPT genes were observed in the genome of R .…”

Plant geranylgeranyl diphosphate synthases: every (gene) family has a story

“…GGPP synthase (GGPPS) enzymes generate GGPP by three sequential IPP condensation steps to DMAPP, via GPP and finally FPP. Consistent with the requirement of GGPP in multiple locations and growth stages to ensure proper development and response to environmental challenges, plant genomes have retained families of differentially expressed genes encoding GGPPS isoforms that interact with specific protein partners and localize to particular cell compartments, including cytosol, plastids, mitochondria, and endoplasmic reticulum (Barja et al 2021;Beck et al 2013;Coman et al 2014;Ruiz-Sola et al 2016b;Wang and Dixon 2009;Wang et al 2018;You et al 2020;Zhou and Pichersky 2020;Zhou et al 2017). Multiple copies of phylogenetically related (i.e., homologous) GGPPS-encoding genes that result from duplication events involving individual genes, chromosomal segments, or entire genomes are referred to as paralogs (in the same species) and orthologs (in different species).…”

“…GFP fusions of OsGGPPS1, OsGPPS and OsSSU-II proteins were targeted to chloroplasts (Fig. 1) (You et al 2020;Zhou et al 2017). Interestingly, OsSSU-II was found to recruit OsGGPPS1 from the chloroplast stroma to the thylakoid membranes, directing it to a large protein complex containing GGR and other components of the chlorophyll biosynthetic pathway, such as the light-harvesting-like protein LIL3 and the chlorophyll synthase CHLG (Fig.…”

“…The rice genome harbors several genes with homology to PTs, of which only two clustered with GGPPS-like enzymes and one with SSU-II proteins (You et al 2020;Zhou et al 2017). Similar to Arabidopsis, no gene encoding SSU-I was found in the rice genome.…”