Evolution and molecular mechanism of four‐electron reducing ferredoxin‐dependent bilin reductases from oceanic phages

Ledermann, Benjamin; Schwan, Meike; Sommerkamp, Johannes A.; Hofmann, Eckhard; Béjà, Oded; Frankenberg‐Dinkel, Nicole

doi:10.1111/febs.14341

Cited by 17 publications

(30 citation statements)

References 46 publications

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“…For many years, our laboratory has been interested in the biosynthesis of these open‐chain tetrapyrrole pigments and we have mostly concentrated on the biosynthesis of the pink pigment PEB . The biosynthesis of PEB starts with the heme oxygenase reaction, in which heme is cleaved at the α‐meso carbon to produce biliverdin IXα (BV) with the concomitantly liberation of carbon monoxide and ferric iron .…”

Section: Introductionmentioning

confidence: 99%

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Proximity channeling during cyanobacterial phycoerythrobilin synthesis

Aras

Hartmann

et al. 2019

The FEBS Journal

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Substrate channeling is a widespread mechanism in metabolic pathways to avoid decomposition of unstable intermediates, competing reactions, and to accelerate catalytic turnover. During the biosynthesis of light‐harvesting phycobilins in cyanobacteria, two members of the ferredoxin‐dependent bilin reductases are involved in the reduction of the open‐chain tetrapyrrole biliverdin IXα to the pink pigment phycoerythrobilin. The first reaction is catalyzed by 15,16‐dihydrobiliverdin:ferredoxin oxidoreductase and produces the unstable intermediate 15,16‐dihydrobiliverdin (DHBV). This intermediate is subsequently converted by phycoerythrobilin:ferredoxin oxidoreductase to the final product phycoerythrobilin. Although substrate channeling has been postulated already a decade ago, detailed experimental evidence was missing. Using a new on‐column assay employing immobilized enzyme in combination with UV‐Vis and fluorescence spectroscopy revealed that both enzymes transiently interact and that transfer of the intermediate is facilitated by a significantly higher binding affinity of DHBV toward phycoerythrobilin:ferredoxin oxidoreductase. Concluding from the presented data, the intermediate DHBV is transferred via proximity channeling.

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Section: Introductionmentioning

confidence: 99%

“…Although PebA and PebS share a high structural similarity, the reaction of PebA is terminated directly after DHBV formation, whereas PebS proceeds further to produce PEB via the intermediate DHBV . PcyX on the other hand, although catalyzing formally the same reaction, does this by a different catalytic mechanism .…”

Section: Introductionmentioning

confidence: 99%

Proximity channeling during cyanobacterial phycoerythrobilin synthesis

Aras

Hartmann

et al. 2019

The FEBS Journal

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“…Some other genes reported in Cyanophage genomes 31 were detected in phages reported here. Two genes found in both Cyanophages and Cyanobacteria from global ocean habitats 32 , a heme oxygenase ( ho1 ) and a pcyX -like phycocyanobilin:ferredoxin oxidoreductase are involved in the production of phycobiliprotein pigment 32,33 . The ho1 and pcyX -like genes are adjacent in TP6_1, BML_S_1 and CB_1 and one-gene-apart in CB_2 ( Supplementary Fig.…”

Section: Metabolic Potentials Of Pmoc-phages and Their Relativesmentioning

confidence: 99%

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

Chen

Méheust

Crits-Christoph

et al. 2020

Preprint

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There is growing evidence that phages with unusually large genomes are common across various natural and human microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. Here, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Twenty-two manually curated genomes (18 are complete) ranging from 159 to 527 kbp in length were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC show high similarity (> 90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associated pmoC genes are actively expressed in situ . Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment.

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“…The Prochlorococcus P-SSM2 phage Fd (pssm2-Fd) supports the reduction of phage phycoerythrobilin synthase (PebS), which catalyzes the reduction of biliverdin IXα to 3E/3Z phycoerythrobilin (27,28). While prior studies showed that some Fds support ET to diverse partner oxidoreductases (29)(30)(31)(32), it remains unclear how the biophysical properties of this and other phage Fds compare to host Fds, which can function as ET hubs that couple light harvesting to a range of reductive metabolic reactions (31)(32)(33).…”

Section: Introductionmentioning

confidence: 99%

Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

Campbell

Olmos

et al. 2020

Preprint

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Marine cyanobacteria are infected by phage whose genomes encode ferredoxin (Fd) electron carriers. While these Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, it is not clear how the biochemical and biophysical properties of phage Fds relate to those in photosynthetic organisms. Bioinformatic analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects Prochlorococcus marinus, revealed high similarity to cyanobacterial Fds (≤0.5 Å RMSD). Additionally, pssm2-Fd exhibits a low midpoint reduction potential (-336 mV vs. SHE) similar to other photosynthetic Fds, albeit lower thermostability (Tm = 28°C) than many Fds. When expressed in an Escherichia coli strain with a sulfite assimilation defect, pssm2-Fd complemented growth when coexpressed with a Prochlorococcus marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggests that phage Fds evolved to transfer electrons to both phage-and cyanobacterial-encoded oxidoreductases.

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Evolution and molecular mechanism of four‐electron reducing ferredoxin‐dependent bilin reductases from oceanic phages

Abstract: Suggested EC number for PcyX: 1.3.7.6 DATABASES: The PcyX X-ray structure was deposited in the PDB with the accession code 5OWG.

Cited by 17 publications

References 46 publications

Proximity channeling during cyanobacterial phycoerythrobilin synthesis

Proximity channeling during cyanobacterial phycoerythrobilin synthesis

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

Prochlorococcusphage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

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