Structure and Mutation Analysis of Archaeal Geranylgeranyl Reductase

Sasaki, Daisuke; Fujihashi, M.; Iwata, Yuji; Murakami, Mayuko; Yoshimura, Teizo; Hemmi, Hisashi; Miki, Kunio

doi:10.1016/j.jmb.2011.04.002

Cited by 38 publications

(75 citation statements)

References 71 publications

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“…5. This idea contrasts with the proposed reduction mechanism of an archaeal membrane lipid synthetic GGR, whereby the isoalloxazine ring of FAD resides near the entrance of a substrate pocket which makes it potentially accessible to the full length of a geranylgeranyl chain in order to achieve complete reduction [31,32].…”

Section: Discussionmentioning

confidence: 87%

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

et al. 2014

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Saturation of a prenyl group to various levels is a frequently observed modification of isoprenoids. The members of the geranylgeranyl reductase family, however, are the only known enzymes responsible for such reductive modifications in archaea. A methanogenic archaeon, Methanosarcina acetivorans, has proteins homologous to phytoene desaturase CrtI, which is the carotenogenic enzyme that catalyzes oxidation/isomerization of phytoene to lycopene, but their function in carotenogenesis is unlikely in a methanogen that does not produce carotenoids. In the present study, we identified one of the homologues, MA1492, as a new type of archaeal geranylgeranyl reductase that is not homologous to known geranylgeranyl reductases. The expression of MA1492 in Escherichia coli cells, which were genetically modified to produce unsaturated archaeal‐type lipids, led to the production of partially saturated lipid derivatives. Furthermore, we analyzed the substrate specificity of recombinant MA1492 via in vitro assays. The LC‐MS, or radio‐TLC, analysis of the reaction products showed that the enzyme was definitely specific to compounds containing C20 geranylgeranyl groups and reduced only one of four double bonds in a geranylgeranyl chain. The GC‐MS analysis of the product from geranylgeraniol confirmed that the reduction selectively occurred on the ω‐terminal double bond. The available crystallographic structure of an orthologue enzyme may explain the reaction mechanism that achieves the substrate specificity and regiospecificity. Database Microbial Genome Database (http://mbgd.genome.ad.jp/), EMBOSS Needle (https://www.ebi.ac.uk/Tools/psa/emboss_needle)

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Section: Discussionmentioning

confidence: 87%

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

et al. 2014

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“…This finding was unexpected because a few characterized GGR enzymes from prokaryotes and plants have been shown to perform their reactions without requiring the presence of additional proteins (25,40). The exclusive distribution of LIL3 to the green lineage of photosynthetic eukaryotes also raises the question why only Viridiplantae GGR requires LIL3 (6,7).…”

Section: Discussionmentioning

confidence: 99%

“…The exclusive distribution of LIL3 to the green lineage of photosynthetic eukaryotes also raises the question why only Viridiplantae GGR requires LIL3 (6,7). Considering that GGRs from various organisms are known to accept multiple substrates, such as GGPP, Chl-GG, or 2,3-di-O-geranylgeranylglyceryl phosphate (25,40), it is reasonable to consider that LIL3 is involved in the supply of certain substrates to the GGR reactions in Viridiplantae. In particular, it is interesting to consider that LIL3 holds the tetrapyrrole groups of the substrates of the GGR reaction with its LHC motif to provide them to GGR.…”

Section: Discussionmentioning

confidence: 99%

Functional Analysis of Light-harvesting-like Protein 3 (LIL3) and Its Light-harvesting Chlorophyll-binding Motif in Arabidopsis

Takahashi

Takabayashi

Tanaka

et al. 2014

Journal of Biological Chemistry

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Background:The light-harvesting complex (LHC) motif is an amino acid consensus sequence found in various thylakoid proteins. Results: Modification and replacement of the transmembrane domain encompassing the LHC motif of a plant protein retains its membrane-anchoring function but impairs its protein-protein interaction. Conclusion: This domain functions in membrane anchoring and complex formation. Significance: This study provides new insights regarding the function of the LHC motif.

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“…4) (52, 53). The cofactor for GGR is FADH 2 , and it is most likely regenerated by e − supplied by NAD(P)H 2 (54). Thus, the saturation step in GDGT synthesis requires the cell to supply not only e − but also additional chemical energy (ATP) and/or proton-motive force to rereduce the cofactors; the energetic needs may be similar to transhydrogenation in bacteria (55).…”

Section: Cellular Energy Balance and The Synthesis Of Gdgts: The Redumentioning

confidence: 99%

Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX ₈₆ temperature proxy

Hurley

Elling

Könneke

et al. 2016

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

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Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX 86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX 86 and sea surface temperature (SST) remains unresolved: How does TEX 86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX 86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R 2 = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX 86 ratio decreases by an equivalent of 5.4°C of calculated temperature over a 5.5 fmol·cell −1 ·d −1 increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX 86 . Depth profiles from the marine water column show minimum TEX 86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX 86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX 86 -SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature.T he glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids of Archaea are abundant in marine water columns and sediments. The major source of GDGTs to ocean sediments is thought to be planktonic, ammonia-oxidizing Archaea (AOA) affiliated with the phylum Thaumarchaeota (formerly Marine Group I Crenarchaeota) (1, 2). Thaumarchaeota play a primary role in the nitrogen cycle, performing the first and rate-limiting step of nitrification-namely, the oxidation of ammonia to nitrite (3-5). Accordingly, Thaumarchaeota are most abundant at the base of, or below, the euphotic zone (6-9). Based on the phylogeny of their ammonia monooxygenase gene, the planktonic Thaumarchaeota are divided into two distinct clusters, the Water Column Cluster A that is most abundant in the epi-and upper mesopelagic (above ∼200 to ∼500 m, depending on location) and the Water Column Cluster B that dominates thaumarchaeal assemblages in the deeper mesopelagic and bathypelagic (7-10). These clusters putatively represent thaumarchaeal ecotypes adapted to high and low ammonium flux, respectively (11,12).Thaumarchaeota produce GDGTs containing from zero to four cyclopentane rings (GDGT-0 to GDGT-4) or four cyclopentane rings and one additional cyclohexane ring (e.g., in crenarchaeol;...

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Structure and Mutation Analysis of Archaeal Geranylgeranyl Reductase

Cited by 38 publications

References 71 publications

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

Functional Analysis of Light-harvesting-like Protein 3 (LIL3) and Its Light-harvesting Chlorophyll-binding Motif in Arabidopsis

Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX ₈₆ temperature proxy

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Structure and Mutation Analysis of Archaeal Geranylgeranyl Reductase

Cited by 38 publications

References 71 publications

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity

Functional Analysis of Light-harvesting-like Protein 3 (LIL3) and Its Light-harvesting Chlorophyll-binding Motif in Arabidopsis

Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX 86 temperature proxy

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Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX ₈₆ temperature proxy