Asparagine hydroxylation is likely to be a reversible post-translational modification

Rodríguez, Javier; Haydinger, Cameron D.; Peet, Daniel J.; Nguyen, Lan K.; Kriegsheim, Alex von

doi:10.1101/2020.03.22.002436

Cited by 7 publications

(4 citation statements)

References 54 publications

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“…The pathogenic strains harbor a significant amount of Asn residues, while the non-pathogenic ones display more Gly and Gln residues. Asn residues are highly susceptible to hydroxylation which is a post-translational modification shown recently as reversible [37]. Therefore, one cannot exclude the hydroxylation of Asn residues, which could contribute to protein modification, flexibility and anchoring at the PG.…”

Section: Analysis Of the Differences At The 2d And 3d Levelsmentioning

confidence: 99%

Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains

Tran

Cormontagne

Vidić

et al. 2020

Toxins

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The emergence of B. cereus as an opportunistic food-borne pathogen has intensified the need to distinguish strains of public health concern. The heterogeneity of the diseases associated with B. cereus infections emphasizes the versatility of these bacteria strains to colonize their host. Nevertheless, the molecular basis of these differences remains unclear. Several toxins are involved in virulence, particularly in gastrointestinal disorders, but there are currently no biological markers able to differentiate pathogenic from harmless strains. We have previously shown that CwpFM is a cell wall peptidase involved in B. cereus virulence. Here, we report a sequence/structure/function characterization of 39 CwpFM sequences, chosen from a collection of B. cereus with diverse virulence phenotypes, from harmless to highly pathogenic strains. CwpFM is homology-modeled in silico as an exported papain-like endopeptidase, with an N-terminal end composed of three successive bacterial Src Homology 3 domains (SH3b1–3) likely to control protein–protein interactions in signaling pathways, and a C-terminal end that contains a catalytic NLPC_P60 domain primed to form a competent active site. We confirmed in vitro that CwpFM is an endopeptidase with a moderate peptidoglycan hydrolase activity. Remarkably, CwpFMs from pathogenic strains harbor a specific stretch of twenty residues intrinsically disordered, inserted between the SH3b3 and the catalytic NLPC_P60 domain. This strongly suggests this linker as a marker of differentiation between B. cereus strains. We believe that our findings improve our understanding of the pathogenicity of B. cereus while advancing both clinical diagnosis and food safety.

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Section: Analysis Of the Differences At The 2d And 3d Levelsmentioning

confidence: 99%

Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains

Tran

Cormontagne

Vidić

et al. 2020

Toxins

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“…Unlike proline hydroxylation, targets of FIH outside the HIF factors have been readily identified by mass spectrometry approaches (Cockman et al, 2009a;Rodriguez et al, 2016). In fact, in this case, even evidence for a de-hydroxylase activity existing in cells has been provided, even though its identity has remained elusive (Rodriguez et al, 2020). FIH has been shown to mediate the hydroxylation of asparagine residues in many different proteins, including ankyrin-containing proteins such as nuclear factor kappa B subunit 1 (NFKB1), NFKB2, NFKB inhibitor alpha (NFKBIA; Cockman et al, 2009b;Singleton et al, 2011) and deubiquitinases such as OTU deubiquitinase, ubiquitin aldehyde binding 1 (OTUB1; Scholz et al, 2016) and Cezanne (Mader et al, 2020).…”

Section: Asparagine Hydroxylationmentioning

confidence: 99%

Oxygen‐regulated post‐translation modifications as master signalling pathway in cells

Batie,

Fasanya,

Kenneth

et al. 2023

EMBO Reports

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Oxygen is essential for viability in mammalian organisms. However, cells are often exposed to changes in oxygen availability, due to either increased demand or reduced oxygen supply, herein called hypoxia. To be able to survive and/or adapt to hypoxia, cells activate a variety of signalling cascades resulting in changes to chromatin, gene expression, metabolism and viability. Cellular signalling is often mediated via post‐translational modifications (PTMs), and this is no different in response to hypoxia. Many enzymes require oxygen for their activity and oxygen can directly influence several PTMS. Here, we review the direct impact of changes in oxygen availability on PTMs such as proline, asparagine, histidine and lysine hydroxylation, lysine and arginine methylation and cysteine dioxygenation, with a focus on mammalian systems. In addition, indirect hypoxia‐dependent effects on phosphorylation, ubiquitination and sumoylation will also be discussed. Direct and indirect oxygen‐regulated changes to PTMs are coordinated to achieve the cell's ultimate response to hypoxia. However, specific oxygen sensitivity and the functional relevance of some of the identified PTMs still require significant research.

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“…We identified Asn hydroxylation, but only on HIF-2α and at 1% O2. These observations are likely explained by the fact that Asn hydroxylation has recently been shown to be reversible (Rodriguez et al 2020), and that hydroxy-Asn containing HIFα molecules are likely additionally hydroxy-Pro and thus degraded, indirectly limiting their abundance.…”

Section: Hif-1α and Hif-2α Proteins Are Extensively Modified In Both ...mentioning

confidence: 99%

Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α

et al. 2021

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Cellular adaptation to low-oxygen environments is mediated in part by the hypoxia-inducible factors (HIFs). Like other transcription factors, the stability and transcriptional activity of HIFs—and consequently, the hypoxic response—are regulated by post-translational modifications (PTMs) and changes in protein-protein interactions. Our current understanding of PTM-mediated regulation of HIFs is primarily based on in vitro protein fragment–based studies typically validated in fragment-expressing cells treated with hypoxia-mimicking compounds. Here, we used immunoprecipitation-based mass spectrometry to characterize the PTMs and binding partners for full-length HIF-1α and HIF-2α under normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. Hypoxia substantially altered the complexity and composition of the HIFα protein interaction networks, particularly for HIF-2α, with the hypoxic networks of both isoforms being enriched for mitochondrial proteins. Moreover, both HIFα isoforms were heavily covalently modified. We identified ~40 PTM sites composed of 13 different types of modification on both HIFα isoforms, including multiple cysteine modifications and an unusual phosphocysteine. More than 80% of the PTMs identified were not previously known and about half exhibited oxygen dependency. We further characterized an evolutionarily conserved phosphorylation of Ser31 in HIF-1α as a regulator of its transcriptional function, and we propose functional roles for Thr406, Thr528, and Ser581 in HIF-2α. These data will help to delineate the different physiological roles of these closely related isoforms in fine-tuning the hypoxic response.

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Asparagine hydroxylation is likely to be a reversible post-translational modification

Cited by 7 publications

References 54 publications

Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains

Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains

Oxygen‐regulated post‐translation modifications as master signalling pathway in cells

Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α

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