Illuminating the impact of N-terminal acetylation: from protein to physiology

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 15, 2025

N-terminal acetylation is a highly abundant protein modification in eukaryotic cells. This catalysed by acetyltransferases acting co- or post-translationally. Here, we review the machinery: enzymes involved and their substrate specificities. We also provide an overview of impact acetylation, including its effects on folding, subcellular targeting, complex formation, turnover. In particular, there may be competition between other defining fate. At organismal level, influential, impairment was recently linked to cardiac dysfunction neurodegenerative diseases. ubiquitous eukaryotes. authors machinery, function fate, role physiology human disease.

Язык: Английский

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Protein N-terminal modifications: molecular machineries and biological implications

Trends in Biochemical Sciences, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

The majority of eukaryotic proteins undergo N-terminal (Nt) modifications facilitated by various enzymes. These enzymes, which target the initial amino acid a polypeptide in sequence-dependent manner, encompass peptidases, transferases, cysteine oxygenases, and ligases. Nt - such as acetylation, fatty acylations, methylation, arginylation, oxidation enhance proteome complexity regulate protein targeting, stability, complex formation. Modifications at N termini are thereby core components large number biological processes, including cell signaling motility, autophagy regulation, plant animal oxygen sensing. Dysregulation Nt-modifying enzymes is implicated several human diseases. In this feature review we provide an overview occurring either co- or post-translationally, involved, impact.

Язык: Английский

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Development of an enhanced anti-pan-N-formylmethionine-specific antibody

BioTechniques, Год журнала: 2025, Номер unknown, С. 1 - 10

Опубликована: Фев. 20, 2025

Both bacterial and eukaryotic ribosomes can initiate protein synthesis with formylmethionine (fMet), but detecting fMet-bearing peptides proteins has been challenging due to the lack of effective anti-pan-fMet antibodies. Previously, we developed a polyclonal anti-fMet antibody using fMet-Gly-Ser-Gly-Cys pentapeptide that detects those regardless their sequence context. In this study, significantly improved antibody's specificity affinity by mixture fMet-Xaa-Cys tripeptides (Xaa, any 20 amino acids) as immunogen. This newly optimized is powerful, cost-effective tool for across species. Furthermore, approach provides foundation developing anti-pan-specific antibodies targeting other N-terminal modifications through acylation, alkylation, oxidation, arginylation, etc.

Язык: Английский

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Revisiting the structure of UBR box from human UBR6

Protein Science, Год журнала: 2025, Номер 34(4)

Опубликована: Март 18, 2025

Abstract Eukaryotic N‐degron pathways are proteolytic systems with the ability to recognize specific N‐terminal residues of substrate proteins, which essential parts their degradation signals. Domains, referred as UBR boxes, several E3 ubiquitin ligases can basic N‐degrons. UBR6 is among seven mammalian family proteins containing box domain. However, recognition type‐1 N‐degrons by still not well understood. The crystal structure from human revealed zinc‐mediated dimerization, a structural feature distinct other monomeric boxes. Furthermore, its folding pattern differed that fold, although sequences aligned those In this study, we re‐determined investigate whether unusual domain‐swapped dimer was structurally relevant. newly determined at 1.5 Å resolution monomer classical fold. Our compared previously reported structures and features were further analyzed using binding assays.

Язык: Английский

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The nascent polypeptide-associated complex (NAC) as regulatory hub on ribosomes

Biological Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Abstract The correct synthesis of new proteins is essential for maintaining a functional proteome and cell viability. This process tightly regulated, with ribosomes associated protein biogenesis factors ensuring proper production, modification, targeting. In eukaryotes, the conserved nascent polypeptide-associated complex (NAC) plays central role in coordinating early processing by regulating ribosome access multiple factors. NAC recruits modifying enzymes to ribosomal exit site N-terminus directs secretory into SRP-mediated targeting pathway. this review we will focus on these pathways, which are critical summarize recent advances understanding cotranslational functions mechanisms higher eukaryotes.

Язык: Английский

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Contribution of UbrA, a ubiquitin ligase essential for Arg/N-degron pathway, to peptidase gene expression inAspergillus oryzae

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 16, 2025

ABSTRACT The degradation of intracellular proteins by N-degron pathways depends on their N-terminal amino acids. In budding yeast, the Arg/N-degron pathway controls expression di/tri-peptide transporter gene degrading transcriptional repressor. However, there is no detailed information in filamentous fungi, and its role regulating microbial nitrogen metabolism unclear. Here, we demonstrated that E3 ubiquitin ligase, UbrA, which required for pathway, regulates peptidase fungus Aspergillus oryzae . Using ubiquitin-fused green fluorescent protein as a reporter, showed A. similar to yeast. Disruption ubrA significantly reduced activities acidic endopeptidase carboxypeptidase submerged culture using soy source. addition, disruption dramatically mRNA major genes but increased alkaline production. Moreover, levels di peptidyl- tripeptidyl- genes. This regulation was independent PrtR, transcription factor extracellular Our data UbrA involved various concert with IMPORTANCE Peptidases produced are important production Japanese fermented foods used industrial enzymes food-processing pharmaceutical applications. yeast controlled positive feedback mechanism through dipeptide-mediated activation Ubr1, essential determines lifetime proteins. this study, (an ortholog Ubr1) addition decreases increases gene. di/tri-peptidyl were disruption. These results suggest facilitate

Язык: Английский

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The multifunctional regulatory post-proline protease dipeptidyl peptidase 9 and its inhibitors: new opportunities for therapeutics

Cellular and Molecular Life Sciences, Год журнала: 2025, Номер 82(1)

Опубликована: Апрель 28, 2025

Abstract Dipeptidyl Peptidase 9 (DPP9) is a prolyl amino dipeptidylpeptidase that can cut post-proline peptide bond at the penultimate position N-terminus. By removing N-terminal prolines, this intracellular peptidase acts as an upstream regulator of N-degron pathway. DPP9 has crucial roles in inflammatory regulation, DNA repair, cellular homeostasis, and proliferation, while its deregulation linked to cancer immunological disorders. Currently, there no fully selective chemical inhibitor knockout transgenic mouse model conditional. Mice humans which catalytic activity absent die neonatally. inhibition for manipulating vivo potential uses rapid progress towards selectivity, with 170x selectivity achieved. This review discusses biology diseases applications compounds inhibit related proteases.

Язык: Английский

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Design of PROTACs utilizing the E3 ligase GID4 for targeted protein degradation

Nature Structural & Molecular Biology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 28, 2025

Язык: Английский

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Implementing N-terminomics and machine learning to probe in vivo Nt-arginylation

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Май 12, 2025

N-terminal arginylation (Nt-arginylation) is a degradation signal in the ubiquitin-proteasome and autophagy-lysosomal pathways, but its study has been limited by technical challenges. Here, we developed an integrated approach combining N-terminomics with machine learning-based filtering to identify vivo Nt-arginylation. By using Arg-starting missed cleavage peptides as proxies for ATE1-mediated arginylation, trained transfer learning model predict MS2 spectra retention times. applying prediction models additional statistical filter, identified 134 Nt-arginylation sites thapsigargin-treated HeLa cells. Arginylation was enriched proteins from various organelles, especially at caspase peptide processing sites. Several were further validated their interaction p62 ZZ domain. Temporal profiling revealed that ATF4 increased early post-stress, followed caspase-3 substrates ER signal-cleaved proteins. Our enables sensitive detection of rare modifications, offering potential biomarker drug target discovery.

Язык: Английский

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Deciphering Glutaminyl Cyclase Catalytic Pathways Enables Recognition of Anchor Pharmacophores for Inhibitor Discovery

Journal of Chemical Information and Modeling, Год журнала: 2025, Номер unknown

Опубликована: Май 14, 2025

Glutaminyl cyclases are responsible for N-terminal pyroglutamate modifications of various protein/peptide substrates, influencing their metabolic stability or biological functions. However, the precise chemical pathways by which glutaminyl catalyze conversion glutamine/glutamate to not yet fully understood. We initially identified catalytically essential components cross-species structural analysis, followed ab initio quantum mechanics/molecular mechanics (QM/MM) calculations human secretory cyclase (sQC) with two tripeptide QFA and EFA. The results revealed that sQC processes similar reaction EFA, but distinctly different energy barriers. In both pathways, catalytic triad E201 directly mediates multiple proton transfers, while D248 D305 primarily maintain orientation stabilize substrate binding. Based on anchor pharmacophores recognized analysis intermediates, we successfully imidazole-sulfonamide inhibitors mimic binding, as validated cocrystallographic analysis.

Язык: Английский

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