Proteasomes from Structure to Function: Perspectives from Archaea

Maupin-Furlow, Julie A.; Humbard, Matthew A.; Kirkland, P. Aaron; Li, Wei; Reuter, Christopher J.; Wright, Andrew Martin; Zhou, Guannan

doi:10.1016/s0070-2153(06)75005-0

Cited by 53 publications

(53 citation statements)

References 292 publications

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“…Although they share similarities to both prokaryotes and eukaryotes they have evolved many unique ecological and life-style adaptations. Archaea have become models for the characterization of specific cellular machineries they share with eukaryotes such as those involved in replication (Grabowski and Kelman 2003) and protein degradation (Maupin-Furlow et al 2006). Despite the increasing availability of genome sequences, the use of archaea as model organisms has been slow, mainly because most archaeal organisms cannot be cultured under standard laboratory conditions and few archaeal genetic systems have been developed (Allers and Mevarech 2005).…”

Section: Introductionmentioning

confidence: 99%

A Gateway platform for functional genomics inHaloferax volcanii: deletion of three tRNA modification genes

Yacoubi

Phillips

Blaby‐Haas

et al. 2009

Archaea

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SummaryIn part due to the existence of simple methods for its cultivation and genetic manipulation, Haloferax volcanii is a major archaeal model organism. It is the only archaeon for which the whole set of post-transcriptionally modified tRNAs has been sequenced, allowing for an in silico prediction of all RNA modification genes present in the organism. One approach to check these predictions experimentally is via the construction of targeted gene deletion mutants. Toward this goal, an integrative "Gateway vector" that allows gene deletion in H. volcanii uracil auxotrophs was constructed. The vector was used to delete three predicted tRNA modification genes: HVO_2001 (encoding an archaeal transglycosyl tranferase or arcTGT), which is involved in archeosine biosynthesis; HVO_2348 (encoding a newly discovered GTP cyclohydrolase I), which catalyzes the first step common to archaeosine and folate biosynthesis; and HVO_2736 (encoding a member of the COG1444 family), which is involved in N 4 -acetylcytidine (ac 4 C) formation. Preliminary phenotypic analysis of the deletion mutants was conducted, and confirmed all three predictions.

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Section: Introductionmentioning

confidence: 99%

A Gateway platform for functional genomics inHaloferax volcanii: deletion of three tRNA modification genes

Yacoubi

Phillips

Blaby‐Haas

et al. 2009

Archaea

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“…Proteasomes are energy-dependent proteases that are highly conserved and universally distributed within the Archaea and Eucarya domains (Maupin-Furlow et al, 2006). These enzymes form nanocompartments within the cell that selectively degrade specific proteins into oligopeptides that are hydrolysed to free amino acids by downstream peptidases.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional linkage of Haloferax volcanii proteasomal genes with non-proteasomal gene neighbours including RNase P, MOSC domain and SAM-methyltransferase homologues

2007

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Comparative genomics reveals a common theme of 20S proteasome and proteasome-activating nucleotidase genes dispersed throughout archaeal genomes yet arranged in conserved linkages with gene homologues of translation and/or transcription machineries. To provide biological evidence for these linkages as well as insight into proteasome operon organization, transcripts of the five proteasomal genes of the halophilic archaeon Haloferax volcanii were analysed by Northern (RNA) blotting, RT-PCR and primer extension. These included psmA, psmB and psmC, encoding the 20S proteasomal subunits a1, b and a2, as well as panA and panB, encoding the PanA and PanB proteasome-activating nucleotidase proteins, respectively. All five of these genes are dispersed throughout the H. volcanii genome. For each proteasomal gene, a distinct transcript was detected by Northern blotting that was similar in size to the respective coding region. For both psmA and psmC, an additional transcript was detected that was 1.34 and 0.85 kb greater, respectively, than the coding region. Further analysis by Northern blotting and RT-PCR revealed that psmA was co-transcribed with genes encoding a Pop5 homologue of the RNase P endoRNase as well as an S-adenosylmethionine (SAM)-dependent methyltransferase. Likewise, psmC was co-transcribed with a downstream gene encoding a molybdenum cofactor sulfurase C-terminal (MOSC) domain protein. Additional proteasomal and neighbouring gene-specific transcriptional linkages were detected by RT-PCR. These results provide the first evidence that proteasome and tRNA modification genes are co-transcribed, reveal that a number of additional enzymes including those predicted to facilitate metal-sulfur cluster assembly are co-regulated with proteasomes at the transcriptional level, and provide further insight into proteasome gene transcription in archaea.

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“…The levels of ␣2 protein increase severalfold, while the levels of ␣1 and ␤ proteins remain relatively constant as cells enter stationary phase (41). This is likely to allow for the regulated control of different 20S proteasome subtypes in the cell.Previous studies have shown that different post-and cotranslational modifications take place on the subunits of proteasomes and their regulatory particles in eukaryotic cells (33,42). These modifications, which include phosphorylation, N-terminal acetylation, autocatalytic cleavage of ␤ propeptides, and N myristoylation, are suggested to control a variety of functions.…”

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confidence: 99%

“…Although several of these events have been demonstrated, few phenotypes that are associated with these proteasomal modifications have been analyzed. Suggested biological functions include the steric hindrance of the 20S proteasome aperture, the association of regulatory particles with the 20S core, and the subcellular distribution of proteasomes (33,42). In this study, we identified N-terminal acetylation and phosphorylation sites on 20S proteasome proteins of H. volcanii.…”

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confidence: 99%

Posttranslational Modification of the 20S Proteasomal Proteins of the Archaeon Haloferax volcanii

2006

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20S proteasomes are large, multicatalytic proteases that play an important role in intracellular protein degradation. The barrel-like architecture of 20S proteasomes, formed by the stacking of four heptameric protein rings, is highly conserved from archaea to eukaryotes. The outer two rings are composed of ␣-type subunits, and the inner two rings are composed of ␤-type subunits. The halophilic archaeon Haloferax volcanii synthesizes two different ␣-type proteins, ␣1 and ␣2, and one ␤-type protein that assemble into at least two 20S proteasome subtypes. In this study, we demonstrate that all three of these 20S proteasomal proteins (␣1, ␣2, and ␤) are modified either post-or cotranslationally. Using electrospray ionization quadrupole time-of-flight mass spectrometry, a phosphorylation site of the ␤ subunit was identified at Ser129 of the deduced protein sequence. In addition, ␣1 and ␣2 contained N-terminal acetyl groups. These findings represent the first evidence of acetylation and phosphorylation of archaeal proteasomes and are one of the limited examples of post-and/or cotranslational modification of proteins in this unusual group of organisms.26S proteasomes are central proteolytic enzymes of the ubiquitin-mediated degradation pathway in eukaryotes. The 20S core particle of 26S proteasomes is responsible for the hydrolysis of peptide bonds, and the overall architecture of this complex is conserved from archaea to eukaryotes (12). The 20S proteasomes are chambered proteases with the proteolytic N-terminal Thr active site sequestered within a cylindrical complex composed of 28 proteins associated as four heptameric rings of ␣-and ␤-type subunits (2). The ␣-type subunits form the outer two rings, and the ␤-type subunits form the inner two rings that comprise the central proteolytic chamber.In the halophilic archaeon Haloferax volcanii, there are two ␣-type (␣1 and ␣2) subunits and one ␤-type proteasomal subunit (54). The N-terminal protein sequence of the ␤ subunit purified from 20S proteasomes reveals an N-terminal Thr residue exposed via posttranslational cleavage which is likely to form the active site (54). In contrast, the ␣ subunits are not amenable to N-terminal sequencing, suggesting that these proteins are modified at their N termini (54).Two subtypes of 20S proteasome complexes have been identified in stationary-phase cells and are denoted ␣1␤-and ␣1␤␣2-20S, with the latter containing both ␣-type subunits in a single 20S proteasome (20). Interestingly, both ␣1 and ␣2 proteins form homo-oligomeric rings and ␣1-␣1 and ␣2-␣2 contacts (versus ␣1-␣2 contacts) are detected in 20S proteasome complexes (20). Thus, the ␣1␤␣2-20S core particle is proposed to be an asymmetric proteasome, with the stacked rings arranged in an ␣1:␤:␤:␣2 configuration. The ␣1␤-20S proteasome, in contrast, is in a symmetrical ␣1:␤:␤:␣1 configuration. The levels of ␣2 protein increase severalfold, while the levels of ␣1 and ␤ proteins remain relatively constant as cells enter stationary phase (41). This is likely to allow for the regul...

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Proteasomes from Structure to Function: Perspectives from Archaea

Cited by 53 publications

References 292 publications

A Gateway platform for functional genomics inHaloferax volcanii: deletion of three tRNA modification genes

A Gateway platform for functional genomics inHaloferax volcanii: deletion of three tRNA modification genes

Transcriptional linkage of Haloferax volcanii proteasomal genes with non-proteasomal gene neighbours including RNase P, MOSC domain and SAM-methyltransferase homologues

Posttranslational Modification of the 20S Proteasomal Proteins of the Archaeon Haloferax volcanii

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