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Novel hopanoid cyclases from the environment

Pearson, Ann and Flood Page, Sarah R. and Jorgenson, Tyler L. and Fischer, Woodward W. and Higgins, Meytal B. (2007) Novel hopanoid cyclases from the environment. Environmental Microbiology, 9 (9). pp. 2175-2188. ISSN 1462-2912. doi:10.1111/j.1462-2920.2007.01331.x. https://resolver.caltech.edu/CaltechAUTHORS:20091116-092735268

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Abstract

Hopanoids are ubiquitous isoprenoid lipids found in modern biota, in recent sediments and in low-maturity sedimentary rocks. Because these lipids primarily are derived from bacteria, they are used as proxies to help decipher geobiological communities. To date, much of the information about sources of hopanoids has come from surveys of culture collections, an approach that does not address the vast fraction of prokaryotic communities that remains uncharacterized. Here we investigated the phylogeny of hopanoid producers using culture-independent methods. We obtained 79 new sequences of squalene-hopene cyclase genes (sqhC) from marine and lacustrine bacterioplankton and analysed them along with all 31 sqhC fragments available from existing metagenomics libraries. The environmental sqhCs average only 60% translated amino acid identity to their closest relatives in public databases. The data imply that the sources of these important geologic biomarkers remain largely unknown. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analysed here, yet the geologic record contains abundant hopanoids apparently of cyanobacterial origin. The data also suggest that hopanoid biosynthesis is uncommon: < 10% of bacterial species may be capable of producing hopanoids. A better understanding of the contemporary distribution of hopanoid biosynthesis may reveal fundamental insight about the function of these compounds, the organisms in which they are found, and the environmental signals preserved in the sedimentary record.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1111/j.1462-2920.2007.01331.xDOIArticle
http://www3.interscience.wiley.com/journal/118491310/abstractPublisherArticle
ORCID:
AuthorORCID
Pearson, Ann0000-0003-2785-8405
Fischer, Woodward W.0000-0002-8836-3054
Additional Information:© 2007 The Authors. Journal compilation © 2007 Society for Applied Microbiology and Blackwell Publishing Ltd. Received 9 January, 2007; accepted 2 April, 2007. We thank A.H. Knoll and R.E. Summons for helpful discussions; E.F. DeLong for discussions and editorial assistance; and K.-U. Hinrichs and an anonymous reviewer for their thorough reviews. M.C. Fisher, A.E. Ingalls, S.R. Shah, S.J. Carter, L.I. Aluwihare and R. Hansman are thanked for field assistance. This work was supported by NSF EAR-0311937 and NSF OCE-0241363 (to A.P.) and the David and Lucille Packard Foundation. Funding for genomic sequencing of selected microbial species and the availability of these data in the public domain are supported by The Institute for Genome Research (TIGR), the US Department of Energy (DOE and the J. Craig Venter Institute. We acknowledge the United Kingdom as the country of origin for the Sargasso Sea metagenome data. Supplementary material: The following supplementary material is available for this article online: Additional Methods. Description of PCR, cloning and sequencing protocols. Fig. S1. Pictorial representation of sample–primer–program combinations. Samples TJ1 and TJ2 are from LM; sample HIS is from the NCP. Fig. S2. Sample TJ1. Amplification of a 900 bp region of sqhC using fully degenerate primers designed to the cyanobacterial/actinomycetes group. Primers SHCF, SHCcyR. M, DNA marker; (–), template containing no SHC; (+), sample TJ1. Fig. S3. Sample TJ1. Amplification of sqhC using touchdown-nested programs. Primers SHCF, SHCcyR; amplicon 900 bp. Second amplification of this sample using nested primers SHCF and SHCNR; intended amplicon 700 bp and truncated amplicon 350 bp. M, DNA marker; Td, touchdown amplicon; N, nested amplicon. Table S1. Data for LM and NCP clones. Columns: (1) clone; (2) letter codes corresponding to Fig. 2; (3) closest described genus by TBLASTN; (4–8) expectation values and AA statistics; (9) other clones obtained by PCR with 99% translated AA identity to the named clone; (10) total frequency data used to create Fig. 2A and C; (11,12) confirmation of conserved motifs expected for SHCs (p., primer region). Table S2. Data for environmental metagenomes SS, FS, IM. Columns: (1) name; (2) GenBank GI number; (3) sequence coverage type; (4) closest described genus by TBLASTN; (5–8) expectation values and AA statistics. Table S3. Summary of the eight combinations of primer sets and PCR programs attempted for samples TJ1, TJ2 and HISurf. Symbols indicate (+) sequences obtained; (–) attempted, but no sqhC sequences obtained; n.a., no amplicon; shaded, not attempted. Table S4. Genera matched by forward and reverse primers, based on bacterial genomes available through JGI. Table S5. Translation of each degenerate primer, with melting temperatures. This material is available as part of the online article from http://www.blackwell-synergy.com
Funders:
Funding AgencyGrant Number
NSFEAR-0311937
NSFOCE-0241363
David and Lucille Packard FoundationUNSPECIFIED
The Institute for Genome Research (TIGR)UNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
J. Craig Venter InstituteUNSPECIFIED
Issue or Number:9
DOI:10.1111/j.1462-2920.2007.01331.x
Record Number:CaltechAUTHORS:20091116-092735268
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20091116-092735268
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16712
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:25 Nov 2009 21:46
Last Modified:08 Nov 2021 23:29

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