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Pheno- and Genotyping of Hopanoid Production in Acidobacteria
Sinninghe Damsté, J.S.; Rijpstra, W.I.C.; Dedysh, S.N.; Foesel, B.U.; Villanueva, L. (2017). Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front. Microbiol. 8: 968. https://dx.doi.org/10.3389/fmicb.2017.00968
In: Frontiers in Microbiology. Frontiers Media: Lausanne. ISSN 1664-302X, meer
Peer reviewed article  

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Trefwoord
Author keywords
    Hopanoids; Acidobacteria; lipid biosynthesis; lipid analysis; methylation; genomes; metagenomes

Auteurs  Top 
  • Sinninghe Damsté, J.S., meer
  • Rijpstra, W.I.C., meer
  • Dedysh, S.N.
  • Foesel, B.U.
  • Villanueva, L., meer

Abstract
    Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups.Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria andaerobic methanotrophs until the genes encoding for the methylation at the C-2 andC-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain,invalidating their use as specific biomarkers. These genes have been detected in thegenome of the Acidobacterium “Ca. Koribacter versatilis,” but our knowledge of thesynthesis of hopanoids and the presence of genes of their biosynthetic pathway inother member of the Acidobacteria is limited. We analyzed 38 different strains of sevenAcidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenesand C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/orC30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (exceptingChloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement withthe presence of genes required for hopanoid biosynthesis in the 31 available wholegenomes of cultivated Acidobacteria. All genomes encode the enzymes involved in thenon-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3Acidobacteria and C. thermophilum encode all three enzymes required for the synthesisof squalene, its cyclization (shc), and addition and modification of the extended sidechain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalizedBHPs were detected; three strains contained variable relative abundances (up to 45%)of pentafunctionalized BHPs. Only “Ca. K. versatilis” contained methylated hopanoids(i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes arenot present in any other Acidobacterium, consistent with the absence of methylatedBHPs in the other examined strains. These data are in agreement with the scatteredoccurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-,and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential.Metagenomes of Acidobacteria were also examined for the presence of genes requiredfor hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident inSD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with thelimited occurrence of BHPs in acidobacterial cultures.

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