Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling

The Arg/N-degron pathway targets proteins for degradation by recognizing their N-terminal (Nt) residues. If a substrate bears, for example, Nt-Asn, its targeting involves deamidation of Nt-Asn, arginylation of resulting Nt-Asp, binding of resulting (conjugated) Nt-Arg to the UBR1-RAD6 E3-E2 ubiquitin ligase, ligase-mediated synthesis of a substrate-linked polyubiquitin chain, its capture by the proteasome, and substrate’s degradation. We discovered that the human Nt-Asn–specific Nt-amidase NTAN1, Nt-Gln–specific Nt-amidase NTAQ1, arginyltransferase ATE1, and the ubiquitin ligase UBR1-UBE2A/B (or UBR2-UBE2A/B) form a complex in which NTAN1 Nt-amidase binds to NTAQ1, ATE1, and UBR1/UBR2. In addition, NTAQ1 Nt-amidase and ATE1 arginyltransferase also bind to UBR1/UBR2. In the yeast Saccharomyces cerevisiae, the Nt-amidase, arginyltransferase, and the double-E3 ubiquitin ligase UBR1-RAD6/UFD4-UBC4/5 are shown to form an analogous targeting complex. These complexes may enable substrate channeling, in which a substrate bearing, for example, Nt-Asn, would be captured by a complex-bound Nt-amidase, followed by sequential Nt modifications of the substrate and its polyubiquitylation at an internal Lys residue without substrate’s dissociation into the bulk solution. At least in yeast, the UBR1/UFD4 ubiquitin ligase interacts with the 26S proteasome, suggesting an even larger Arg/N-degron–targeting complex that contains the proteasome as well. In addition, specific features of protein-sized Arg/N-degron substrates, including their partly sequential and partly nonsequential enzymatic modifications, led us to a verifiable concept termed “superchanneling.” In superchanneling, the synthesis of a substrate-linked poly-Ub chain can occur not only after a substrate’s sequential Nt modifications, but also before them, through a skipping of either some or all of these modifications within a targeting complex.

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Tat-binding protein-1, a component of the 26S proteasome, contributes to the E3 ubiquitin ligase function of the von Hippel–Lindau protein

Nature Genetics ◽

10.1038/ng1254 ◽

2003 ◽

Vol 35 (3) ◽

pp. 229-237 ◽

Cited By ~ 51

Author(s):

Paul G Corn ◽

E Robert McDonald ◽

James G Herman ◽

Wafik S El-Deiry

Keyword(s):

Ubiquitin Ligase ◽

Binding Protein ◽

E3 Ubiquitin Ligase ◽

26S Proteasome ◽

Von Hippel Lindau ◽

Ligase Function

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A Nucleus-based Quality Control Mechanism for Cytosolic Proteins

Molecular Biology of the Cell ◽

10.1091/mbc.e10-02-0111 ◽

2010 ◽

Vol 21 (13) ◽

pp. 2117-2127 ◽

Cited By ~ 110

Author(s):

Rupali Prasad ◽

Shinichi Kawaguchi ◽

Davis T.W. Ng

Keyword(s):

Quality Control ◽

Control Systems ◽

Ubiquitin Ligase ◽

Nuclear Import ◽

Control Mechanism ◽

E3 Ubiquitin Ligase ◽

26S Proteasome ◽

Cytosolic Proteins ◽

Hsp70 Chaperone ◽

Quality Control Mechanism

Intracellular quality control systems monitor protein conformational states. Irreversibly misfolded proteins are cleared through specialized degradation pathways. Their importance is underscored by numerous pathologies caused by aberrant proteins. In the cytosol, where most proteins are synthesized, quality control remains poorly understood. Stress-inducible chaperones and the 26S proteasome are known mediators but how their activities are linked is unclear. To better understand these mechanisms, a panel of model misfolded substrates was analyzed in detail. Surprisingly, their degradation occurs not in the cytosol but in the nucleus. Degradation is dependent on the E3 ubiquitin ligase San1p, known previously to direct the turnover of damaged nuclear proteins. A second E3 enzyme, Ubr1p, augments this activity but is insufficient by itself. San1p and Ubr1p are not required for nuclear import of substrates. Instead, the Hsp70 chaperone system is needed for efficient import and degradation. These data reveal a new function of the nucleus as a compartment central to the quality control of cytosolic proteins.

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Rad7 E3 Ubiquitin Ligase Attenuates Polyubiquitylation of Rpn10 and Dsk2 Following DNA Damage in <i>Saccharomyces cerevisiae</i>

Advances in Biological Chemistry ◽

10.4236/abc.2015.57021 ◽

2015 ◽

Vol 05 (07) ◽

pp. 239-254

Author(s):

Joseph M. Benoun ◽

Danielle Lalimar-Cortez ◽

Analila Valencia ◽

Adriana Granda ◽

Destaye M. Moore ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Damage ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase

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TaClpS1, Negatively Regulates Wheat Resistance Against Puccinia striiformis f. sp. tritici

10.21203/rs.3.rs-25890/v2 ◽

2020 ◽

Author(s):

Qian Yang ◽

Md Ashraful Islam ◽

Kunyan Cai ◽

Shuxin Tian ◽

Yan Liu ◽

...

Keyword(s):

Immune Response ◽

Ubiquitin Ligase ◽

Puccinia Striiformis ◽

E3 Ubiquitin Ligase ◽

Transit Peptide ◽

26S Proteasome ◽

Plant Responses ◽

Virus Induced Gene Silencing ◽

Chloroplast Transit Peptide

Abstract Background: The degradation of intracellular proteins plays an essential role in plant responses to stressful environments. ClpS1 and E3 ubiquitin ligase function as adaptors for selecting target substrates in caseinolytic peptidase (Clp) proteases pathways and the 26S proteasome system, respectively. Currently, the role of E3 ubiquitin ligase in the plant immune response to pathogens is well defined. However, the role of ClpS1 in the plant immune response to pathogens remains unknown. Results: Here, we identified and characterized wheat (Triticum aestivum) ClpS1 (TaClpS1). TaClpS1 encoded 161 amino acids, contained a conserved ClpS domain and a chloroplast transit peptide (1-32 aa). TaClpS1 was found to be specifically localized in the chloroplast when expressed transiently in wheat protoplasts. The transcript level of TaClpS1 in wheat was significantly induced during infection by Puccinia striiformis f. sp. tritici (Pst). Knock-down of TaClpS1 via virus-induced gene silencing (VIGS) resulted in an increase in resistance against Pst, accompanied by an increase in the hypersensitive response (HR), accumulation of reactive oxygen species (ROS) and expression of TaPR1 and TaPR2, and a reduction in the growth of Pst. Furthermore, heterologous expression of TaClpS1 in Nicotiana benthamiana enhanced the infection by Phytophthora parasitica. Conclusions: These results suggest that TaClpS1 negatively regulates the resistance of wheat to Pst.

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The ARRE RING-Type E3 Ubiquitin Ligase Negatively Regulates Cuticular Wax Biosynthesis in Arabidopsis thaliana by Controlling ECERIFERUM1 and ECERIFERUM3 Protein Levels

Frontiers in Plant Science ◽

10.3389/fpls.2021.752309 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shuang Liu ◽

Meixuezi Tong ◽

Lifang Zhao ◽

Xin Li ◽

Ljerka Kunst

Keyword(s):

Ubiquitin Ligase ◽

Uv Light ◽

E3 Ubiquitin Ligase ◽

E3 Ligase ◽

Cuticular Wax ◽

26S Proteasome ◽

Covalent Attachment ◽

Wax Deposition ◽

E3 Ligases ◽

Ring Type

The outer epidermal cell walls of plant shoots are covered with a cuticle, a continuous lipid structure that provides protection from desiccation, UV light, pathogens, and insects. The cuticle is mostly composed of cutin and cuticular wax. Cuticular wax synthesis is synchronized with surface area expansion during plant development and is associated with plant responses to biotic and abiotic stresses. Cuticular wax deposition is tightly regulated by well-established transcriptional and post-transcriptional regulatory mechanisms, as well as post-translationally via the ubiquitin-26S proteasome system (UPS). The UPS is highly conserved in eukaryotes and involves the covalent attachment of polyubiquitin chains to the target protein by an E3 ligase, followed by the degradation of the modified protein by the 26S proteasome. A large number of E3 ligases are encoded in the Arabidopsis genome, but only a few have been implicated in the regulation of cuticular wax deposition. In this study, we have conducted an E3 ligase reverse genetic screen and identified a novel RING-type E3 ubiquitin ligase, AtARRE, which negatively regulates wax biosynthesis in Arabidopsis. Arabidopsis plants overexpressing AtARRE exhibit glossy stems and siliques, reduced fertility and fusion between aerial organs. Wax load and wax compositional analyses of AtARRE overexpressors showed that the alkane-forming branch of the wax biosynthetic pathway is affected. Co-expression of AtARRE and candidate target proteins involved in alkane formation in both Nicotiana benthamiana and stable Arabidopsis transgenic lines demonstrated that AtARRE controls the levels of wax biosynthetic enzymes ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3). CER1 has also been confirmed to be a ubiquitination substrate of the AtARRE E3 ligase by an in vivo ubiquitination assay using a reconstituted Escherichia coli system. The AtARRE gene is expressed throughout the plant, with the highest expression detected in fully expanded rosette leaves and oldest stem internodes. AtARRE gene expression can also be induced by exposure to pathogens. These findings reveal that wax biosynthesis in mature plant tissues and in response to pathogen infection is controlled post-translationally.

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TaClpS1, Negatively Regulates Wheat Resistance Against Puccinia striiformis f. sp. tritici

10.21203/rs.3.rs-25890/v5 ◽

2020 ◽

Author(s):

Qian Yang ◽

Md Ashraful Islam ◽

Kunyan Cai ◽

Shuxin Tian ◽

Yan Liu ◽

...

Keyword(s):

Immune Response ◽

Ubiquitin Ligase ◽

Puccinia Striiformis ◽

E3 Ubiquitin Ligase ◽

Transit Peptide ◽

26S Proteasome ◽

Plant Responses ◽

Virus Induced Gene Silencing ◽

Chloroplast Transit Peptide

Abstract Background: The degradation of intracellular proteins plays an essential role in plant responses to stressful environments. ClpS1 and E3 ubiquitin ligase function as adaptors for selecting target substrates in caseinolytic peptidase (Clp) proteases pathways and the 26S proteasome system, respectively. Currently, the role of E3 ubiquitin ligase in the plant immune response to pathogens is well defined. However, the role of ClpS1 in the plant immune response to pathogens remains unknown. Results: Here, wheat (Triticum aestivum) ClpS1 (TaClpS1) was studied and resulted to encode 161 amino acids, containing a conserved ClpS domain and a chloroplast transit peptide (1-32 aa). TaClpS1 was found to be specifically localized in the chloroplast when expressed transiently in wheat protoplasts. The transcript level of TaClpS1 in wheat was significantly induced during infection by Puccinia striiformis f. sp. tritici (Pst). Knockdown of TaClpS1 via virus-induced gene silencing (VIGS) resulted in an increase in wheat resistance against Pst, accompanied by an increase in the hypersensitive response (HR), accumulation of reactive oxygen species (ROS) and expression of TaPR1 and TaPR2, and a reduction in the number of haustoria, length of infection hypha and infection area of Pst. Furthermore, heterologous expression of TaClpS1 in Nicotiana benthamiana enhanced the infection by Phytophthora parasitica. Conclusions: These results suggest that TaClpS1 negatively regulates the resistance of wheat to Pst.

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TaClpS1, Negatively Regulates Wheat Resistance Against Puccinia striiformis f. sp. tritici

10.21203/rs.3.rs-25890/v4 ◽

2020 ◽

Author(s):

Qian Yang ◽

Md Ashraful Islam ◽

Kunyan Cai ◽

Shuxin Tian ◽

Yan Liu ◽

...

Keyword(s):

Immune Response ◽

Ubiquitin Ligase ◽

Puccinia Striiformis ◽

E3 Ubiquitin Ligase ◽

Transit Peptide ◽

26S Proteasome ◽

Plant Responses ◽

Virus Induced Gene Silencing ◽

Chloroplast Transit Peptide

Abstract Background: The degradation of intracellular proteins plays an essential role in plant responses to stressful environments. ClpS1 and E3 ubiquitin ligase function as adaptors for selecting target substrates in caseinolytic peptidase (Clp) proteases pathways and the 26S proteasome system, respectively. Currently, the role of E3 ubiquitin ligase in the plant immune response to pathogens is well defined. However, the role of ClpS1 in the plant immune response to pathogens remains unknown. Results: Here, wheat (Triticum aestivum) ClpS1 (TaClpS1) was studied and resulted to encode 161 amino acids, containing a conserved ClpS domain and a chloroplast transit peptide (1-32 aa). TaClpS1 was found to be specifically localized in the chloroplast when expressed transiently in wheat protoplasts. The transcript level of TaClpS1 in wheat was significantly induced during infection by Puccinia striiformis f. sp. tritici (Pst). Knockdown of TaClpS1 via virus-induced gene silencing (VIGS) resulted in an increase in wheat resistance against Pst, accompanied by an increase in the hypersensitive response (HR), accumulation of reactive oxygen species (ROS) and expression of TaPR1 and TaPR2, and a reduction in the number of haustoria, length of infection hypha and infection area of Pst. Furthermore, heterologous expression of TaClpS1 in Nicotiana benthamiana enhanced the infection by Phytophthora parasitica. Conclusions: These results suggest that TaClpS1 negatively regulates the resistance of wheat to Pst.

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Faculty Opinions recommendation of Heat shock protein cognate 70-4 and an E3 ubiquitin ligase, CHIP, mediate plastid-destined precursor degradation through the ubiquitin-26S proteasome system in Arabidopsis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.2577985.2232085 ◽

2010 ◽

Author(s):

Judy Callis

Keyword(s):

Heat Shock ◽

Heat Shock Protein ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

26S Proteasome

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Endocytosis of the Aspartic Acid/Glutamic Acid Transporter Dip5 Is Triggered by Substrate-Dependent Recruitment of the Rsp5 Ubiquitin Ligase via the Arrestin-Like Protein Aly2

Molecular and Cellular Biology ◽

10.1128/mcb.00464-10 ◽

2010 ◽

Vol 30 (24) ◽

pp. 5598-5607 ◽

Cited By ~ 61

Author(s):

Riko Hatakeyama ◽

Masao Kamiya ◽

Terunao Takahara ◽

Tatsuya Maeda

Keyword(s):

Saccharomyces Cerevisiae ◽

Plasma Membrane ◽

Glutamic Acid ◽

Aspartic Acid ◽

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

Acid Transporter ◽

Py Motif ◽

Related Proteins

ABSTRACT Endocytosis of nutrient transporters is stimulated under various conditions, such as elevated nutrient availability. In Saccharomyces cerevisiae, endocytosis is triggered by ubiquitination of transporters catalyzed by the E3 ubiquitin ligase Rsp5. However, how the ubiquitination is accelerated under certain conditions remains obscure. Here we demonstrate that closely related proteins Aly2/Art3 and Aly1/Art6, which are poorly characterized members of the arrestin-like protein family, mediate endocytosis of the aspartic acid/glutamic acid transporter Dip5. In aly2Δ cells, Dip5 is stabilized at the plasma membrane and is not endocytosed efficiently. Efficient ubiquitination of Dip5 is dependent on Aly2. aly1Δ cells also show deficiency in Dip5 endocytosis, although less remarkably than aly2Δ cells. Aly2 physically interacts in vivo with Rsp5 at its PY motif and also with Dip5, thus serving as an adaptor linking Rsp5 with Dip5 to achieve Dip5 ubiquitination. Importantly, the interaction between Aly2 and Dip5 is accelerated in response to elevated aspartic acid availability. This result indicates that the regulation of Dip5 endocytosis is accomplished by dynamic recruitment of Rsp5 via Aly2.

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