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Lažetić V, Batachari LE, Russell AB, Troemel ER. Similarities in the induction of the intracellular pathogen response in Caenorhabditis elegans and the type I interferon response in mammals. Bioessays 2023; 45:e2300097. [PMID: 37667453 PMCID: PMC10694843 DOI: 10.1002/bies.202300097] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023]
Abstract
Although the type-I interferon (IFN-I) response is considered vertebrate-specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional immunological programs. The IPR is induced during infection with natural intracellular fungal and viral pathogens of the intestine and promotes resistance against these pathogens. Similarly, the IFN-I response is induced by viruses and other intracellular pathogens and promotes resistance against infection. Whether the IPR and the IFN-I response evolved in a divergent or convergent manner is an unanswered and exciting question, which could be addressed by further studies of immunity against intracellular pathogens in C. elegans and other simple host organisms. Here we highlight similar roles played by RIG-I-like receptors, purine metabolism enzymes, proteotoxic stressors, and transcription factors to induce the IPR and IFN-I response, as well as the similar consequences of these defense programs on organismal development.
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Affiliation(s)
- Vladimir Lažetić
- School of Biological SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of Biological SciencesThe George Washington UniversityWashingtonDCUSA
| | - Lakshmi E. Batachari
- School of Biological SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Alistair B. Russell
- School of Biological SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Emily R. Troemel
- School of Biological SciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
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2
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Mallik S, Tawfik DS, Levy ED. How gene duplication diversifies the landscape of protein oligomeric state and function. Curr Opin Genet Dev 2022; 76:101966. [PMID: 36007298 PMCID: PMC9548406 DOI: 10.1016/j.gde.2022.101966] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
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Affiliation(s)
- Saurav Mallik
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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3
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Takagi J, Cho C, Duvalyan A, Yan Y, Halloran M, Hanson-Smith V, Thorner J, Finnigan GC. Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1. G3-GENES GENOMES GENETICS 2021; 11:6025175. [PMID: 33561226 PMCID: PMC7849910 DOI: 10.1093/g3journal/jkaa006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/13/2020] [Indexed: 11/21/2022]
Abstract
Septins are GTP-binding proteins conserved across metazoans. They can polymerize into extended filaments and, hence, are considered a component of the cytoskeleton. The number of individual septins varies across the tree of life—yeast (Saccharomyces cerevisiae) has seven distinct subunits, a nematode (Caenorhabditis elegans) has two, and humans have 13. However, the overall geometric unit (an apolar hetero-octameric protomer and filaments assembled there from) has been conserved. To understand septin evolutionary variation, we focused on a related pair of yeast subunits (Cdc11 and Shs1) that appear to have arisen from gene duplication within the fungal clade. Either Cdc11 or Shs1 occupies the terminal position within a hetero-octamer, yet Cdc11 is essential for septin function and cell viability, whereas Shs1 is not. To discern the molecular basis of this divergence, we utilized ancestral gene reconstruction to predict, synthesize, and experimentally examine the most recent common ancestor (“Anc.11-S”) of Cdc11 and Shs1. Anc.11-S was able to occupy the terminal position within an octamer, just like the modern subunits. Although Anc.11-S supplied many of the known functions of Cdc11, it was unable to replace the distinct function(s) of Shs1. To further evaluate the history of Shs1, additional intermediates along a proposed trajectory from Anc.11-S to yeast Shs1 were generated and tested. We demonstrate that multiple events contributed to the current properties of Shs1: (1) loss of Shs1–Shs1 self-association early after duplication, (2) co-evolution of heterotypic Cdc11–Shs1 interaction between neighboring hetero-octamers, and (3) eventual repurposing and acquisition of novel function(s) for its C-terminal extension domain. Thus, a pair of duplicated proteins, despite constraints imposed by assembly into a highly conserved multi-subunit structure, could evolve new functionality via a complex evolutionary pathway.
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Affiliation(s)
- Julie Takagi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Christina Cho
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Angela Duvalyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Yao Yan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Megan Halloran
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Jeremy Thorner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
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4
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Mallik S, Tawfik DS. Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PLoS Comput Biol 2020; 16:e1008145. [PMID: 32853212 PMCID: PMC7480870 DOI: 10.1371/journal.pcbi.1008145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/09/2020] [Accepted: 07/12/2020] [Indexed: 12/16/2022] Open
Abstract
Oligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only ~10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available. About half of all proteins assemble as oligomers, either by self-interaction (homomers) or via interaction with another protein (heteromers). The latter can be unrelated, yet, quite commonly, the interacting proteins are paralogs, namely two genes that arose by gene duplication. Indeed, while a homomer is encoded by a single gene, heteromers demand two genes as a minimum. Duplication can therefore yield two discrete homomeric complexes or a single heteromer. Do paralogs tend to retain the ancestral homomeric interaction, or do they mostly diverge into heteromeric complexes? Despite several studies addressing this question, to date, we lack a systematic, rigorous approach for delineating the oligomeric fates of paralogs on an organism scale. To this end, we developed a new pipeline for analysis of molecular interaction databases that includes various filtering steps and unambiguous definitions of all possible oligomeric fates. Applying this method to Escherichia coli and Saccharomyces cerevisiae we noted that paralogous pairs tend to remain homomeric in the former while in the latter heteromeric complexes dominate. We consequently note a systematic trend of homomeric bacterial proteins diverging into heteromeric complexes in eukaryotes.
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Affiliation(s)
- Saurav Mallik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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5
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Zhang G, Zhang W. Direct protein-protein interaction network for insecticide resistance based on subcellular localization analysis in Drosophila melanogaster. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2020; 55:732-748. [PMID: 32567974 DOI: 10.1080/03601234.2020.1782114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In present study, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the key proteins and potential mechanisms from macro-perspective. The problem of resistance has not been solved fundamentally, because the development of new insecticides can't keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. As the further analysis to reduce data noise, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. The interaction between proteins located at the same subcellular location belongs to direct interactions, thus eliminating indirect interaction. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the hub proteins and potential mechanisms from macro-perspective. This is the first study to explore the insecticide resistance molecular mechanism of Drosophila melanogaster based on subcellular localization analysis. It can provide the bioinformatics foundation for further understanding the mechanisms of insecticide resistance. It also provides a reference for the study of molecular mechanism of insecticide resistance of other insects.
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Affiliation(s)
- Guilu Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenjun Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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6
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Henderson LD, Matthews-Palmer TRS, Gulbronson CJ, Ribardo DA, Beeby M, Hendrixson DR. Diversification of Campylobacter jejuni Flagellar C-Ring Composition Impacts Its Structure and Function in Motility, Flagellar Assembly, and Cellular Processes. mBio 2020; 11:e02286-19. [PMID: 31911488 PMCID: PMC6946799 DOI: 10.1128/mbio.02286-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial flagella are reversible rotary motors that rotate external filaments for bacterial propulsion. Some flagellar motors have diversified by recruiting additional components that influence torque and rotation, but little is known about the possible diversification and evolution of core motor components. The mechanistic core of flagella is the cytoplasmic C ring, which functions as a rotor, directional switch, and assembly platform for the flagellar type III secretion system (fT3SS) ATPase. The C ring is composed of a ring of FliG proteins and a helical ring of surface presentation of antigen (SPOA) domains from the switch proteins FliM and one of two usually mutually exclusive paralogs, FliN or FliY. We investigated the composition, architecture, and function of the C ring of Campylobacter jejuni, which encodes FliG, FliM, and both FliY and FliN by a variety of interrogative approaches. We discovered a diversified C. jejuni C ring containing FliG, FliM, and both FliY, which functions as a classical FliN-like protein for flagellar assembly, and FliN, which has neofunctionalized into a structural role. Specific protein interactions drive the formation of a more complex heterooligomeric C. jejuni C-ring structure. We discovered that this complex C ring has additional cellular functions in polarly localizing FlhG for numerical regulation of flagellar biogenesis and spatial regulation of division. Furthermore, mutation of the C. jejuni C ring revealed a T3SS that was less dependent on its ATPase complex for assembly than were other systems. Our results highlight considerable evolved flagellar diversity that impacts motor output, biogenesis, and cellular processes in different species.IMPORTANCE The conserved core of bacterial flagellar motors reflects a shared evolutionary history that preserves the mechanisms essential for flagellar assembly, rotation, and directional switching. In this work, we describe an expanded and diversified set of core components in the Campylobacter jejuni flagellar C ring, the mechanistic core of the motor. Our work provides insight into how usually conserved core components may have diversified by gene duplication, enabling a division of labor of the ancestral protein between the two new proteins, acquisition of new roles in flagellar assembly and motility, and expansion of the function of the flagellum beyond motility, including spatial regulation of cell division and numerical control of flagellar biogenesis in C. jejuni Our results highlight that relatively small changes, such as gene duplications, can have substantial ramifications on the cellular roles of a molecular machine.
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Affiliation(s)
- Louie D Henderson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Connor J Gulbronson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deborah A Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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7
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Howell LA, Tomko RJ, Kusmierczyk AR. Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s11515-017-1439-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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8
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Abstract
All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome activators (PAs), which control the entrance of substrates. These include the PA700 (19S complex), which assembles with the 20S and forms the 26S proteasome and allows the efficient degradation of proteins usually labeled by ubiquitin tags, PA200 and PA28, which are involved in proteolysis through ubiquitin-independent mechanisms and PI31, which was initially identified as a 20S inhibitor in vitro. Unlike 20S proteasome, shown to be present in all Eukaryotes and Archaea, the evolutionary history of PAs remained fragmentary. Here, we made a comprehensive survey and phylogenetic analyses of the four types of regulators in 17 clades covering most of the eukaryotic supergroups. We found remarkable conservation of each PA700 subunit in all eukaryotes, indicating that the current complex PA700 structure was already set up in the last eukaryotic common ancestor (LECA). Also present in LECA, PA200, PA28, and PI31 showed a more contrasted evolutionary picture, because many lineages have subsequently lost one or two of them. The paramount conservation of PA700 composition in all eukaryotes and the dynamic evolution of PA200, PA28, and PI31 are discussed in the light of current knowledge on their physiological roles.
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Affiliation(s)
- Philippe Fort
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
| | - Andrey V Kajava
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - Fredéric Delsuc
- Université de Montpellier, France CNRS, IRD, Institut des Sciences de l'Evolution, UMR 5554, Montpellier, France
| | - Olivier Coux
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
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9
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Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex. ACTA ACUST UNITED AC 2014; 22:117-28. [PMID: 25544043 PMCID: PMC4306531 DOI: 10.1016/j.chembiol.2014.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/07/2014] [Accepted: 11/07/2014] [Indexed: 02/05/2023]
Abstract
Describing, understanding, and modulating the function of the cell require elucidation of the structures of macromolecular assemblies. Here, we describe an integrative method for modeling heteromeric complexes using as a starting point disassembly pathways determined by native mass spectrometry (MS). In this method, the pathway data and other available information are encoded as a scoring function on the positions of the subunits of the complex. The method was assessed on its ability to reproduce the native contacts in five benchmark cases with simulated MS data and two cases with real MS data. To illustrate the power of our method, we purified the yeast initiation factor 3 (eIF3) complex and characterized it by native MS and chemical crosslinking MS. We established substoichiometric binding of eIF5 and derived a model for the five-subunit eIF3 complex, at domain level, consistent with its role as a scaffold for other initiation factors. Integrative MS method allows topological characterization of heteromeric complexes Intersubunit crosslinks increase the precision of the predicted topologies A 3D model of eIF3:eIF5 complex was built using restraints from MS-based methods Integrative modeling reveals two submodules within eIF3: eIF3b:i:g and eIF3a:c
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10
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Magill L, Walker B, Irvine AE. The Proteasome: A Novel Therapeutic Target in Haematopoietic Malignancy. Hematology 2013; 8:275-83. [PMID: 14530169 DOI: 10.1080/10245330310001604755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The proteasome plays a key role in regulating protein degradation in eukaryotic cells. A range of synthetic inhibitors of proteasome activity have been developed which have helped elucidate its role in the cell. These inhibitors have selectively induced apoptosis in malignant cells in vitro suggesting that the proteasome may be a novel therapeutic target. First generation proteasome inhibitors are currently showing promise in phase II/III clinical trials for patients with multiple myeloma.
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Affiliation(s)
- Laura Magill
- Department of Haemotology, Queen's University of Belfast, UK
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11
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Förster F, Unverdorben P, Śledź P, Baumeister W. Unveiling the Long-Held Secrets of the 26S Proteasome. Structure 2013; 21:1551-62. [DOI: 10.1016/j.str.2013.08.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 01/23/2023]
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12
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Abstract
The eukaryotic ubiquitin-proteasome system is responsible for most aspects of regulatory and quality-control protein degradation in cells. Its substrates, which are usually modified by polymers of ubiquitin, are ultimately degraded by the 26S proteasome. This 2.6-MDa protein complex is separated into a barrel-shaped proteolytic 20S core particle (CP) of 28 subunits capped on one or both ends by a 19S regulatory particle (RP) comprising at least 19 subunits. The RP coordinates substrate recognition, removal of substrate polyubiquitin chains, and substrate unfolding and translocation into the CP for degradation. Although many atomic structures of the CP have been determined, the RP has resisted high-resolution analysis. Recently, however, a combination of cryo-electron microscopy, biochemical analysis, and crystal structure determination of several RP subunits has yielded a near-atomic-resolution view of much of the complex. Major new insights into chaperone-assisted proteasome assembly have also recently emerged. Here we review these novel findings.
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Affiliation(s)
- Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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13
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Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly. Proc Natl Acad Sci U S A 2012; 109:E1001-10. [PMID: 22460800 DOI: 10.1073/pnas.1116538109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 26S proteasome, a molecular machine responsible for regulated protein degradation, consists of a proteolytic core particle (20S CP) associated with 19S regulatory particles (19S RPs) subdivided into base and lid subcomplexes. The assembly of 19S RP base subcomplex is mediated by multiple dedicated chaperones. Among these, Hsm3 is important for normal growth and directly targets the carboxyl-terminal (C-terminal) domain of Rpt1 of the Rpt1-Rpt2-Rpn1 assembly intermediate. Here, we report crystal structures of the yeast Hsm3 chaperone free and bound to the C-terminal domain of Rpt1. Unexpectedly, the structure of the complex suggests that within the Hsm3-Rpt1-Rpt2 module, Hsm3 also contacts Rpt2. We show that in both yeast and mammals, Hsm3 actually directly binds the AAA domain of Rpt2. The Hsm3 C-terminal region involved in this interaction is required in vivo for base assembly, although it is dispensable for binding Rpt1. Although Rpt1 and Rpt2 exhibit weak affinity for each other, Hsm3 unexpectedly acts as an essential matchmaker for the Rpt1-Rpt2-Rpn1 assembly by bridging both Rpt1 and Rpt2. In addition, we provide structural and biochemical evidence on how Hsm3/S5b may regulate the 19S RP association to the 20S CP proteasome. Our data point out the diverse functions of assembly chaperones.
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14
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Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A 2012; 109:1380-7. [PMID: 22307589 PMCID: PMC3277140 DOI: 10.1073/pnas.1120559109] [Citation(s) in RCA: 376] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been determined by X-ray crystallography, the structure of the 19S regulatory particle (RP), which recruits substrates, unfolds them, and translocates them to the CP for degradation, has remained elusive. Here, we describe the molecular architecture of the 26S holocomplex determined by an integrative approach based on data from cryoelectron microscopy, X-ray crystallography, residue-specific chemical cross-linking, and several proteomics techniques. The "lid" of the RP (consisting of Rpn3/5/6/7/8/9/11/12) is organized in a modular fashion. Rpn3/5/6/7/9/12 form a horseshoe-shaped heterohexamer, which connects to the CP and roofs the AAA-ATPase module, positioning the Rpn8/Rpn11 heterodimer close to its mouth. Rpn2 is rigid, supporting the lid, while Rpn1 is conformationally variable, positioned at the periphery of the ATPase ring. The ubiquitin receptors Rpn10 and Rpn13 are located in the distal part of the RP, indicating that they were recruited to the complex late in its evolution. The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates.
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Affiliation(s)
- Keren Lasker
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, 1700 4th Street, University of California, San Francisco, CA 94158
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stefan Bohn
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Thomas Walzthoeni
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische, Technische Hochschule, 8093 Zürich, Switzerland
- PhD Program in Molecular Life Sciences, University of Zurich/ETH Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; and
| | - Elizabeth Villa
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Pia Unverdorben
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische, Technische Hochschule, 8093 Zürich, Switzerland
- Faculty of Science, University of Zürich, 8093 Zürich, Switzerland
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences, 1700 4th Street, University of California, San Francisco, CA 94158
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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15
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Assembly, structure, and function of the 26S proteasome. Trends Cell Biol 2010; 20:391-401. [PMID: 20427185 DOI: 10.1016/j.tcb.2010.03.007] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2009] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 01/15/2023]
Abstract
The 26S proteasome is a large multiprotein complex involved in the regulated degradation of ubiquitinated proteins in the cell. The 26S proteasome has been shown to control an increasing number of essential biochemical mechanisms of the cellular lifecycle including DNA synthesis, repair, transcription, translation, and cell signal transduction. Concurrently, it is increasingly seen that malfunction of the ubiquitin proteasome system contributes to the pathogenesis of disease. The recent identification of four molecular chaperones, in addition to five previously identified chaperones, have provided mechanistic insight into how this cellular megastructure is assembled in the cell. These data, together with new insights into the structure and function of the proteasome, provide a much better understanding of this complex protease.
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16
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Rotanova TV, Melnikov EE. The ATP-dependent proteases and proteolytic complexes involved into intracellular protein degradation. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2008. [DOI: 10.1134/s1990750808030049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Kurepa J, Smalle JA. Structure, function and regulation of plant proteasomes. Biochimie 2008; 90:324-35. [PMID: 17825468 DOI: 10.1016/j.biochi.2007.07.019] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 07/20/2007] [Indexed: 11/24/2022]
Abstract
Proteasomes are large multisubunit, multicatalytic proteases responsible for most of the cytosolic and nuclear protein degradation, and their structure and functions are conserved in eukaryotes. Proteasomes were originally identified as the proteolytic module of the ubiquitin-dependent proteolysis pathway. Today we know that proteasomes also mediate ubiquitin-independent proteolysis, that they have RNAse activity, and play a non-proteolytic role in transcriptional regulation. Here we present an overview of the current knowledge of proteasome function and regulation in plants and highlight the role of proteasome-dependent protein degradation in the control of plant development and responses to the environment.
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Affiliation(s)
- Jasmina Kurepa
- Plant Physiology, Biochemistry and Molecular Biology Program, Department of Plant and Soil Sciences, KTRDC, University of Kentucky, Lexington, KY 40546, USA
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Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S. Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochem Biophys Res Commun 2007; 359:503-9. [PMID: 17555716 DOI: 10.1016/j.bbrc.2007.05.138] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 05/18/2007] [Indexed: 11/15/2022]
Abstract
The 26S proteasome-dependent protein degradation is an evolutionarily conserved process. The mammalian oncoprotein gankyrin, which associates with S6 of the proteasome, facilitates the degradation of pRb, and thus possibly acts as a bridging factor between the proteasome and its substrates. However, the mechanism of the proteasome-dependent protein degradation in yeast is poorly understood. Here, we report the tertiary structure of the complex between Nas6 and a C-terminal domain of Rpt3, which are the yeast orthologues of gankyrin and S6, respectively. The concave region of Nas6 bound to the alpha-helical domain of Rpt3. The stable interaction between Nas6 and Rpt3 was mediated by intermolecular interactions composed of complementary charged patches. The recognition of Rpt3 by Nas6 in the crystal suggests that Nas6 is indeed a subunit of the 26S proteasome. These results provide a structural basis for the association between Nas6 and the heterohexameric ATPase ring of the proteasome through Rpt3.
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Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S. Purification, crystallization and preliminary X-ray diffraction analysis of the non-ATPase subunit Nas6 in complex with the ATPase subunit Rpt3 of the 26S proteasome from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:190-2. [PMID: 17329811 PMCID: PMC2330193 DOI: 10.1107/s1744309107004848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 01/30/2007] [Indexed: 05/14/2023]
Abstract
The non-ATPase subunit Nas6, which is the human orthologue of gankyrin, was co-expressed with the C-terminal domain of the ATPase subunit Rpt3 of the yeast 26S proteasome in Escherichia coli, purified to near-homogeneity and crystallized using the hanging-drop vapour-diffusion method. The protein crystallized in space group P2(1), with unit-cell parameters a = 60.38, b = 100.22, c = 72.20 A, beta = 94.70 degrees and with three Nas6-Rpt3C molecules per asymmetric unit. The crystal diffracted to beyond 2.2 A resolution using synchrotron radiation.
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Affiliation(s)
- Yoshihiro Nakamura
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Umehara
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Masami Horikoshi
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | | | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006; 1:19. [PMID: 16834776 PMCID: PMC1586193 DOI: 10.1186/1745-6150-1-19] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/11/2006] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed--the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it; previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial. RESULTS I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Posibacteria are derived from Eurybacteria and ancestral to neomura. RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane beta-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria. CONCLUSION Chlorobacteria are probably the oldest and Archaebacteria the youngest bacteria, with Posibacteria of intermediate age, requiring radical reassessment of dominant views of bacterial evolution. The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery, not a heterotrophic posibacterium with one membrane.
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Müller D, Nagel AC, Maier D, Preiss A. A molecular link A molecular link between Hairless and Pros26.4, a member of the AAA-ATPase subunits of the proteasome 19S regulatory particle in Drosophila. J Cell Sci 2006; 119:250-8. [PMID: 16410550 DOI: 10.1242/jcs.02743] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proteasome is the major degradation machinery of the cell that regulates multiple cellular processes as diverse as cell cycle, signal transduction and gene expression. Recognition and unfolding of target proteins involves the regulatory cap whose base contains six AAA-ATPases that display reverse chaperone activity. One of them, Rpt2 (also known as S4), has an essential role in gating the degradative central core. We have isolated the orthologous gene Pros26.4 from Drosophila melanogaster as a molecular interaction partner of Hairless. Hairless plays a major role as antagonist of Notch signalling in Drosophila, prompting our interest in the Hairless-Pros26.4 interaction. We find that Pros26.4 negatively regulates Hairless at the genetic and molecular level. Depletion of Pros26.4 by using tissue-specific RNA interference (RNAi) resulted in a specific stabilization of the Hairless protein, but not in stabilization of the intracellular domain of Notch or the effector protein Suppressor of Hairless. Thus, the Hairless-Pros26.4 interaction provides a novel mechanism of positive regulation of Notch signalling.
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Affiliation(s)
- Dominik Müller
- Universität Hohenheim, Institut für Genetik (240), Garbenstr. 30, 70599 Stuttgart, Germany
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Reuter CJ, Kaczowka SJ, Maupin-Furlow JA. Differential regulation of the PanA and PanB proteasome-activating nucleotidase and 20S proteasomal proteins of the haloarchaeon Haloferax volcanii. J Bacteriol 2004; 186:7763-72. [PMID: 15516591 PMCID: PMC524898 DOI: 10.1128/jb.186.22.7763-7772.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii produces three different proteins (alpha1, alpha2, and beta) that assemble into at least two 20S proteasome isoforms. This work reports the cloning and sequencing of two H. volcanii proteasome-activating nucleotidase (PAN) genes (panA and panB). The deduced PAN proteins were 60% identical with Walker A and B motifs and a second region of homology typical of AAA ATPases. The most significant region of divergence was the N terminus predicted to adopt a coiled-coil conformation involved in substrate recognition. Of the five proteasomal proteins, the alpha1, beta, and PanA proteins were the most abundant. Differential regulation of all five genes was observed, with a four- to eightfold increase in mRNA levels as cells entered stationary phase. In parallel with this mRNA increase, the protein levels of PanB and alpha2 increased severalfold during the transition from exponential growth to stationary phase, suggesting that these protein levels are regulated at least in part by mechanisms that control transcript levels. In contrast, the beta and PanA protein levels remained relatively constant, while the alpha1 protein levels exhibited only a modest increase. This lack of correlation between the mRNA and protein levels for alpha1, beta, and PanA suggests posttranscriptional mechanisms are involved in regulating the levels of these major proteasomal proteins. Together these results support a model in which the cell regulates the ratio of the different 20S proteasome and PAN proteins to modulate the structure and ultimately the function of this central energy-dependent proteolytic system.
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Affiliation(s)
- Christopher J Reuter
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA
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Abstract
Proteasomes are large, multisubunit proteases that are found, in one form or another, in all domains of life and play a critical role in intracellular protein degradation. Although they have substantial structural similarity, the proteasomes of bacteria, archaea, and eukaryotes show many differences in architecture and subunit composition. This article discusses possible paths by which proteasomes may have evolved from simple precursors to the highly complicated and diverse complexes observed today.
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Affiliation(s)
- C Volker
- SmithKline Beecham Pharmaceuticals, UP 1345, 1250 South Collegeville Road, Collegeville, PA 19426-0989, USA
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Ulrich HD. Degradation or maintenance: actions of the ubiquitin system on eukaryotic chromatin. EUKARYOTIC CELL 2002; 1:1-10. [PMID: 12455966 PMCID: PMC118055 DOI: 10.1128/ec.1.1.1-10.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Helle D Ulrich
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.
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