A proteomic determination of cold adaptation in the Antarctic archaeon, <i>Methanococcoides burtonii</i>

Goodchild, Amber; Saunders, Neil F. W.; Ertan, Haluk; Raftery, Mark J.; Guilhaus, Michael; Curmi, Paul M. G.; Cavicchioli, Ricardo

doi:10.1111/j.1365-2958.2004.04130.x

Cited by 141 publications

(186 citation statements)

References 54 publications

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“…Hence, an interaction of Rpb7 with the clamp during initiation is very likely 3 but the role of this interaction and the exact function of Rpb7 in initiation are unclear. The observation that the intracellular levels of EЈ increase during growth at low temperatures (29) suggest that this EЈ facilitates transcription at low temperatures and our present data show a role of EЈ in open-complex formation. It is unclear whether EЈ is essential for growth of archaeal cells but cell-free transcription data demonstrate that EЈ is dispensable for cell-free transcription of the gdh promoter at temperatures between 70 (Fig.…”

Section: Discussionsupporting

confidence: 49%

The RPB7 Orthologue E′ Is Required for Transcriptional Activity of a Reconstituted Archaeal Core Enzyme at Low Temperatures and Stimulates Open Complex Formation

Naji

Grünberg

Thomm

2007

Journal of Biological Chemistry

121

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RNA polymerases from Archaea and Eukaryotes consist of a core enzyme associated with a dimeric E F (Rpb7/Rpb4) subcomplex but the functional contribution of the two subunit subcomplexes to the transcription process is poorly understood. Here we report the reconstitution of the 11-subunit RNA polymerase and of the core enzyme from the hyperthermophilic Archaeon Pyrococcus furiosus. The core enzyme showed significant activity between 70 and 80°C but was almost inactive at 60°C. E stimulated the activity of the core enzyme at 60°C, dramatically suggesting an important role of this subunit at low growth temperatures. Subunit F did not contribute significantly to catalytic activity. Permanganate footprinting at low temperatures dissected the contributions of the core enzyme, subunit E , and of archaeal TFE to open complex formation. Opening in the ؊2 and ؊4 region could be achieved by the core enzyme, subunit E stimulated bubble formation in general and opening at the upstream end of the transcription bubble was preferably stimulated by TFE. Analyses of the kinetic stabilities of open complexes revealed an unexpected E -independent role of TFE in the stabilization of open complexes. Transcription in cells of Archaea andBacteria is catalyzed by a single RNA polymerase (RNAP), 2 whereas eukaryotic cells contain three different types of RNAPs (I, II, and III) that carry out specialized functions. Despite their morphological similarity to Bacteria, Archaea have a transcriptional machinery that is more akin to the eukaryotic machinery (1-3).Like eukaryotes, Archaea use extrinsic transcription factors for initiation. The process of transcription initiation in Archaea can be dissected in three steps. The general transcription factor TATA-binding protein (TBP) interacts with the archaeal TATA box, transcription factor B (TFB) stabilizes the binding of TBP to the promoter. The TBP-TFB promoter complex mediates recruitment of RNAP (4, 5). These extrinsic factors show the major structural features of eukaryotic TBP and TFIIB and interact with DNA and RNAP in a similar fashion as their eukaryotic counterparts (6, 7). This exceptional degree of similarity between the archaeal and eukaryotic transcriptional machineries extends also to the RNAP.Archaeal RNAP consist of 11 or 12 different subunits (8 -10) that display a high level of primary sequence similarity to the subunits present in eukaryotic RNAPII. With the exception of subunits RPB8 and RPB9, orthologs of other RNAPII subunits have been identified in all archaeal genomes studied so far. A recent in silico study revealed a high degree of conservation of subunits shared by pol II and Archaea in particular in the regions of RNAP comprising the catalytic center and proteinprotein binding studies showed a similar pattern of subunit interactions between the subunits of pol II and of Pyrococcus RNAP (11). Although very similar to eukaryotic RNAP in subunit composition and transcription initiation factor requirement the archaeal machinery is less complex than the eukaryotic machine...

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Section: Discussionsupporting

confidence: 49%

The RPB7 Orthologue E′ Is Required for Transcriptional Activity of a Reconstituted Archaeal Core Enzyme at Low Temperatures and Stimulates Open Complex Formation

Naji

Grünberg

Thomm

2007

Journal of Biological Chemistry

121

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“…Finally, GB was recently found to be demethylated by some marine archaea in the methanogenic genus Methanococcoides (62,63). Only the genome of Methanococcoides burtonii has been sequenced and is publically available (64), but it is the only methanogen presently known to carry a non-Pyl MttB, and it will be interesting to see whether this enzyme plays a role in quaternary amine demethylation.…”

Section: Discussionmentioning

confidence: 99%

A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase

Ticak

Kountz²,

Girosky³

et al. 2014

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

157

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Significance Pyrrolysine, the 22nd amino acid, is found in few proteins. One, the trimethylamine methyltransferase MttB, forms a small portion of a large family of proteins. Most in this family lack pyrrolysine and have no known activity. We show that one such protein, MtgB, is a glycine betaine methyltransferase, providing functional context that may explain the relationship between family members with and without pyrrolysine. Close relatives of MtgB are encoded in many of the abundant bacteria in the oceans, as well as different microbes undertaking symbioses ranging from plants to humans. This finding implies that MtgB might partake in a widespread and underappreciated pathway of GB metabolism contributing significantly to global carbon and nitrogen cycling as well as human health.

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“…Cotranscription of pylTSBCD is likely by inspection of the M. acetivorans sequence (8) and has been demonstrated for pylTSBC in M. barkeri (7). The same pylTSBCD arrangement has been maintained in all sequenced Methanosarcina and Methanococcoides genomes (7,(14)(15)(16). Surprisingly, this order of genes has also been found in a single genus of Gram-positive bacterium, Desulfitobacterium hafniense (ref.…”

mentioning

confidence: 96%

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

Longstaff

Larue

Faust

et al. 2007

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

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Pyrrolysine has entered natural genetic codes by the translation of UAG, a canonical stop codon. UAG translation as pyrrolysine requires the pylT gene product, an amber-decoding tRNA Pyl that is aminoacylated with pyrrolysine by the pyrrolysyl-tRNA synthetase produced from the pylS gene. The pylTS genes form a gene cluster with pylBCD, whose functions have not been investigated. The pylTSBCD gene order is maintained not only in methanogenic Archaea but also in a distantly related Gram-positive Bacterium, indicating past horizontal gene transfer of all five genes. Here we show that lateral transfer of pylTSBCD introduces biosynthesis and genetic encoding of pyrrolysine into a naïve organism. PylS-based assays demonstrated that pyrrolysine was biosynthesized in Escherichia coli expressing pylBCD from Methanosarcina acetivorans. Production of pyrrolysine did not require tRNA Pyl or PylS. However, when pylTSBCD were coexpressed with mtmB1, encoding the methanogen monomethylamine methyltransferase, UAG was translated as pyrrolysine to produce recombinant monomethylamine methyltransferase. Expression of pylTSBCD also suppressed an amber codon introduced into the E. coli uidA gene. Strains lacking one of the pylBCD genes did not produce pyrrolysine or translate UAG as pyrrolysine. These results indicated that pylBCD gene products biosynthesize pyrrolysine using metabolites common to Bacteria and Archaea and, furthermore, that the pyl gene cluster represents a ''genetic code expansion cassette,'' previously unprecedented in natural organisms, whose transfer allows an existing codon to be translated as a novel endogenously synthesized free amino acid. Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code.T ranslated in-frame amber (TAG/UAG) codons in the genes encoding methylamine methyltransferases from Methanosarcina barkeri (1-3) were early clues to the existence of pyrrolysine as the 22nd genetically encoded amino acid from nature. Crystallography of MtmB1, the monomethylamine methyltransferase, demonstrated that the UAG codon of the encoding mtmB1 gene corresponds to pyrrolysine, whose structure was proposed as lysine with N in amide linkage with the D-isomer of 4-methyl-pyrroline-5-carboxylate (4, 5). This structure is consistent with the UAG-encoded residue's mass in three distinct methylamine methyltransferases (6).Near the mtmB1 gene in Methanosarcina spp. are the pyl genes (ref. 7; Fig. 1). Two of these genes are known to underlie the genetic encoding of pyrrolysine. The pylT encodes tRNA Pyl , whose CUA anticodon complements the UAG codon corresponding to pyrrolysine. Deletion of the pyl gene promoter and pylT leads to loss of pyrrolysine-dependent monomethylamine methyltransferase and methylamine metabolism (8). The pylS gene encodes the pyrrolysyl-tRNA synthetase, PylS, which charges tRNA Pyl with chemically synthesized pyrrolysine and further carries out a pyrrolysine-dependent ATP:pyrophosphate exchange reaction (5, 9-11)...

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A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii

Cited by 141 publications

References 54 publications

The RPB7 Orthologue E′ Is Required for Transcriptional Activity of a Reconstituted Archaeal Core Enzyme at Low Temperatures and Stimulates Open Complex Formation

The RPB7 Orthologue E′ Is Required for Transcriptional Activity of a Reconstituted Archaeal Core Enzyme at Low Temperatures and Stimulates Open Complex Formation

A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine

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