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George N Phillips - One of the best experts on this subject based on the ideXlab platform.
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Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N Phillips, Brian G FoxAbstract:Background Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
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evolution of substrate specificity in bacterial aa10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N PhillipsAbstract:Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
Adam J Book - One of the best experts on this subject based on the ideXlab platform.
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Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N Phillips, Brian G FoxAbstract:Background Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
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evolution of substrate specificity in bacterial aa10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N PhillipsAbstract:Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
Wei Jen Chang - One of the best experts on this subject based on the ideXlab platform.
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diversity and universality of endosymbiotic rickettsia in the fish parasite ichthyophthirius multifiliis
Frontiers in Microbiology, 2017Co-Authors: Kassandra E. Zaila, Hannah Ellerbrock, Donna Cassidyhanley, Che Huang Tung, Daniel Kolbin, Thomas G Doak, Mauricio Laterca Martins, Wei Jen Chang, T G ClarkAbstract:Although the presence of endosymbiotic rickettsial bacteria, specifically Candidatus Megaira, has been reported in diverse habitats and a wide range of eukaryotic hosts, it remains unclear how broadly Ca. Megaira are distributed in a single host species. In this study we seek to address whether Ca. Megaira are present in most, if not all isolates, of the parasitic ciliate Ichthyophthirius multifiliis. Conserved regions of bacterial 16S rRNA genes were either PCR amplified, or assembled from deep sequencing data, from 18 isolates/populations of I. multifiliis sampled worldwide (Brazil, Taiwan, and United States). We found that rickettsial rRNA sequences belonging to three out of four Ca. Megaira Subclades could be consistently detected in all I. multifiliis samples. I. multifiliis collected from local fish farms tend to be inhabited by the same Subclade of Ca. Megaira, whereas those derived from pet fish are often inhabited by more than one Subclade of Ca. Megaira. Distributions of Ca. Megaira in I. multifiliis thus better reflect the travel history, but not the phylogeny, of I. multifiliis. In summary, our results suggest that I. multifiliis may be dependent on this endosymbiotic relationship, and the association between Ca. Megaira and I. multifiliis is more diverse than previously thought.
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Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis
Frontiers in Microbiology, 2017Co-Authors: Kassandra E. Zaila, Hannah Ellerbrock, Che Huang Tung, Daniel Kolbin, Thomas G Doak, Mauricio Laterca Martins, T G Clark, Meng Chao Yao, Donna Cassidy-hanley, Wei Jen ChangAbstract:Although the presence of endosymbiotic rickettsial bacteria, specifically Candidatus Megaira, has been reported in diverse habitats and a wide range of eukaryotic hosts, it remains unclear how broadly Ca. Megaira are distributed in a single host species. In this study we seek to address whether Ca. Megaira are present in most, if not all isolates, of the parasitic ciliate Ichthyophthirius multifiliis. Conserved regions of bacterial 16S rRNA genes were either PCR amplified, or assembled from deep sequencing data, from 18 isolates/populations of I. multifiliis sampled worldwide (Brazil, Taiwan, and USA). We found that rickettsial rRNA sequences belonging to three out of four Ca. Megaira Subclades could be consistently detected in all I. multifiliis samples. I. multifiliis collected from local fish farms tend to be inhabited by the same Subclade of Ca. Megaira, whereas those derived from pet fish are often inhabited by more than one Subclade of Ca. Megaira. Distributions of Ca. Megaira in I. multifiliis thus better reflect the travel history, but not the phylogeny, of I. multifiliis. In summary, our results suggest that I. multifiliis may be dependent on this endosymbiotic relationship, and the association between Ca. Megaira and I. multifiliis is more diverse than previously thought.
Taichi E Takasuka - One of the best experts on this subject based on the ideXlab platform.
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Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N Phillips, Brian G FoxAbstract:Background Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
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evolution of substrate specificity in bacterial aa10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N PhillipsAbstract:Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
Cameron R Currie - One of the best experts on this subject based on the ideXlab platform.
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Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N Phillips, Brian G FoxAbstract:Background Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
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evolution of substrate specificity in bacterial aa10 lytic polysaccharide monooxygenases
Biotechnology for Biofuels, 2014Co-Authors: Adam J Book, Ragothaman M Yennamalli, Taichi E Takasuka, Cameron R Currie, George N PhillipsAbstract:Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 Subclades showed distinct selective pressures between putative cellulolytic genes (Subclade A) and CBP21-like chitinolytic genes (Subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all Subclades. Furthermore, all codons in the Subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic Subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a Subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
