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AUA codon decoding by preferential use of tRNA^Ile(UAU) in Lactobacillus casei. 干酪乳杆菌优先使用tRNAIle（UAU）解码AUA密码子。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-16 DOI: 10.1261/rna.081092.126

Chie Tomikawa, Satoshi Okura, Gakuto Uesugi, Kodai Toda, Kazuyuki Takai

{"title":"AUA codon decoding by preferential use of tRNA<sup>Ile</sup>(UAU) in <i>Lactobacillus casei</i>.","authors":"Chie Tomikawa, Satoshi Okura, Gakuto Uesugi, Kodai Toda, Kazuyuki Takai","doi":"10.1261/rna.081092.126","DOIUrl":"10.1261/rna.081092.126","url":null,"abstract":"<p><p>Modified nucleosides at the first (wobble) position of tRNA anticodons play critical roles in accurate decoding of the genetic code. In bacteria, the isoleucine AUA codon is typically decoded by tRNA<sup>Ile</sup>(LAU), in which lysidine (L) at the wobble position of tRNA<sup>Ile</sup> with a CAU anticodon ensures discrimination from the methionine AUG codon. However, some bacteria, such as <i>Mycoplasma mobile</i>, lack tRNA<sup>Ile</sup>(LAU) and instead utilize tRNA<sup>Ile</sup>(UAU). In this organism, the unmodified uridine at the wobble position is thought to enable specific decoding of AUA while avoiding AUG recognition. In our previous study, we identified a lactic acid bacterium in which both tRNA<sup>Ile</sup>(LAU) and tRNA<sup>Ile</sup>(UAU) coexist. Here, we show that tRNA<sup>Ile</sup>(LAU) is scarcely aminoacylated in vivo, whereas tRNA<sup>Ile</sup>(UAU) is efficiently aminoacylated. Notably, the presence of 4-thiouridine (s<sup>4</sup>U) at position 8 inhibits IleRS-dependent aminoacylation of tRNA<sup>Ile</sup>(UAU) in vitro, suggesting a regulatory role of tRNA modification in this process. Moreover, tRNA<sup>Ile</sup>(LAU) exhibits incomplete discrimination between AUA and AUG codons and binds to AUG in the ribosomal A-site binding assays. In contrast, tRNA<sup>Ile</sup>(UAU) containing <i>N</i> <sup>6</sup>-threonylcarbamoyladenosine (t<sup>6</sup>A) at position 37 showed a tendency toward improved discrimination between AUA and AUG codons and preferentially recognized AUA at the ribosomal A site. These results indicate that AUA decoding is predominantly mediated by preferential use of tRNA<sup>Ile</sup>(UAU) rather than canonical tRNA<sup>Ile</sup>(LAU), revealing an alternative mechanism of codon decoding based on differential utilization of tRNA isoacceptors, and providing an additional layer of translational control in bacteria.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1590-1602"},"PeriodicalIF":4.3,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient production of a self-amplifying RNA vaccine sequence with the single subunit RNA polymerase from Klebsiella phage 32 utilizing the native AU initiating dinucleotide. 利用天然AU起始二核苷酸，利用来自克雷伯氏菌噬菌体32的单亚基RNA聚合酶高效生产自扩增RNA疫苗序列。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-16 DOI: 10.1261/rna.081020.126

Marcus A Price, Maryia Trubitsyna, Jane E Paget, Benjamin W Baker, Frances Turner, Susan J Rosser

引用次数: 0

18S rRNA 3' end cleavage by the phosphorylated endoribonuclease NOB1 is interconnected with early small subunit biogenesis. 磷酸化核糖核酸内切酶NOB1的18S rRNA 3'端切割与早期小亚基生物发生有关。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-10 DOI: 10.1261/rna.081089.126

Katja I Bloch von Blottnitz, Mona Honemann-Capito, Philipp Hackert, Olexandr Dybkov, Christof Lenz, Markus T Bohnsack, Sonja Lorenz, Henning Urlaub, Claudia Schneider, Katherine E Bohnsack

{"title":"18S rRNA 3' end cleavage by the phosphorylated endoribonuclease NOB1 is interconnected with early small subunit biogenesis.","authors":"Katja I Bloch von Blottnitz, Mona Honemann-Capito, Philipp Hackert, Olexandr Dybkov, Christof Lenz, Markus T Bohnsack, Sonja Lorenz, Henning Urlaub, Claudia Schneider, Katherine E Bohnsack","doi":"10.1261/rna.081089.126","DOIUrl":"https://doi.org/10.1261/rna.081089.126","url":null,"abstract":"<p><p>Processing of the precursor ribosomal RNAs (pre-rRNAs) is a key aspect of ribosomal subunit assembly that is closely coordinated with other maturation events. The ribonucleases that mediate pre-rRNA cleavages require regulation to ensure that their activities are exerted in a timely manner. Post-translational modifications can influence protein functions, and although many human ribosome assembly factors are reported to be post-translationally modified, most of these sites remain unconfirmed and functional insights are lacking. Here, we show that NOB1, the PIN domain endoribonuclease responsible for cleavage of the 3' end of the 18S rRNA, is phosphorylated within an evolutionarily conserved acidic tract that can be modified by casein kinase II in vitro. Association of NOB1 with pre-ribosomes is independent of these phosphorylations, and lack of NOB1 phosphorylation only mildly perturbs the efficiency of SSU maturation events upstream of 3' end cleavage of the 18S rRNA. Interestingly, our analyses of pre-rRNA levels in cells depleted of NOB1 or lacking its catalytic activity revealed not only accumulation of the 18SE precursor of the 18S rRNA, but also altered levels of pre-rRNAs containing 5' external transcribed spacer (ETS) sequences (43S, 26S and 30S). This suggests that lack of NOB1-mediated pre-rRNA cleavage impairs recycling of assembly factors required during early biogenesis steps, leading to altered kinetics of 5' ETS processing. Taken together, these data provide new insights into the role of NOB1 during SSU biogenesis and the post-translational regulation of this ribonuclease.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circular-pre-rRNA-dependent and -independent rRNA maturation pathways in Archaea. 古细菌循环pre-rRNA依赖和不依赖的rRNA成熟途径。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-09 DOI: 10.1261/rna.081051.126

Daniela Strauß, Maximilian Liebl, Pranav Sharma, Michael Jüttner, Robert Reichelt, Aurore Gorlas, Sarah J Berkemer, Sébastien Ferreira-Cerca

{"title":"Circular-pre-rRNA-dependent and -independent rRNA maturation pathways in Archaea.","authors":"Daniela Strauß, Maximilian Liebl, Pranav Sharma, Michael Jüttner, Robert Reichelt, Aurore Gorlas, Sarah J Berkemer, Sébastien Ferreira-Cerca","doi":"10.1261/rna.081051.126","DOIUrl":"https://doi.org/10.1261/rna.081051.126","url":null,"abstract":"<p><p>Ribosome biogenesis in archaea is uniquely characterized by the formation of circular pre-rRNA intermediates, a process dependent on bulge-helix-bulge (bhb) motifs-structured RNA elements located in the processing stems flanking the rRNA and critical for cleavage and ligation by the tRNA splicing machinery. In this study, we confirm the existence of circular-dependent rRNA maturation pathways across diverse archaeal species. In addition, we also reveal the presence of circular-independent rRNA maturation pathways. Using a pan-archaeal assay, we detected circular pre-16S rRNA in most analysed species, but notably, Thermoplasma acidophilum lacks both circular pre-16S intermediate and a bhb motif in the 16S processing stem, indicating a novel, bhb- and circular-independent pre-16S maturation mechanism. In Haloarcula marismortui, we identified hybrid pathways, where different operons utilize either circular-dependent or -independent maturation routes. Additionally, we uncovered unprecedented diversity in bhb motifs, with central helix lengths ranging from 3 to 6 nucleotides, contrasting with the canonical 4-nucleotide helix typically observed in the context of tRNA splicing. These findings expand our understanding of rRNA maturation in archaea, demonstrating that circular pre-16S rRNA formation in archaea is not a universal requirement and highlighting the adaptability of archaeal ribosome biogenesis.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

2''F-NAD⁺ is a broad-spectrum RNA 2'-phosphotransferase (Tpt1) poison that traps the enzyme on its abortive RNA-2'-phospho-(2''F-ADP-ribose) reaction intermediate. 2' F-NAD+是一种广谱RNA 2'-磷酸转移酶（Tpt1）毒药，它将酶困在其流产的RNA-2'-磷酸（2' f - adp核糖）反应中间体上。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-03 DOI: 10.1261/rna.081192.126

Renata Kasprzyk, Shreya Ghosh, Stewart Shuman

{"title":"2''F-NAD<sup>+</sup> is a broad-spectrum RNA 2'-phosphotransferase (Tpt1) poison that traps the enzyme on its abortive RNA-2'-phospho-(2''F-ADP-ribose) reaction intermediate.","authors":"Renata Kasprzyk, Shreya Ghosh, Stewart Shuman","doi":"10.1261/rna.081192.126","DOIUrl":"https://doi.org/10.1261/rna.081192.126","url":null,"abstract":"<p><p>RNA 2'-phosphotransferase Tpt1 catalyzes the removal of an internal RNA 2'-PO4 via a two-step mechanism in which: (i) the 2'-PO4 attacks NAD+ C1'' to form an RNA-2'-phospho-(ADP-ribose) intermediate and nicotinamide; and (ii) transesterification of the ADP-ribose O2'' to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1'',2''-cyclic phosphate. Although Tpt1 enzymes are prevalent in bacteria, archaea, and eukarya, Tpt1 is uniquely essential in fungi, where it erases the 2'-PO4 mark installed by tRNA ligases during tRNA splicing. A Tpt1 \"poison\" that arrests the reaction after step 1 could aid in the design of antifungals that interdict tRNA biogenesis. Whereas our previous studies of 2''OMeNAD+ established its efficacy in poisoning Runella slithyformis Tpt1 (RslTpt1, a bacterial enzyme), its application was limited insofar as Tpt1 enzymes from fungal pathogens were unable to utilize 2''OMeNAD<sup>+</sup> for step 1 catalysis. Here we report the chemical synthesis of 2''F-NAD<sup>+</sup>, which proved to be a broad-spectrum poison against Tpt1 enzymes from five different taxa, including human pathogens Candida albicans and Candida auris. The resulting RNA-2'-phospho-(2''F-ADP-ribose) dead-end product remains stably trapped in a complex with Tpt1. A modified analog, 2''F-NAD-DTB, containing desthiobiotin (DTB) linked to adenine C2, provides an improved affinity-tag probe of RNA 2'-phosphate modification.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inositol hexakisphosphate is a Cofactor and Modulator of ADAR1 RNA Editing Activity. 磷酸己肌醇是ADAR1 RNA编辑活性的辅助因子和调节剂。

IF 4.3 3区生物学

RNA Pub Date : 2026-09-03 DOI: 10.1261/rna.081004.126

Francisco Antonio Venegas Solis, Mengsi Lu, Roni Cohen-Fultheim, Felix Bender, Valeria Fedeli, Takuya Masunaga, Mikako Fujita, Thomas Zillinger, Sabine Schneider, Andreas Kaufmann, Adolfo Saiardi, Erez Y Levanon, Henning Jessen, Stefan Bauer

{"title":"Inositol hexakisphosphate is a Cofactor and Modulator of ADAR1 RNA Editing Activity.","authors":"Francisco Antonio Venegas Solis, Mengsi Lu, Roni Cohen-Fultheim, Felix Bender, Valeria Fedeli, Takuya Masunaga, Mikako Fujita, Thomas Zillinger, Sabine Schneider, Andreas Kaufmann, Adolfo Saiardi, Erez Y Levanon, Henning Jessen, Stefan Bauer","doi":"10.1261/rna.081004.126","DOIUrl":"https://doi.org/10.1261/rna.081004.126","url":null,"abstract":"<p><p>Adenosine-to-inosine (A-to-I) RNA editing by ADAR1 is a key post-transcriptional modification, and mutations in ADAR1 lead to Aicardi-Goutières syndrome (AGS), an autoimmune disorder. Despite its biological and clinical relevance, the regulation of ADAR1 activity remains incompletely understood. Using a combination of biochemical approaches, inositol-pentakisphosphate 2-kinase (IPPK)-knockout cells, molecular dynamics simulations, and a cell-permeable inositol hexakisphosphate (IP6) prodrug (Pro-IP6), we demonstrate that IP6 depletion drastically reduces global RNA editing, while supplementation with Pro-IP6 restores and even enhances editing levels. Furthermore, we identify the C6-phosphate of IP6 as a critical determinant of ADAR1 catalytic efficiency, functioning within a hydrogen-bonding network that indirectly coordinates a Zn²⁺-ion. Finally, we show that the AGS-associated ADAR1 mutation N907S impairs RNA editing activity, most likely by altering the hydrogen-bond interaction network linking IP6 to the ADAR1 catalytic center. Together, these findings identify IP6 as an essential cofactor and regulator of ADAR1 activity and highlight cofactor availability and interaction networks as strategies for therapeutically modulating RNA editing.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative analysis of the m⁶A epitranscriptome in HeLa-expressed HPV18 early transcripts reveals its potential impact on splicing. 对hela表达的HPV18早期转录本中m6A表转录组的比较分析揭示了其对剪接的潜在影响。

IF 4.3 3区生物学

RNA Pub Date : 2026-08-17 DOI: 10.1261/rna.080698.125

Ida Rye Hellebek, Malte Storm Lau Schlosser, Johanna Jönsson, Jamie Yam Auxillos, Sarah Rennie

{"title":"Integrative analysis of the m<sup>6</sup>A epitranscriptome in HeLa-expressed HPV18 early transcripts reveals its potential impact on splicing.","authors":"Ida Rye Hellebek, Malte Storm Lau Schlosser, Johanna Jönsson, Jamie Yam Auxillos, Sarah Rennie","doi":"10.1261/rna.080698.125","DOIUrl":"10.1261/rna.080698.125","url":null,"abstract":"<p><p>Human papillomavirus (HPV)-driven cancers remain a major global health burden, and understanding how posttranscriptional regulation shapes viral gene expression may inform new therapeutic strategies. Here, we reanalyzed independently generated public HeLa data sets to identify candidate RNA modification sites on integrated HPV18 transcripts expressed from the HeLa genome. Using Oxford Nanopore direct RNA sequencing of native RNAs and in vitro transcribed controls, together with GLORI, eTAM-seq and staged 4sU-GLORI data sets, we identified a set of candidate m<sup>6</sup>A sites on HPV18 early transcripts. m<sup>6</sup>A levels at a subset of these sites were reduced following perturbation of the m<sup>6</sup>A pathway, most clearly after METTL3 inhibition, WTAP knockdown, or FTO overexpression. We further show that the <i>E6*I</i>-proximal m<sup>6</sup>A site at position 224 is enriched on unspliced transcripts in direct RNA sequencing, as supported by several of the analyzed data sets. In contrast, we find no convincing evidence for m<sup>5</sup>C or pseudouridine within the HPV18 regions covered by these data sets. Together, our analyses provide a candidate map of RNA modifications on HeLa-expressed HPV18 early transcripts.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1422-1435"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimized tRNA structure-seq reveals robust tRNA secondary structures in S. cerevisiae under mild stress conditions. 优化后的tRNA结构序列揭示了在轻度应力条件下酿酒酵母中强健的tRNA二级结构。

IF 4.3 3区生物学

RNA Pub Date : 2026-08-17 DOI: 10.1261/rna.081029.126

Komei Yanagihara, Futa Konishi, Teppei Matsuda, Akira Hirata, Hiroyuki Hori, Philip C Bevilacqua, Ryota Yamagami

{"title":"Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.","authors":"Komei Yanagihara, Futa Konishi, Teppei Matsuda, Akira Hirata, Hiroyuki Hori, Philip C Bevilacqua, Ryota Yamagami","doi":"10.1261/rna.081029.126","DOIUrl":"10.1261/rna.081029.126","url":null,"abstract":"<p><p>RNA structure plays a crucial role in diverse biological processes beyond the translation of genetic information. Therefore, the development of reliable methods for RNA structure prediction is essential for understanding RNA structure-related functions. However, accurate and comprehensive RNA structure prediction remains challenging. Here, we focus on secondary structure prediction of transfer RNA (tRNA) using structure probing coupled with next-generation sequencing (tRNA structure-seq). In silico prediction of <i>Saccharomyces cerevisiae</i> tRNA secondary structures achieves only 56.9% accuracy on average. Incorporation of dimethyl sulfate (DMS) probing data improves prediction accuracy to 87.4%, which is still not sufficient for practical tRNA structure prediction. To overcome this, we optimized the tRNA structure-seq analysis pipeline by explicitly incorporating natural tRNA modifications detected in tRNA sequencing data and by refining pseudo-free energy parameters specifically optimized for tRNA structure prediction. Using this optimized pipeline, the average prediction accuracy is remarkably improved to 93.3%. Furthermore, analysis of multiple structural conformations predicted from DMS probing data indicates that <i>S. cerevisiae</i> tRNAs predominantly adopt the canonical cloverleaf secondary structure under in vivo conditions. Finally, we examined tRNA structures under mild stress conditions, including heat stress, osmotic stress, and antibiotic stress. These perturbations had minimal effects on in vivo tRNA secondary structure, demonstrating that <i>S. cerevisiae</i> tRNAs maintain structural stability under physiologically relevant stress conditions. In summary, our results establish an optimized tRNA structure-seq analysis that enables highly accurate tRNA secondary structure prediction and reveals the intrinsic robustness of tRNA structures in living cells.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1494-1513"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148339962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reduced sensitivity to RNA structural differences distinguishes eukaryotic Pus4 from bacterial TruB. 真核生物Pus4与细菌TruB对RNA结构差异敏感性的差异

IF 4.3 3区生物学

RNA Pub Date : 2026-08-17 DOI: 10.1261/rna.080960.126

Amelia Cochran, David Muzyka, Jacqueline Anthenien, Fiona Tillyer, Markos Koutmos, Kristin S Koutmou

{"title":"Reduced sensitivity to RNA structural differences distinguishes eukaryotic Pus4 from bacterial TruB.","authors":"Amelia Cochran, David Muzyka, Jacqueline Anthenien, Fiona Tillyer, Markos Koutmos, Kristin S Koutmou","doi":"10.1261/rna.080960.126","DOIUrl":"10.1261/rna.080960.126","url":null,"abstract":"<p><p>Pseudouridine is an abundant posttranscriptional modification important to RNA structure and function. The isomerization of uridine (U) to pseudouridine (Ψ) is catalyzed by members of the pseudouridine synthase (Pus) family throughout all domains of life. All Pus enzymes modify noncoding RNAs, and a subset also pseudouridylate protein-coding messenger RNAs (mRNAs). Although the precise role of Ψ in mRNAs remains to be established, emerging evidence suggests that Ψ might contribute to the posttranscriptional control of gene expression. However, the mechanisms driving mRNA target selection by individual Pus enzymes still need to be defined. The bacterial Pus enzyme TruB has been well characterized and modifies tRNA at position U55 within T-loops. In addition to catalyzing Ψ55 in most tRNAs, eukaryotic TruB orthologs also pseudouridylate mRNAs. While it has been proposed that eukaryotic TruB orthologs modify mRNA at sites that mimic their tRNA targets in sequence and secondary structure, only a fraction of such sites are pseudouridylated in cells. Here, we demonstrate that the <i>Saccharomyces cerevisiae</i> TruB ortholog Pus4 binds and modifies RNAs that differ in secondary structure from its established tRNA substrates in vitro. Comparison of Pus4 and TruB activities on structurally diverse substrates reveals that while both enzymes can modify a variety of substrates, TruB does so less robustly than Pus4. We also find that the bacterial-specific PUA domain modulates TruB substrate selection. These findings are consistent with reports demonstrating that other mRNA-modifying Pus enzymes are more promiscuous in vitro than in cells. Our results suggest that Pus4 substrate selection might rely on additional factors beyond protein-RNA recognition in cells.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1373-1387"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148318544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4. 在缺乏Not4的细胞中，Puf3参与了mRNA溶解度的改变、罕见精氨酸密码子翻译延伸动力学的改变以及蛋白质稳态的丧失。

IF 4.3 3区生物学

RNA Pub Date : 2026-08-17 DOI: 10.1261/rna.080953.126

Léna Audebert, George E Allen, Siyu Chen, Olesya O Panasenko, Susanne Huch, Christine Polte, Zoya Ignatova, Vicent Pelechano, Martine A Collart

{"title":"Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.","authors":"Léna Audebert, George E Allen, Siyu Chen, Olesya O Panasenko, Susanne Huch, Christine Polte, Zoya Ignatova, Vicent Pelechano, Martine A Collart","doi":"10.1261/rna.080953.126","DOIUrl":"10.1261/rna.080953.126","url":null,"abstract":"<p><p>The Not proteins of the Ccr4-Not complex regulate translation elongation dynamics, essential for proper folding and assembly of new proteins. In yeast, ribosomes with nonoptimal codons in the A-site are enriched within the pool of ribosomes bound by Not4 and Not5. Such ribosomes accumulate in cells lacking Not4 or Not5 that show defects in co-translational assembly and aggregation of new proteins. Recently, we observed that depletion of Not1 and Not4 inversely regulate changes in mRNA solubility, correlating with inverse codon-specific changes in A-site ribosome dwelling occupancies (RDOs). Here we describe that mRNAs less soluble upon Not4 depletion are enriched for targets of the RNA-binding protein Puf3. We determine that Puf3 contributes to differential changes of A-site RDOs upon Not1 and Not4 depletion, in particular at rare arginine codons, and it contributes to changes in mRNA solubility in <i>not4</i>Δ. Moreover, deletion of Puf3 suppresses temperature sensitivity and protein aggregation in the <i>not4</i>Δ strain, while overexpression of Puf3 is toxic. Interestingly, the Puf3 interactome is altered in <i>not4</i>Δ. Taken together, our results associate alterations in Puf3 to <i>not4</i> mutant phenotypes, in particular to changes in translation elongation dynamics and protein aggregation.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1473-1493"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148278675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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