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Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis.

Francis WR, Shaner NC, Christianson LM, Powers ML, Haddock SH - PLoS ONE (2015)

Bottom Line: Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species.Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence.Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present.

View Article: PubMed Central - PubMed

Affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA 95039, United States of America; Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America.

ABSTRACT
The biosynthesis of the luciferin coelenterazine has remained a mystery for decades. While not all organisms that use coelenterazine appear to make it themselves, it is thought that ctenophores are a likely producer. Here we analyze the transcriptome data of 24 species of ctenophores, two of which have published genomes. The natural precursors of coelenterazine have been shown to be the amino acids L-tyrosine and L-phenylalanine, with the most likely biosynthetic pathway involving cyclization and further modification of the tripeptide Phe-Tyr-Tyr ("FYY"). Therefore, we searched the ctenophore transcriptome data for genes with the short peptide "FYY" as part of their coding sequence. We recovered a group of candidate genes for coelenterazine biosynthesis in the luminous species which encode a set of highly conserved non-heme iron oxidases similar to isopenicillin-N-synthase. These genes were absent in the transcriptomes and genome of the two non-luminous species. Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species. Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence. Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present. Given the known functions of other members of this protein superfamily are involved in heterocycle formation, we consider these genes to be top candidates for laboratory characterization or gene knockouts in the investigation of coelenterazine biosynthesis.

No MeSH data available.


Related in: MedlinePlus

Maximum-likelihood tree of all putative ctenophore non-heme oxygenase protein sequences.Maximum-likelihood tree of all ctenophore non-heme oxygenase proteins including both FYY-containing (blue branches) and two non-FYY groups (green and purple branches). Outgroups from top BLAST hits (gold branches) and model enzymes (brown and red branches) show long branches compared to the FYY proteins. Sequence names are grayed out to emphasize branch lengths and clustering of the proteins. Scale bar indicates substitutions per site. Partial or incomplete sequences are indicated by -p as in Fig 4. Species abbreviations are as follows: Anid, Aspergillus nidulans; Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Cgig, Crassostrea gigas; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Odio, Oikopleura dioica; Omac, Ocyropsis maculata; Otri, Oxytricha trifallax; Pbac, Pleurobrachia bachei; Scla, Streptomyces clavuligerus; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
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pone.0128742.g005: Maximum-likelihood tree of all putative ctenophore non-heme oxygenase protein sequences.Maximum-likelihood tree of all ctenophore non-heme oxygenase proteins including both FYY-containing (blue branches) and two non-FYY groups (green and purple branches). Outgroups from top BLAST hits (gold branches) and model enzymes (brown and red branches) show long branches compared to the FYY proteins. Sequence names are grayed out to emphasize branch lengths and clustering of the proteins. Scale bar indicates substitutions per site. Partial or incomplete sequences are indicated by -p as in Fig 4. Species abbreviations are as follows: Anid, Aspergillus nidulans; Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Cgig, Crassostrea gigas; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Odio, Oikopleura dioica; Omac, Ocyropsis maculata; Otri, Oxytricha trifallax; Pbac, Pleurobrachia bachei; Scla, Streptomyces clavuligerus; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum

Mentions: Several BLAST searches (blastn, blastp, and tblastn) failed to identify a similar sequence to the FYY proteins in Hormiphora transcriptome, although the searches did find proteins similar to the non-FYY IPNS-homologs (S2 and S3 Figs). We considered that this absence could be due to a very low expression of the FYY protein which was removed during assembly. To address this, we then examined whether any fragments of the FYY proteins could be identified in the pre-assembled contigs (called “contigs.fa” by Velvet and “inchworm.K25.L25.DS.fa” by the first stage of Trinity.) We found 75 contigs this way and most were redundant when translated. Two putatively full-length proteins were identified from the contigs both of which group to non-FYY homologs in other ctenophores in the phylogenetic tree of the IPNS-homologs (Fig 5).


Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis.

Francis WR, Shaner NC, Christianson LM, Powers ML, Haddock SH - PLoS ONE (2015)

Maximum-likelihood tree of all putative ctenophore non-heme oxygenase protein sequences.Maximum-likelihood tree of all ctenophore non-heme oxygenase proteins including both FYY-containing (blue branches) and two non-FYY groups (green and purple branches). Outgroups from top BLAST hits (gold branches) and model enzymes (brown and red branches) show long branches compared to the FYY proteins. Sequence names are grayed out to emphasize branch lengths and clustering of the proteins. Scale bar indicates substitutions per site. Partial or incomplete sequences are indicated by -p as in Fig 4. Species abbreviations are as follows: Anid, Aspergillus nidulans; Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Cgig, Crassostrea gigas; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Odio, Oikopleura dioica; Omac, Ocyropsis maculata; Otri, Oxytricha trifallax; Pbac, Pleurobrachia bachei; Scla, Streptomyces clavuligerus; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4488382&req=5

pone.0128742.g005: Maximum-likelihood tree of all putative ctenophore non-heme oxygenase protein sequences.Maximum-likelihood tree of all ctenophore non-heme oxygenase proteins including both FYY-containing (blue branches) and two non-FYY groups (green and purple branches). Outgroups from top BLAST hits (gold branches) and model enzymes (brown and red branches) show long branches compared to the FYY proteins. Sequence names are grayed out to emphasize branch lengths and clustering of the proteins. Scale bar indicates substitutions per site. Partial or incomplete sequences are indicated by -p as in Fig 4. Species abbreviations are as follows: Anid, Aspergillus nidulans; Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Cgig, Crassostrea gigas; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Odio, Oikopleura dioica; Omac, Ocyropsis maculata; Otri, Oxytricha trifallax; Pbac, Pleurobrachia bachei; Scla, Streptomyces clavuligerus; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
Mentions: Several BLAST searches (blastn, blastp, and tblastn) failed to identify a similar sequence to the FYY proteins in Hormiphora transcriptome, although the searches did find proteins similar to the non-FYY IPNS-homologs (S2 and S3 Figs). We considered that this absence could be due to a very low expression of the FYY protein which was removed during assembly. To address this, we then examined whether any fragments of the FYY proteins could be identified in the pre-assembled contigs (called “contigs.fa” by Velvet and “inchworm.K25.L25.DS.fa” by the first stage of Trinity.) We found 75 contigs this way and most were redundant when translated. Two putatively full-length proteins were identified from the contigs both of which group to non-FYY homologs in other ctenophores in the phylogenetic tree of the IPNS-homologs (Fig 5).

Bottom Line: Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species.Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence.Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present.

View Article: PubMed Central - PubMed

Affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA 95039, United States of America; Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America.

ABSTRACT
The biosynthesis of the luciferin coelenterazine has remained a mystery for decades. While not all organisms that use coelenterazine appear to make it themselves, it is thought that ctenophores are a likely producer. Here we analyze the transcriptome data of 24 species of ctenophores, two of which have published genomes. The natural precursors of coelenterazine have been shown to be the amino acids L-tyrosine and L-phenylalanine, with the most likely biosynthetic pathway involving cyclization and further modification of the tripeptide Phe-Tyr-Tyr ("FYY"). Therefore, we searched the ctenophore transcriptome data for genes with the short peptide "FYY" as part of their coding sequence. We recovered a group of candidate genes for coelenterazine biosynthesis in the luminous species which encode a set of highly conserved non-heme iron oxidases similar to isopenicillin-N-synthase. These genes were absent in the transcriptomes and genome of the two non-luminous species. Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species. Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence. Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present. Given the known functions of other members of this protein superfamily are involved in heterocycle formation, we consider these genes to be top candidates for laboratory characterization or gene knockouts in the investigation of coelenterazine biosynthesis.

No MeSH data available.


Related in: MedlinePlus