Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum
ABSTRACT Inositols (cyclohexanehexols) comprise nine isomeric cyclic sugar alcohols, several of which occur in all domains of life with various functions. Many bacteria can utilize inositols as carbon and energy sources via a specific pathway involving inositol dehydrogenases (IDHs) as the first ste...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-10-01
|
| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01950-22 |
| _version_ | 1811198196568817664 |
|---|---|
| author | Paul Ramp Christopher Pfleger Jonas Dittrich Christina Mack Holger Gohlke Michael Bott |
| author_facet | Paul Ramp Christopher Pfleger Jonas Dittrich Christina Mack Holger Gohlke Michael Bott |
| author_sort | Paul Ramp |
| collection | DOAJ |
| description | ABSTRACT Inositols (cyclohexanehexols) comprise nine isomeric cyclic sugar alcohols, several of which occur in all domains of life with various functions. Many bacteria can utilize inositols as carbon and energy sources via a specific pathway involving inositol dehydrogenases (IDHs) as the first step of catabolism. The microbial cell factory Corynebacterium glutamicum can grow with myo-inositol as a sole carbon source. Interestingly, this species encodes seven potential IDHs, raising the question of the reason for this multiplicity. We therefore investigated the seven IDHs to determine their function, activity, and selectivity toward the biologically most important isomers myo-, scyllo-, and d-chiro-inositol. We created an ΔIDH strain lacking all seven IDH genes, which could not grow on the three inositols. scyllo- and d-chiro-inositol were identified as novel growth substrates of C. glutamicum. Complementation experiments showed that only four of the seven IDHs (IolG, OxiB, OxiD, and OxiE) enabled growth of the ΔIDH strain on two of the three inositols. The kinetics of the four purified enzymes agreed with the complementation results. IolG and OxiD are NAD+-dependent IDHs accepting myo- and d-chiro-inositol but not scyllo-inositol. OxiB is an NAD+-dependent myo-IDH with a weak activity also for scyllo-inositol but not for d-chiro-inositol. OxiE on the other hand is an NAD+-dependent scyllo-IDH showing also good activity for myo-inositol and a very weak activity for d-chiro-inositol. Structural models, molecular docking experiments, and sequence alignments enabled the identification of the substrate binding sites of the active IDHs and of residues allowing predictions on the substrate specificity. IMPORTANCE myo-, scyllo-, and d-chiro-inositol are C6 cyclic sugar alcohols with various biological functions, which also serve as carbon sources for microbes. Inositol catabolism starts with an oxidation to keto-inositols catalyzed by inositol dehydrogenases (IDHs). The soil bacterium C. glutamicum encodes seven potential IDHs. Using a combination of microbiological, biochemical, and modeling approaches, we analyzed the function of these enzymes and identified four IDHs involved in the catabolism of inositols. They possess distinct substrate preferences for the three isomers, and modeling and sequence alignments allowed the identification of residues important for substrate specificity. Our results expand the knowledge of bacterial inositol metabolism and provide an important basis for the rational development of producer strains for these valuable inositols, which show pharmacological activities against, e.g., Alzheimer’s disease, polycystic ovarian syndrome, or type II diabetes. |
| first_indexed | 2024-04-12T01:26:43Z |
| format | Article |
| id | doaj.art-d9a3acc54cdf4ef585f10b05418c41f5 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-12T01:26:43Z |
| publishDate | 2022-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-d9a3acc54cdf4ef585f10b05418c41f52022-12-22T03:53:38ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-10-0110510.1128/spectrum.01950-22Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicumPaul Ramp0Christopher Pfleger1Jonas Dittrich2Christina Mack3Holger Gohlke4Michael Bott5IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, GermanyInstitut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, GermanyThe Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, GermanyIBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, GermanyThe Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, GermanyIBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, GermanyABSTRACT Inositols (cyclohexanehexols) comprise nine isomeric cyclic sugar alcohols, several of which occur in all domains of life with various functions. Many bacteria can utilize inositols as carbon and energy sources via a specific pathway involving inositol dehydrogenases (IDHs) as the first step of catabolism. The microbial cell factory Corynebacterium glutamicum can grow with myo-inositol as a sole carbon source. Interestingly, this species encodes seven potential IDHs, raising the question of the reason for this multiplicity. We therefore investigated the seven IDHs to determine their function, activity, and selectivity toward the biologically most important isomers myo-, scyllo-, and d-chiro-inositol. We created an ΔIDH strain lacking all seven IDH genes, which could not grow on the three inositols. scyllo- and d-chiro-inositol were identified as novel growth substrates of C. glutamicum. Complementation experiments showed that only four of the seven IDHs (IolG, OxiB, OxiD, and OxiE) enabled growth of the ΔIDH strain on two of the three inositols. The kinetics of the four purified enzymes agreed with the complementation results. IolG and OxiD are NAD+-dependent IDHs accepting myo- and d-chiro-inositol but not scyllo-inositol. OxiB is an NAD+-dependent myo-IDH with a weak activity also for scyllo-inositol but not for d-chiro-inositol. OxiE on the other hand is an NAD+-dependent scyllo-IDH showing also good activity for myo-inositol and a very weak activity for d-chiro-inositol. Structural models, molecular docking experiments, and sequence alignments enabled the identification of the substrate binding sites of the active IDHs and of residues allowing predictions on the substrate specificity. IMPORTANCE myo-, scyllo-, and d-chiro-inositol are C6 cyclic sugar alcohols with various biological functions, which also serve as carbon sources for microbes. Inositol catabolism starts with an oxidation to keto-inositols catalyzed by inositol dehydrogenases (IDHs). The soil bacterium C. glutamicum encodes seven potential IDHs. Using a combination of microbiological, biochemical, and modeling approaches, we analyzed the function of these enzymes and identified four IDHs involved in the catabolism of inositols. They possess distinct substrate preferences for the three isomers, and modeling and sequence alignments allowed the identification of residues important for substrate specificity. Our results expand the knowledge of bacterial inositol metabolism and provide an important basis for the rational development of producer strains for these valuable inositols, which show pharmacological activities against, e.g., Alzheimer’s disease, polycystic ovarian syndrome, or type II diabetes.https://journals.asm.org/doi/10.1128/spectrum.01950-22inositol metabolismmyo-inositolscyllo-inositold-chiro-inositolenzyme kineticsstructural models |
| spellingShingle | Paul Ramp Christopher Pfleger Jonas Dittrich Christina Mack Holger Gohlke Michael Bott Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum Microbiology Spectrum inositol metabolism myo-inositol scyllo-inositol d-chiro-inositol enzyme kinetics structural models |
| title | Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum |
| title_full | Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum |
| title_fullStr | Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum |
| title_full_unstemmed | Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum |
| title_short | Physiological, Biochemical, and Structural Bioinformatic Analysis of the Multiple Inositol Dehydrogenases from Corynebacterium glutamicum |
| title_sort | physiological biochemical and structural bioinformatic analysis of the multiple inositol dehydrogenases from corynebacterium glutamicum |
| topic | inositol metabolism myo-inositol scyllo-inositol d-chiro-inositol enzyme kinetics structural models |
| url | https://journals.asm.org/doi/10.1128/spectrum.01950-22 |
| work_keys_str_mv | AT paulramp physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum AT christopherpfleger physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum AT jonasdittrich physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum AT christinamack physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum AT holgergohlke physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum AT michaelbott physiologicalbiochemicalandstructuralbioinformaticanalysisofthemultipleinositoldehydrogenasesfromcorynebacteriumglutamicum |