The specificities of yeast methionine aminopeptidase and acetylation of amino-terminal methionine in vivo. Processing of altered iso-1-cytochromes c created by oligonucleotide transformation.

Moerschell, Richard P.; Hosokawa, Yu; Tsunasawa, Susumu; Sherman, Fred

doi:10.1016/s0021-9258(17)45419-6

Cited by 191 publications

(30 citation statements)

References 54 publications

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“…Although Gid4 recognizes substrates such as Mdh2 via N-degrons with an N-terminal proline ( Chen et al., 2017 ; Hämmerle et al., 1998 ), the partially overlapping specificity of Gid10 is less understood ( Melnykov et al., 2019 ). In the case of Mdh2, proline is exposed at the N terminus after co-translational removal of the initiator methionine by methionine aminopeptidases (MetAPs), whose substrates comprise N termini with small residues (A, S, T, V, C, G, P) after the initiator methionine ( Moerschell et al., 1990 ; Varland et al., 2015 ). As expected, Mdh2 was stabilized in the absence of Gid4 in the tFT assay.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, we tested how Gid11-dependent protein turnover depends on the substrate N terminus. As controls, we mutated the N-terminal proline of Mdh2 to alanine (Mdh2 P2A ) or glycine residues (Mdh2 P2G ), which do not prevent removal of the initiator methionine by MetAPs ( Moerschell et al., 1990 ; Varland et al., 2015 ). Both mutations preclude Gid4 binding to the Mdh2 N terminus and largely abolished Gid4-dependent turnover of Mdh2-tFT ( Chen et al., 2017 ; Hämmerle et al., 1998 ; Figure 6 H).…”

Section: Resultsmentioning

confidence: 99%

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Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase

et al. 2021

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Summary Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae . Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase

et al. 2021

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“…Eight constructs were made, with substitutions representing each of the amino acid types and, more importantly, representing examples of COOH-terminal residues previously shown to have either a positive or negative influence on transport (15,17). All of the constructs studied contain an initiating methionine that is predicted to be removed by methionyl aminopeptidase (30), and which has therefore been eliminated from the nomenclature.…”

Section: Ace-mediated Rescue Of a Panel Of 11-mermentioning

confidence: 99%

Murine Transporter Associated with Antigen Presentation (TAP) Preferences Influence Class I–restricted T Cell Responses

Yellen-Shaw

Laughlin

Metrione

et al. 1997

The Journal of Experimental Medicine

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The transporter associated with antigen presentation (TAP) complex shuttles cytosolic peptides into the exocytic compartment for association with nascent major histocompatibility complex class I molecules. Biochemical studies of murine and human TAP have established that substrate length and COOH-terminal residue identity are strong determinants of transport efficiency. However, the existence of these specificities in the intact cell and their influences on T cell responses have not been demonstrated. We have devised a method for studying TAP- mediated transport in intact cells, using T cell activation as a readout. The approach makes use of a panel of recombinant vaccinia viruses expressing peptides containing the Kd-restricted nonamer influenza nucleoprotein residues 147–155. The COOH terminus of each construct was appended with a dipeptide composed of an internal threonine residue followed by a varying amino acid. Synthetic peptide versions of these 11-mers exhibit vastly different transport capabilities in streptolysin O–permeabilized cells, in accordance with the predicted influence of the COOH-terminal residues. Presentation of the endogenously expressed version of each construct requires TAP-mediated transport and cooexpression with a vac-encoded exocytic COOH-terminal dipeptidase, angiotensin converting enzyme, to allow liberation of the minimal epitope. Recognition by epitope-specific CTLs therefore signifies TAP-mediated transport of a complete 11-mer within the target cell. Under normal assay conditions no influences of the COOH-terminal residue were revealed. However, when T cell recognition was limited, either by blocking CD8 coreceptor interactions or by decreasing the amount of transport substrate synthesized, significant COOH-terminal effects were revealed. Under such conditions, those peptides that transported poorly in biochemical assays were less efficiently presented. Therefore, TAP specificity operates in the intact cell, appears to reflect previously defined rules with regard to the influence of the COOH-terminal residue, and can strongly influence T cell responses.

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“…In a previous study (Moerschell et al, 1990), iso-1cytochromes c with all 20 amino acid replacements at a specific site were generated with 20 different oligonucleotides. This study uses oligonucleotides with mixed codons at the site of interest to generate functional variants of cytochrome c (Figure 2, Table 1).…”

Section: Methodsmentioning

confidence: 99%

Site Specific Combinations of Stabilizing and Destabilizing Amino Acid Replacements in Yeast Cytochrome c: In Vivo and in Vitro Effects

Linske-O'Connell¹,

Sherman²,

McLendon³

1995

Biochemistry

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Oligonucleotide-directed mutagenesis in vivo was used to create destabilizing site specific changes at position 6 in iso-1-cytochrome c in Saccharomyces cerevisiae. These changes were made in combination with the stabilizing N52I substitution. The resulting proteins showed that a variety of forces and interactions are responsible for these destabilizations. Increasing side chain size was the strongest predictor of decreases in cytochrome c levels in vivo. With intermediate size replacements, increasing hydrophobicity correlated with the proteins' thermostability. Some differences in protein levels in vivo could not be explained by side chain size and hydrophobicity alone. Therefore, specific interactions of individual amino acids may also be involved. The N52I-stabilizing mutation tended to increase the protein levels to the same degree relative to the amino acid at position 6. These stabilized cytochromes had an increased specific activity when compared to the series with the original N52. Strains with these altered cytochromes c showed temperature sensitivities for protein levels and function. Thermodynamic measurements in vivo of the WT (C102A), N52I, G6A, G6A N52I, and G6S N52I correlated with the in vivo data. The variant G6A N52I showed additivity (Wells, 1990) of the Cm's and delta delta G's of unfolding for guanidine hydrochloride denaturation.

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The specificities of yeast methionine aminopeptidase and acetylation of amino-terminal methionine in vivo. Processing of altered iso-1-cytochromes c created by oligonucleotide transformation.

Cited by 191 publications

References 54 publications

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase

Murine Transporter Associated with Antigen Presentation (TAP) Preferences Influence Class I–restricted T Cell Responses

Site Specific Combinations of Stabilizing and Destabilizing Amino Acid Replacements in Yeast Cytochrome c: In Vivo and in Vitro Effects

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