Pairs of dipeptides synergistically activate the binding of substrate by ubiquitin ligase through dissociation of its autoinhibitory domain

Du, Fei; Navarro‐García, Federico; Xia, Zanxian; Tasaki, Takafumi; Varshavsky, Alexander

doi:10.1073/pnas.172527399

Cited by 103 publications

(176 citation statements)

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“…However, di/ tripeptides with basic (Type 1: Arg, His, or Lys) and bulky (Type 2: Ile, Leu, Phe, Trp, or Tyr) N-terminal residues can compete with larger protein substrates for binding at the Type 1 and Type 2 Ubr1p substrate-binding sites. Upon binding, these peptides allosterically activate Ubr1p-mediated degradation of Cup9p by release of the Ubr1p autoinhibitory domain, thus exposing a substrate-binding domain that binds an internal degron in Cup9p [32]. Relief of Cup9p repression of PTR2 results in enhanced PTR2 expression.…”

Section: Introductionmentioning

confidence: 99%

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Harnessing Natural Diversity to Probe Metabolic Pathways

Homann¹,

Cai²,

Becker³

et al. 2005

PLoS Genet

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Analyses of cellular processes in the yeast Saccharomyces cerevisiae rely primarily upon a small number of highly domesticated laboratory strains, leaving the extensive natural genetic diversity of the model organism largely unexplored and unexploited. We asked if this diversity could be used to enrich our understanding of basic biological processes. As a test case, we examined a simple trait: the utilization of di/tripeptides as nitrogen sources. The capacity to import small peptides is likely to be under opposing selective pressures (nutrient utilization versus toxin vulnerability) and may therefore be sculpted by diverse pathways and strategies. Hitherto, dipeptide utilization in S. cerevisiae was solely ascribed to the activity of a single protein, the Ptr2p transporter. Using high-throughput phenotyping and several genetically diverse strains, we identified previously unknown cellular activities that contribute to this trait. We find that the Dal5p allantoate/ureidosuccinate permease is also capable of facilitating di/ tripeptide transport. Moreover, even in the absence of Dal5p and Ptr2p, an additional activity-almost certainly the periplasmic asparaginase II Asp3p-facilitates the utilization of dipeptides with C-terminal asparagine residues by a different strategy. Another, as-yet-unidentified activity enables the utilization of dipeptides with C-terminal arginine residues. The relative contributions of these activities to the utilization of di/tripeptides vary among the strains analyzed, as does the vulnerability of these strains to a toxic dipeptide. Only by sampling the genetic diversity of multiple strains were we able to uncover several previously unrecognized layers of complexity in this metabolic pathway. High-throughput phenotyping facilitates the rapid exploration of the molecular basis of biological complexity, allowing for future detailed investigation of the selective pressures that drive microbial evolution.Citation: Homann OR, Cai H, Becker JM, Lindquist SL (2005) Harnessing natural diversity to probe metabolic pathways. PLoS Genet 1(6): e80.

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Section: Introductionmentioning

confidence: 99%

“…Relief of Cup9p repression of PTR2 results in enhanced PTR2 expression. This initiates a positive regulatory feedback loop in which di/ tripeptide uptake perpetuates Ubr1p-mediated degradation of Cup9p, up-regulation of PTR2, and additional di/tripeptide uptake [32][33][34].…”

Section: Introductionmentioning

confidence: 99%

Harnessing Natural Diversity to Probe Metabolic Pathways

Homann¹,

Cai²,

Becker³

et al. 2005

PLoS Genet

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“…An essential determinant of one class of degrons, called N-degrons, is a substrate's destabilizing N-terminal residue. The set of destabilizing residues in a given cell type yields a rule, called the N-end rule, which relates the in vivo half-life of a protein to the identity of its N-terminal residue (7)(8)(9)(10)(11)(12). In eukaryotes, the N-degron consists of three main determinants, a destabilizing N-terminal residue of a substrate, its internal Lys (K) residue(s) (the site of formation of a poly-Ub chain), and a conformationally flexible region(s) in the vicinity of these determinants (7,13,14).…”

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Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen

Graciet

Hu²,

Piatkov³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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115

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The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Primary destabilizing N-terminal residues (Nd p ) are recognized directly by the targeting machinery. The recognition of secondary destabilizing N-terminal residues (Nd s ) is preceded by conjugation of an Nd p residue to Nd s of a polypeptide substrate. In eukaryotes, ATE1 -encoded arginyl-transferases (R D,E,C* -transferases) conjugate Arg (R), an Nd p residue, to Nd s residues Asp (D), Glu (E), or oxidized Cys residue (C*). Ubiquitin ligases recognize the N-terminal Arg of a substrate and target the (ubiquitylated) substrate to the proteasome. In prokaryotes such as Escherichia coli , Nd p residues Leu (L) or Phe (F) are conjugated, by the aat -encoded Leu/Phe-transferase (L/F K,R -transferase), to N-terminal Arg or Lys, which are Nd s in prokaryotes but Nd p in eukaryotes. In prokaryotes, substrates bearing the Nd p residues Leu, Phe, Trp, or Tyr are degraded by the proteasome-like ClpAP protease. Despite enzymological similarities between eukaryotic R D,E,C* -transferases and prokaryotic L/F K,R -transferases, there is no significant sequelogy (sequence similarity) between them. We identified an aminoacyl-transferase, termed Bpt, in the human pathogen Vibrio vulnificus . Although it is a sequelog of eukaryotic R D,E,C* -transferases, this prokaryotic transferase exhibits a “hybrid” specificity, conjugating Nd p Leu to Nd s Asp or Glu. Another aminoacyl-transferase, termed ATEL1, of the eukaryotic pathogen Plasmodium falciparum , is a sequelog of prokaryotic L/F K,R -transferases (Aat), but has the specificity of eukaryotic R D,E,C* -transferases (ATE1). Phylogenetic analysis suggests that the substrate specificity of R-transferases arose by two distinct routes during the evolution of eukaryotes.

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“…1) 10,13 . Several other N-terminal residues function as tertiary (Asn and Gln) and secondary (Asp and Glu) destabilizing residues in that they are recognized by UBR1 after their enzymatic conjugation to Arg, a primary destabilizing residue.…”

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confidence: 99%

“…The UBR1 Ub ligase of the S. cerevisiae N-end rule pathway contains a distinct (third) substrate-binding site 13 that recognizes an internal (non-N-terminal) degron in the pathway's substrates, such as the transcriptional repressor CUP9. Dipeptides with destabilizing N-terminal residues bind to UBR1, thereby increasing the ability of UBR1 to target CUP9 for degradation 11 .…”

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confidence: 99%