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The GTPase Nog1 co-ordinates assembly, maturation and quality control of distant ribosomal functional centers

ABSTRACT: Yeast ribosome assembly analysis, using APMS on various 60S tagged subunits (SSF1, RIX1, ARX1, KRE35, ARX1_bud20D, KRE35_DRG1, KRE35_drg-dn, YEP, G223, NOG1)

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Diploid Cell

DISEASE(S): Mixed Disorder As Reaction To Stress

SUBMITTER: Ludovic Gillet

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD011382 | Pride | 2020-01-06

REPOSITORIES: Pride

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			Action	DRS
	ConsLib_yeast_LARS2-1All.sptxt	Other
	ConsLib_yeast_LARS2-1All_openSWATH_curated.tsv	Tabular
	Crapome_above20.csv	Csv
	E1701271515_feature_alignment.tsv	Tabular
	Heatmap_proteins.csv	Csv

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Publications

The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers.

Klingauf-Nerurkar Purnima P Gillet Ludovic C LC Portugal-Calisto Daniela D Oborská-Oplová Michaela M Jäger Martin M Schubert Olga T OT Pisano Agnese A Peña Cohue C Rao Sanjana S Altvater Martin M Chang Yiming Y Aebersold Ruedi R Panse Vikram G VG

eLife 20200107

Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the pre-60S, these steps include removal of placeholders Rlp24, Arx1 and Mrt4 that prevent premature loading of the ribosomal protein eL24, the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities lice ...[more]

PMID: 31909713

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The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers.

Project description:Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the pre-60S, these steps include removal of placeholders Rlp24, Arx1 and Mrt4 that prevent premature loading of the ribosomal protein eL24, the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities license release factors Rei1 and Yvh1 to trigger Arx1 and Mrt4 removal. Drg1-ATPase activity removes Rlp24 from the GTPase Nog1 on the pre-60S; consequently, the C-terminal tail of Nog1 is extracted from the PET. These events enable Rei1 to probe PET integrity and catalyze Arx1 release. Concomitantly, Nog1 eviction from the pre-60S permits peptidyl transferase center maturation, and allows Yvh1 to mediate Mrt4 release for stalk assembly. Thus, Nog1 co-ordinates the assembly, maturation and quality control of distant functional centers during ribosome formation.

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Interleukin-7 co-ordinates proliferation, differentiation and TCRA recombination during thymocyte β-selection

Project description:We used Illumina global gene expression profiling to compare IL7-regulated pathways in post-beta-selected DN3b and DN4 versus pre-beta-selected DN3a cell stages. We found that IL7 induced fewer genes in both DN3b and DN4 cells (800 and 300 respectively, versus 1800 in DN3a). We found several direct JAK/STAT target genes were significantly induced in all 3 stages. This group included Bcl2 and Cish, Socs2 and Socs3, feedback regulators of JAK-STAT signaling, as well as Pim1, Tfrc (Cd71) and Ccnd2. Thus, in addition to inducing survival genes, here we show that IL7 acutely regulates expression of trophic receptors and cell cycle regulators in pre- and post-beta-selection DN thymocytes.

2015-02-05 | GSE63932 | GEO

In situ spatial reconstruction of distinct normal and pathological cell populations within the human adrenal gland

Project description:The human adrenal gland consists of concentrically organized functionally distinct regions responsible for hormone production. Dysregulation of adrenocortical cell differentiation alters the proportion and organization of the functional zones of the adrenal cortex leading to disease. Current models of adrenocortical cell differentiation are based on mouse studies, but there are known organizational and functional differences between human and mouse adrenal glands. This study aimed to investigate the centripetal differentiation model in the human adrenal cortex and characterize aldosterone-producing micronodules (APMs) to better understand adrenal diseases such as primary aldosteronism. We applied spatially resolved in situ transcriptomics to human adrenal tissue sections from two individuals and identified distinct cell populations and their positional relationships. The results supported the centripetal differentiation model in humans, with cells progressing from the outer capsule to the zona glomerulosa, zona fasciculata, and zona reticularis. Additionally, we characterized two APMs in a 72-year-old female. Comparison with earlier APM transcriptomes indicated a subset of core genes, but also heterogeneity between APMs. The findings contribute to our understanding of normal and pathological cellular differentiation in the human adrenal cortex.

2023-11-15 | GSE244084 | GEO

Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.

Project description:X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.

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Urinary proteome in diabetic nephropathy

Project description:Urinary proteome was analyzed and quantified by Tandem Mass Tag (TMT) labeling followed by bioinformatics analysis to study DN pathophysiology and to identify biomarkers of clinical outcome. We included type 2 diabetic normotensive non-obese males with and without incipient DN (microalbuminuria). Sample collection included blood and urine at baseline (control and DN-basal) and, in DN patients, after 3 months of losartan treatment (DN-treated). Urinary proteome analysis identified 166 differentially abundant proteins between controls and DN patients, 27 comparing DN-treated and DN-basal patients, and 182 between DN-treated patients and controls. Mathematical modeling analysis identified 80 key proteins involved in DN pathophysiology, 15 in losartan effect and 7 of these 95 are essential in both processes. VCAM-1 and neprilysin are the only ones that are differentially expressed in the urinary proteome. We observed an increase of VCAM-1 urine levels in DN-basal patients compared to diabetic controls and an increase of urinary neprilysin in DN-treated patients with persistent albuminuria, the latter confirmed by ELISA . Our results point to neprilysin and VCAM-1 as potential candidates in DN pathology and treatment.

2018-05-22 | PXD009303 | Pride

Sympathetic nerves and arrector pili muscles form a dual component niche to regulate hair follicle stem cells

Project description:Piloerection (goosebump) requires concerted actions of the hair follicle, the arrector pili muscle (APM), and the sympathetic nerve, providing a model to study interactions across epithelium, mesenchyme, and nerves. Here, we show that APMs and sympathetic nerves form a dual component niche to modulate hair follicle stem cell (HFSC) activity. Sympathetic nerves form synapse-like structures with HFSCs and regulate HFSCs through norepinephrine, whereas APMs maintain sympathetic innervation to HFSCs. Without norepinephrine signaling, HFSCs enter a deep quiescence state by down-regulating cell cycle machinery and mitochondria metabolism, while up-regulating quiescence regulators Lhx2, Foxp1, and Fgf18. During development, HFSC progeny secrets Sonic Hedgehog (SHH) to direct the formation of this APM-sympathetic nerve niche, which in turn controls hair follicle regeneration in adults. Our results reveal a reciprocal interdependence between a regenerative tissue and its niche at different stages, and illustrate that nerves can modulate stem cell quiescence through synapses and neurotransmitters.

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C-type natriuretic peptide co-ordinates cardiac structure and function.

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