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Watanabe S. Characterization of a novel L-fuconate dehydratase involved in the non-phosphorylated pathway of L-fucose metabolism from bacteria. Biosci Biotechnol Biochem 2024; 88:177-180. [PMID: 38017627 DOI: 10.1093/bbb/zbad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
A sugar acid dehydratase from Paraburkholderia mimosarum, potentially involved in the non-phosphorylated L-fucose pathway, was functionally characterized. A biochemical analysis revealed its unique heterodimeric structure and higher specificity toward L-fuconate than D-arabinonate, D-altronate, and L-xylonate, which differed from homomeric homologs. This unique L-fuconate dehydratase has a poor phylogenetic relationship with other functional members of the D-altronate dehydratase/galactarate dehydratase protein family.
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Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
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Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
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Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
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Rosas‐Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF. Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. Protein Sci 2020; 29:711-722. [PMID: 31811683 PMCID: PMC7021002 DOI: 10.1002/pro.3796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/24/2019] [Accepted: 12/04/2019] [Indexed: 11/06/2022]
Abstract
Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca2+ . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.
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Affiliation(s)
- Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Ludmilla Shuvalova
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center–LS‐CATNorthwestern UniversityArgonneIllinois
| | - Olga Kiryukhina
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
| | - Nathan Mih
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
| | - Lukasz Jaroszewski
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Bernhard Palsson
- Department of BioengineeringUniversity of California San DiegoLa JollaCalifornia
- Systems Biology Center for Antibiotic ResistanceUniversity of California San DiegoLa JollaCalifornia
| | - Adam Godzik
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Department of Biomedical SciencesUniversity of California at RiversideRiversideCalifornia
| | - Karla J. F. Satchell
- Department of Microbiology‐ImmunologyNorthwestern University, Feinberg School of MedicineChicagoIllinois
- Center for Structural Genomics of Infectious DiseasesNorthwestern University, Feinberg School of MedicineChicagoIllinois
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