The Experts below are selected from a list of 816 Experts worldwide ranked by ideXlab platform

Paul F Long - One of the best experts on this subject based on the ideXlab platform.

  • Global genome analysis of the Shikimic Acid Pathway reveals greater gene loss in host-associated than in free-living bacteria
    BMC Genomics, 2010
    Co-Authors: Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Jamal Williams, Daslav Hranueli, Paul F Long
    Abstract:

    Background A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete Shikimic Acid Pathway, whereas metazoans lacking this Pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the Pathway, we report the presence of genes encoding shikimate Pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes. Results Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete Shikimic Acid Pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-Acid sequences of enzymes of the Pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate Pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete Shikimic Acid Pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic Pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic Pathways. Conclusions These results challenge the conventional belief that the Shikimic Acid Pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this Pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential Pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching.
    Public Library of Science (PLoS), 2010
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F Long
    Abstract:

    The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues.A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a 'shared metabolic adaptation' between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca(2+)-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis.Bioinformatics analyses of DNA sequences obtained by differential gene expression of a coral exposed to high solar irradiance has revealed the identification of putative genes encoding key steps of the MAA biosynthetic Pathway. Revealed also by this treatment are genes that implicate exocytosis as a cellular process contributing to a breakdown in the metabolically essential partnership between the coral host and endosymbiotic algae, which manifests as coral bleaching

  • enzymes of the Shikimic Acid Pathway encoded in the genome of a basal metazoan nematostella vectensis have microbial origins
    Proceedings of the National Academy of Sciences of the United States of America, 2008
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Shamima Akthar, Malcolm J Shick, Paul F Long
    Abstract:

    The Shikimic Acid Pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this Pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino Acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate Pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the Shikimic Acid Pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a “shared metabolic adaptation” between the partners.

Eckhard Boles - One of the best experts on this subject based on the ideXlab platform.

  • an expanded enzyme toolbox for production of cis cis muconic Acid and other shikimate Pathway derivatives in saccharomyces cerevisiae
    Fems Yeast Research, 2018
    Co-Authors: Christine Bruckner, Eckhard Boles, Mislav Oreb, Gotthard Kunze, Joanna Tripp
    Abstract:

    A wide range of commercially relevant aromatic chemicals can be synthesized via the Shikimic Acid Pathway. Thus, this Pathway has been the target of diverse metabolic engineering strategies. In the present work, an optimized yeast strain for production of the Shikimic Acid Pathway intermediate 3-dehydroshikimate (3-DHS) was generated, which is a precursor for the production of the valuable compounds cis, cis-muconic Acid (CCM) and gallic Acid (GA). Production of CCM requires the overexpression of the heterologous enzymes 3-DHS dehydratase AroZ, protocatechuic Acid (PCA) decarboxylase AroY and catechol dioxygenase CatA. The activity of AroY limits the yield of the Pathway. This repertoire of enzymes was expanded by a novel fungal decarboxylase. Introducing this enzyme into the Pathway in the optimized strain, a titer of 1244 mg L-1 CCM could be achieved, yielding 31 mg g-1 glucose. This represents the highest yield of this compound reported in Saccharomyces cerevisiae to date. To demonstrate the applicability of the optimized strain for production of other compounds from 3-DHS, we overexpressed AroZ together with a mutant of a para-hydroxybenzoic Acid hydroxylase with improved substrate specificity for PCA, PobAY385F. Thereby, we could demonstrate the production of GA for the first time in S. cerevisiae.

  • engineering of hydroxymandelate synthases and the aromatic amino Acid Pathway enables de novo biosynthesis of mandelic and 4 hydroxymandelic Acid with saccharomyces cerevisiae
    Metabolic Engineering, 2018
    Co-Authors: Mara Reifenrath, Eckhard Boles
    Abstract:

    Mandelic Acid (MA) and 4-hydroxymandelic Acid (HMA) are valuable specialty chemicals used as precursors for flavors as well as for cosmetic and pharmaceutical purposes. Today they are mainly synthesized chemically. Their synthesis through microbial fermentation would allow for environmentally sustainable production. In this work, we engineered the yeast Saccharomyces cerevisiae for high-level production of MA and HMA. Expressing the hydroxymandelate synthase from Amycolatopsis orientalis in a yeast wild type strain resulted in the production of 119mg/L HMA from glucose. As the enzyme also accepts phenylpyruvate as a substrate aside from its native substrate 4-hydroxyphenylpyruvate, 0.7mg/L MA was also produced. Preventing binding of 4-hydroxyphenylpyruvate to the hydroxymandelate synthase by introducing a S201V replacement in its substrate binding site nearly completely prevented HMA production but increased MA production only 3.5-fold. To further increase HMA and MA production, the aromatic amino Acid Pathway was engineered. We increased the precursor supply by introducing modifications in the Shikimic Acid Pathway (ARO1↑, ARO3K222L↑, ARO4K220L↑) and reducing flux into the Ehrlich Pathway (aro10Δ), and thereby enhanced the HMA titer to 465mg/L and the MA titer to 2.9mg/L. A further increase in HMA and MA titers was achieved by replacing the hydroxymandelate synthase from A. orientalis with the corresponding enzyme from Nocardia uniformis. Subsequently, we introduced additional deletions to block the competing tryptophan branch (trp2Δ), to further decrease flux into the Ehrlich Pathway (pdc5Δ) and to avoid transamination of phenylpyruvate and 4-hydroxyphenylpyruvate (aro8Δ, aro9Δ). We achieved more than 1g/L 4-hydroxymandelate when additionally preventing formation of phenylpyruvate by deleting PHA2. When deleting TYR1 to prevent formation of 4-hydroxyphenylpyruvate instead, an MA titer of 236mg/L was achieved. This is a more than 200-fold increase in MA production compared to the wild type strain expressing the hydroxymandelate synthase from A. orientalis. Finally, we showed that S. cerevisiae tolerates HMA and MA to concentrations as high as 3g/L and 7.5g/L, respectively. Our results demonstrate that S. cerevisiae is a promising host for sustainable MA and HMA production.

Walter C Dunlap - One of the best experts on this subject based on the ideXlab platform.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching. PLoS One 2010
    2016
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F
    Abstract:

    Background: The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues. Methodology/Principal Findings: A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a ‘shared metabolic adaptation ’ between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca2+-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis

  • Global genome analysis of the Shikimic Acid Pathway reveals greater gene loss in host-associated than in free-living bacteria
    BMC Genomics, 2010
    Co-Authors: Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Jamal Williams, Daslav Hranueli, Paul F Long
    Abstract:

    Background A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete Shikimic Acid Pathway, whereas metazoans lacking this Pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the Pathway, we report the presence of genes encoding shikimate Pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes. Results Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete Shikimic Acid Pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-Acid sequences of enzymes of the Pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate Pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete Shikimic Acid Pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic Pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic Pathways. Conclusions These results challenge the conventional belief that the Shikimic Acid Pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this Pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential Pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching.
    Public Library of Science (PLoS), 2010
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F Long
    Abstract:

    The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues.A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a 'shared metabolic adaptation' between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca(2+)-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis.Bioinformatics analyses of DNA sequences obtained by differential gene expression of a coral exposed to high solar irradiance has revealed the identification of putative genes encoding key steps of the MAA biosynthetic Pathway. Revealed also by this treatment are genes that implicate exocytosis as a cellular process contributing to a breakdown in the metabolically essential partnership between the coral host and endosymbiotic algae, which manifests as coral bleaching

  • enzymes of the Shikimic Acid Pathway encoded in the genome of a basal metazoan nematostella vectensis have microbial origins
    Proceedings of the National Academy of Sciences of the United States of America, 2008
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Shamima Akthar, Malcolm J Shick, Paul F Long
    Abstract:

    The Shikimic Acid Pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this Pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino Acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate Pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the Shikimic Acid Pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a “shared metabolic adaptation” between the partners.

John Cullum - One of the best experts on this subject based on the ideXlab platform.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching. PLoS One 2010
    2016
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F
    Abstract:

    Background: The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues. Methodology/Principal Findings: A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a ‘shared metabolic adaptation ’ between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca2+-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis

  • Global genome analysis of the Shikimic Acid Pathway reveals greater gene loss in host-associated than in free-living bacteria
    BMC Genomics, 2010
    Co-Authors: Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Jamal Williams, Daslav Hranueli, Paul F Long
    Abstract:

    Background A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete Shikimic Acid Pathway, whereas metazoans lacking this Pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the Pathway, we report the presence of genes encoding shikimate Pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes. Results Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete Shikimic Acid Pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-Acid sequences of enzymes of the Pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate Pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete Shikimic Acid Pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic Pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic Pathways. Conclusions These results challenge the conventional belief that the Shikimic Acid Pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this Pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential Pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching.
    Public Library of Science (PLoS), 2010
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F Long
    Abstract:

    The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues.A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a 'shared metabolic adaptation' between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca(2+)-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis.Bioinformatics analyses of DNA sequences obtained by differential gene expression of a coral exposed to high solar irradiance has revealed the identification of putative genes encoding key steps of the MAA biosynthetic Pathway. Revealed also by this treatment are genes that implicate exocytosis as a cellular process contributing to a breakdown in the metabolically essential partnership between the coral host and endosymbiotic algae, which manifests as coral bleaching

  • enzymes of the Shikimic Acid Pathway encoded in the genome of a basal metazoan nematostella vectensis have microbial origins
    Proceedings of the National Academy of Sciences of the United States of America, 2008
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Shamima Akthar, Malcolm J Shick, Paul F Long
    Abstract:

    The Shikimic Acid Pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this Pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino Acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate Pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the Shikimic Acid Pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a “shared metabolic adaptation” between the partners.

Daslav Hranueli - One of the best experts on this subject based on the ideXlab platform.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching. PLoS One 2010
    2016
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F
    Abstract:

    Background: The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues. Methodology/Principal Findings: A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a ‘shared metabolic adaptation ’ between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca2+-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis

  • Global genome analysis of the Shikimic Acid Pathway reveals greater gene loss in host-associated than in free-living bacteria
    BMC Genomics, 2010
    Co-Authors: Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Jamal Williams, Daslav Hranueli, Paul F Long
    Abstract:

    Background A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete Shikimic Acid Pathway, whereas metazoans lacking this Pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the Pathway, we report the presence of genes encoding shikimate Pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes. Results Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete Shikimic Acid Pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-Acid sequences of enzymes of the Pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate Pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete Shikimic Acid Pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic Pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic Pathways. Conclusions These results challenge the conventional belief that the Shikimic Acid Pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this Pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential Pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.

  • Gene expression in the scleractinian Acropora microphthalma exposed to high solar irradiance reveals elements of photoprotection and coral bleaching.
    Public Library of Science (PLoS), 2010
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Malcolm J Shick, Paul F Long
    Abstract:

    The success of tropical reef-building corals depends on the metabolic co-operation between the animal host and the photosynthetic performance of endosymbiotic algae residing within its cells. To examine the molecular response of the coral Acropora microphthalma to high levels of solar irradiance, a cDNA library was constructed by PCR-based suppression subtractive hybridisation (PCR-SSH) from mRNA obtained by transplantation of a colony from a depth of 12.7 m to near-surface solar irradiance, during which the coral became noticeably paler from loss of endosymbionts in sun-exposed tissues.A novel approach to sequence annotation of the cDNA library gave genetic evidence for a hypothetical biosynthetic Pathway branching from the Shikimic Acid Pathway that leads to the formation of 4-deoxygadusol. This metabolite is a potent antioxidant and expected precursor of the UV-protective mycosporine-like amino Acids (MAAs), which serve as sunscreens in coral phototrophic symbiosis. Empirical PCR based evidence further upholds the contention that the biosynthesis of these MAA sunscreens is a 'shared metabolic adaptation' between the symbiotic partners. Additionally, gene expression induced by enhanced solar irradiance reveals a cellular mechanism of light-induced coral bleaching that invokes a Ca(2+)-binding synaptotagmin-like regulator of SNARE protein assembly of phagosomal exocytosis, whereby algal partners are lost from the symbiosis.Bioinformatics analyses of DNA sequences obtained by differential gene expression of a coral exposed to high solar irradiance has revealed the identification of putative genes encoding key steps of the MAA biosynthetic Pathway. Revealed also by this treatment are genes that implicate exocytosis as a cellular process contributing to a breakdown in the metabolically essential partnership between the coral host and endosymbiotic algae, which manifests as coral bleaching

  • enzymes of the Shikimic Acid Pathway encoded in the genome of a basal metazoan nematostella vectensis have microbial origins
    Proceedings of the National Academy of Sciences of the United States of America, 2008
    Co-Authors: Antonio Starcevic, Walter C Dunlap, John Cullum, Daslav Hranueli, Shamima Akthar, Malcolm J Shick, Paul F Long
    Abstract:

    The Shikimic Acid Pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this Pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino Acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate Pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the Shikimic Acid Pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a “shared metabolic adaptation” between the partners.