Affinity Purification of an Archaeal DNA Replication Protein Network

Li, Zhuo; Santangelo, Thomas J.; Čuboňová, Ľubomíra; Reeve, John N.; Kelman, Zvi

doi:10.1128/mbio.00221-10

Cited by 78 publications

(118 citation statements)

References 44 publications

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“…These results suggested that PolD is the major replicative DNA polymerase in methanococci and PolB plays a secondary role or is redundant with another protein. In support of this conclusion, in Thermococcus kodakarensis PolD can be coisolated with proliferating cell nuclear antigen (PCNA) and other proteins of the archaeal replication fork (15). Although PolB coisolated with the replication proteins minichromosome maintenance 2 (MCM2) and replication protein A-3 (RPA3), most of its associations were with proteins whose roles have yet to be defined.…”

Section: Resultsmentioning

confidence: 70%

“…Two other genes of M. maripaludis S2 that encode hypothetical proteins share homology with proteins that copurified with the replication fork complex of T. kodakarensis (15). Although their functions are unknown in both archaea, MMP0668 (homolog to TK1313) and MMP1392 (homolog to TK0358) were both possibly essential and may play important roles in archaeal replication.…”

Section: Resultsmentioning

confidence: 99%

“…In contrast, a homolog of the bacterial DnaG-type primase, MMP1286, was nonessential. A homolog of this protein in T. kodakarensis (TK1410) copurified with the exosome complex (15), and the presence of both primase activities has been reported in Sulfolobus solfataricus (21). Other possibly essential genes related to replication were the processivity factors PCNA (MMP1126 and 1711), DNA topoisomerases (MMP0956, 0989, and 1437), and DNA ligase (MMP0970).…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

Sarmiento

Mrázek

Whitman

2013

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

132

140

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A comprehensive whole-genome analysis of gene function by transposon mutagenesis and deep sequencing methodology has been implemented successfully in a representative of the Archaea domain. Libraries of transposon mutants were generated for the hydrogenotrophic, methanogenic archaeon Methanococcus maripaludis S2 using a derivative of the Tn5 transposon. About 89,000 unique insertions were mapped to the genome, which allowed for the classification of 526 genes or about 30% of the genome as possibly essential or strongly advantageous for growth in rich medium. Many of these genes were homologous to eukaryotic genes that encode fundamental processes in replication, transcription, and translation, providing direct evidence for their importance in Archaea. Some genes classified as possibly essential were unique to the archaeal or methanococcal lineages, such as that encoding DNA polymerase PolD. In contrast, the archaeal homolog to the gene encoding DNA polymerase B was not essential for growth, a conclusion confirmed by construction of an independent deletion mutation. Thus PolD, and not PolB, likely plays a fundamental role in DNA replication in methanococci. Similarly, 121 hypothetical ORFs were classified as possibly essential and likely play fundamental roles in methanococcal information processing or metabolism that are not established outside this group of prokaryotes.Tn-seq | polyploidy | methanogenesis

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Section: Resultsmentioning

confidence: 70%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis

Sarmiento

Mrázek

Whitman

2013

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

132

140

View full text Add to dashboard Cite

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“…This observation indicates that, as in eukaryotes, the multiple MCMs in M. maripaludis have evolved to perform specialized functions. Interestingly, protein interaction studies in T. kodakarensis show that nonessential MCM1 and MCM2 co-purify with proteins with known roles in DNA repair [51]; although a role for these MCMs in DNA repair has not be established. Our data demonstrating that multiple functional MCMs are present in M. maripaludis indicate that this organism provides a useful biochemical and genetic system that could provide further insight into eukaryotic MCM function.…”

Section: Discussionmentioning

confidence: 99%

Non-essential MCM-related proteins mediate a response to DNA damage in the archaeon Methanococcus maripaludis

Walters

Chong

2017

Microbiology

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The single minichromosome maintenance (MCM) protein found in most archaea has been widely studied as a simplified model for the MCM complex that forms the catalytic core of the eukaryotic replicative helicase. Organisms of the order Methanococcales are unusual in possessing multiple MCM homologues. The Methanococcus maripaludis S2 genome encodes four MCM homologues, McmA-McmD. DNA helicase assays reveal that the unwinding activity of the three MCM-like proteins is highly variable despite sequence similarities and suggests additional motifs that influence MCM function are yet to be identified. While the gene encoding McmA could not be deleted, strains harbouring individual deletions of genes encoding each of the other MCMs display phenotypes consistent with these proteins modulating DNA damage responses. M. maripaludis S2 is the first archaeon in which MCM proteins have been shown to influence the DNA damage response.

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“…While many replication factors have been identified using in silico approaches, it is clear that some factors and enzymes involved in archaeal replication have not yet been identified. In vivo tagging of known replication proteins and the isolation of complexes that copurified with them resulted in the identification of several putative new replication proteins (Li et al, 2010). For example, this strategy identified an archaeal protein that interacts with the GINS complex (Li et al, 2011).…”

Section: The Genetics Eramentioning

confidence: 99%