Distribution and Origin of Oxygen-Dependent and Oxygen-Independent Forms of Mg-Protoporphyrin Monomethylester Cyclase among Phototrophic Proteobacteria

Abstract

b Magnesium-protoporphyrin IX monomethylester cyclase is one of the key enzymes of the bacteriochlorophyll biosynthesis pathway. There exist two fundamentally different forms of this enzyme. The oxygen-dependent form, encoded by the gene acsF, catalyzes the formation of the bacteriochlorophyll fifth ring using oxygen, whereas the oxygen-independent form encoded by the gene bchE utilizes an oxygen atom extracted from water. The presence of acsF and bchE genes was surveyed in various phototrophic Proteobacteria using the available genomic data and newly designed degenerated primers. It was found that while the majority of purple nonsulfur bacteria contained both forms of the cyclase, the purple sulfur bacteria contained only the oxygenindependent form. All tested species of aerobic anoxygenic phototrophs contained acsF genes, but some of them also retained the bchE gene. In contrast to bchE phylogeny, the acsF phylogeny was in good agreement with 16S inferred phylogeny. Moreover, the survey of the genome data documented that the acsF gene occupies a conserved position inside the photosynthesis gene cluster, whereas the bchE location in the genome varied largely between the species. This suggests that the oxygen-dependent cyclase was recruited by purple phototrophic bacteria very early during their evolution. The primary sequence and immunochemical similarity with its cyanobacterial counterparts suggests that acsF may have been acquired by Proteobacteria via horizontal gene transfer from cyanobacteria. The acquisition of the gene allowed purple nonsulfur phototrophic bacteria to proliferate in the mildly oxygenated conditions of the Proterozoic era.

Three classes of oxygen-dependent cyclase involved in chlorophyll and bacteriochlorophyll biosynthesis

“…Our phylogenetic analysis is consistent with this theory, with Ycf54-requiring AcsF sequences clustering in a well-defined clade. In addition, it is believed that acsF was horizontally transferred from cyanobacteria to Proteobacteria before the divergence of Alphaproteobacterial, Betaproteobacterial, and Gammaproteobacterial lineages, because cyanobacteria were initially oxygenating the atmosphere, conferring an advantage to anoxygenic phototrophs previously reliant solely on O 2 -sensitive BchE (26). A newly discovered bacterial phototroph belonging to the phylum Gemmatimonadetes is believed to have acquired an acsF-containing purple bacterial PGC via horizontal gene transfer (39), and thus is more recent than the acquisition of acsF by the Proteobacteria.…”

“…Analysis of the PGC of Rba. sphaeroides revealed a small ORF (rsp_6110) found directly upstream of, and overlapping with, acsF; orthologs of this gene are conserved upstream of acsF in all studied Alphaproteobacteria containing acsF but are absent in all other taxonomic groups (26), including the betaproteobacterium Rvi. gelatinosus (Table S1).…”

Novel acsF Gene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China)

“…Unfortunately, these markers did not clearly distinguish phototrophic Gemmatimonadetes, probably because of their high similarity to the sequences of phototrophic Proteobacteria. To avoid this ambiguity, we recently introduced a novel marker, the acsF gene, which in our previous studies proved to be a reliable phylogenetic marker for a large range of anoxygenic bacteria (10). The novel primer successfully amplified acsF genes from Lake Taihu samples and showed high efficiency and specificity.…”

“…The newly designed primers were first tested with cultured species. The cultures were grown, and the DNA was isolated as described previously (3,10). Six strains of phototrophic Proteobacteria (Rhodovulum sulfidophilum, Erythrobacter sp.…”

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

“…S6); however, whether they originate from heterotrophic or phototrophic species is unclear. To target specifically phototrophic Gemmatimonadetes, we ran a search of protein homologs of oxygen-dependent Mg-protoporphyrin monomethylester cyclase (AcsF), a recently developed phylogenetic marker for aerobic and semiaerobic chlorophototrophs (33). The survey of available metagenomes stored in the CAMERA database (34) and in the National Center for Biotechnology Information (NCBI) whole-genome shotgun database identified five partial homologs predicted from Yellowstone Lake metagenomes (129-173 predicted amino acid positions with 88∼94% identities) and one fulllength homolog from a Danish wastewater metagenome (362 positions with 88% identity) (SI Appendix, Table S8).…”