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Ma A, Zhang D, Wang G, Wang K, Li Z, Gao Y, Li H, Bian C, Cheng J, Han Y, Yang S, Gong Z, Qi J. Verticillium dahliae effector VDAL protects MYB6 from degradation by interacting with PUB25 and PUB26 E3 ligases to enhance Verticillium wilt resistance. THE PLANT CELL 2021; 33:3675-3699. [PMID: 34469582 PMCID: PMC8643689 DOI: 10.1093/plcell/koab221] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/26/2021] [Indexed: 05/30/2023]
Abstract
Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophic Verticillium dahliae-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leaves in vitro but enhances the resistance to V. dahliae when overexpressed in Arabidopsis or cotton without affecting the plant growth and development. VDAL protein interacts with Arabidopsis E3 ligases plant U-box 25 (PUB25) and PUB26 and is ubiquitinated by PUBs in vitro. However, VDAL is not degraded by PUB25 or PUB26 in planta. Besides, the pub25 pub26 double mutant shows higher resistance to V. dahliae than the wild-type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist the V. dahliae infection without causing a hypersensitive response (HR); alternatively, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance.
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Affiliation(s)
- Aifang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dingpeng Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Neurosurgery, University of Florida, Gainesville, Florida 32608, USA
| | - Guangxing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanhui Gao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengchang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chao Bian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yinan Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- College of Life Science, Hebei University, Baoding 071002, China
| | - Junsheng Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Luo Q, Li Y, Wang W, Fei X, Deng X. Genome-wide survey and expression analysis of Chlamydomonas reinhardtii U-box E3 ubiquitin ligases (CrPUBs) reveal a functional lipid metabolism module. PLoS One 2015; 10:e0122600. [PMID: 25822994 PMCID: PMC4378952 DOI: 10.1371/journal.pone.0122600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
E3 ubiquitin ligases determine the substrate specificity of ubiquitination. Plant U-box (PUB) E3 ligases, with a typical 70-amino acid U-box domain, participate in plant developmental processes and environmental responses. Thus far, 64 PUB proteins have been identified in Arabidopsis and 77 PUB proteins have been identified in Oryza. However, detailed studies on U-box genes in the model microalgae Chlamydomonas reinhardtii are lacking. Here, we present a comprehensive analysis of the genes encoding U-box family proteins in C. reinhardtii. Following BLASTP analysis, 30 full-length U-box genes were identified in the C. reinhardtii genome sequence. Bioinformatics analyses of CrPUB genes were performed to characterize the phylogenetic relationships, chromosomal locations and gene structures of each member. The 30 identified CrPUB proteins are clustered into 3 distinct subfamilies, and the genes for these proteins are unevenly distributed among 14 chromosomes. Furthermore, the quantitative real-time RT-PCR or semi-quantitative RT-PCR analysis of 30 CrPUB mRNA abundances under nitrogen starvation showed that 18 CrPUB genes were induced by N starvation and that 7 genes were repressed in the N-poor environment. We selected five CrPUB genes exhibiting marked changes in expression under N-free conditions for further analysis in RNAi experiments and examined the oil content of these gene-silenced transgenic strains. The silencing of CrPUB5 and CrPUB14, which are typically down-regulated under N starvation, induced 9.8%-45.0% and 14.4%-61.8% lipid accumulation, respectively. In contrast, the silencing of CrPUB11, CrPUB23 and CrPUB28, which are markedly up-regulated under N-free conditions, decreased the lipid content by 5.5%-27.8%, 8.1%-27.3% and 6.6%-27.9%, respectively. These results provide a useful reference for the identification and functional analysis of this gene family and fundamental information for microalgae lipid metabolism research.
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Affiliation(s)
- Qiulan Luo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Yajun Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Wenquan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Xiaowen Fei
- School of Science, Hainan Medical College, Haikou, 571101, China
| | - Xiaodong Deng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
- * E-mail:
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Vogelmann K, Subert C, Danzberger N, Drechsel G, Bergler J, Kotur T, Burmester T, Hoth S. Plasma membrane-association of SAUL1-type plant U-box armadillo repeat proteins is conserved in land plants. FRONTIERS IN PLANT SCIENCE 2014; 5:37. [PMID: 24600457 PMCID: PMC3928556 DOI: 10.3389/fpls.2014.00037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/27/2014] [Indexed: 05/08/2023]
Abstract
Post-translational protein modification plays a pivotal role in the regulation and specific turnover of proteins. One of these important modifications is the ubiquitination of target proteins, which can occur at distinct cellular compartments. At the plasma membrane, ubiquitination regulates the internalization and thus trafficking of membrane proteins such as receptors and channels. The Arabidopsis plant U-box (PUB) armadillo repeat (PUB-ARM) ubiquitin ligase SAUL1 (SENESCENCE-ASSOCIATED UBIQUITIN LIGASE1) is part of the ubiquitination machinery at the plasma membrane. In contrast to most other PUB-ARM proteins, SAUL1 carries additional C-terminal ARM repeats responsible for plasma membrane-association. Here, we demonstrated that the C-terminal ARM repeat domain is also essential and sufficient to mediate plasma membrane-association of the closest Arabidopis paralog AtPUB43. We investigated targeting of PUB-ARM ubiquitin ligases of different plant species to find out whether plasma membrane-association of SAUL1-type PUB-ARM proteins is conserved. Phylogenetic analysis identified orthologs of SAUL1 in these plant species. Intracellular localization of transiently expressed GFP fusion proteins revealed that indeed plasma membrane-association due to additional C-terminal ARM repeats represents a conserved feature of SAUL1-type proteins. Analyses of transgenic Arabidopsis plants overexpressing N-terminally masked or truncated proteins revealed that interfering with the function of SAUL1-type proteins resulted in severe growth defects. Our results suggest an ancient origin of ubiquitination at the plasma membrane in the evolution of land plants.
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Affiliation(s)
- Katja Vogelmann
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Christa Subert
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Nina Danzberger
- Department Biologie, Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Gabriele Drechsel
- Zentrum für Molekularbiologie der Pflanzen, Allgemeine Genetik, Universität TübingenTübingen, Germany
| | - Johannes Bergler
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Tanja Kotur
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
| | - Thorsten Burmester
- Stoffwechselphysiologie, Biozentrum Grindel, Universität HamburgHamburg, Germany
| | - Stefan Hoth
- Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität HamburgHamburg, Germany
- *Correspondence: Stefan Hoth, Molekulare Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany e-mail:
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Ishizaki K, Mizutani M, Shimamura M, Masuda A, Nishihama R, Kohchi T. Essential role of the E3 ubiquitin ligase nopperabo1 in schizogenous intercellular space formation in the liverwort Marchantia polymorpha. THE PLANT CELL 2013; 25:4075-84. [PMID: 24170128 PMCID: PMC3877802 DOI: 10.1105/tpc.113.117051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/25/2013] [Accepted: 10/08/2013] [Indexed: 05/17/2023]
Abstract
The vast majority of land plants develop gas-exchange tissues with intercellular spaces (ICSs) connected directly to the air. Although the developmental processes of ICS have been described in detail at the morphological and ultrastructural level in diverse land plants, little is known about the molecular mechanism responsible for ICS formation. The liverwort Marchantia polymorpha develops a multilayered tissue with a large ICS (air chamber), whose formation is initiated at selected positions of epidermal cells. We isolated a mutant of M. polymorpha showing impaired air-chamber formation, nopperabo1 (nop1), from T-DNA-tagged lines. In nop1 plants, no ICS was formed; consequently, a single-layered epidermis developed on the dorsal side of the thallus. The causal gene NOP1 encodes a Plant U-box (PUB) E3 ubiquitin ligase carrying tandem ARMADILLO (ARM) repeats in the C terminus. An in vitro ubiquitination assay indicated that the NOP1 protein possesses E3 ubiquitin ligase activity in a U-box-dependent manner. Confocal microscopy and biochemical analysis showed that NOP1 was localized to the plasma membrane. Our investigation demonstrated the essential role of the PUB-ARM-type ubiquitin ligase in ICS formation in M. polymorpha, which sheds light on the molecular mechanism of schizogenous ICS formation in land plants.
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Affiliation(s)
- Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Miya Mizutani
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masaki Shimamura
- Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Akihide Masuda
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Intrinsically disordered proteins undergo and assist folding transitions in the proteome. Arch Biochem Biophys 2012; 531:80-9. [PMID: 23142500 DOI: 10.1016/j.abb.2012.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 11/20/2022]
Abstract
The common notion in the protein world holds that proteins are synthesized as a linear polypeptide chain, followed by folding into a unique, functional 3D-structure. As outlined in many articles of this volume, this is in fact the case for a great proportion of the proteome. Many proteins and protein domains, however, are intrinsically disordered (IDPs), i.e., they cannot fold on their own, but often undergo a folding transition in the presence of a binding partner. This binding-induced folding process shows strong conceptual parallels with the folding of globular proteins, in a sense that it can proceed via two routes, either induction of the folded conformation from an initial random state or selection of a pre-formed state already present in the ensemble. In addition, we show that IDPs not only undergo folding themselves, they also assist the folding process of other proteins as chaperones, and even contribute to the quality control processes of the cell, in which irreparably misfolded proteins are recognized and tagged for proteasomal degradation. These various mechanisms suggest that structural disorder, in a biological context, is linked with protein folding in several ways, in which both the IDP and its partner may undergo reciprocal structural transitions.
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Rampuria S, Joshi U, Palit P, Deokar AA, Meghwal RR, Mohapatra T, Srinivasan R, Bhatt KV, Sharma R. Construction and analysis of an SSH cDNA library of early heat-induced genes of Vigna aconitifolia variety RMO-40. Genome 2012. [PMID: 23199573 DOI: 10.1139/g2012-064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Moth bean ( Vigna aconitifolia (Jacq.) Marechal) is an important grain legume crop grown in rain fed areas of hot desert regions of Thar, India, under scorching sun rays with very little supplementation of water. An SSH cDNA library was generated from leaf tissues of V. aconitifolia var. RMO-40 exposed to an elevated temperature of 42 °C for 5 min to identify early-induced genes. A total of 488 unigenes (114 contigs and 374 singletons) were derived by cluster assembly and sequence alignment of 738 ESTs; out of 206 ESTs (28%) of unknown proteins, 160 ESTs (14%) were found to be novel to moth bean. Only 578 ESTs (78%) showed significant BLASTX similarity (<1 × 10(-6)) in the NCBI non-redundant database. Gene ontology functional classification terms were retrieved for 479 (65%) sequences, and 339 sequences were annotated with 165 EC codes and mapped to 68 different KEGG pathways. Four hundred and fifty-two ESTs were further annotated with InterProScan (IPS), and no IPS was assigned to 153 ESTs. In addition, the expression level of 27 ESTs in response to heat stress was evaluated through semiquantitative RT-PCR assay. Approximately 20 different signaling genes and 16 different transcription factors have been shown to be associated with heat stress in moth bean for the first time.
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Affiliation(s)
- Sakshi Rampuria
- Plant Biotechnology Centre, Swami Keshwanand Rajasthan Agricultural University, Bikaner, Rajasthan, India
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Metzger MB, Hristova VA, Weissman AM. HECT and RING finger families of E3 ubiquitin ligases at a glance. J Cell Sci 2012; 125:531-7. [PMID: 22389392 DOI: 10.1242/jcs.091777] [Citation(s) in RCA: 442] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Meredith B Metzger
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute-Frederick, 1050 Boyles Street, Frederick, MD 21702, USA
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Zawaski C, Ma C, Strauss SH, French D, Meilan R, Busov VB. PHOTOPERIOD RESPONSE 1 (PHOR1)-like genes regulate shoot/root growth, starch accumulation, and wood formation in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5623-34. [PMID: 22915748 PMCID: PMC3444277 DOI: 10.1093/jxb/ers217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This study describes functional characterization of two putative poplar PHOTOPERIOD RESPONSE 1 (PHOR1) orthologues. The expression and sequence analyses indicate that the two poplar genes diverged, at least partially, in function. PtPHOR1_1 is most highly expressed in roots and induced by short days, while PtPHOR1_2 is more uniformly expressed throughout plant tissues and is not responsive to short days. The two PHOR1 genes also had distinct effects on shoot and root growth when their expression was up- and downregulated transgenically. PtPHOR1_1 effects were restricted to roots while PtPHOR1_2 had similar effects on aerial and below-ground development. Nevertheless, both genes seemed to be upregulated in transgenic poplars that are gibberellin-deficient and gibberellin-insensitive, suggesting interplay with gibberellin signalling. PHOR1 suppression led to increased starch accumulation in both roots and stems. The effect of PHOR1 suppression on starch accumulation was coupled with growth-inhibiting effects in both roots and shoots, suggesting that PHOR1 is part of a mechanism that regulates the allocation of carbohydrate to growth or storage in poplar. PHOR1 downregulation led to significant reduction of xylem formation caused by smaller fibres and vessels suggesting that PHOR1 likely plays a role in the growth of xylem cells.
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Affiliation(s)
- Christine Zawaski
- School of Forest Resources and Environmental Science, Michigan Technological UniversityHoughton, MI 49931-1295USA
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR 97331-5752USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR 97331-5752USA
| | - Darla French
- Department of Forestry and Natural Resources, Purdue UniversityWest Lafayette, IN 47907-2061USA
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue UniversityWest Lafayette, IN 47907-2061USA
| | - Victor B. Busov
- School of Forest Resources and Environmental Science, Michigan Technological UniversityHoughton, MI 49931-1295USA
- *To whom correspondence should be addressed: E-mail:
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Ying M, Huang X, Zhao H, Wu Y, Wan F, Huang C, Jie K. Comprehensively surveying structure and function of RING domains from Drosophila melanogaster. PLoS One 2011; 6:e23863. [PMID: 21912646 PMCID: PMC3166285 DOI: 10.1371/journal.pone.0023863] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/26/2011] [Indexed: 12/22/2022] Open
Abstract
Using a complete set of RING domains from Drosophila melanogaster, all the solved RING domains and cocrystal structures of RING-containing ubiquitin-ligases (RING-E3) and ubiquitin-conjugating enzyme (E2) pairs, we analyzed RING domains structures from their primary to quarternary structures. The results showed that: i) putative orthologs of RING domains between Drosophila melanogaster and the human largely occur (118/139, 84.9%); ii) of the 118 orthologous pairs from Drosophila melanogaster and the human, 117 pairs (117/118, 99.2%) were found to retain entirely uniform domain architectures, only Iap2/Diap2 experienced evolutionary expansion of domain architecture; iii) 4 evolutionary structurally conserved regions (SCRs) are responsible for homologous folding of RING domains at the superfamily level; iv) besides the conserved Cys/His chelating zinc ions, 6 equivalent residues (4 hydrophobic and 2 polar residues) in the SCRs possess good-consensus and conservation- these 4 SCRs function in the structural positioning of 6 equivalent residues as determinants for RING-E3 catalysis; v) members of these RING proteins located nucleus, multiple subcellular compartments, membrane protein and mitochondrion are respectively 42 (42/139, 30.2%), 71 (71/139, 51.1%), 22 (22/139, 15.8%) and 4 (4/139, 2.9%); vi) CG15104 (Topors) and CG1134 (Mul1) in C3HC4, and CG3929 (Deltex) in C3H2C3 seem to display broader E2s binding profiles than other RING-E3s; vii) analyzing intermolecular interfaces of E2/RING-E3 complexes indicate that residues directly interacting with E2s are all from the SCRs in RING domains. Of the 6 residues, 2 hydrophobic ones contribute to constructing the conserved hydrophobic core, while the 2 hydrophobic and 2 polar residues directly participate in E2/RING-E3 interactions. Based on sequence and structural data, SCRs, conserved equivalent residues and features of intermolecular interfaces were extracted, highlighting the presence of a nucleus for RING domain fold and formation of catalytic core in which related residues and regions exhibit preferential evolutionary conservation.
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Affiliation(s)
- Muying Ying
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People's Republic of China.
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Abstract
Background The patterns of emergence and diversification of the families of ubiquitin ligases provide insights about the evolution of the eukaryotic ubiquitination system. U-box ubiquitin ligases (UULs) are proteins characterized by containing a peculiar protein domain known as U box. In this study, the origin of the animal UUL genes is described. Results Phylogenetic and structural data indicate that six of the seven main UUL-encoding genes found in humans (UBE4A, UBE4B, UIP5, PRP19, CHIP and CYC4) were already present in the ancestor of all current metazoans and the seventh (WDSUB1) is found in placozoans, cnidarians and bilaterians. The fact that only 4 - 5 genes orthologous to the human ones are present in the choanoflagellate Monosiga brevicollis suggests that several animal-specific cooptions of the U box to generate new genes occurred. Significantly, Monosiga contains five additional UUL genes that are not present in animals. One of them is also present in distantly-related protozoans. Along animal evolution, losses of UUL-encoding genes are rare, except in nematodes, which lack three of them. These general patterns are highly congruent with those found for other two families (RBR, HECT) of ubiquitin ligases. Conclusions Finding that the patterns of emergence, diversification and loss of three unrelated families of ubiquitin ligases (RBR, HECT and U-box) are parallel indicates that there are underlying, linage-specific evolutionary forces shaping the complexity of the animal ubiquitin system.
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Pemberton TJ, Kay JE. Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. Comp Funct Genomics 2010; 6:277-300. [PMID: 18629211 PMCID: PMC2447506 DOI: 10.1002/cfg.482] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/01/2005] [Accepted: 05/26/2005] [Indexed: 11/11/2022] Open
Abstract
The peptidyl-prolyl cis/trans isomerase (PPIase) class of proteins comprises three
member families that are found throughout nature and are present in all the major
compartments of the cell. Their numbers appear to be linked to the number of genes in
their respective genomes, although we have found the human repertoire to be smaller
than expected due to a reduced cyclophilin repertoire. We show here that whilst the
members of the cyclophilin family (which are predominantly found in the nucleus
and cytoplasm) and the parvulin family (which are predominantly nuclear) are
largely conserved between different repertoires, the FKBPs (which are predominantly
found in the cytoplasm and endoplasmic reticulum) are not. It therefore appears
that the cyclophilins and parvulins have evolved to perform conserved functions,
while the FKBPs have evolved to fill ever-changing niches within the constantly
evolving organisms. Many orthologous subgroups within the different PPIase families
appear to have evolved from a distinct common ancestor, whereas others, such as the
mitochondrial cyclophilins, appear to have evolved independently of one another. We
have also identified a novel parvulin within Drosophila melanogaster that is unique to
the fruit fly, indicating a recent evolutionary emergence. Interestingly, the fission yeast
repertoire, which contains no unique cyclophilins and parvulins, shares no PPIases
solely with the budding yeast but it does share a majority with the higher eukaryotes
in this study, unlike the budding yeast. It therefore appears that, in comparison with
Schizosaccharomyces pombe, Saccharomyces cerevisiae is a poor representation of the
higher eukaryotes for the study of PPIases.
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Affiliation(s)
- Trevor J Pemberton
- The Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton ,East Sussex BN1 9PX, United Kingdom.
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Pemberton TJ. Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires. BMC Genomics 2006; 7:244. [PMID: 16995943 PMCID: PMC1618848 DOI: 10.1186/1471-2164-7-244] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 09/22/2006] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The peptidyl-prolyl cis/trans isomerase (PPIase) class of proteins is present in all known eukaryotes, prokaryotes, and archaea, and it is comprised of three member families that share the ability to catalyze the cis/trans isomerisation of a prolyl bond. Some fungi have been used as model systems to investigate the role of PPIases within the cell, however how representative these repertoires are of other fungi or humans has not been fully investigated. RESULTS PPIase numbers within these fungal repertoires appears associated with genome size and orthology between repertoires was found to be low. Phylogenetic analysis showed the single-domain FKBPs to evolve prior to the multi-domain FKBPs, whereas the multi-domain cyclophilins appear to evolve throughout cyclophilin evolution. A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. However, no such commonality was found with the FKBPs. Twelve of the 17 human cyclophilins and both human parvulins, but only one of the 13 human FKBPs, identified orthologues within these fungi. hPar14 orthologues were restricted to the Pezizomycotina fungi, and R. oryzae is unique in the known fungi in possessing an hCyp33 orthologue and a TPR-containing FKBP. The repertoires of Cryptococcus neoformans, Aspergillus fumigatus, and Aspergillus nidulans were found to exhibit the highest orthology to the human repertoire, and Saccharomyces cerevisiae one of the lowest. CONCLUSION Given this data, we would hypothesize that: (i) the evolution of the fungal PPIases is driven, at least in part, by the size of the proteome, (ii) evolutionary pressures differ both between the different PPIase families and the different fungi, and (iii) whilst the cyclophilins and parvulins have evolved to perform conserved functions, the FKBPs have evolved to perform more variable roles. Also, the repertoire of Cryptococcus neoformans may represent a better model fungal system within which to study the functions of the PPIases as its genome size and genetic tractability are equal to those of Saccharomyces cerevisiae, whilst its repertoires exhibits greater orthology to that of humans. However, further experimental investigations are required to confirm this.
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Affiliation(s)
- Trevor J Pemberton
- Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, 2250 Alcazar Street, Los Angeles, CA 90033, USA.
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Ardley HC, Robinson PA. The role of ubiquitin-protein ligases in neurodegenerative disease. NEURODEGENER DIS 2006; 1:71-87. [PMID: 16908979 DOI: 10.1159/000080048] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 02/19/2004] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease and Parkinson's disease are the most common neurodegenerative conditions associated with the ageing process. The pathology of these and other neurodegenerative disorders, including polyglutamine diseases, is characterised by the presence of inclusion bodies in brain tissue of affected patients. In general, these inclusion bodies consist of insoluble, unfolded proteins that are commonly tagged with the small protein, ubiquitin. Covalent tagging of proteins with chains of ubiquitin generally targets them for degradation. Indeed, the ubiquitin/proteasome system (UPS) is the major route through which intracellular proteolysis is regulated. This strongly implicates the UPS in these disease-associated inclusions, either due to malfunction (of specific UPS components) or overload of the system (due to aggregation of unfolded/mutant proteins), resulting in subsequent cellular toxicity. Protein targeting for degradation is a highly regulated process. It relies on transfer of ubiquitin molecules to the target protein via an enzyme cascade and specific recognition of a substrate protein by ubiquitin-protein ligases (E3s). Recent advances in our knowledge gained from the Human Genome Mapping Project have revealed the presence of potentially hundreds of E3s within the human genome. The discovery that parkin, mutations in which are found in at least 50% of patients with autosomal recessive juvenile parkinsonism, is an E3 further highlights the importance of the UPS in neurological disease. To date, parkin is the only E3 confirmed to have a direct causal role in neurodegenerative disorders. However, a number of other (putative) E3s have now been identified that may cause disease directly or interact with neurological disease-associated proteins. Many of these are either lost or mutated in a given disease or fail to process disease-associated mutant proteins correctly. In this review, we will discuss the role(s) of E3s in neurodegenerative disorders.
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Affiliation(s)
- Helen C Ardley
- Molecular Medicine Unit, University of Leeds, St. James's University Hospital, Leeds, UK.
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González-Lamothe R, Tsitsigiannis DI, Ludwig AA, Panicot M, Shirasu K, Jones JDG. The U-box protein CMPG1 is required for efficient activation of defense mechanisms triggered by multiple resistance genes in tobacco and tomato. THE PLANT CELL 2006; 18:1067-83. [PMID: 16531490 PMCID: PMC1425846 DOI: 10.1105/tpc.106.040998] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 02/13/2006] [Accepted: 02/20/2006] [Indexed: 05/07/2023]
Abstract
We previously identified three Avr9/Cf-9 Rapidly Elicited (ACRE) genes essential for Cf-9- and Cf-4-dependent hypersensitive response (HR) production in Nicotiana benthamiana. Two of them encode putative E3 ubiquitin ligase components. This led us to investigate other ACRE genes associated with the ubiquitination pathway. ACRE74 encodes a U-box E3 ligase homolog, highly related to parsley (Petroselinum crispum) CMPG1 and Arabidopsis thaliana PLANT U-BOX20 (PUB20) and PUB21 proteins, and was called Nt CMPG1. Transcript levels of Nt CMPG1 and the homologous tomato (Solanum lycopersicum) Cmpg1 are induced in Cf9 tobacco (Nicotiana tabacum) and Cf9 tomato after Avr9 elicitation. Tobacco CMPG1 possesses in vitro E3 ligase activity. N. benthamiana plants silenced for Nt CMPG1 show reduced HR after Cf-9/Avr9 elicitation, while overexpression of Nt CMPG1 induces a stronger HR in Cf9 tobacco plants after Avr9 infiltration. In tomato, silencing of Cmpg1 decreased resistance to Cladosporium fulvum. Overexpression of epitope-tagged tobacco CMPG1 mutated in the U-box domain confers a dominant-negative phenotype. We also show that Nt CMPG1 is involved in the Pto/AvrPto and Inf1 responses. In summary, we show that the E3 ligase Nt CMPG1 is essential for plant defense and disease resistance.
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Pemberton TJ, Kay JE. The cyclophilin repertoire of the fission yeast Schizosaccharomyces pombe. Yeast 2005; 22:927-45. [PMID: 16134115 DOI: 10.1002/yea.1288] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The cyclophilin repertoire of the fission yeast Schizosaccharomyces pombe is comprised of nine members that are distributed over all three of its chromosomes and range from small single-domain to large multi-domain proteins. Each cyclophilin possesses only a single prolyl-isomerase domain, and these vary in their degree of consensus, including at positions that are likely to affect their drug-binding ability and catalytic activity. The additional identified motifs are involved in putative protein or RNA interactions, while a novel domain that is specific to SpCyp7 and its orthologues may have functions that include an interaction with hnRNPs. The Sz. pombe cyclophilins are found throughout the cell but appear to be absent from the mitochondria, which is unique among the characterized eukaryotic repertoires. SpCyp5, SpCyp6 and SpCyp8 have exhibited significant upregulation of their expression during the meiotic cycle and SpCyp5 has exhibited significant upregulation of its expression during heat stress. All nine have identified members in the repertoires of H. sapiens, D. melanogaster and A. thaliana. However, only three identified members in the cyclophilin repertoire of S. cerevisiae with SpCyp7 identifying a fourth protein that is not a member of the recognized repertoire due to its possession of a degenerate prolyl-isomerase domain. The cyclophilin repertoire of Sz. pombe therefore represents a better model group for the study of cyclophilin function in the higher eukaryotes.
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Affiliation(s)
- Trevor J Pemberton
- The Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, East Sussex BN1 9PX, UK.
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16
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Ye L, Li X, Chen Y, Sun H, Wang W, Su T, Jiang L, Cui B, Ning G. Autosomal dominant neurohypophyseal diabetes insipidus with linkage to chromosome 20p13 but without mutations in the AVP-NPII gene. J Clin Endocrinol Metab 2005; 90:4388-93. [PMID: 15811933 DOI: 10.1210/jc.2004-2000] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Autosomal dominant neurohypophyseal diabetes insipidus (ADNDI) has been known as a rare disorder transmitted as an autosomal dominant trait, characterized by polyuria and polydipsia, and caused by deficient neurosecretion of arginine vasopressin precursor (AVP-NPII). We reported an ADNDI family with linkage to chromosome 20p13 but without mutations in the AVP-NPII gene. OBJECTIVE The objective of this study was to identify the corresponding locus responsible for ADNDI in a family without AVP-NP II gene mutations. SUBJECTS AND METHODS Two families with ADNDI were diagnosed by water deprivation test. The AVP-NPII gene was amplified by PCR and sequenced. A genomewide scan was performed in one family using 400 microsatellite markers covering 22 autosomes. RESULTS A 3-bp deletion (1827-1829delAGG) of AVP-NPII gene was identified in the affected individuals in one family. Although no mutations could be detected in the coding, the promoter, and intronic regions of AVP-NPII gene in the other family, a maximum LOD score of 1.202999 (theta = 0.00) was obtained at marker D20S889 by genomewide scan, and a 7-cM interval on chromosome 20p13 was defined by fine mapping with markers D20S199-D20S849. Furthermore, the intragenic region that regulates AVP-NPII and oxytocin expression as an enhancer element and the UBCE7IP5 gene that participates in prohormone degradation were sequenced. No alterations could be detected either. CONCLUSION The corresponding locus responsible for ADNDI is possibly heterogeneous regarding the slightly different clinical features in these two families.
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Affiliation(s)
- Lei Ye
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Second Medical University, Ruijin Er Lu, Shanghai 200025, People's Republic of China
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17
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Esser C, Alberti S, Höhfeld J. Cooperation of molecular chaperones with the ubiquitin/proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1695:171-88. [PMID: 15571814 DOI: 10.1016/j.bbamcr.2004.09.020] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular chaperones and energy-dependent proteases have long been viewed as opposing forces that control protein biogenesis. Molecular chaperones are specialized in protein folding, whereas energy-dependent proteases such as the proteasome mediate efficient protein degradation. Recent data, however, suggest that molecular chaperones directly cooperate with the ubiquitin/proteasome system during protein quality control in eukaryotic cells. Modulating the intracellular balance of protein folding and protein degradation may open new strategies for the treatment of human diseases that involve chaperone pathways such as cancer and diverse amyloid diseases.
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Affiliation(s)
- Claudia Esser
- Institut für Zellbiologie und Bonner Forum Biomedizin, Rheinische Friedrich-Wilhelms-Universität Bonn,Ulrich-Haberland-Str. 61a, D-53121 Bonn, Germany
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18
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Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1695:55-72. [PMID: 15571809 DOI: 10.1016/j.bbamcr.2004.09.019] [Citation(s) in RCA: 964] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ubiquitin is the founding member of a family of structurally conserved proteins that regulate a host of processes in eukaryotic cells. Ubiquitin and its relatives carry out their functions through covalent attachment to other cellular proteins, thereby changing the stability, localization, or activity of the target protein. This article reviews the basic biochemistry of these protein conjugation reactions, focusing on ubiquitin itself and emphasizing recent insights into mechanism and specificity.
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Affiliation(s)
- Cecile M Pickart
- Department of Biochemistry and Molecular Biology/Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA.
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19
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Jang JH. FIGC, a novel FGF-induced ubiquitin-protein ligase in gastric cancers. FEBS Lett 2005; 578:21-5. [PMID: 15581609 DOI: 10.1016/j.febslet.2004.10.071] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 10/11/2004] [Indexed: 11/24/2022]
Abstract
We have previously shown that fibroblast growth factor receptor 2 (FGFR2) plays an important role in gastric carcinogenesis. In this study, we have used a differential display approach to identify basic fibroblast growth factor (bFGF)-inducible genes in gastric cancer cells. Here, we report that one of these genes is predicted to encode a RING finger protein, designated FIGC. The FIGC gene was found to encode a polypeptide of 381 amino acids with a novel RING finger module at the NH2-terminus and the COOH-terminal proline-rich region. Using an in vitro ubiquitination assay with recombinant protein, we demonstrate that FIGC has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. Our data indicate that FIGC upregulation in response to bFGF in gastric cancer might be implicated in carcinogenesis through dysregulation of growth modulator.
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Affiliation(s)
- Jun-Hyeog Jang
- Department of Biochemistry, Inha University College of Medicine, Jung Gu, Incheon 400-712, Republic of Korea.
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20
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Abstract
Post-translational covalent attachment of ubiquitin and ubiquitin-like proteins (ubls) has emerged as a predominant cellular regulatory mechanism, with important roles in controlling cell division, signal transduction, embryonic development, endocytic trafficking and the immune response. Ubls function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways. A number of biochemical and structural studies have provided insights into the mechanism of ubl-activating enzymes and their roles in ubl conjugation cascades.
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Affiliation(s)
- Danny T Huang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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21
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Abstract
Recent molecular biological and genetical studies have identified several positive and negative regulators of gibberellin (GA) signalling pathways in higher plants. The DELLA protein functions as a negative regulator of GA signalling; its degradation through the ubiquitin/proteasome pathway is a key event in the regulation of GA-stimulated processes.
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Affiliation(s)
- Kenji Gomi
- BioScience Centre, Nagoya University, Nagoya 464-8601, Japan
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22
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Friedman AD, Nimbalkar D, Quelle FW. Erythropoietin receptors associate with a ubiquitin ligase, p33RUL, and require its activity for erythropoietin-induced proliferation. J Biol Chem 2003; 278:26851-61. [PMID: 12746455 DOI: 10.1074/jbc.m210039200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proliferation and survival of hematopoietic cells is strictly regulated by cytokine growth factors that act through receptors of the Type I cytokine receptor family, including erythropoietin (Epo) and its receptor, EpoR. Mitogenic signaling by these receptors depends on activation of Jak tyrosine kinases. However, other required components of this pathway have not been fully identified. In a screen for proteins that interact with EpoR and Jak2, we identified a novel member of the U-box family of ubiquitin ligases. This receptor-associated ubiquitin ligase, RUL, co-precipitated with EpoR from mammalian cells and mediated ubiquitination of EpoR. Also, endogenously expressed RUL was rapidly and transiently phosphorylated on serine after cytokine treatment of factor-dependent hematopoietic cells. Expression of ubiquitin ligase-deficient mutants of RUL inhibited Epo-induced expression of c-myc and bcl-2, two immediate-early genes normally associated with Epo-induced cell growth. Consistent with that finding, expression of mutant RUL also inhibited Epo-dependent proliferation and survival of factor-dependent cells. Together, these observations suggest that RUL is a required component of mitogenic signaling by EpoR. We also show that RUL is phosphorylated in response to growth factors that act through non-cytokine receptors, suggesting that RUL may function as a common regulator of mitogenesis.
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Affiliation(s)
- Ann D Friedman
- Department of Pharmacology and The Immunology Graduate Program, The University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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23
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Ohi MD, Vander Kooi CW, Rosenberg JA, Chazin WJ, Gould KL. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat Struct Mol Biol 2003; 10:250-5. [PMID: 12627222 PMCID: PMC5881891 DOI: 10.1038/nsb906] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2002] [Accepted: 01/15/2003] [Indexed: 11/08/2022]
Abstract
The structure of the U-box in the essential Saccharomyces cerevisiae pre-mRNA splicing factor Prp19p has been determined by NMR. The conserved zinc-binding sites supporting the cross-brace arrangement in RING-finger domains are replaced by hydrogen-bonding networks in the U-box. These hydrogen-bonding networks are necessary for the structural stabilization and activity of the U-box. A conservative Val-->Ile point mutation in the Prp19p U-box domain leads to pre-mRNA splicing defects in vivo. NMR analysis of this mutant shows that the substitution disrupts structural integrity of the U-box domain. Furthermore, comparison of the Prp19p U-box domain with known RING-E2 complex structures demonstrates that both U-box and RING-fingers contain a conserved interaction surface. Mutagenesis of residues at this interface, while not perturbing the structure of the U-box, abrogates Prp19p function in vivo. These comparative structural and functional analyses imply that the U-box and its associated ubiquitin ligase activity are critical for Prp19p function in vivo.
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Affiliation(s)
- Melanie D Ohi
- Howard Hughes Medical Institute School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
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24
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Abstract
Ubiquitin-protein ligases (E3s) determine the substrate specificity of ubiquitylation and, until recently, had been classified into two families, the HECT and RING-finger families. The U-box is a domain of approximately 70 amino acids that is present in proteins from yeast to humans. The prototype U-box protein, yeast Ufd2, was identified as a ubiquitin chain assembly factor (E4) that cooperates with a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and an E3 to catalyze the formation of a ubiquitin chain on artificial substrates. We recently showed that mammalian U-box proteins, in conjunction with an E1 and an E2, mediate polyubiquitylation in the absence of a HECT type or RING-finger type E3. U-box proteins have thus been defined as a third family of E3s. We here review recent progress in the characterization of U-box proteins and of their role in the quality control system that underlies the cellular stress response to the intracellular accumulation of abnormal proteins.
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Affiliation(s)
- Shigetsugu Hatakeyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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25
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Cyr DM, Höhfeld J, Patterson C. Protein quality control: U-box-containing E3 ubiquitin ligases join the fold. Trends Biochem Sci 2002; 27:368-75. [PMID: 12114026 DOI: 10.1016/s0968-0004(02)02125-4] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular chaperones act with folding co-chaperones to suppress protein aggregation and refold stress damaged proteins. However, it is not clear how slowly folding or misfolded polypeptides are targeted for proteasomal degradation. Generally, selection of proteins for degradation is mediated by E3 ubiquitin ligases of the mechanistically distinct HECT and RING domain sub-types. Recent studies suggest that the U-box protein family represents a third class of E3 enzymes. CHIP, a U-box-containing protein, is a degradatory co-chaperone of heat-shock protein 70 (Hsp70) and Hsp90 that facilitates the polyubiquitination of chaperone substrates. These data indicate a model for protein quality control in which the interaction of Hsp70 and Hsp90 with co-chaperones that have either folding or degradatory activity helps to determine the fate of non-native cellular proteins.
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Affiliation(s)
- Douglas M Cyr
- Dept of Cell and Developmental Biology and The UNC-Cystic Fibrosis Center, 524 Taylor Hall, University of North Carolina, Chapel Hill, NC 27599-7060, USA.
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26
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Aravind L, Anantharaman V, Koonin EV. Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins 2002; 48:1-14. [PMID: 12012333 DOI: 10.1002/prot.10064] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein sequence and structure comparisons show that the catalytic domains of Class I aminoacyl-tRNA synthetases, a related family of nucleotidyltransferases involved primarily in coenzyme biosynthesis, nucleotide-binding domains related to the UspA protein (USPA domains), photolyases, electron transport flavoproteins, and PP-loop-containing ATPases together comprise a distinct class of alpha/beta domains designated the HUP domain after HIGH-signature proteins, UspA, and PP-ATPase. Several lines of evidence are presented to support the monophyly of the HUP domains, to the exclusion of other three-layered alpha/beta folds with the generic "Rossmann-like" topology. Cladistic analysis, with patterns of structural and sequence similarity used as discrete characters, identified three major evolutionary lineages within the HUP domain class: the PP-ATPases; the HIGH superfamily, which includes class I aaRS and related nucleotidyltransferases containing the HIGH signature in their nucleotide-binding loop; and a previously unrecognized USPA-like group, which includes USPA domains, electron transport flavoproteins, and photolyases. Examination of the patterns of phyletic distribution of distinct families within these three major lineages suggests that the Last Universal Common Ancestor of all modern life forms encoded 15-18 distinct alpha/beta ATPases and nucleotide-binding proteins of the HUP class. This points to an extensive radiation of HUP domains before the last universal common ancestor (LUCA), during which the multiple class I aminoacyl-tRNA synthetases emerged only at a late stage. Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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27
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Martinez-Noel G, Müller U, Harbers K. Identification of molecular determinants required for interaction of ubiquitin-conjugating enzymes and RING finger proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5912-9. [PMID: 11722579 DOI: 10.1046/j.0014-2956.2001.02541.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent results from several laboratories suggest that the interaction of E2 ubiquitin-conjugating enzymes with the RING finger domain has a central role in mediating the transfer of ubiquitin to proteins. Here we present a mutational analysis of the interaction between the E2 enzyme UbcM4/UbcH7 and three different RING finger proteins, termed UIPs, which, like Parkin, contain a RING1-IBR-RING2 motif. The results show that the E2 enzyme binds to the RING1 domain but not to the other cysteine/histidine-rich domains of the RING1-IBR-RING2 motif. Three regions within the UbcM4 molecule are involved in this interaction: the H1 alpha helix, loop L1, connecting the third and fourth strand of the beta sheet, and loop L2, located between the fourth beta strand and the second alpha helix. Loop L2 plays an important role in determining the specificity of interaction. The effects of L2 mutations on UbcM4/UIP interaction are different for each UIP, indicating that RING finger domains can vary considerably in their structural requirements for binding to E2 enzymes. The result that single amino-acid changes can regulate binding of E2 enzymes to different RING finger proteins suggests a novel approach to experimentally manipulate proteolytic pathways mediated by RING finger proteins.
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Affiliation(s)
- G Martinez-Noel
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität Hamburg, Hamburg, Germany
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28
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Abstract
The latest advances in ubiquitin-mediated signaling were discussed at a recent FASEB meeting in Vermont. New findings show that besides signaling proteolysis, ubiquitination can be a signal for trafficking, kinase activation, and other nonproteolytic fates.
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Affiliation(s)
- C M Pickart
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA.
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