A Methanocaldococcus jannaschii Archaeal Signature Gene Encodes for a 5-Formaminoimidazole-4-carboxamide-1-β-d-ribofuranosyl 5′-Monophosphate Synthetase

Ownby, Katie E.; Xu, Huimin; White, Robert H.

doi:10.1074/jbc.m413937200

Cited by 25 publications

(38 citation statements)

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“…Given the requirement for 10-formyltetrahydrofolate (and not an archaeal folate analogue), a different enzyme must participate in the conversion of AICAR to FAICAR in non-folate-containing archaea. The search for AICAR formyltransferase activity in these archaea led to the discovery that the archaeal signature purP gene product served this function in some archaeal species, using formate as a carbon source [8]. …”

Section: Resultsmentioning

confidence: 99%

“…Except for Methanosaeta thermophila , the Methanosarcinales also have a full-length purH -like gene, in addition to multiple genes (typically two) encoding a protein similar to the well-characterized M. jannaschii PurP [8]. It is unclear whether these PurP-like proteins are functional in these species, or whether the PurH-like protein catalyzes the necessary conversions alone.…”

Section: Resultsmentioning

confidence: 99%

“…M. jannaschii MJ0136, in cluster Ia, is the formate-dependent AICAR formyltransferase originally designated PurP [8]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have no AICAR formyltransferase activity previously [66], although activity under different conditions or with different substrates cannot be ruled out.…”

Section: Resultsmentioning

confidence: 99%

“…For decades, the story of purine biosynthesis seemed mostly complete, with only a few new enzymes added to the pathway [4-6]. However, with increased study of archaea and the availability of archaeal genomes, it became clear that the purine biosynthesis pathway in many archaea included several unique enzymes [7,8]. …”

Section: Introductionmentioning

confidence: 99%

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Purine biosynthesis in archaea: variations on a theme

et al. 2011

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BackgroundThe ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains.ResultsWe searched the Integrated Microbial Genome system (IMG) for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function.Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified.Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected) or Enzyme Commission (E. C.) numbers (57 proteins, 7.7%). There were also 57 proteins (7.7%) assigned overly generic names and 78 proteins (10.6%) without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified.ConclusionsThe patchy distribution of purine biosynthetic genes in archaea is consistent with a pathway that has been shaped by horizontal gene transfer, duplication, and gene loss. Our results indicate that manual curation can improve upon automated annotation for a small number of automatically-annotated proteins and can reveal a need to identify further pathway components even in well-studied pathways.ReviewersThis article was reviewed by Dr. Céline Brochier-Armanet, Dr Kira S Makarova (nominated by Dr. Eugene Koonin), and Dr. Michael Galperin.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Purine biosynthesis in archaea: variations on a theme

et al. 2011

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“…Methanocaldococcus jannaschii purP gene Mj0136 was cloned into the expression vector pET19b and overexpressed in Escherichia coli B834(DE3), a methionine auxotrophic strain (15). For overexpression of native protein, cells were grown in LB medium supplemented with 100 µg/mL ampicillin.…”

Section: Overexpression and Purification Of Mjpurpmentioning

confidence: 99%

Crystal Structure and Function of 5-Formaminoimidazole-4-carboxamide Ribonucleotide Synthetase from Methanocaldococcus jannaschii^,

2007

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Purine biosynthesis requires ten enzymatic steps in higher organisms while prokaryotes require an additional enzyme for step six. In most organisms steps nine and ten are catalyzed by the purH gene product, a bifunctional enzyme with both 5-formaminoimidazole-4-carboxamide-5′-monophosphate ribonucleotide (FAICAR) synthase and inosine monophosphate (IMP) cyclohydrolase activity. Recently it was discovered that Archaea utilize different enzymes to catalyze steps nine and ten. An ATP dependent FAICAR synthetase is encoded by the purP gene and IMP cyclohydrolase is encoded by the purO gene. We have determined the X-ray crystal structures of FAICAR synthetase from Methanocaldococcus jannaschii complexed with various ligands, including the tertiary substrate complex and product complex. The enzyme belongs to the ATP grasp superfamily and is predicted to use a formylphosphate intermediate formed by an ATP-dependent phosphorylation. In addition, we have determined the structures of a PurP ortholog from Pyrococcus furiosus, which is functionally unclassified, in three crystal forms. With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP.The purine biosynthetic pathway generates inosine monophosphate, which is subsequently converted to either adenosine monophosphate or guanosine monophosphate. Buchanan worked out the details of the vertebrate pathway in the 1950's identifying ten enzymatic conversions (1). Later, Stubbe and coworkers showed that in prokaryotes the conversion of aminoamidazole ribonucleotide to carboxyaminoamidazole ribonucleotide catalyzed by PurE in step 6 requires an additional enzyme (PurK) (2-4), resulting in a total of eleven enzymatic conversions. In Escherichia coli each step of the pathway is catalyzed by a monofunctional enzyme, with the exception of the last two steps, while in vertebrates steps 2 (PurD), 3 (PurN) and 5 (PurM) comprise a trifunctional enzyme (5), steps 6 (PurE) and 7 (PurC) comprise a bifunctional enzyme (6,7) and steps 9 and 10 are catalyzed by the bifunctional enzyme PurH (8-11). Additional species dependent gene fusions have been observed.Other deviations from the vertebrate purine biosynthetic pathway have also been observed. In vertebrates, formyltransferase reactions occur in steps 3 (PurN) and 9 (PurH), with N 10 - † This work was supported by National Institutes of Health grants RR15301 and GM073220. SEE is indebted to the W. MATERIALS AND METHODS Overexpression and Purification of MjPurPMethanocaldococcus jannaschii purP gene Mj0136 was cloned into the expression vector pET19b and overexpressed in Escherichia coli B834(DE3), a methionine auxotrophic strain (15). For overexpression of native protein, cells were grown in LB medium supplemented with 100 µg/mL ampicillin. For overexpression of selenomethionine (SeMet) substituted protein, cells were grown in M9 minimal salts supplemented with 4% (w/v) glucos...

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Geochemische Kontinuität und Katalysator/Cofaktor‐Austausch für Ursprung und Evolution des Lebens

Fontecilla‐Camps

2018

Angewandte Chemie

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Zwei Hypothesen konkurrieren vorrangig um eine Erklärung des Ursprungs allen Lebens: “Genetics First” und “Metabolism First”. Die Erste basiert auf dem Miller‐Uray‐Experiment und auf organischen Molekülen, die auf Meteoriten und Kometen gefunden wurden. Sie geht von einem heterotrophen Ursprung des Lebens aus und steht im Einklang mit dem Konzept einer “RNA‐Welt”. Die “Metabolism‐First”‐Hypothese postuliert einen autotrophen Ursprung des Lebens, basierend auf Mineralien und/oder hydrothermalen Quellen. Unmittelbare Beweise zur Untersützung einer der beiden Hypothesen fehlen. Der “Metabolism‐First”‐Hypothese kann jedoch nachgegangen werden, wenn man einen kontinuierlichen, geochemischen, katalytisch‐dynamischen Prozess zugrunde legt. Unter Anwendung dieses Ansatzes stelle ich die Vermutung an, dass sich die Purin‐ und Pyrimidinsynthese auf sich auf mineralischen Oberflächen entwickelt hat, die später durch ATP ersetzt wurden. Dieses Konzept lässt sich auf Redoxprozesse erweitern, bei denen metallgebundene Hydride später durch NAD ersetzt werden konnten.

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A Methanocaldococcus jannaschii Archaeal Signature Gene Encodes for a 5-Formaminoimidazole-4-carboxamide-1-β-d-ribofuranosyl 5′-Monophosphate Synthetase

Cited by 25 publications

References 46 publications

Purine biosynthesis in archaea: variations on a theme

Purine biosynthesis in archaea: variations on a theme

Crystal Structure and Function of 5-Formaminoimidazole-4-carboxamide Ribonucleotide Synthetase from Methanocaldococcus jannaschii^,

Geochemische Kontinuität und Katalysator/Cofaktor‐Austausch für Ursprung und Evolution des Lebens

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A Methanocaldococcus jannaschii Archaeal Signature Gene Encodes for a 5-Formaminoimidazole-4-carboxamide-1-β-d-ribofuranosyl 5′-Monophosphate Synthetase

Cited by 25 publications

References 46 publications

Purine biosynthesis in archaea: variations on a theme

Purine biosynthesis in archaea: variations on a theme

Crystal Structure and Function of 5-Formaminoimidazole-4-carboxamide Ribonucleotide Synthetase from Methanocaldococcus jannaschii,

Geochemische Kontinuität und Katalysator/Cofaktor‐Austausch für Ursprung und Evolution des Lebens

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Crystal Structure and Function of 5-Formaminoimidazole-4-carboxamide Ribonucleotide Synthetase from Methanocaldococcus jannaschii^,