Evidence map›Paper›PMID 25535391›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2015

Terpene synthases are widely distributed in bacteria.

Yuuki Yamada, Tomohisa Kuzuyama, Mamoru Komatsu, Kazuo Shin-Ya, Satoshi Omura, David E Cane, Haruo Ikeda

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 226 papers.

0numbers the graph read from it
0cells of the map it votes in
226citing papers in PubMed
14.9field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

226 citing papers in PubMed, 541 citations in OpenAlex.

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  7. Designed Water Capture in Terpene Synthase Catalysis.Chembiochem : a European journal of chemical biology · 2026
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166 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 4 institutions in 2 countries.

Yuuki YamadaLaboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan;
Tomohisa KuzuyamaBiotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan;
Mamoru KomatsuLaboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan;
Kazuo Shin-YaNational Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
Satoshi OmuraLaboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8461, Japan; and omuras@insti.kitasato-u.ac.jp ikeda@ls.kitasato-u.ac.jp.
David E CaneDepartment of Chemistry, Brown University, Providence, RI 02912-9108.
Haruo IkedaLaboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan; omuras@insti.kitasato-u.ac.jp ikeda@ls.kitasato-u.ac.jp.
Kitasato University · JPBrown University · USNational Institute of Advanced Industrial Science and Technology · JPThe University of Tokyo · JP

Funding

STEREOCHEMICAL STUDIES OF ISOPRENOID BIOSYNTHESISR01GM030301 · NIGMS · BROWN UNIVERSITY · PI CANE, DAVID E · 1985 to 2015
$5.4M
STEROCHEMICAL STUDIES 0F ISOPRENOID BIOSYNTHESISR37GM030301 · NIGMS · BROWN UNIVERSITY · PI CANE, DAVID E · 1994 to 2003
$1.8M
NIGMS NIH HHS GM30301NIGMS NIH HHS R01 GM030301NIGMS NIH HHS R37 GM030301
6 · The paper itself

Abstract

Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes.

Indexed as

Alkyl and Aryl TransferasesBacteriaMarkov ChainsAlkyl and Aryl Transferasesterpene synthasebacteriaheterologous expressionterpene synthase

Identifiers

PMID25535391
PMCPMC4311827
OpenAlexW2073073672

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.