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Abstract
Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and biological function of plant PUSs. In this study, we identified 20 AtPUSs and 22 ZmPUSs from Arabidopsis and maize (Zea mays), respectively. Our phylogenetic analysis indicated that both AtPUSs and ZmPUSs could be clustered into six known subfamilies: RluA, RsuA, TruA, TruB, PUS10, and TruD. RluA subfamily is the largest subfamily in both Arabidopsis and maize. It’s noteworthy that except the canonical XXHRLD-type RluAs, another three conserved RluA variants, including XXNRLD-, XXHQID-, and XXHRLG-type were also identified in those key nodes of vascular plants. Subcellular localization analysis of representative AtPUSs and ZmPUSs in each subfamily revealed that PUS proteins were localized in different organelles including nucleus, cytoplasm and chloroplasts. Transcriptional expression analysis indicated that AtPUSs and ZmPUSs were differentially expressed in various tissues and diversely responsive to abiotic stresses, especially suggesting their potential roles in response to heat and salt stresses. All these results would facilitate the functional identification of these pseudouridylation in the future.
Highlights
Received: 29 December 2021Up to date, more than 170 RNA modifications have been identified [1]
Proteins, an unrooted phylogenetic tree of plant Pseudouridine synthases (PUSs) genes was constructed based on the sequences of PUS catalytic domains from A. thaliana, Glycine max, Zea mays, Oryza sativa, and Solanum lycopersicum (Figure 1 and Table S4)
Combined with the typical features of the conserved catalytic motif in enzymatic domain, the phylogenetic analysis showed that the PUS proteins were clustered into two groups: the first group share homological conserved catalytic domain with bacteria ribosomal RNAs (rRNAs) pseudouridine synthase, which could be further divided into two subfamilies, RluA and RsuA; the second group share homological conserved catalytic domain with bacteria transfer RNAs (tRNAs) pseudouridine synthase, which could be further divided into four subfamilies, TruA, TruB, TruD, and Pus10
Summary
Received: 29 December 2021Up to date, more than 170 RNA modifications have been identified [1]. Instead of the canonical C-N glycosidic bond between the base and ribose in uridine, Ψ is an isomer of uridine with a more inert C-C bond produced through enzymatic isomerization, at the N1 of which there is an extra hydrogen bond donor. Due to these structural differences, RNAs with pseudouridylation have more rigid phosphodiester backbone and more stable Ψ-A base pairs through improved base stacking and water coordination [4]. The pseudouridines have been identified in a wide range of various noncoding RNAs, such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear. In the past few years, several deep-sequencing technologies based on N-cyclohexyl-N 0 -[β-(N-methylmorpholino)-ethyl]-carbodiimide-ptoluene sulfonate (CMCT) labeling were developed for the high–resolution identification of transcriptome-wide pseudouridylation and novel pseudouridylation sites were found in protein-encoding mRNAs and some other non-coding RNAs as well [5–8], expanding the Accepted: 25 February 2022
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