Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system

Fuchs, Adrian C. D.; Maldoner, Lorena; Wojtynek, Matthias; Hartmann, M.D.; Martin, Jörg

doi:10.1038/s41467-018-05198-1

Cited by 23 publications

(17 citation statements)

References 60 publications

(92 reference statements)

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“…The catalytic groove in the MPN domain of JAMM-family DUBs accommodates the C-terminal tail of Ub for cleavage 25,26,37 . The first insertion in the JAMM core (i.e., Ins-1) forms a β-sheet with the C-terminal tail of Ub in the catalytic groove (Fig.…”

Section: Resultsmentioning

confidence: 99%

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

et al. 2019

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Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48–UN complex and its assembly.

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Section: Resultsmentioning

confidence: 99%

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

et al. 2019

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“…Archaebacteria and hadobacterium Thermus have a tagging mechanism whose tags (SAMPs) are distantly related to ubiquitin, but sampylation requires only the E1 enzyme, not E1, E2, and E3 like eukaryotic ubiquitylation (Fu et al 2016). A few filarchaeote archaebacteria (some Asgards, and thaumarchaeote Candidatus Caldiarchaeum subterraneum) have genuine ubiquitylation (Fuchs et al 2018); though that was assumed to be 'ancestral', ubiquitylation more likely evolved in eubacteria as E2 homologues abound in Planctobacteria and also occur i n Posibacteria, Cyanobacteria, and Myxococcus. Attributing all these eubacterial ubiquitylating enzymes to multiple LGTs from eukaryotes (Arcas et al 2013) seems just to reflect the widespread, essentially evidence-free, prejudice that the universal root is in the neomuran stem: in fact on their ML tree, the eukaryotic E2s are a clade robustly within paraphyletic eubacteria and closer to Planctomycetia than to most posibacterial and cyanobacterial sequences (Arcas et al 2013).…”

Section: Planctobacterial Origin Of Neomuramentioning

confidence: 99%

“…It was also once thought that ubiquitin (Ub) was restricted to eukaryotes, but Ub and ubiquitylation involving a cascade of E1, E2, and E3 enzymes is now well established in the thaumarchaeote Candidatus Caldiarchaeum subterraneum and related enzymes are known in Asgards (Fuchs et al 2018), so ubiquitylation was likely present in the last common ancestor of Filarchaeota. E2 homologues have now been discovered in Planctomycetes and in Cyanobacteria, both posibacteria phyla, and δ-proteobacterial genus Myxococcus.…”

Section: Planctobacterial Origin Of Neomuran Ubiquitin Systemmentioning

confidence: 99%

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Cavalier‐Smith

Chao

2020

Protoplasma

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Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many ‘rDNA-phyla’ belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including ‘Asgardia’) and Euryarchaeota sensu-lato (including ultrasimplified ‘DPANN’ whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

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“…To verify these results in vitro, we incorporated the M. mazei MtrA-derived (5)KDPGA(10) sequence in a different protein, Caldiarchaeum subterraneum ubiquitin (26), and found that Connectase modifies it just like MtrA. Surprisingly, though, when we followed the time course of the reaction we found only a constant fraction (∼7%) of Ub-( 5)KDPGA( 10) modified at any time (Fig.…”

Section: Resultsmentioning

confidence: 83%

Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits

Fuchs

Ammelburg

Martin

et al. 2021

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

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Sequence-specific protein ligations are widely used to produce customized proteins “on demand.” Such chimeric, immobilized, fluorophore-conjugated or segmentally labeled proteins are generated using a range of chemical, (split) intein, split domain, or enzymatic methods. Where short ligation motifs and good chemoselectivity are required, ligase enzymes are often chosen, although they have a number of disadvantages, for example poor catalytic efficiency, low substrate specificity, and side reactions. Here, we describe a sequence-specific protein ligase with more favorable characteristics. This ligase, Connectase, is a monomeric homolog of 20S proteasome subunits in methanogenic archaea. In pulldown experiments with Methanosarcina mazei cell extract, we identify a physiological substrate in methyltransferase A (MtrA), a key enzyme of archaeal methanogenesis. Using microscale thermophoresis and X-ray crystallography, we show that only a short sequence of about 20 residues derived from MtrA and containing a highly conserved KDPGA motif is required for this high-affinity interaction. Finally, in quantitative activity assays, we demonstrate that this recognition tag can be repurposed to allow the ligation of two unrelated proteins. Connectase catalyzes such ligations at substantially higher rates, with higher yields, but without detectable side reactions when compared with a reference enzyme. It thus presents an attractive tool for the development of new methods, for example in the preparation of selectively labeled proteins for NMR, the covalent and geometrically defined attachment of proteins on surfaces for cryo-electron microscopy, or the generation of multispecific antibodies.

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Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system

Cited by 23 publications

References 60 publications

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits

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