tRNA‐like structures and their functions

Wu, Sipeng; Li, Xiang; Wang, Geng

doi:10.1111/febs.16070

Cited by 8 publications

(8 citation statements)

References 123 publications

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“…ABC transport is broadly associated with various physiological functions in the body [51]. Notably, aminoacyl tRNA regulates RNA replication, translation, and protein interactions, which produce, transport, and store sperm [52]. This may be related to the enhancement of sperm density, sperm motility, number of rectilinear sperm, and sperm mitochondrial membrane potential by L-Cit in rams…”

Section: Discussionmentioning

confidence: 99%

Metabolomic and Transcriptomic Changes Underlying the Effects of L-Citrulline Supplementation on Ram Semen Quality

Zhao

Bai

et al. 2023

Animals

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This study examined the effects of L-Cit supplementation on ram semen quality through metabolomics and transcriptomics. A total of 16 rams were randomly categorized into two groups. The control group was fed a basic diet, whereas the experimental group received feed supplemented with 12 g/d of L-Cit. Semen and blood were collected from the rams on days 0 and 72 to measure sugar, pyruvate, amino acid, and nontargeted metabolite contents. Additionally, hypothalamic and testicular tissues were collected for a transcriptomic analysis. We found 27 differential metabolites between the control and experimental groups, of which 21 were downregulated (p < 0.05) and 6 were upregulated (p < 0.05). Compared with the control group, xylose and pyruvate contents in seminal plasma increased by 43.86% and 162.71%, respectively (p < 0.01). Additionally, the levels of 11 amino acids showed a significant increase in seminal plasma (p < 0.01). Furthermore, 961 and 715 differentially expressed genes were detected in the hypothalamic and testicular tissues, respectively. The pathways of significant enrichment in the hypothalamus and testes were protein digestion, absorption, glycolysis/gluconeogenesis, and amino as well as nucleotide sugar metabolisms. In the present study, L-Cit improved protein synthesis and blood metabolism, consequently increasing the contents of most amino acids in ram seminal plasma. Specifically, the hypothalamus controlled the expression of glycolysis/gluconeogenesis-related genes in the testes through its metabolites released into the serum, thereby providing energy for sperm production, which led to a decrease in the sugar content of seminal plasma.

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Section: Discussionmentioning

confidence: 99%

Metabolomic and Transcriptomic Changes Underlying the Effects of L-Citrulline Supplementation on Ram Semen Quality

Zhao

Bai

et al. 2023

Animals

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“…In some previous studies, sequences with identical anticodons were regarded as tRNA-like sequences [ 27 , 60 ], while alternative anticodons can be utilized in other studies [ 26 , 61 ]; a consistent standard has not been established [ 62 ]. In the tRNA-like analysis in this study, the same anticodon was used as a criterion for identification.…”

Section: Discussionmentioning

confidence: 99%

“…As the forward and reverse strands are transcribed separately and the start is in the control region, the tRNA at the intersection should theoretically be closer to the typical structure. Despite the discovery of multiple tRNA-like structures in plant and animal viruses and studies of their essential activities [ 62 ], few studies have evaluated their evolutionary characteristics and functions in insect mitogenomes. The conventional and tRNA-like structures differed in sequence homology by 47.14% to 69.12% in this study.…”

Section: Discussionmentioning

confidence: 99%

Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences

Wang,

Hu,

et al. 2023

Genes

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Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.

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“…coli strain with rnpA knockout served as an efficient means to enhance recombinant protein production of difficult targets including the highly‐repetitive glycine‐rich spider silk protein, the Cas9 protein and an antibody fragment (Chung et al, 2023). Several plant viruses responsible for worldwide crop yield loss rely on tRNA‐like structures (TLSs) to carry out efficient viral RNA genome replication and other infection‐critical processes (Dreher, 2009; S. Wu, Li, & Wang, 2022). A unique strategy to confer resistance in such plant crops against viruses was envisioned via cytosolic RNase P (cytoRP) technology (Gobert et al, 2021), wherein plant PRORPs were re‐localized to accumulate in the cytoplasm to target TLSs, thereby disrupting viral replication.…”

Section: Applications Of Rnase Pmentioning

confidence: 99%

Multiple structural flavors of RNase P in precursor tRNA processing

Sridhara

2024

WIREs RNA

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The precursor transfer RNAs (pre‐tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5′‐processing, 3′‐processing, modifications at specific sites, if any, and 3′‐CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre‐tRNA sequences at the 5′ end by the removal of phosphodiester linkages between nucleotides at position −1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless‐position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion‐mediated conserved catalytic reaction. While the canonical RNA‐based ribonucleoprotein RNase P has been well‐known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA‐free protein‐only RNase P in eukaryotes and RNA‐free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA‐based and RNA‐free RNase P holoenzymes towards harnessing critical RNA–protein and protein–protein interactions in achieving conserved pre‐tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications.This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes

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tRNA‐like structures and their functions

Cited by 8 publications

References 123 publications

Metabolomic and Transcriptomic Changes Underlying the Effects of L-Citrulline Supplementation on Ram Semen Quality

Metabolomic and Transcriptomic Changes Underlying the Effects of L-Citrulline Supplementation on Ram Semen Quality

Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences

Multiple structural flavors of RNase P in precursor tRNA processing

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