Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures DOI Creative Commons
Patrick J. Willems, Jingjing Huang, Joris Messens

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 17, 2022

ABSTRACT Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional annotation. Here, we used predicted structures fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the kingdom. In addition identification metal ligands coordinated by residues, systematically analyzed disulfides present these predictions. Our analysis demonstrates most are trustworthy due their agreement (~96%) those X-ray NMR structures, characteristic disulfide stereochemistry, biased subcellular distribution proteins a higher degree oxidation respective cysteines measured proteomics. Adopting perspective, zinc binding sites increasingly at expense iron-sulfur clusters plants. Interestingly, formation is increased secreted land plants, likely promoting sequence evolution adapt changing environments encountered summary, Alphafold2 rich source information studying role interest redox biology general.

Language: Английский

The tRNA identity landscape for aminoacylation and beyond DOI Creative Commons
Richard Giegé, Gilbert Eriani

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(4), P. 1528 - 1570

Published: Feb. 6, 2023

tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily sets identities within molecules composed determinants antideterminants preventing mischarging non-cognate synthetases. Such identity were discovered a few model organisms, their properties generalized as universal rules. Since then, panel elements governing accuracy has expanded considerably, but increasing number reported functional idiosyncrasies led to some confusion. In parallel, description other processes involving tRNAs, often well beyond aminoacylation, progressed greatly expanding interactome uncovering multiple novel same molecule. review highlights findings mechanistics evolution tRNA-like identities. addition, new methods results for searching single discussed. Taken together, this knowledge shows that comprehensive understanding role individual collective nucleotide needed medical, biotechnological applications.

Language: Английский

Citations

91
Redox regulation: mechanisms, biology and therapeutic targets in diseases DOI Creative Commons
Bowen Li, Hui Ming, Siyuan Qin

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2025, Volume and Issue: 10(1)

Published: March 7, 2025

Redox signaling acts as a critical mediator in the dynamic interactions between organisms and their external environment, profoundly influencing both onset progression of various diseases. Under physiological conditions, oxidative free radicals generated by mitochondrial respiratory chain, endoplasmic reticulum, NADPH oxidases can be effectively neutralized NRF2-mediated antioxidant responses. These responses elevate synthesis superoxide dismutase (SOD), catalase, well key molecules like nicotinamide adenine dinucleotide phosphate (NADPH) glutathione (GSH), thereby maintaining cellular redox homeostasis. Disruption this finely tuned equilibrium is closely linked to pathogenesis wide range Recent advances have broadened our understanding molecular mechanisms underpinning dysregulation, highlighting pivotal roles genomic instability, epigenetic modifications, protein degradation, metabolic reprogramming. findings provide foundation for exploring regulation mechanistic basis improving therapeutic strategies. While antioxidant-based therapies shown early promise conditions where stress plays primary pathological role, efficacy diseases characterized complex, multifactorial etiologies remains controversial. A deeper, context-specific signaling, particularly redox-sensitive proteins, designing targeted aimed at re-establishing balance. Emerging small molecule inhibitors that target specific cysteine residues proteins demonstrated promising preclinical outcomes, setting stage forthcoming clinical trials. In review, we summarize current intricate relationship disease also discuss how these insights leveraged optimize strategies practice.

Language: Английский

Citations

4
N-degron pathways DOI Creative Commons
Alexander Varshavsky

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(39)

Published: Sept. 12, 2024

An N-degron is a degradation signal whose main determinant “destabilizing” N-terminal residue of protein. Specific N-degrons, discovered in 1986, were the first identified signals short-lived intracellular proteins. These N-degrons are recognized by ubiquitin-dependent proteolytic system called Arg/N-degron pathway. Although bacteria lack ubiquitin system, they also have pathways. Studies after 1986 shown that all 20 amino acids genetic code can act, specific sequence contexts, as destabilizing residues. Eukaryotic proteins targeted for conditional or constitutive at least five systems differ both functionally and mechanistically: pathway, Ac/N-degron Pro/N-degron fMet/N-degron newly named, this perspective, GASTC/N-degron pathway (GASTC = Gly, Ala, Ser, Thr, Cys). I discuss these expanded terminology now encompasses entire gamut known

Language: Английский

Citations

13
Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes DOI
Nan Shen,

Haoyu Xie,

Kefang Liu

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 263, P. 130610 - 130610

Published: March 5, 2024

Language: Английский

Citations

5
Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates DOI Creative Commons

Bong Heon Kim,

Min Kyung Kim,

Sun Joo Oh

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(31)

Published: July 25, 2022

N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues can be recognized as destabilizing ones by the Arg/N-degron pathway. A cleavage generate Arg at N terminus resulting C-terminal (Ct) fragment either directly or after Nt-arginylation Ct-fragment Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNA cosubstrate. Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate Cys-sulfonate) short peptides. genes fungi, animals, plants have been cloned decades ago, but three-dimensional structure remained unknown. detailed mechanism arginylation unknown well. We describe here crystal R-transferase from budding yeast Kluyveromyces lactis . The 58-kDa comprises two domains recognize, together, an acidic Nt-residue acceptor substrate, residue , 3′-proximal segment tRNA moiety. enzyme’s active site located, least in part, between domains. In vitro vivo assays with site-directed mutants were suggested structural results yielded inferences about specific binding sites Ate1. also analyzed inhibition activity hemin (Fe 3+ -heme), found induced previously undescribed disulfide-mediated oligomerization Together, these advance understanding

Language: Английский

Citations

21
The structural basis of tRNA recognition by arginyl-tRNA-protein transferase DOI Creative Commons
Thilini Abeywansha, Wei Huang, Xuan Ye

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 19, 2023

Abstract Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto substrates in tRNA-dependent manner. However, how (and other aminoacyl-tRNA transferases) hijacks tRNA the highly efficient ribosomal synthesis pathways catalyzes arginylation reaction remains mystery. Here, we describe three-dimensional structures Saccharomyces cerevisiae with without cofactor. Importantly, putative substrate binding domain adopts previously uncharacterized fold that contains atypical zinc-binding site critical for stability function. recognition Arg by coordinated through interactions major groove acceptor arm tRNA. Binding induces conformational changes helps explain mechanism arginylation.

Language: Английский

Citations

11
Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function DOI Creative Commons

Xin Lan,

Wei Huang, Su Kim

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 28, 2024

The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to protein substrate. Conserved from yeast humans, deficiency in mice correlates with defects cardiovascular development and angiogenesis results embryonic lethality, while conditional knockouts exhibit reproductive, developmental, neurological deficiencies. Despite the recent revelation of tRNA binding mechanism catalytic cycle ATE1, structure-function relationship higher organisms not well understood. In this study, we present three-dimensional structure human apo-state complex its cofactor peptide contrast counterpart, forms symmetric homodimer, which dissociates upon Furthermore, includes unique extended loop wraps around tRNAArg, creating extensive contacts T-arm cofactor. Substituting key residues identified substrate site abolishes enzymatic activity accumulation substrates cells. essential gene mammals recognized as master regulator Here, authors describe structural insights into revealing mechanisms regulate arginylation

Language: Английский

Citations

4
Global Profiling of N-terminal Cysteine-Dependent Degradation Mechanisms DOI Open Access
Aizat Bekturova, Yaara Makaros,

Shahar Ben-David

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Abstract Hypoxia, a condition characterized by insufficient oxygen supply, challenges cellular homeostasis and energy production, driving the activation of adaptive responses to maintain survival under these stress-inducing conditions. One key strategy involves enzymatic oxidation N-terminal cysteine residues coupled with proteolysis through Cys-Arg/N-degron pathway. Despite presence hundreds proteins in humans, only two have been identified as substrates this pathway, its substrate selectivity remains unclear. Moreover, biological role pathway response hypoxia is not well defined. By employing systematic proteomics approach, we discovered that nearly half cysteine-commencing proteome could be regulated Mutagenesis experiments revealed specificty showing preference for hydrophobic positively charged following cysteine. Furthermore, uncovered are during hypoxia, including IP6K1. The loss IP6K1 impaired glucose uptake, glycolytic ATP overall mitochondrial morphology function. As result, IP6K1-deficient cells exhibited disrupted metabolic adaptation hypoxic conditions decreased stress. These findings underscore importance regulating highlight potential hypoxia-related disorders.

Language: Английский

Citations

0
The N-degron pathway: From basic science to therapeutic applications DOI
Ah Jung Heo, Su Kim, Yong Tae Kwon

et al.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Journal Year: 2023, Volume and Issue: 1866(2), P. 194934 - 194934

Published: March 28, 2023

Language: Английский

Citations

7
An Unbiased Proteomic Platform for Activity-based Arginylation Profiling DOI Creative Commons
Zongtao Lin, Yixuan Xie,

Joanna Gongora

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 2, 2024

Abstract Protein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. Arginylation features a post-translational conjugation of arginyl to protein, making it extremely challenging differentiate from translational arginine residues with the same mass protein sequence. Here we present general activity-based profiling (ABAP) platform for unbiased discovery substrates and their precise sites. This method integrates isotopic labeling into ATE1 assay utilizing biological lysates ( ex vivo ) rather than live cells, thus eliminating bias derived ribosomal activity enabling bona fide identification using features. ABAP has been successfully applied array peptide, cell, patient, animal tissue samples 20 µg sample input, 229 unique sites revealed human proteomes. Representative were validated followed up functions. The developed globally applicable aforementioned types therefore paves way functional studies this difficult-to-characterize modification.

Language: Английский

Citations

2