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Wladek Minor - One of the best experts on this subject based on the ideXlab platform.
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correction to classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Psychiatry, 2019Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:Following publication of the original article [1], we have been notified that some important information was omitted by the authors from the Competing interests section. The declaration should read as below.
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classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Evolutionary Biology, 2018Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:The family of D-isomer specific 2-Hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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structural biochemical and evolutionary characterizations of glyoxylate hydroxypyruvate reductases show their division into two distinct subfamilies
Biochemistry, 2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGh...
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Additional file 2: of Classification, substrate specificity and structural features of D-2-Hydroxyacid dehydrogenases: 2HADH knowledgebase
2018Co-Authors: Dorota Matelska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Ivan Shabalin, Jagoda JabĹoĹska, Wladek MinorAbstract:Figure S1. Maximum-likelihood evolutionary tree of the 2HADH family. The branch labels correspond to UniProt accessions of proteins with studied substrate specificities (orange dots), known crystal structures (green dots), or both (red dots). The scale bar represents the number of estimated changes per position. A crystal structure of GHRC from Desulfovibrio vulgaris (PDB ID: 5tx7) was solved after the analysis was performed, and is not shown in the figure. (PDF 56 kb
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Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies
2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site
Dorota Matelska - One of the best experts on this subject based on the ideXlab platform.
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correction to classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Psychiatry, 2019Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:Following publication of the original article [1], we have been notified that some important information was omitted by the authors from the Competing interests section. The declaration should read as below.
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classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Evolutionary Biology, 2018Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:The family of D-isomer specific 2-Hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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structural biochemical and evolutionary characterizations of glyoxylate hydroxypyruvate reductases show their division into two distinct subfamilies
Biochemistry, 2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGh...
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Additional file 2: of Classification, substrate specificity and structural features of D-2-Hydroxyacid dehydrogenases: 2HADH knowledgebase
2018Co-Authors: Dorota Matelska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Ivan Shabalin, Jagoda JabĹoĹska, Wladek MinorAbstract:Figure S1. Maximum-likelihood evolutionary tree of the 2HADH family. The branch labels correspond to UniProt accessions of proteins with studied substrate specificities (orange dots), known crystal structures (green dots), or both (red dots). The scale bar represents the number of estimated changes per position. A crystal structure of GHRC from Desulfovibrio vulgaris (PDB ID: 5tx7) was solved after the analysis was performed, and is not shown in the figure. (PDF 56 kb
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Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies
2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site
Jan Kutner - One of the best experts on this subject based on the ideXlab platform.
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correction to classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Psychiatry, 2019Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:Following publication of the original article [1], we have been notified that some important information was omitted by the authors from the Competing interests section. The declaration should read as below.
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classification substrate specificity and structural features of d 2 Hydroxyacid dehydrogenases 2hadh knowledgebase
BMC Evolutionary Biology, 2018Co-Authors: Dorota Matelska, Ivan G Shabalin, Jagoda Jablonska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Wladek MinorAbstract:The family of D-isomer specific 2-Hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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structural biochemical and evolutionary characterizations of glyoxylate hydroxypyruvate reductases show their division into two distinct subfamilies
Biochemistry, 2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGh...
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Additional file 2: of Classification, substrate specificity and structural features of D-2-Hydroxyacid dehydrogenases: 2HADH knowledgebase
2018Co-Authors: Dorota Matelska, M J Domagalski, Jan Kutner, Krzysztof Ginalski, Ivan Shabalin, Jagoda JabĹoĹska, Wladek MinorAbstract:Figure S1. Maximum-likelihood evolutionary tree of the 2HADH family. The branch labels correspond to UniProt accessions of proteins with studied substrate specificities (orange dots), known crystal structures (green dots), or both (red dots). The scale bar represents the number of estimated changes per position. A crystal structure of GHRC from Desulfovibrio vulgaris (PDB ID: 5tx7) was solved after the analysis was performed, and is not shown in the figure. (PDF 56 kb
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Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies
2018Co-Authors: Jan Kutner, Dorota Matelska, Ivan G Shabalin, Krzysztof Ginalski, Katarzyna B Handing, Olga Gasiorowska, Piotr Sroka, Maria W Gorna, Krzysztof Wozniak, Wladek MinorAbstract:The d-2-Hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site
Sijae Park - One of the best experts on this subject based on the ideXlab platform.
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Biosynthesis of 2-Hydroxyacid-containing polyhydroxyalkanoates by employing butyryl-CoA transferases in metabolically engineered Escherichia coli†
Biotechnology Journal, 2017Co-Authors: Yokimiko David, Young Hoon Oh, Jung-eun Yang, Sijae ParkAbstract:The authors previously reported the production of polyhydroxyalkanoates (PHAs) containing 2-Hydroxyacid monomers by expressing evolved Pseudomonas sp. 6-19 PHA synthase and Clostridium propionicum propionyl-CoA transferase in engineered microorganisms. Here, the authors examined four butyryl-CoA transferases from Roseburia sp., Eubacterium hallii, Faecalibacterium prausnitzii, and Anaerostipes caccae as potential CoA-transferases to support synthesis of polymers having 2HA monomer. In vitro activity analyses of the four butyryl-CoA transferases suggested that each butyryl-CoA transferase has different activities towards 2-hydroxybutyrate (2HB), 3-hydroxybutyrate (3HB), and lactate (LA). When Escherichia coli XL1-Blue expressing Pseudomonas sp. 6-19 PhaC1437 along with one butyryl-CoA transferase is cultured in chemically defined MR medium containing 20 g L of glucose, 2 g L of sodium 3-hydroxybutyrate, and various concentrations of sodium 2-hydroxybutyrate, PHAs consisting of 3HB, 2HB, and LA are produced. The monomer composition of PHAs agreed well with the substrate specificities of butyryl-CoA transferases from E. hallii, F. prausnitzii, and A. caccae, but not Roseburia sp. When E. coli XL1-Blue expressing PhaC1437 and E. hallii butyryl-CoA transferase is cultured in MR medium containing 20 g L of glucose and 2 g L of sodium 2-hydroxybutyrate, P(65.7 mol% 2HB-co-34.3 mol% LA) is produced with the highest PHA content of 30 wt%. Butyryl-CoA transferases also supported the production of P(3HB-co-2HB-co-LA) from glucose as the sole carbon source in E. coli XL1-Blue strains when one of these bct genes is expressed with phaC1437, cimA3.7, leuBCD, panE, and phaAB genes. Butyryl-CoA transferases characterized in this study can be used for engineering of microorganisms that produce PHAs containing novel 2-Hydroxyacid monomers.
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metabolic engineering of ralstonia eutropha for the biosynthesis of 2 Hydroxyacid containing polyhydroxyalkanoates
Metabolic Engineering, 2013Co-Authors: Sijae Park, Youngah Jang, Jihoon Shin, Young Hoon Oh, Bongkeun Song, Areum Park, Jung-eun Yang, Jong-geon JegalAbstract:Abstract Polyhydroxyalkanoates (PHAs) are bio-based and biodegradable polyesters synthesized by numerous microorganisms. PHAs containing 2-Hydroxyacids as monomer units have attracted much attention, but their production has not been efficient. Here, we metabolically engineered Ralstonia eutropha strains for the in vivo synthesis of PHAs containing 2-Hydroxyacids as monomers. This was accomplished by replacing the R. eutropha phaC gene in the chromosome with either the R. eutropha phaC S506G A510K gene, which contains two point mutations, or the Pseudomonas sp. MBEL 6–19 phaC1437 gene. In addition, the R. eutropha phaAB genes in the chromosome were replaced with the Clostridium propionicum pct540 gene. All of the engineered R. eutropha strains produced PHAs containing 2-Hydroxyacid monomers, including lactate and 2-hydroxybutyrate (2HB), along with 3-hydroxybutyrate (3HB) and/or 3-hydroxyvalerate (3HV), when they were cultured in nitrogen-free medium containing 5 g/L lactate or 4 g/L 2HB and 20 g/L glucose as carbon sources. Expression of the Escherichia coli ldhA gene in engineered R. eutropha strains allowed production of poly(3-hydroxybutyrate-co-lactate) [P(3HB-co-LA)] from glucose as the sole carbon source. This is the first report on the production of 2-Hydroxyacid-containing PHAs by metabolically engineered R. eutropha.
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propionyl coa dependent biosynthesis of 2 hydroxybutyrate containing polyhydroxyalkanoates in metabolically engineered escherichia coli
Journal of Biotechnology, 2013Co-Authors: Sijae Park, Young Hoon Oh, Kyounghee Kang, Bongkeun Song, Areum Park, Jung-eun Yang, Jong-geon JegalAbstract:Abstract We have previously reported in vivo biosynthesis of 2-Hydroxyacid containing polyesters including polylactic acid (PLA), poly(3-hydroxybutyrate- co -lactate) [P(3HB- co -LA)], and poly(3-hydroxybutyrate- co -2-hydroxybutyrate- co -lactate) [P(3HB- co -2HB- co -LA)] employing metabolically engineered Escherichia coli strains by the introduction of evolved Clostridium propionicum propionyl-CoA transferase (Pct Cp ) and Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1 Ps 6–19 ). In this study, we further engineered in vivo PLA biosynthesis system in E. coli to synthesize 2HB-containing PHA, in which propionyl-CoA was used as precursor for 2-ketobutyrate that was converted into 2HB-CoA by the sequential actions of Lactococcus lactis ( d )-2-hydroxybutyrate dehydrogenase (PanE) and Pct Cp and then 2HB-CoA was polymerized by PhaC1 Ps 6–19 . The recombinant E. coli XL1-blue expressing the phaC1437 gene, the pct540 gene, and the Ralstonia eutropha prpE gene together with the panE gene could be grown to 0.66 g/L and successfully produced P(70 mol%3HB- co -18 mol%2HB- co -12 mol%LA) up to the PHA content of 66 wt% from 20 g/L of glucose, 2 g/L of 3HB and 1 g/L of sodium propionate. Removal of the prpC gene in the chromosome of E. coli XL1-blue could increase the mole fraction of 2HB in copolymer, but the PHA content was decreased. The metabolic engineering strategy reported here suggests that propionyl-CoA can be successfully used as the precursor to provide PHA synthase with 2HB-CoA for the production of PHAs containing 2HB monomer.
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metabolic engineering of escherichia coli for the production of 2 Hydroxyacid containing polyesters
한국생물공학회 학술대회, 2013Co-Authors: Sijae Park, Seung Hwan Lee, Sang Yup LeeAbstract:As the concerns about environmental problems, climate change and limited fossil resources increase, bio-based production of chemicals and polymers from renewable resources gains much attention as one of the promising solutions to deal with these problems. Polyhydroxyalkanoates (PHAs) are polyesters produced and accumulated in various microorganisms. PHAs are synthesized using monomers provided from metabolite precursors of diverse metabolic pathways and are accumulated as distinct granules inside the cells. On the other hand, most so called bio-based polymers including polybutylene succinate (PBS), polytrimethylene terephthalate (PTT), and polylactic acid (PLA) are synthesized by a chemical process using fermentation-derived monomers. PLA, an attractive biomass-derived thermoplastic, is currently synthesized by ring opening polymerization (ROP) of (L)-lactide that is made from fermentation-derived (L)-lactic acid. Recently, we have developed one-step fermentative synthesis process for the production of PLA and PLA copolymers from renewable resources employing recombinant bacteria equipped with PHA biosynthesis pathways coupled with a novel metabolic pathway. This could be accomplished by establishing a pathway for generating lactyl- CoA and engineering PHA synthase to accept lactyl-CoA as a monomer combined with systems metabolic engineering. In this presentation, we report recent advances in the production of lactate-containing homo- and co- polyesters, and furthermore 2-Hydroxyacid containing polyesters in recombinant microorganisms. We will discuss challenges remaining to efficiently produce 2-Hydroxyacid containing polyesters such as PLA, PLA copolymers and 2-hydroxybutyrate containing PHA and development of the metabolic engineering strategies to overcome these challenges.
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advanced bacterial polyhydroxyalkanoates towards a versatile and sustainable platform for unnatural tailor made polyesters
Biotechnology Advances, 2012Co-Authors: Sijae Park, Tae Wan Kim, Minkyung Kim, Sang Yup Lee, Sungchul LimAbstract:Polyhydroxyalkanoates (PHAs) are biopolyesters that generally consist of 3-, 4-, 5-, and 6-hydroxycarboxylic acids, which are accumulated as carbon and energy storage materials in many bacteria in limited growth conditions with excess carbon sources. Due to the diverse substrate specificities of PHA synthases, the key enzymes for PHA biosynthesis, PHAs with different material properties have been synthesized by incorporating different monomer components with differing compositions. Also, engineering PHA synthases using in vitro-directed evolution and site-directed mutagenesis facilitates the synthesis of PHA copolymers with novel material properties by broadening the spectrum of monomers available for PHA biosynthesis. Based on the understanding of metabolism of PHA biosynthesis, recombinant bacteria have been engineered to produce different types of PHAs by expressing heterologous PHA biosynthesis genes, and by creating and enhancing the metabolic pathways to efficiently generate precursors for PHA monomers. Recently, the PHA biosynthesis system has been expanded to produce unnatural biopolyesters containing 2-Hydroxyacid monomers such as glycolate, lactate, and 2-hydroxybutyrate by employing natural and engineered PHA synthases. Using this system, polylactic acid (PLA), one of the major commercially-available bioplastics, can be synthesized from renewable resources by direct fermentation of recombinant bacteria. In this review, we discuss recent advances in the development of the PHA biosynthesis system as a platform for tailor-made polyesters with novel material properties.
Frank Schmitz - One of the best experts on this subject based on the ideXlab platform.
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ribeye a component of synaptic ribbons a protein s journey through evolution provides insight into synaptic ribbon function
Neuron, 2000Co-Authors: Frank Schmitz, Andreas Konigstorfer, Thomas C SudhofAbstract:Abstract Photoreceptor cells utilize ribbon synapses to transmit sensory signals at high resolution. Ribbon synapses release neurotransmitters tonically, with a high release rate made possible by continuous docking of synaptic vesicles on presynaptic ribbons. We have partially purified synaptic ribbons from retina and identified a major protein component called RIBEYE. RIBEYE is composed of a unique A domain specific for ribbons, and a B domain identical with CtBP2, a transcriptional repressor that in turn is related to 2-Hydroxyacid dehydrogenases. The A domain mediates assembly of RIBEYE into large structures, whereas the B domain binds NAD + with high affinity, similar to 2-Hydroxyacid dehydrogenases. Our results define a unique component of synaptic ribbons and suggest that RIBEYE evolved in vertebrates under utilization of a preexisting protein to build a unique scaffold for a specialized synapse.
