bims-tricox 2022-10-16 papers

Issue of 2022‒10‒16
five papers selected by
Yash Verma
University of Delhi South Campus

Cells. 2022 Sep 20. pii: 2943. [Epub ahead of print]11(19):

The RNA-Binding Landscape of HAX1 Protein Indicates Its Involvement in Translation and Ribosome Assembly.

Anna Balcerak, Ewelina Macech-Klicka, Maciej Wakula, Rafal Tomecki, Krzysztof Goryca, Malgorzata Rydzanicz, Mateusz Chmielarczyk, Malgorzata Szostakowska-Rodzos, Marta Wisniewska, Filip Lyczek, Aleksandra Helwak, David Tollervey, Grzegorz Kudla, Ewa A Grzybowska.

HAX1 is a human protein with no known homologues or structural domains. Mutations in the HAX1 gene cause severe congenital neutropenia through mechanisms that are poorly understood. Previous studies reported the RNA-binding capacity of HAX1, but the role of this binding in physiology and pathology remains unexplained. Here, we report the transcriptome-wide characterization of HAX1 RNA targets using RIP-seq and CRAC, indicating that HAX1 binds transcripts involved in translation, ribosome biogenesis, and rRNA processing. Using CRISPR knockouts, we find that HAX1 RNA targets partially overlap with transcripts downregulated in HAX1 KO, implying a role in mRNA stabilization. Gene ontology analysis demonstrated that genes differentially expressed in HAX1 KO (including genes involved in ribosome biogenesis and translation) are also enriched in a subset of genes whose expression correlates with HAX1 expression in four analyzed neoplasms. The functional connection to ribosome biogenesis was also demonstrated by gradient sedimentation ribosome profiles, which revealed differences in the small subunit:monosome ratio in HAX1 WT/KO. We speculate that changes in HAX1 expression may be important for the etiology of HAX1-linked diseases through dysregulation of translation.

Keywords: CRAC; HAX1; RIP-seq; RNA–protein binding; ribosome assembly; translation

DOI: https://doi.org/10.3390/cells11192943

Nat Commun. 2022 Oct 11. 13(1): 5989

An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.

Ondřej Gahura, Alexander Mühleip, Carolina Hierro-Yap, Brian Panicucci, Minal Jain, David Hollaus, Martina Slapničková, Alena Zíková, Alexey Amunts.

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

DOI: https://doi.org/10.1038/s41467-022-33588-z

Cell Rep. 2022 Oct 11. pii: S2211-1247(22)01317-1. [Epub ahead of print]41(2): 111467

An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs.

Cornelius Schneider, Florian Erhard, Beyenech Binotti, Alexander Buchberger, Jörg Vogel, Utz Fischer.

In all domains of life, mechanisms exist that adjust translational capacity to nutrient restriction and other growth constraints. The mammalian target of rapamycin (mTOR) regulates the synthesis of ribosomal proteins and translation factors in mammalian cells via phosphorylation of the La-related protein 1 (LARP1). In the present model of starvation-induced translational silencing, LARP1 targets mRNAs carrying a 5' terminal oligopyrimidine (5'TOP) motif to shift these into subpolysomal ribonucleoprotein particles. However, how these mRNAs would be protected from degradation and rapidly made available to restore translation capacity when needed remained enigmatic. Here, to address this, we employ gradient profiling by sequencing (Grad-seq) and monosome footprinting. Challenging the above model, we find that 5'TOP mRNAs, instead of being translationally silenced during starvation, undergo low baseline translation with reduced initiation rates. This mode of regulation ensures a stable 5'TOP mRNA population under starvation and allows fast reversibility of the translational repression.

Keywords: 5'TOP; CP: Molecular biology; LARP1; TOP mRNAs; TOP response; baseline translation; mRNA; mTORC1; starvation; translation initiation; translation regulation

DOI: https://doi.org/10.1016/j.celrep.2022.111467

FEBS Lett. 2022 Oct 11.

Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.

Fay M Allen, Ana S H Costa, Anja V Gruszczyk, Georgina R Bates, Hiran A Prag, Efterpi Nikitopoulou, Carlo Viscomi, Christian Frezza, Andrew M James, Michael P Murphy.

The compartmentation and distribution of metabolites between mitochondria and the rest of the cell is a key parameter of cell signalling and pathology. Here, we have developed a rapid fractionation procedure that enables us to take mouse heart and liver from in vivo and within ~ 30 seconds stabilise the distribution of metabolites between mitochondria and the cytosol by rapid cooling, homogenisation and dilution. This is followed by centrifugation of mitochondria through an oil layer to separate mitochondrial and cytosolic fractions for subsequent metabolic analysis. Using this procedure revealed the in vivo compartmentation of mitochondrial metabolites and will enable assessment of the distribution of metabolites between the cytosol and mitochondria during a range of situations in vivo.

Keywords: compartmentation; in vivo; ischemia; metabolites; mitochondria; rapid fractionation

DOI: https://doi.org/10.1002/1873-3468.14511

Cell Mol Life Sci. 2022 Oct 15. 79(11): 550

Rewiring of the protein-protein-metabolite interactome during the diauxic shift in yeast.

Dennis Schlossarek, Marcin Luzarowski, Ewelina M Sokołowska, Venkatesh P Thirumalaikumar, Lisa Dengler, Lothar Willmitzer, Jennifer C Ewald, Aleksandra Skirycz.

In budding yeast Saccharomyces cerevisiae, the switch from aerobic fermentation to respiratory growth is separated by a period of growth arrest, known as the diauxic shift, accompanied by a significant metabolic rewiring, including the derepression of gluconeogenesis and the establishment of mitochondrial respiration. Previous studies reported hundreds of proteins and tens of metabolites accumulating differentially across the diauxic shift transition. To assess the differences in the protein-protein (PPIs) and protein-metabolite interactions (PMIs) yeast samples harvested in the glucose-utilizing, fermentative phase, ethanol-utilizing and early stationary respiratory phases were analysed using isothermal shift assay (iTSA) and a co-fractionation mass spectrometry approach, PROMIS. Whereas iTSA monitors changes in protein stability and is informative towards protein interaction status, PROMIS uses co-elution to delineate putative PPIs and PMIs. The resulting dataset comprises 1627 proteins and 247 metabolites, hundreds of proteins and tens of metabolites characterized by differential thermal stability and/or fractionation profile, constituting a novel resource to be mined for the regulatory PPIs and PMIs. The examples discussed here include (i) dissociation of the core and regulatory particle of the proteasome in the early stationary phase, (ii) the differential binding of a co-factor pyridoxal phosphate to the enzymes of amino acid metabolism and (iii) the putative, phase-specific interactions between proline-containing dipeptides and enzymes of central carbon metabolism.

Keywords: Co-fractionantion mass spectrometry; Diauxic-shift; Dipeptides; Proteasome; Protein-metabolite interactions; Yeast

DOI: https://doi.org/10.1007/s00018-022-04569-8