bims-tricox 2023-05-28 papers

Issue of 2023–05–28
six papers selected by
Yash Verma, University of Zurich

PLoS Genet. 2023 May 22. 19(5): e1010774

Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis.

Floortje van de Poll, Benjamin M Sutter, Michelle Grace Acoba, Daniel Caballero, Samira Jahangiri, Yu-San Yang, Chien-Der Lee, Benjamin P Tu.

Pbp1 (poly(A)-binding protein-binding protein 1) is a cytoplasmic stress granule marker that is capable of forming condensates that function in the negative regulation of TORC1 signaling under respiratory conditions. Polyglutamine expansions in its mammalian ortholog ataxin-2 lead to spinocerebellar dysfunction due to toxic protein aggregation. Here, we show that loss of Pbp1 in S. cerevisiae leads to decreased amounts of mRNAs and mitochondrial proteins which are targets of Puf3, a member of the PUF (Pumilio and FBF) family of RNA-binding proteins. We found that Pbp1 supports the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase and subunits of mitochondrial ribosomes. We further show that Pbp1 and Puf3 interact through their respective low complexity domains, which is required for Puf3-target mRNA translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration. They may further explain prior associations of Pbp1/ataxin-2 with RNA, stress granule biology, mitochondrial function, and neuronal health.

DOI: https://doi.org/10.1371/journal.pgen.1010774

Biol Chem. 2023 May 29.

Molecular functions of RNA helicases during ribosomal subunit assembly.

Ali Khreiss, Katherine E Bohnsack, Markus T Bohnsack.

During their biogenesis, the ribosomal subunits undergo numerous structural and compositional changes to achieve their final architecture. RNA helicases are a key driving force of such remodelling events but deciphering their particular functions has long been challenging due to lack of knowledge of their molecular functions and RNA substrates. Advances in the biochemical characterisation of RNA helicase activities together with new insights into RNA helicase binding sites on pre-ribosomes and structural snapshots of pre-ribosomal complexes containing RNA helicases now open the door to a deeper understanding of precisely how different RNA helicases contribute to ribosomal subunit maturation.

Keywords: DEAH box protein; DExD box protein; RNA helicase; RNP remodelling; ribosome

DOI: https://doi.org/10.1515/hsz-2023-0135

Biomolecules. 2023 May 18. pii: 853. [Epub ahead of print]13(5):

Ribosomal Protein uS5 and Friends: Protein-Protein Interactions Involved in Ribosome Assembly and Beyond.

Anne-Marie Landry-Voyer, Zabih Mir Hassani, Mariano Avino, François Bachand.

Ribosomal proteins are fundamental components of the ribosomes in all living cells. The ribosomal protein uS5 (Rps2) is a stable component of the small ribosomal subunit within all three domains of life. In addition to its interactions with proximal ribosomal proteins and rRNA inside the ribosome, uS5 has a surprisingly complex network of evolutionarily conserved non-ribosome-associated proteins. In this review, we focus on a set of four conserved uS5-associated proteins: the protein arginine methyltransferase 3 (PRMT3), the programmed cell death 2 (PDCD2) and its PDCD2-like (PDCD2L) paralog, and the zinc finger protein, ZNF277. We discuss recent work that presents PDCD2 and homologs as a dedicated uS5 chaperone and PDCD2L as a potential adaptor protein for the nuclear export of pre-40S subunits. Although the functional significance of the PRMT3-uS5 and ZNF277-uS5 interactions remain elusive, we reflect on the potential roles of uS5 arginine methylation by PRMT3 and on data indicating that ZNF277 and PRMT3 compete for uS5 binding. Together, these discussions highlight the complex and conserved regulatory network responsible for monitoring the availability and the folding of uS5 for the formation of 40S ribosomal subunits and/or the role of uS5 in potential extra-ribosomal functions.

Keywords: PDCD2; PDCD2L; PRMT3; ZNF277; dedicated chaperone; ribosome biogenesis; uS5

DOI: https://doi.org/10.3390/biom13050853

Biomolecules. 2023 May 19. pii: 866. [Epub ahead of print]13(5):

Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly.

Kavan Gor, Olivier Duss.

Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.

Keywords: RNA folding; RNA structure probing; RNP assembly; assembly intermediates; cryo–electron microscopy; in vitro reconstitutions; mass spectrometry; protein–RNA interactions; ribosome assembly; single-molecule fluorescence microscopy

DOI: https://doi.org/10.3390/biom13050866

Acta Pharmacol Sin. 2023 May 22.

COX17 restricts renal fibrosis development by maintaining mitochondrial copper homeostasis and restoring complex IV activity.

Sai-Ya Zhu, Wen-Qian Zhou, Yang-Yang Niu, Chao Zheng, Xi Liu, Ying-Ying Zhang, Chen Yu.

Renal fibrosis relies on multiple proteins and cofactors in its gradual development. Copper is a cofactor of many enzymes involved in renal microenvironment homeostasis. We previously reported that intracellular copper imbalance occurred during renal fibrosis development and was correlated with fibrosis intensity. In this study, we investigated the molecular mechanisms of how copper affected renal fibrosis development. Unilateral ureteral obstruction (UUO) mice were used for in vivo study; rat renal tubular epithelial cells (NRK-52E) treated with TGF-β1 were adapted as an in vitro fibrotic model. We revealed that the accumulation of copper in mitochondria, rather than cytosol, was responsible for mitochondrial dysfunction, cell apoptosis and renal fibrosis in both in vivo and in vitro fibrotic models. Furthermore, we showed that mitochondrial copper overload directly disrupted the activity of respiratory chain complex IV (cytochrome c oxidase), but not complex I, II and III, which hampered respiratory chain and disrupted mitochondrial functions, eventually leading to fibrosis development. Meanwhile, we showed that COX17, the copper chaperone protein, was significantly upregulated in the mitochondria of fibrotic kidneys and NRK-52E cells. Knockdown of COX17 aggravated mitochondrial copper accumulation, inhibited complex IV activity, augmented mitochondrial dysfunction and led to cell apoptosis and renal fibrosis, whereas overexpression of COX17 could discharge copper from mitochondria and protect mitochondrial function, alleviating renal fibrosis. In conclusion, copper accumulation in mitochondria blocks complex IV activity and induces mitochondrial dysfunction. COX17 plays a pivotal role in maintaining mitochondrial copper homeostasis, restoring complex IV activity, and ameliorating renal fibrosis.

Keywords: COX17; NRK-52E cells; copper; cytochrome c oxidase; mitochondria; renal fibrosis

DOI: https://doi.org/10.1038/s41401-023-01098-3

bioRxiv. 2023 May 10. pii: 2023.05.09.539987. [Epub ahead of print]

Structural mechanism of co-import of H2A-H2B and its chaperone Nap1 by nuclear import receptor Kap114.

Jenny Jiou, Ho Yee Joyce Fung, Yuh Min Chook.

Histones are synthesized and processed in the cytoplasm and then transported into the nucleus for assembly into nucleosomes. H2A-H2B is imported into the S. cerevisiae nucleus by the importin Kap114, which also imports the most prominent H2A-H2B chaperone, Nap1. We understand how Kap114 recognizes H2A-H2B for nuclear import, but little is known about how it recognizes Nap1. Furthermore, the ternary complex of Nap1, H2A-H2B and Kap114 was previously detected in both the cytosol and the nucleus, but its role in nuclear import is unclear. Here, we present biophysical analysis of interactions between Nap1, H2A-H2B, Kap114 and RanGTP, and cryo-electron microscopy structures of ternary Kap114, Nap1 and H2A-H2B complexes. Kap114 binds Nap1 very weakly, but H2A-H2B enhances Kap114-Nap1 interaction to form a ternary Kap114/Nap1/H2A-H2B complex that is stable in the absence and presence of RanGTP. Cryogenic electron microscopy structures reveal two distinct ternary Kap114/Nap1/H2A-H2B complexes: a 3.2 Å resolution structure of Nap1 bound to H2A-H2B-bound Kap114 where Nap1 does not contact H2A-H2B, and a 3.5 Å resolution structure of H2A-H2B sandwiched between Nap1 and Kap114. Collectively, these results lead to a mechanistic model of how Nap1•H2A-H2B encounters Kap114 in the cytoplasm and how both H2A-H2B and Nap1 are chaperoned and co-imported by Kap114 into the nucleus. The model also suggests how RanGTP-binding stabilizes a quaternary RanGTP/Kap114/Nap1/H2A-H2B complex that facilitates hand-off of H2A-H2B from Kap114 to Nap1, the assembling nucleosome or other nuclear chaperone.
Significance Statement: Free core histones are highly toxic and must be sequestered by other macromolecules in the cell. The mechanism of H3-H4 import by karyopherin Importin-4 in the presence of its chaperone ASF1 is understood, but the mechanism of how histone chaperone Nap1 influences H2A-H2B import is not resolved. We present biophysical interaction analysis and cryo-EM structures that reveal how Kap114, Nap1 and H2A-H2B assemble into an import complex. These results lead us to a structural mechanism of how Nap1 delivers H2A-H2B to Kap114 in the cytosol, how Nap1 and H2A-H2B are co-imported into the nucleus, and how RanGTP may influence Kap114/Nap1/H2A-H2B interactions to assemble nucleosomes in the nucleus.

DOI: https://doi.org/10.1101/2023.05.09.539987