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Qadri H, Shah AH, Almilaibary A, Mir MA. Microbiota, natural products, and human health: exploring interactions for therapeutic insights. Front Cell Infect Microbiol 2024; 14:1371312. [PMID: 39035357 PMCID: PMC11257994 DOI: 10.3389/fcimb.2024.1371312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/03/2024] [Indexed: 07/23/2024] Open
Abstract
The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.
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Affiliation(s)
- Hafsa Qadri
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdul Haseeb Shah
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdullah Almilaibary
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
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Nakamura S, Kurata R, Miyazaki T. Structural insights into α-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae. FEBS J 2024; 291:3267-3282. [PMID: 38661728 DOI: 10.1111/febs.17139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/07/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Glycoside hydrolase family 97 (GH97) comprises enzymes like anomer-inverting α-glucoside hydrolases (i.e., glucoamylase) and anomer-retaining α-galactosidases. In a soil bacterium, Flavobacterium johnsoniae, we previously identified a GH97 enzyme (FjGH97A) within the branched dextran utilization locus. It functions as an α-glucoside hydrolase, targeting α-(1→6)-glucosidic linkages in dextran and isomaltooligosaccharides (i.e., glucodextranase). FjGH97A exhibits a preference for α-(1→6)-glucoside linkages over α-(1→4)-linkages, while Bacteroides thetaiotaomicron glucoamylase SusB (with 69% sequence identity), which is involved in the starch utilization system, exhibits the highest specificity for α-(1→4)-glucosidic linkages. Here, we examined the crystal structures of FjGH97A in complexes with glucose, panose, or isomaltotriose, and analyzed the substrate preferences of its mutants to identify the amino acid residues that determine the substrate specificity for α-(1→4)- and α-(1→6)-glucosidic linkages. The overall structure of FjGH97A resembles other GH97 enzymes, with conserved catalytic residues similar to anomer-inverting GH97 enzymes. A comparison of active sites between FjGH97A and SusB revealed differences in amino acid residues at subsites +1 and +2 (specifically Ala195 and Ile378 in FjGH97A). Among the three mutants (A195S, I378F, and A195S-I378F), A195S and A195S-I378F exhibited increased activity toward α-(1→4)-glucoside bonds compared to α-(1→6)-glucoside bonds. This suggests that Ala195, located on the Gly184-Thr203 loop (named loop-N) conserved within the GH97 subgroup, including FjGH97A and SusB, holds significance in determining linkage specificity. The conservation of alanine in the active site of the GH97 enzymes, within the same gene cluster as the putative dextranase, indicates its crucial role in determining the specificity for α-(1→6)-glucoside linkage.
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Affiliation(s)
- Shuntaro Nakamura
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Japan
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3
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Boukouvala S, Kontomina E, Olbasalis I, Patriarcheas D, Tzimotoudis D, Arvaniti K, Manolias A, Tsatiri MA, Basdani D, Zekkas S. Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism. Sci Rep 2024; 14:14905. [PMID: 38942826 PMCID: PMC11213898 DOI: 10.1038/s41598-024-65342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Microbial NAT enzymes, which employ acyl-CoA to acylate aromatic amines and hydrazines, have been well-studied for their role in xenobiotic metabolism. Some homologues have also been linked to secondary metabolism, but this function of NAT enzymes is not as well-known. For this comparative study, we surveyed sequenced microbial genomes to update the list of formally annotated NAT genes, adding over 4000 new sequences (mainly bacterial, but also archaeal, fungal and protist) and portraying a broad but not universal distribution of NATs in the microbiocosmos. Localization of NAT sequences within microbial gene clusters was not a rare finding, and this association was evident across all main types of biosynthetic gene clusters (BGCs) implicated in secondary metabolism. Interrogation of the MIBiG database for experimentally characterized clusters with NAT genes further supports that secondary metabolism must be a major function for microbial NAT enzymes and should not be overlooked by researchers in the field. We also show that NAT sequences can be associated with bacterial plasmids potentially involved in horizontal gene transfer. Combined, our computational predictions and MIBiG literature findings reveal the extraordinary functional diversification of microbial NAT genes, prompting further research into their role in predicted BGCs with as yet uncharacterized function.
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Affiliation(s)
- Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece.
| | - Evanthia Kontomina
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Ioannis Olbasalis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dionysios Patriarcheas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimosthenis Tzimotoudis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Konstantina Arvaniti
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Aggelos Manolias
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Maria-Aggeliki Tsatiri
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Dimitra Basdani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
| | - Sokratis Zekkas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100, Alexandroupolis, Greece
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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Du Y, Han W, Hao P, Hu Y, Hu T, Zeng Y. A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel Strain Streptomyces sp. 21So2-11 Isolated from Antarctic Soil. Microorganisms 2024; 12:1228. [PMID: 38930610 PMCID: PMC11205464 DOI: 10.3390/microorganisms12061228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed that this strain is most closely related to Streptomyces drozdowiczii NBRC 101007T, with a similarity of 98.02%. Genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) showed that strain 21So2-11 represents a novel species of the genus Streptomyces. In addition to a large number of genes related to environmental adaptation and ecological function, a total of 28 putative biosynthetic gene clusters (BGCs) responsible for the biosynthesis of known and/or novel secondary metabolites, including terpenes, lantipeptides, polyketides, nonribosomal peptides, RiPPs and siderophores, were detected in the genome of strain 21So2-11. In addition, a total of 1456 BGCs were predicted to contribute to the biosynthesis of more than 300 secondary metabolites based on the genomes of 47 Streptomyces strains originating from polar regions. The results indicate the potential of Streptomyces sp. 21So2-11 for bioactive secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold terrestrial environments.
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Affiliation(s)
- Yu Du
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Wei Han
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Puyu Hao
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yongqiang Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Ting Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
| | - Yinxin Zeng
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; (Y.D.); (W.H.); (P.H.); (Y.H.); (T.H.)
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
- Shanghai Key Laboratory of Polar Life and Environment Sciences, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, Shanghai 200030, China
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Deb S, Wild MA, LeClair T, Shah DH. Discovery of novel treponemes associated with pododermatitis in elk ( Cervus canadensis). Appl Environ Microbiol 2024; 90:e0010524. [PMID: 38742897 PMCID: PMC11218636 DOI: 10.1128/aem.00105-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.
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Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Margaret A. Wild
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Thomas LeClair
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Devendra H. Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA
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7
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Maroniche GA, Puente ML, García JE, Mongiardini E, Coniglio A, Nievas S, Labarthe MM, Wisniewski-Dyé F, Rodriguez Cáceres E, Díaz-Zorita M, Cassán F. Phenogenetic profile and agronomic contribution of Azospirillum argentinense Az39 T, a reference strain for the South American inoculant industry. Microbiol Res 2024; 283:127650. [PMID: 38452553 DOI: 10.1016/j.micres.2024.127650] [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: 12/15/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20-38 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance.
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Affiliation(s)
- G A Maroniche
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), CONICET, Balcarce, Buenos Aires, Argentina
| | - M L Puente
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - J E García
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - E Mongiardini
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET, La Plata, Buenos Aires, Argentina
| | - A Coniglio
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - S Nievas
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina
| | - M M Labarthe
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), CONICET, Balcarce, Buenos Aires, Argentina
| | - F Wisniewski-Dyé
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne 69622, France
| | | | - M Díaz-Zorita
- Facultad de Agronomía, Universidad Nacional de La Pampa (UNLPam), CONICET, Santa Rosa, La Pampa, Argentina
| | - F Cassán
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba, Argentina.
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8
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Höing L, Sowa ST, Toplak M, Reinhardt JK, Jakob R, Maier T, Lill MA, Teufel R. Biosynthesis of the bacterial antibiotic 3,7-dihydroxytropolone through enzymatic salvaging of catabolic shunt products. Chem Sci 2024; 15:7749-7756. [PMID: 38784727 PMCID: PMC11110157 DOI: 10.1039/d4sc01715c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
The non-benzenoid aromatic tropone ring is a structural motif of numerous microbial and plant natural products with potent bioactivities. In bacteria, tropone biosynthesis involves early steps of the widespread CoA-dependent phenylacetic acid (paa) catabolon, from which a shunt product is sequestered and surprisingly further utilized as a universal precursor for structurally and functionally diverse tropone derivatives such as tropodithietic acid or (hydroxy)tropolones. Here, we elucidate the biosynthesis of the antibiotic 3,7-dihydroxytropolone in Actinobacteria by in vitro pathway reconstitution using paa catabolic enzymes as well as dedicated downstream tailoring enzymes, including a thioesterase (TrlF) and two flavoprotein monooxygenases (TrlCD and TrlE). We furthermore mechanistically and structurally characterize the multifunctional key enzyme TrlE, which mediates an unanticipated ipso-substitution involving a hydroxylation and subsequent decarboxylation of the CoA-freed side chain, followed by ring oxidation to afford tropolone. This study showcases a remarkably efficient strategy for 3,7-dihydroxytropolone biosynthesis and illuminates the functions of the involved biosynthetic enzymes.
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Affiliation(s)
- Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Sven T Sowa
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marina Toplak
- Hilde-Mangold-Haus (CIBSS), University of Freiburg Habsburgerstrasse 49 79104 Freiburg im Breisgau Germany
| | - Jakob K Reinhardt
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Timm Maier
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Li TT, Chen X, Huo D, Arifuzzaman M, Qiao S, Jin WB, Shi H, Li XV, Iliev ID, Artis D, Guo CJ. Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. Cell Host Microbe 2024; 32:661-675.e10. [PMID: 38657606 DOI: 10.1016/j.chom.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The intestine and liver are thought to metabolize dietary nutrients and regulate host nutrient homeostasis. Here, we find that the gut microbiota also reshapes the host amino acid (aa) landscape via efficiently metabolizing intestinal aa. To identify the responsible microbes/genes, we developed a metabolomics-based assay to screen 104 commensals and identified candidates that efficiently utilize aa. Using genetics, we identified multiple responsible metabolic genes in phylogenetically diverse microbes. By colonizing germ-free mice with the wild-type strain and their isogenic mutant deficient in individual aa-metabolizing genes, we found that these genes regulate the availability of gut and circulatory aa. Notably, microbiota genes for branched-chain amino acids (BCAAs) and tryptophan metabolism indirectly affect host glucose homeostasis via peripheral serotonin. Collectively, at single-gene level, this work characterizes a microbiota-encoded metabolic activity that affects host nutrient homeostasis and provides a roadmap to interrogate microbiota-dependent activity to improve human health.
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Affiliation(s)
- Ting-Ting Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xi Chen
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Da Huo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Shanshan Qiao
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Huiqing Shi
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xin V Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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10
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Gu B, Goldfuss B, Dickschat JS. Two Sesterterpene Synthases from Lentzea atacamensis Demonstrate the Role of Conformational Variability in Terpene Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202401539. [PMID: 38372063 DOI: 10.1002/anie.202401539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024]
Abstract
Mining of two multiproduct sesterterpene synthases from Lentzea atacamensis resulted in the identification of the synthases for lentzeadiene (LaLDS) and atacamatriene (LaATS). The main product of LaLDS (lentzeadiene) is a new compound, while one of the side products (lentzeatetraene) is the enantiomer of brassitetraene B and the other side product (sestermobaraene F) is known from a surprisingly distantly related sesterterpene synthase. LaATS produces six new compounds, one of which is the enantiomer of the known sesterterpene Bm1. Notably, for both enzymes the products cannot all be explained from one and the same starting conformation of geranylfarnesyl diphosphate, demonstrating the requirement of conformational flexibility of the substrate in the enzymes' active sites. For lentzeadiene an intriguing thermal [1,5]-sigmatropic rearrangement was discovered, reminiscent of the biosynthesis of vitamin D3. All enzyme reactions and the [1,5]-sigmatropic rearrangement were investigated through isotopic labeling experiments and DFT calculations. The results also emphasize the importance of conformational changes during terpene cyclizations.
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Affiliation(s)
- Binbin Gu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department for Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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11
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Djorić D, Atkinson SN, Kristich CJ. Reciprocal regulation of enterococcal cephalosporin resistance by products of the autoregulated yvcJ-glmR-yvcL operon enhances fitness during cephalosporin exposure. PLoS Genet 2024; 20:e1011215. [PMID: 38512984 PMCID: PMC10986989 DOI: 10.1371/journal.pgen.1011215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/02/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Enterococci are commensal members of the gastrointestinal tract and also major nosocomial pathogens. They possess both intrinsic and acquired resistance to many antibiotics, including intrinsic resistance to cephalosporins that target bacterial cell wall synthesis. These antimicrobial resistance traits make enterococcal infections challenging to treat. Moreover, prior therapy with antibiotics, including broad-spectrum cephalosporins, promotes enterococcal proliferation in the gut, resulting in dissemination to other sites of the body and subsequent infection. As a result, a better understanding of mechanisms of cephalosporin resistance is needed to enable development of new therapies to treat or prevent enterococcal infections. We previously reported that flow of metabolites through the peptidoglycan biosynthesis pathway is one determinant of enterococcal cephalosporin resistance. One factor that has been implicated in regulating flow of metabolites into cell wall biosynthesis pathways of other Gram-positive bacteria is GlmR. In enterococci, GlmR is encoded as the middle gene of a predicted 3-gene operon along with YvcJ and YvcL, whose functions are poorly understood. Here we use genetics and biochemistry to investigate the function of the enterococcal yvcJ-glmR-yvcL gene cluster. Our results reveal that YvcL is a DNA-binding protein that regulates expression of the yvcJ-glmR-yvcL operon in response to cell wall stress. YvcJ and GlmR bind UDP-GlcNAc and reciprocally regulate cephalosporin resistance in E. faecalis, and binding of UDP-GlcNAc by YvcJ appears essential for its activity. Reciprocal regulation by YvcJ/GlmR is essential for fitness during exposure to cephalosporin stress. Additionally, our results indicate that enterococcal GlmR likely acts by a different mechanism than the previously studied GlmR of Bacillus subtilis, suggesting that the YvcJ/GlmR regulatory module has evolved unique targets in different species of bacteria.
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Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Samantha N. Atkinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Christopher J. Kristich
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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12
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Kwon T, Hovde BT. Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures. Sci Rep 2024; 14:1534. [PMID: 38233413 PMCID: PMC10794256 DOI: 10.1038/s41598-023-50095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.
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Affiliation(s)
- Taehyung Kwon
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Blake T Hovde
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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13
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Yang Z, Yang X, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Zhu D, Cheng A. Genome-wide association study reveals serovar-associated genetic loci in Riemerella anatipestifer. BMC Genomics 2024; 25:57. [PMID: 38216873 PMCID: PMC10787497 DOI: 10.1186/s12864-024-09988-4] [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: 04/26/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND The disease caused by Riemerella anatipestifer (R. anatipestifer, RA) results in large economic losses to the global duck industry every year. Serovar-related genomic variation, such as the O-antigen and capsular polysaccharide (CPS) gene clusters, has been widely used for serotyping in many gram-negative bacteria. RA has been classified into at least 21 serovars based on slide agglutination, but the molecular basis of serotyping is unknown. In this study, we performed a pan-genome-wide association study (Pan-GWAS) to identify the genetic loci associated with RA serovars. RESULTS The results revealed a significant association between the putative CPS synthesis gene locus and the serological phenotype. Further characterization of the CPS gene clusters in 11 representative serovar strains indicated that they were highly diverse and serovar-specific. The CPS gene cluster contained the key genes wzx and wzy, which are involved in the Wzx/Wzy-dependent pathway of CPS synthesis. Similar CPS loci have been found in some other species within the family Weeksellaceae. We have also shown that deletion of the wzy gene in RA results in capsular defects and cross-agglutination. CONCLUSIONS This study indicates that the CPS synthesis gene cluster of R. anatipestifer is a serotype-specific genetic locus. Importantly, our finding provides a new perspective for the systematic analysis of the genetic basis of the R anatipestifer serovars and a potential target for establishing a complete molecular serotyping scheme.
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Affiliation(s)
- Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Xueqin Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China.
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China.
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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14
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Hirsch P, Tagirdzhanov A, Kushnareva A, Olkhovskii I, Graf S, Schmartz GP, Hegemann JD, Bozhüyük KAJ, Müller R, Keller A, Gurevich A. ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome. Nucleic Acids Res 2024; 52:D579-D585. [PMID: 37994699 PMCID: PMC10767846 DOI: 10.1093/nar/gkad1086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
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Affiliation(s)
- Pascal Hirsch
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Azat Tagirdzhanov
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Aleksandra Kushnareva
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ilia Olkhovskii
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Simon Graf
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Kenan A J Bozhüyük
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alexey Gurevich
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
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15
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Li J, Mui JWY, da Silva BM, Pires DEV, Ascher DB, Madiedo Soler N, Goddard-Borger ED, Williams SJ. A Broad-Spectrum α-Glucosidase of Glycoside Hydrolase Family 13 from Marinovum sp., a Member of the Roseobacter Clade. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04820-3. [PMID: 38180643 DOI: 10.1007/s12010-023-04820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Glycoside hydrolases (GHs) are a diverse group of enzymes that catalyze the hydrolysis of glycosidic bonds. The Carbohydrate-Active enZymes (CAZy) classification organizes GHs into families based on sequence data and function, with fewer than 1% of the predicted proteins characterized biochemically. Consideration of genomic context can provide clues to infer possible enzyme activities for proteins of unknown function. We used the MultiGeneBLAST tool to discover a gene cluster in Marinovum sp., a member of the marine Roseobacter clade, that encodes homologues of enzymes belonging to the sulfoquinovose monooxygenase pathway for sulfosugar catabolism. This cluster lacks a gene encoding a classical family GH31 sulfoquinovosidase candidate, but which instead includes an uncharacterized family GH13 protein (MsGH13) that we hypothesized could be a non-classical sulfoquinovosidase. Surprisingly, recombinant MsGH13 lacks sulfoquinovosidase activity and is a broad-spectrum α-glucosidase that is active on a diverse array of α-linked disaccharides, including maltose, sucrose, nigerose, trehalose, isomaltose, and kojibiose. Using AlphaFold, a 3D model for the MsGH13 enzyme was constructed that predicted its active site shared close similarity with an α-glucosidase from Halomonas sp. H11 of the same GH13 subfamily that shows narrower substrate specificity.
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Affiliation(s)
- Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Janice W-Y Mui
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Bruna M da Silva
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia
- School of Computing and Information Systems, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia
- School of Computing and Information Systems, University of Melbourne, Parkville, Victoria, 3010, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Niccolay Madiedo Soler
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Ethan D Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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16
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Beller P, Fink P, Wolf F, Männle D, Helmle I, Kuttenlochner W, Unterfrauner D, Engelbrecht A, Staudt ND, Kulik A, Groll M, Gross H, Kaysser L. Characterization of the cystargolide biosynthetic gene cluster and functional analysis of the methyltransferase CysG. J Biol Chem 2024; 300:105507. [PMID: 38029966 PMCID: PMC10776993 DOI: 10.1016/j.jbc.2023.105507] [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: 07/24/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Cystargolides are natural products originally isolated from Kitasatospora cystarginea NRRL B16505 as inhibitors of the proteasome. They are composed of a dipeptide backbone linked to a β-lactone warhead. Recently, we identified the cystargolide biosynthetic gene cluster, but systematic genetic analyses had not been carried out because of the lack of a heterologous expression system. Here, we report the discovery of a homologous cystargolide biosynthetic pathway in Streptomyces durhamensis NRRL-B3309 by genome mining. The gene cluster was cloned via transformation-associated recombination and heterologously expressed in Streptomyces coelicolor M512. We demonstrate that it contains all genes necessary for the production of cystargolide A and B. Single gene deletion experiments reveal that only five of the eight genes from the initially proposed gene cluster are essential for cystargolide synthesis. Additional insights into the cystargolide pathway could be obtained from in vitro assays with CysG and chemical complementation of the respective gene knockout. This could be further supported by the in vitro investigation of the CysG homolog BelI from the belactosin biosynthetic gene cluster. Thereby, we confirm that CysG and BelI catalyze a cryptic SAM-dependent transfer of a methyl group that is critical for the construction of the cystargolide and belactosin β-lactone warheads.
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Affiliation(s)
- Patrick Beller
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Phillipp Fink
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Felix Wolf
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Daniel Männle
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Irina Helmle
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Wolfgang Kuttenlochner
- Department of Bioscience, Center for Protein Assemblies (CPA), TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Daniel Unterfrauner
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Alicia Engelbrecht
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Nicole D Staudt
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Michael Groll
- Department of Bioscience, Center for Protein Assemblies (CPA), TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, Institute for Drug Discovery, University of Leipzig, Leipzig, Germany.
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17
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Vacheron J, Heiman CM, Garneau JR, Kupferschmied P, de Jonge R, Garrido-Sanz D, Keel C. Molecular and evolutionary basis of O-antigenic polysaccharide-driven phage sensitivity in environmental pseudomonads. Microbiol Spectr 2023; 11:e0204923. [PMID: 37800913 PMCID: PMC10715155 DOI: 10.1128/spectrum.02049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE The application of plant-beneficial microorganisms to protect crop plants is a promising alternative to the usage of chemicals. However, biocontrol research often faces difficulties in implementing this approach due to the inconsistency of the bacterial inoculant to establish itself within the root microbiome. Beneficial bacterial inoculants can be decimated by the presence of their natural predators, notably bacteriophages (also called phages). Thus, it is important to gain knowledge regarding the mechanisms behind phage-bacteria interactions to overcome this challenge. Here, we evidence that the major long O-antigenic polysaccharide (O-PS, O-antigen) of the widely used model plant-beneficial bacterium Pseudomonas protegens CHA0 is the receptor of its natural predator, the phage ΦGP100. We examined the distribution of the gene cluster directing the synthesis of this O-PS and identified signatures of horizontal gene acquisitions. Altogether, our study highlights the importance of bacterial cell surface structure variation in the complex interplay between phages and their Pseudomonas hosts.
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Affiliation(s)
- Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Clara M. Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Julian R. Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Peter Kupferschmied
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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18
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Seibel E, Um S, Dayras M, Bodawatta KH, de Kruijff M, Jønsson KA, Poulsen M, Kim KH, Beemelmanns C. Genome mining for macrolactam-encoding gene clusters allowed for the network-guided isolation of β-amino acid-containing cyclic derivatives and heterologous production of ciromicin A. Commun Chem 2023; 6:257. [PMID: 37985888 PMCID: PMC10662134 DOI: 10.1038/s42004-023-01034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
β-Amino acid-containing macrolactams represent a structurally diverse group of bioactive natural products derived from polyketides; however we are currently lacking a comprehensive overview about their abundance across bacterial families and the underlying biosynthetic diversity. In this study, we employed a targeted β-amino acid-specific homology-based multi-query search to identify potential bacterial macrolactam producers. Here we demonstrate that approximately 10% of each of the identified actinobacterial genera harbor a biosynthetic gene cluster (BGC) encoding macrolactam production. Based on our comparative study, we propose that mutations occurring in specific regions of polyketide synthases (PKS) are the primary drivers behind the variation in macrolactam ring sizes. We successfully validated two producers of ciromicin A from the genus Amycolatopsis, revised the composition of the biosynthetic gene cluster region mte of macrotermycins, and confirmed the ciromicin biosynthetic pathway through heterologous expression. Additionally, network-based metabolomic analysis uncovered three previously unreported macrotermycin congeners from Amycolatopsis sp. M39. The combination of targeted mining and network-based analysis serves as a powerful tool for identifying macrolactam producers and our studies will catalyze the future discovery of yet unreported macrolactams.
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Affiliation(s)
- Elena Seibel
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Soohyun Um
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Songdogwahak-ro, Incheon, 12983, Republic of Korea
| | - Marie Dayras
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Kasun H Bodawatta
- Globe Institute, Section for Molecular Ecology and Evolution, University of Copenhagen, 1350, Copenhagen K, Denmark
- Natural History Museum of Denmark - Research and Collections, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Martinus de Kruijff
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany
| | - Knud A Jønsson
- Natural History Museum of Denmark - Research and Collections, University of Copenhagen, 2100, Copenhagen East, Denmark
- Section for Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18, Stockholm, Sweden
| | - Michael Poulsen
- Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745, Jena, Germany.
- Anti-Infectives from Microbiota, Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany.
- Saarland University, 66123, Saarbrücken, Germany.
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19
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Sharma M, Kaur A, Madiedo Soler N, Lingford JP, Epa R, Goddard-Borger ED, Davies GJ, Williams SJ. Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases. J Biol Chem 2023; 299:105338. [PMID: 37838169 PMCID: PMC10665668 DOI: 10.1016/j.jbc.2023.105338] [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: 08/19/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant, algal, and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for SQ breakdown is the sulfoglycolytic Embden-Meyerhof-Parnas pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is understood for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures of complexes with substrate SFP and product dihydroxyacetone phosphate reveal a dimer-of-dimers (tetrameric) assembly, the sulfonate-binding pocket, two metal-binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal-dependent and exhibited high KM values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfoglycolytic Embden-Meyerhof-Parnas gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases have mututally exclusive occurrence within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar.
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Affiliation(s)
- Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Niccolay Madiedo Soler
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - James P Lingford
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ruwan Epa
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ethan D Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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20
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Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat Biotechnol 2023; 41:1416-1423. [PMID: 36782070 PMCID: PMC10423304 DOI: 10.1038/s41587-023-01675-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2023] [Indexed: 02/15/2023]
Abstract
The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
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Affiliation(s)
| | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Changzhou Medical Center, Nanjing Medical University, Changzhou, China
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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21
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Salamzade R, Tran P, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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22
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Bown L, Hirota R, Goettge MN, Cui J, Krist DT, Zhu L, Giurgiu C, van der Donk WA, Ju KS, Metcalf WW. A Novel Pathway for Biosynthesis of the Herbicidal Phosphonate Natural Product Phosphonothrixin Is Widespread in Actinobacteria. J Bacteriol 2023; 205:e0048522. [PMID: 37074199 PMCID: PMC10210982 DOI: 10.1128/jb.00485-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Phosphonothrixin is an herbicidal phosphonate natural product with an unusual, branched carbon skeleton. Bioinformatic analyses of the ftx gene cluster, which is responsible for synthesis of the compound, suggest that early steps of the biosynthetic pathway, up to production of the intermediate 2,3-dihydroxypropylphosphonic acid (DHPPA) are identical to those of the unrelated phosphonate natural product valinophos. This conclusion was strongly supported by the observation of biosynthetic intermediates from the shared pathway in spent media from two phosphonothrixin producing strains. Biochemical characterization of ftx-encoded proteins confirmed these early steps, as well as subsequent steps involving the oxidation of DHPPA to 3-hydroxy-2-oxopropylphosphonate and its conversion to phosphonothrixin by the combined action of an unusual heterodimeric, thiamine-pyrophosphate (TPP)-dependent ketotransferase and a TPP-dependent acetolactate synthase. The frequent observation of ftx-like gene clusters within actinobacteria suggests that production of compounds related to phosphonothrixin is common within these bacteria. IMPORTANCE Phosphonic acid natural products, such as phosphonothrixin, have great potential for biomedical and agricultural applications; however, discovery and development of these compounds requires detailed knowledge of the metabolism involved in their biosynthesis. The studies reported here reveal the biochemical pathway phosphonothrixin production, which enhances our ability to design strains that overproduce this potentially useful herbicide. This knowledge also improves our ability to predict the products of related biosynthetic gene clusters and the functions of homologous enzymes.
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Affiliation(s)
- Luke Bown
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ryuichi Hirota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Michelle N. Goettge
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - David T. Krist
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lingyang Zhu
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Constantin Giurgiu
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A. van der Donk
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
| | - William W. Metcalf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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23
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Sharon I, Schmeing TM. Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation. Sci Rep 2023; 13:8314. [PMID: 37221236 PMCID: PMC10206079 DOI: 10.1038/s41598-023-34587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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24
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van den Belt M, Gilchrist C, Booth TJ, Chooi YH, Medema MH, Alanjary M. CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters. BMC Bioinformatics 2023; 24:181. [PMID: 37131131 PMCID: PMC10155394 DOI: 10.1186/s12859-023-05311-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/27/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) that produce specialized metabolites with medicinal, agricultural, and industrial value (e.g. antimicrobials). Comparative analysis of BGCs can aid in the discovery of novel metabolites by highlighting distribution and identifying variants in public genomes. Unfortunately, gene-cluster-level homology detection remains inaccessible, time-consuming and difficult to interpret. RESULTS The comparative gene cluster analysis toolbox (CAGECAT) is a rapid and user-friendly platform to mitigate difficulties in comparative analysis of whole gene clusters. The software provides homology searches and downstream analyses without the need for command-line or programming expertise. By leveraging remote BLAST databases, which always provide up-to-date results, CAGECAT can yield relevant matches that aid in the comparison, taxonomic distribution, or evolution of an unknown query. The service is extensible and interoperable and implements the cblaster and clinker pipelines to perform homology search, filtering, gene neighbourhood estimation, and dynamic visualisation of resulting variant BGCs. With the visualisation module, publication-quality figures can be customized directly from a web-browser, which greatly accelerates their interpretation via informative overlays to identify conserved genes in a BGC query. CONCLUSION Overall, CAGECAT is an extensible software that can be interfaced via a standard web-browser for whole region homology searches and comparison on continually updated genomes from NCBI. The public web server and installable docker image are open source and freely available without registration at: https://cagecat.bioinformatics.nl .
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Affiliation(s)
- Matthias van den Belt
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Cameron Gilchrist
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University and Research, 6708PB, Wageningen, The Netherlands.
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25
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Mihelj P, Abreu I, Moreyra T, González-Guerrero M, Raimunda D. Functional Characterization of the Co 2+ Transporter AitP in Sinorhizobium meliloti: A New Player in Fe 2+ Homeostasis. Appl Environ Microbiol 2023; 89:e0190122. [PMID: 36853042 PMCID: PMC10057888 DOI: 10.1128/aem.01901-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
Co2+ induces the increase of the labile-Fe pool (LIP) by Fe-S cluster damage, heme synthesis inhibition, and "free" iron import, which affects cell viability. The N2-fixing bacteria, Sinorhizobium meliloti, is a suitable model to determine the roles of Co2+-transporting cation diffusion facilitator exporters (Co-eCDF) in Fe2+ homeostasis because it has a putative member of this subfamily, AitP, and two specific Fe2+-export systems. An insertional mutant of AitP showed Co2+ sensitivity and accumulation, Fe accumulation and hydrogen peroxide sensitivity, but not Fe2+ sensitivity, despite AitP being a bona fide low affinity Fe2+ exporter as demonstrated by the kinetic analyses of Fe2+ uptake into everted membrane vesicles. Suggesting concomitant Fe2+-dependent induced stress, Co2+ sensitivity was increased in strains carrying mutations in AitP and Fe2+ exporters which did not correlate with the Co2+ accumulation. Growth in the presence of sublethal Fe2+ and Co2+ concentrations suggested that free Fe-import might contribute to Co2+ toxicity. Supporting this, Co2+ induced transcription of Fe-import system and genes associated with Fe homeostasis. Analyses of total protoporphyrin content indicates Fe-S cluster attack as the major source for LIP. AitP-mediated Fe2+-export is likely counterbalanced via a nonfutile Fe2+-import pathway. Two lines of evidence support this: (i) an increased hemin uptake in the presence of Co2+ was observed in wild-type (WT) versus AitP mutant, and (ii) hemin reversed the Co2+ sensitivity in the AitP mutant. Thus, the simultaneous detoxification mediated by AitP aids cells to orchestrate an Fe-S cluster salvage response, avoiding the increase in the LIP caused by the disassembly of Fe-S clusters or free iron uptake. IMPORTANCE Cross-talk between iron and cobalt has been long recognized in biological systems. This is due to the capacity of cobalt to interfere with proper iron utilization. Cells can detoxify cobalt by exporting mechanisms involving membrane proteins known as exporters. Highlighting the cross-talk, the capacity of several cobalt exporters to also export iron is emerging. Although biologically less important than Fe2+, Co2+ induces toxicity by promoting intracellular Fe release, which ultimately causes additional toxic effects. In this work, we describe how the rhizobia cells solve this perturbation by clearing Fe through a Co2+ exporter, in order to reestablish intracellular Fe levels by importing nonfree Fe, heme. This piggyback-ride type of transport may aid bacterial cells to survive in free-living conditions where high anthropogenic Co2+ content may be encountered.
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Affiliation(s)
- Paula Mihelj
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Tomás Moreyra
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Daniel Raimunda
- Instituto de Investigación Médica Mercedes y Martín Ferreyra-INIMEC-CONICET, UNC, Córdoba, Argentina
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Zhang J, Guan J, Wang M, Li G, Djordjevic M, Tai C, Wang H, Deng Z, Chen Z, Ou HY. SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems. SCIENCE CHINA. LIFE SCIENCES 2023; 66:626-634. [PMID: 36346548 DOI: 10.1007/s11427-022-2172-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
Type VI Secretion System (T6SS) plays significant roles in microbial activities via injecting effectors into adjacent cells or environments. T6SS increasingly gained attention due to its important influence on pathogenesis, microbial competition, etc. T6SS-associated research is explosively expanding on numerous grounds that call for an efficient resource. The SecReT6 version 3 provides comprehensive information on T6SS and the interactions between T6SS and T6SS-related proteins such as T6SS regulators and T6SS effectors. To assist T6SS researches like microbial competition and regulatory mechanisms, SecReT6 v3 developed online tools for detection and analysis of T6SS and T6SS-related proteins and estimation of T6SS-dependent killing risk. We have identified a novel T6SS regulator and T6SS-dependent killing capacity in Acinetobacter baumannii clinical isolates with the aid of SecReT6 v3. 17,212 T6SSs and plentiful T6SS-related proteins in 26,573 bacterial complete genomes were also detected, analyzed and incorporated into the database. The database is freely available at https://bioinfo-mml.sjtu.edu.cn/SecReT6/ .
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Affiliation(s)
- Jianfeng Zhang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Intensive Care Unit, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Jiahao Guan
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Meng Wang
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gang Li
- Department of Laboratory Medicine, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, 201500, China
| | - Marko Djordjevic
- Quantitative Biology Group, Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhaoyan Chen
- Intensive Care Unit, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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27
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Lekired A, Cherif-Silini H, Silini A, Ben Yahia H, Ouzari HI. Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments. Genomics 2023; 115:110579. [PMID: 36792019 DOI: 10.1016/j.ygeno.2023.110579] [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: 06/17/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.
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Affiliation(s)
- Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Allaoua Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Hamza Ben Yahia
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.
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Swanson CB, Ford GJ, Mattey AP, Gourbeyre L, Flitsch SL. Biocatalytic Cascades toward Iminosugar Scaffolds Reveal Promiscuous Activity of Shikimate Dehydrogenases. ACS CENTRAL SCIENCE 2023; 9:103-108. [PMID: 36712485 PMCID: PMC9881201 DOI: 10.1021/acscentsci.2c01169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Indexed: 06/18/2023]
Abstract
Iminosugar scaffolds are highly sought-after pharmaceutical targets, but their chemical synthesis is lengthy and can suffer from poor scalability and purification. Here we report protecting-group-free chemoenzymatic and biocatalytic cascades to synthesize iminosugars from sugar-derived aminopolyols in two steps. Using galactose oxidase variant F2 followed by a chemical or enzymatic reduction provided an efficient one-pot route to these targets, with product formation >70%. Key to success of this strategy was the application of genome mining, which identified bacterial shikimate dehydrogenases as promiscuous iminosugar reductases. The cell-free protocols allowed for isolation of highly polar iminosugar products from biotransformations in a single step through development of a gradient-elution cation exchange purification. The two-step pathway provides a short synthetic route that can be used as a cell-free platform for broader iminosugar synthesis.
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29
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Acken KA, Li B. Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila. PLoS One 2023; 18:e0284907. [PMID: 37200397 DOI: 10.1371/journal.pone.0284907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
Quorum sensing is a communication strategy that bacteria use to collectively alter gene expression in response to cell density. Pathogens use quorum sensing systems to control activities vital to infection, such as the production of virulence factors and biofilm formation. The Pseudomonas virulence factor (pvf) gene cluster encodes a signaling system (Pvf) that is present in over 500 strains of proteobacteria, including strains that infect a variety of plant and human hosts. We have shown that Pvf regulates the production of secreted proteins and small molecules in the insect pathogen Pseudomonas entomophila L48. Here, we identified genes that are likely regulated by Pvf using the model strain P. entomophila L48 which does not contain other known quorum sensing systems. Pvf regulated genes were identified through comparing the transcriptomes of wildtype P. entomophila and a pvf deletion mutant (ΔpvfA-D). We found that deletion of pvfA-D affected the expression of approximately 300 genes involved in virulence, the type VI secretion system, siderophore transport, and branched chain amino acid biosynthesis. Additionally, we identified seven putative biosynthetic gene clusters with reduced expression in ΔpvfA-D. Our results indicate that Pvf controls multiple virulence mechanisms in P. entomophila L48. Characterizing genes regulated by Pvf will aid understanding of host-pathogen interactions and development of anti-virulence strategies against P. entomophila and other pvf-containing strains.
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Affiliation(s)
- Katie A Acken
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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30
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Yin CF, Xu Y, Li T, Zhou NY. Wide distribution of the sad gene cluster for sub-terminal oxidation in alkane utilizers. Environ Microbiol 2022; 24:6307-6319. [PMID: 35837858 DOI: 10.1111/1462-2920.16124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/04/2022] [Accepted: 07/01/2022] [Indexed: 01/12/2023]
Abstract
Alkane constitutes major fractions of crude oils, and its microbial aerobic degradation dominantly follows the terminal oxidation and the sub-terminal pathways. However, the latter one received much less attention, especially since the related genes were yet to be fully defined. Here, we isolated a bacterium designated Acinetobacter sp. strain NyZ410, capable of growing on alkanes with a range of chain lengths and derived sub-terminal oxidation products. From its genome, a secondary alcohol degradation gene cluster (sad) was identified to be likely involved in converting the aliphatic secondary alcohols (the sub-terminal oxidation products of alkanes) to the corresponding primary alcohols by removing two-carbon unit. On this cluster, sadC encoded an alcohol dehydrogenase converting the aliphatic secondary alcohols to the corresponding ketones; sadD encoded a Baeyer-Villiger monooxygenase catalysing the conversion of the aliphatic ketones to the corresponding esters; SadA and SadB are two esterases hydrolyzing aliphatic esters to the primary alcohols and acetic acids. Bioinformatics analyses indicated that the sad cluster was widely distributed in the genomes of probable alkane degraders, apparently coexisting (64%) with the signature enzymes AlkM and AlmA for alkane terminal oxidation in 350 bacterial genomes. It suggests that the alkane sub-terminal oxidation may be more ubiquitous than previously thought.
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Affiliation(s)
- Chao-Fan Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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31
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Wang C, Lv Y, Zhou L, Zhang Y, Yao Q, Zhu H. Comparative genomics of Myxococcus and Pyxidicoccus, including the description of four novel species: Myxococcus guangdongensis sp. nov., Myxococcus qinghaiensis sp. nov., Myxococcus dinghuensis sp. nov., and Pyxidicoccus xibeiensis sp. nov. Front Microbiol 2022; 13:995049. [PMID: 36439860 PMCID: PMC9684338 DOI: 10.3389/fmicb.2022.995049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/18/2022] [Indexed: 08/22/2023] Open
Abstract
Myxobacteria are recognized for fascinating social behaviors and producing diverse extracellular active substances. Isolating novel myxobacteria is of great interest in the exploitation of new antibiotics and extracellular enzymes. Herein, four novel strains were isolated from Dinghu Mountain Biosphere Reserve, Guangdong province, and Qinghai virgin forest soils, Qinghai province, China. The phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that the four strains belong to the genera Myxococcus and Pyxidicoccus, sharing the highly similarities of 16S rRNA gene with the genera Myxococcus and Pyxidicoccus (99.3-99.6%, respectively). The four strains had average nucleotide identity (ANI) values of 82.8-94.5%, digital DNA-DNA hybridization (dDDH) values of 22.2-56.6%, average amino acid identity (AAI) values of 75.8-79.1% and percentage of conserved protein (POCP) values of 66.4-74.9% to members of the genera Myxococcus and Pyxidicoccus. Based on phylogenetic analyses, physiological and biochemical characteristics, and comparative genomic analyses, we propose four novel species of the genera Myxococcus and Pyxidicoccus and further supported the two genera above represented the same genus. Description of the four novel species is Myxococcus guangdongensis sp. nov. (K38C18041901T = GDMCC 1.2320T = JCM 39260T), Myxococcus qinghaiensis sp. nov. (QH3KD-4-1T = GDMCC 1.2316T = JCM 39262T), Myxococcus dinghuensis sp. nov. (K15C18031901T = GDMCC 1.2319T = JCM 39259T), and Pyxidicoccus xibeiensis sp. nov. (QH1ED-7-1T = GDMCC 1.2315T = JCM 39261T), respectively. Furthermore, comparative genomics of all 15 species of the genera Myxococcus and Pyxidicoccus revealed extensive genetic diversity. Core genomes enriched more genes associated with housekeeping functional classes while accessory genomes enriched more genes related to environmental interactions, indicating the former is relatively indispensable compared to signaling pathway genes. The 15 species of Myxococcus and Pyxidicoccus also exhibited great gene diversity of carbohydrate-active enzymes (CAZymes) and secondary metabolite biosynthesis gene clusters (BGCs), especially related to glycosyl transferases (GT2 and GT4), glycoside hydrolases (GH13 and GH23), non-ribosomal peptide synthetases (NRPS), and Type I polyketide synthase (PKS)/NRPS hybrids.
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Affiliation(s)
- Chunling Wang
- Guangdong Academy of Sciences, Institute of Microbiology, Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
- College of Life Science, Huizhou University, Huizhou, China
| | - Yingying Lv
- Guangdong Academy of Sciences, Institute of Microbiology, Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Lian Zhou
- Guangdong Academy of Sciences, Institute of Microbiology, Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Yulian Zhang
- Guangdong Academy of Sciences, Institute of Microbiology, Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou, China
| | - Honghui Zhu
- Guangdong Academy of Sciences, Institute of Microbiology, Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
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32
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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. Nat Commun 2022; 13:6044. [PMID: 36229545 PMCID: PMC9561172 DOI: 10.1038/s41467-022-33782-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
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33
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Kusumawardhani H, Hosseini R, Verschoor JA, de Winde JH. Comparative analysis reveals the modular functional structure of conjugative megaplasmid pTTS12 of Pseudomonas putida S12: A paradigm for transferable traits, plasmid stability, and inheritance? Front Microbiol 2022; 13:1001472. [PMID: 36212887 PMCID: PMC9537497 DOI: 10.3389/fmicb.2022.1001472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Originating from various environmental niches, large numbers of bacterial plasmids have been found carrying heavy metal and antibiotic resistance genes, degradation pathways and specific transporter genes for organic solvents or aromatic compounds. Such genes may constitute promising candidates for novel synthetic biology applications. Our systematic analysis of gene clusters encoded on megaplasmid pTTS12 from Pseudomonas putida S12 underscores that a large portion of its genes is involved in stress response to increase survival under harsh conditions like the presence of heavy metal and organic solvent. We investigated putative roles of genes encoded on pTTS12 and further elaborated on their roles in the establishment and maintenance under several stress conditions, specifically focusing on solvent tolerance in P. putida strains. The backbone of pTTS12 was found to be closely related to that of the carbapenem-resistance plasmid pOZ176, member of the IncP-2 incompatibility group, although the carbapenem resistance cassette is absent from pTTS12. Megaplasmid pTTS12 contains multiple transposon-flanked cassettes mediating resistance to various heavy metals such as tellurite, chromate (Tn7), and mercury (Tn5053 and Tn5563). Additionally, pTTS12 also contains a P-type, Type IV secretion system (T4SS) supporting self-transfer to other P. putida strains. This study increases our understanding in the modular structure of pTTS12 as a member of IncP-2 plasmid family and several promising exchangeable gene clusters to construct robust microbial hosts for biotechnology applications.
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Affiliation(s)
- Hadiastri Kusumawardhani
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Rohola Hosseini
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | | | - Johannes H. de Winde
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- *Correspondence: Johannes H. de Winde,
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34
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Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system. Nat Microbiol 2022; 7:1547-1557. [PMID: 36123439 PMCID: PMC9519443 DOI: 10.1038/s41564-022-01209-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/21/2022] [Indexed: 11/24/2022]
Abstract
Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs—so far thought to transfer effectors only into eukaryotic cells—to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture. Pseudomonas putida uses a type IVB secretion system to kill a broad range of Gram-negative bacteria, invade biofilms and prevent phytopathogen Ralstonia solanacearum infection in tomato plants.
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35
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Niveditha L, Fu P, Leao TF, Li T, Wang T, Poulin RX, Gaspar LR, Naman CB, Thavarool Puthiyedathu S. Targeted Isolation of Two New Anti-inflammatory and UV-A Protective Dipyrroloquinones from the Sponge-associated Fungus Aspergillus tamarii MCCF102. PLANTA MEDICA 2022; 88:774-782. [PMID: 35148546 DOI: 10.1055/a-1769-8480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In following up on observed in vitro anti-inflammatory activity of the organic extract of the marine sponge-derived fungus Aspergillus tamarii MCCF102, two new dipyrrolobenzoquinones, terreusinone B and C (1: and 2: ), were discovered along with the known analogue, terreusinone (3: ). The structures of 1: -3: were determined by spectroscopic and spectrometric analyses, along with chemical inter-conversion. In vitro testing on lipopolysaccharide (LPS) stimulated RAW 264.7 murine macrophage cells revealed that 1: -3: exhibit anti-inflammatory activity by inhibiting nitric oxide production in a dose-dependent manner (IC50 < 1 µM) without any cytotoxicity observed at the same concentrations. Due to this and the UV-A absorptive properties imparted by the highly conjugated structures of these molecules, the potential for using 1: -3: or related analogues as natural sunscreen components is suggested. Gene sequencing and informatics biosynthetic gene cluster comparisons were insufficient to confidently elucidate the biosynthetic origins of these compounds, possibly suggesting the occurrence of a gene cluster not detected in the initial sequencing or a non-canonical pathway that should be further investigated.
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Affiliation(s)
- Lekshmi Niveditha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, India
| | - Peng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Tiago F Leao
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Te Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Tingting Wang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Remington X Poulin
- Department of Chemistry and Biochemistry, Center for Marine Science, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Lorena R Gaspar
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - C Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Department of Chemistry and Biochemistry, Center for Marine Science, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Sajeevan Thavarool Puthiyedathu
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, India
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36
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Reitz ZL, Medema MH. Genome mining strategies for metallophore discovery. Curr Opin Biotechnol 2022; 77:102757. [PMID: 35914390 DOI: 10.1016/j.copbio.2022.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Many bacteria use small-molecule chelators called metallophores to acquire trace metals from their environment. These molecules play a central role in interactions between bacteria, plants, and animals. Hence, knowing their full diversity is key to combatting infectious diseases as well as harnessing beneficial microbial communities. Metallophore discovery has been streamlined by advances in genome mining, where genomes are scanned for genes involved in metallophore biosynthesis. This review highlights recent trends and advances in predicting the presence and structure of metallophores based solely on genomic information. Recent work suggests new families of metallophores remain hidden from current homology-based approaches. Their discovery will require new genome mining approaches that move beyond biosynthesis to consider metallophore transporters, regulation, and evolution.
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Affiliation(s)
- Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
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37
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Lee SR, Schalk F, Schwitalla JW, Guo H, Yu JS, Song M, Jung WH, de Beer ZW, Beemelmanns C, Kim KH. GNPS‐Guided Discovery of Madurastatin Siderophores from the Termite‐Associated
Actinomadura
sp. RB99**. Chemistry 2022; 28:e202200612. [PMID: 35404539 PMCID: PMC9325478 DOI: 10.1002/chem.202200612] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 12/14/2022]
Abstract
In this study, we analyzed if Actinomadura sp. RB99 produces siderophores that that could be responsible for the antimicrobial activity observed in co‐cultivation studies. Dereplication of high‐resolution tandem mass spectrometry (HRMS/MS) and global natural product social molecular networking platform (GNPS) analysis of fungus‐bacterium co‐cultures resulted in the identification of five madurastatin derivatives (A1, A2, E1, F, and G1), of which were four new derivatives. Chemical structures were unambiguously confirmed by HR‐ESI‐MS, 1D and 2D NMR experiments, as well as MS/MS data and their absolute structures were elucidated based on Marfey's analysis, DP4+ probability calculation and total synthesis. Structure analysis revealed that madurastatin E1 (2) contained a rare 4‐imidazolidinone cyclic moiety and madurastatin A1 (5) was characterized as a Ga3+‐complex. The function of madurastatins as siderophores was evaluated using the fungal pathogen Cryptococcus neoformans as model organism. Based on homology models, we identified the putative NRPS‐based gene cluster region of the siderophores in Actinomadura sp. RB99.
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Affiliation(s)
- Seoung Rak Lee
- School of Pharmacy Sungkyunkwan University Suwon 16419 (Republic of Korea
- Department of Chemistry Princeton University New Jersey 08544 USA
| | - Felix Schalk
- Chemical Biology of Microbe-Host Interactions Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Jan W. Schwitalla
- Chemical Biology of Microbe-Host Interactions Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Jae Sik Yu
- School of Pharmacy Sungkyunkwan University Suwon 16419 (Republic of Korea
| | - Moonyong Song
- Department of Systems Biotechnology Chung-Ang University Anseong 17546 Republic of Korea
| | - Won Hee Jung
- Department of Systems Biotechnology Chung-Ang University Anseong 17546 Republic of Korea
| | - Z. Wilhelm de Beer
- Department of Biochemistry Genetics and Microbiology Forestry and Agricultural Biotechnology Institute (FABI) University of Pretoria Hatfield 0028 Pretoria South Africa
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Biochemistry of Microbial Metabolism Institute of Biochemistry Leipzig University Johannisallee 21–23 Leipzig 04103 Germany
| | - Ki Hyun Kim
- School of Pharmacy Sungkyunkwan University Suwon 16419 (Republic of Korea
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Amiri Moghaddam J, Guo H, Willing K, Wichard T, Beemelmanns C. Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity. Beilstein J Org Chem 2022; 18:722-731. [PMID: 35821696 PMCID: PMC9235831 DOI: 10.3762/bjoc.18.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Aromatic prenylated metabolites have important biological roles and activities in all living organisms. Compared to their importance in all domains of life, we know relatively little about their substrate scopes and metabolic functions. Here, we describe a new UbiA-like prenyltransferase (Ptase) Ubi-297 encoded in a conserved operon of several bacterial taxa, including marine Flavobacteria and the genus Sacchromonospora. In silico analysis of Ubi-297 homologs indicated that members of this Ptase group are composed of several transmembrane α-helices and carry a conserved and distinct aspartic-rich Mg2+-binding domain. We heterologously produced UbiA-like Ptases from the bacterial genera Maribacter, Zobellia, and Algoriphagus in Escherichia coli. Investigation of their substrate scope uncovered the preferential farnesylation of quinoline derivatives, such as 8-hydroxyquinoline-2-carboxylic acid (8-HQA) and quinaldic acid. The results of this study provide new insights into the abundance and diversity of Ptases in marine Flavobacteria and beyond.
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Affiliation(s)
- Jamshid Amiri Moghaddam
- Chemical Biology Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Huijuan Guo
- Chemical Biology Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Karsten Willing
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr 8, 07743 Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Biochemistry of Microbial Metabolism, Institute of Biochemistry, Leipzig University, Johannisallee 21–23, 04103 Leipzig, Germany
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Abstract
With the overmining of actinomycetes for compounds acting against Gram-negative pathogens, recent efforts to discover novel antibiotics have been focused on other groups of bacteria. Teixobactin, the first antibiotic without detectable resistance that binds lipid II, comes from an uncultured Eleftheria terra, a betaproteobacterium; odilorhabdins, from Xenorhabdus, are broad-spectrum inhibitors of protein synthesis, and darobactins from Photorhabdus target BamA, the essential chaperone of the outer membrane of Gram-negative bacteria. Xenorhabdus and Photorhabdus are symbionts of the nematode gut microbiome and attractive producers of secondary metabolites. Only small portions of their biosynthetic gene clusters (BGC) are expressed in vitro. To access their silent operons, we first separated extracts from a small library of isolates into fractions, resulting in 200-fold concentrated material, and then screened them for antimicrobial activity. This resulted in a hit with selective activity against Escherichia coli, which we identified as a novel natural product antibiotic, 3′-amino 3′-deoxyguanosine (ADG). Mutants resistant to ADG mapped to gsk and gmk, kinases of guanosine. Biochemical analysis shows that ADG is a prodrug that is converted into an active ADG triphosphate (ADG-TP), a mimic of GTP. ADG incorporates into a growing RNA chain, interrupting transcription, and inhibits cell division, apparently by interfering with the GTPase activity of FtsZ. Gsk of the purine salvage pathway, which is the first kinase in the sequential phosphorylation of ADG, is restricted to E. coli and closely related species, explaining the selectivity of the compound. There are probably numerous targets of ADG-TP among GTP-dependent proteins. The discovery of ADG expands our knowledge of prodrugs, which are rare among natural compounds.
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Pseudomonas phenolilytica sp. nov., a novel phenol-degrading bacterium. Arch Microbiol 2022; 204:320. [PMID: 35567652 DOI: 10.1007/s00203-022-02912-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
Abstract
This study describes a bacterium strain RBPA9 isolated from a municipality waste dumping area capable of degrading phenol, proposed as a novel species of Pseudomonas. Cells are Gram-negative, rod shaped, aerobic and motile. The genome is 3.92 Mb, and the G + C content is 64.64%. The overall genome relatedness indices such as in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values were below 70% and 95-96%, respectively. Phylogenetic analysis based on genome-wide core genes and 16S rRNA gene sequences revealed that strain RBPA9 clustered with Pseudomonas stutzeri ATCC 17588 T in both the phylogenetic trees. Maximum growth was recorded at 200 mg /L concentration of phenol which was consumed within 24 h. A gene cluster of phenol degradation pathway was detected. The quantitative real-time PCR (RT-PCR) demonstrated the expression of all the genes required in the meta-cleavage pathway of phenol in RBPA9. Our results reveal that strain RBPA9 represents a novel species for which Pseudomonas phenolilytica sp. nov. is proposed. The type strain is RBPA9T (= TBRC 15231 T = NBRC 115284 T).
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Lin CC, Hoo SY, Ma LT, Lin C, Huang KF, Ho YN, Sun CH, Lee HJ, Chen PY, Shu LJ, Wang BW, Hsu WC, Ko TP, Yang YL. Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors. Commun Biol 2022; 5:454. [PMID: 35551233 PMCID: PMC9098870 DOI: 10.1038/s42003-022-03409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial polyynes are highly active natural products with a broad spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. By integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), in the biosynthesis gene cluster of antifungal polyynes (massilin A 1, massilin B 2, collimonin C 3, and collimonin D 4) of Massilia sp. YMA4. Crystallographic analysis indicated that bacterial polyynes serve as covalent inhibitors of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited the cell viability of Candida albicans by targeting ERG10, the homolog of MasL. Thus, this study demonstrated that acetyl-CoA acetyltransferase is a potential target for developing antifungal agents. In a multi-omics analysis, bacterial polyynes are found to act as antifungal agents by inhibiting the Candida albicans polyyne resistance gene ERG10, the homolog of MasL encoding acetyl-CoA acetyltransferase.
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Affiliation(s)
- Ching-Chih Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Sin Yong Hoo
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Li-Ting Ma
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Chih Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Jhongjheng Dist., Keelung, 202, Taiwan
| | - Chi-Hui Sun
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Han-Jung Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Pi-Yu Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Bo-Wei Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan.,Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Gushan Dist., Kaohsiung, 804, Taiwan
| | - Wei-Chen Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan.,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang Dist., Taipei, 115, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Guiren Dist., Tainan, 711, Taiwan.
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Naguib M, Feldman N, Zarodkiewicz P, Shropshire H, Biamis C, El-Halfawy OM, McCain J, Dezanet C, Décout JL, Chen Y, Cosa G, Valvano MA. An evolutionary conserved detoxification system for membrane lipid-derived peroxyl radicals in Gram-negative bacteria. PLoS Biol 2022; 20:e3001610. [PMID: 35580139 PMCID: PMC9113575 DOI: 10.1371/journal.pbio.3001610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/18/2022] [Indexed: 11/30/2022] Open
Abstract
How double-membraned Gram-negative bacteria overcome lipid peroxidation is virtually unknown. Bactericidal antibiotics and superoxide ion stress stimulate the transcription of the Burkholderia cenocepacia bcnA gene that encodes a secreted lipocalin. bcnA gene orthologs are conserved in bacteria and generally linked to a conserved upstream gene encoding a cytochrome b561 membrane protein (herein named lcoA, lipocalin-associated cytochrome oxidase gene). Mutants in bcnA, lcoA, and in a gene encoding a conserved cytoplasmic aldehyde reductase (peroxidative stress-associated aldehyde reductase gene, psrA) display enhanced membrane lipid peroxidation. Compared to wild type, the levels of the peroxidation biomarker malondialdehyde (MDA) increase in the mutants upon exposure to sublethal concentrations of the bactericidal antibiotics polymyxin B and norfloxacin. Microscopy with lipid peroxidation-sensitive fluorescent probes shows that lipid peroxyl radicals accumulate at the bacterial cell poles and septum and peroxidation is associated with a redistribution of anionic phospholipids and reduced antimicrobial resistance in the mutants. We conclude that BcnA, LcoA, and PsrA are components of an evolutionary conserved, hitherto unrecognized peroxidation detoxification system that protects the bacterial cell envelope from lipid peroxyl radicals.
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Affiliation(s)
- Marwa Naguib
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Nicolás Feldman
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Paulina Zarodkiewicz
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Holly Shropshire
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Christina Biamis
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Omar M. El-Halfawy
- Department of Chemistry and Biochemistry, Faculty of Science, University of Regina, Regina, Saskatchewan, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Julia McCain
- Department of Chemistry and Quebec Center for Advanced Materials, McGill University, Montreal, Québec, Canada
| | - Clément Dezanet
- Department of Molecular Pharmacochemistry, Université Grenoble Alpes/CNRS, Grenoble, France
| | - Jean-Luc Décout
- Department of Molecular Pharmacochemistry, Université Grenoble Alpes/CNRS, Grenoble, France
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials, McGill University, Montreal, Québec, Canada
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
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43
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Liu Y, Chen H, Van Treuren W, Hou BH, Higginbottom SK, Dodd D. Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites. Nat Microbiol 2022; 7:695-706. [PMID: 35505245 PMCID: PMC9089323 DOI: 10.1038/s41564-022-01109-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Gut bacteria face a key problem in how they capture enough energy to sustain their growth and physiology. The gut bacterium Clostridium sporogenes obtains its energy by utilizing amino acids in pairs, coupling the oxidation of one to the reduction of another-the Stickland reaction. Oxidative pathways produce ATP via substrate-level phosphorylation, whereas reductive pathways are thought to balance redox. In the present study, we investigated whether these reductive pathways are also linked to energy generation and the production of microbial metabolites that may circulate and impact host physiology. Using metabolomics, we find that, during growth in vitro, C. sporogenes produces 15 metabolites, 13 of which are present in the gut of C. sporogenes-colonized mice. Four of these compounds are reductive Stickland metabolites that circulate in the blood of gnotobiotic mice and are also detected in plasma from healthy humans. Gene clusters for reductive Stickland pathways suggest involvement of electron transfer proteins, and experiments in vitro demonstrate that reductive metabolism is coupled to ATP formation and not just redox balance. Genetic analysis points to the broadly conserved Rnf complex as a key coupling site for energy transduction. Rnf complex mutants show aberrant amino acid metabolism in a defined medium and are attenuated for growth in the mouse gut, demonstrating a role of the Rnf complex in Stickland metabolism and gut colonization. Our findings reveal that the production of circulating metabolites by a commensal bacterium within the host gut is linked to an ATP-yielding redox process.
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Affiliation(s)
- Yuanyuan Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haoqing Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bi-Huei Hou
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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44
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Giri R, Hoedt EC, Khushi S, Salim AA, Bergot AS, Schreiber V, Thomas R, McGuckin MA, Florin TH, Morrison M, Capon RJ, Ó Cuív P, Begun J. Secreted NF-κB suppressive microbial metabolites modulate gut inflammation. Cell Rep 2022; 39:110646. [PMID: 35417687 DOI: 10.1016/j.celrep.2022.110646] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence suggests that microbiome-host crosstalk regulates intestinal immune activity and predisposition to inflammatory bowel disease (IBD). NF-κB is a master regulator of immune function and a validated target for the treatment of IBD. Here, we identify five Clostridium strains that suppress immune-mediated NF-κB activation in epithelial cell lines, PBMCs, and gut epithelial organoids from healthy human subjects and patients with IBD. Cell-free culture supernatant from Clostridium bolteae AHG0001 strain, but not the reference C. bolteae BAA-613 strain, suppresses inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice. The in vivo responses to Clostridium bolteae AHG0001 and BAA-613 mirror the in vitro activity. Thus, using our in vitro screening of bacteria capable of suppressing NF-κB in the context of IBD and using an ex vivo organoid-based approach, we identify a strain capable of alleviating colitis in a relevant pre-clinical animal model of IBD.
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Affiliation(s)
- Rabina Giri
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Shamsunnahar Khushi
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela A Salim
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Veronika Schreiber
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Michael A McGuckin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Timothy H Florin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Robert J Capon
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Páraic Ó Cuív
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia.
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Domingues Vieira B, Niero H, de Felício R, Giolo Alves LF, Freitas Bazzano C, Sigrist R, Costa Furtado L, Felix Persinoti G, Veras Costa-Lotufo L, Barretto Barbosa Trivella D. Production of Epoxyketone Peptide-Based Proteasome Inhibitors by Streptomyces sp. BRA-346: Regulation and Biosynthesis. Front Microbiol 2022; 13:786008. [PMID: 35401454 PMCID: PMC8988807 DOI: 10.3389/fmicb.2022.786008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Streptomyces sp. BRA-346 is an Actinobacteria isolated from the Brazilian endemic tunicate Euherdmania sp. We have reported that this strain produces epoxyketone peptides, as dihydroeponemycin (DHE) and structurally related analogs. This cocktail of epoxyketone peptides inhibits the proteasome chymotrypsin-like activity and shows high cytotoxicity to glioma cells. However, low yields and poor reproducibility of epoxyketone peptides production by BRA-346 under laboratory cultivation have limited the isolation of epoxyketone peptides for additional studies. Here, we evaluated several cultivation methods using different culture media and chemical elicitors to increase the repertoire of peptide epoxyketone production by this bacterium. Furthermore, BRA-346 genome was sequenced, revealing its broad genetic potential, which is mostly hidden under laboratory conditions. By using specific growth conditions, we were able to evidence different classes of secondary metabolites produced by BRA-346. In addition, by combining genome mining with untargeted metabolomics, we could link the metabolites produced by BRA-346 to its genetic capacity and potential regulators. A single biosynthetic gene cluster (BGC) was related to the production of the target epoxyketone peptides by BRA-346. The candidate BGC displays conserved biosynthetic enzymes with the reported eponemycin (EPN) and TMC-86A (TMC) BGCs. The core of the putative epoxyketone peptide BGC (ORFs A-L), in which ORF A is a LuxR-like transcription factor, was cloned into a heterologous host. The recombinant organism was capable to produce TMC and EPN natural products, along with the biosynthetic intermediates DH-TMC and DHE, and additional congeners. A phylogenetic analysis of the epn/tmc BGC revealed related BGCs in public databases. Most of them carry a proteasome beta-subunit, however, lacking an assigned specialized metabolite. The retrieved BGCs also display a diversity of regulatory genes and TTA codons, indicating tight regulation of this BGC at the transcription and translational levels. These results demonstrate the plasticity of the epn/tmc BGC of BRA-346 in producing epoxyketone peptides and the feasibility of their production in a heterologous host. This work also highlights the capacity of BRA-346 to tightly regulate its secondary metabolism and shed light on how to awake silent gene clusters of Streptomyces sp. BRA-346 to allow the production of pharmacologically important biosynthetic products.
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Affiliation(s)
- Bruna Domingues Vieira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Faculty of Pharmaceutical Sciences (FCF), University of Campinas (UNICAMP), Campinas, Brazil
| | - Henrique Niero
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Faculty of Pharmaceutical Sciences (FCF), University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael de Felício
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luiz Fernando Giolo Alves
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Cristina Freitas Bazzano
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Institute of Computing (IC), University of Campinas (UNICAMP), Campinas, Brazil
| | - Renata Sigrist
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Luciana Costa Furtado
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniela Barretto Barbosa Trivella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- *Correspondence: Daniela Barretto Barbosa Trivella,
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Williams K, de Mattos-Shipley KMJ, Willis CL, Bailey AM. In silico analyses of maleidride biosynthetic gene clusters. Fungal Biol Biotechnol 2022; 9:2. [PMID: 35177129 PMCID: PMC8851701 DOI: 10.1186/s40694-022-00132-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/23/2022] [Indexed: 01/09/2023] Open
Abstract
Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the 'core' set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel putative maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS 125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.
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Affiliation(s)
- Katherine Williams
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
| | - Kate M. J. de Mattos-Shipley
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
| | - Christine L. Willis
- grid.5337.20000 0004 1936 7603School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS UK
| | - Andrew M. Bailey
- grid.5337.20000 0004 1936 7603School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ UK
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Jin WB, Li TT, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi HQ, Wang A, Putzel GG, Longman RS, Artis D, Guo CJ. Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell 2022; 185:547-562.e22. [PMID: 35051369 PMCID: PMC8919858 DOI: 10.1016/j.cell.2021.12.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/01/2021] [Accepted: 12/21/2021] [Indexed: 02/05/2023]
Abstract
Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.
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Affiliation(s)
- Wen-Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Ting-Ting Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Da Huo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sophia Qu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xin V Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Svetlana F Lima
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Hui-Qing Shi
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Aolin Wang
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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48
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Jin X, Yang Y, Cao H, Gao B, Zhao Z. Eco-phylogenetic analyses reveal divergent evolution of vitamin B 12 metabolism in the marine bacterial family 'Psychromonadaceae'. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:147-163. [PMID: 34921716 DOI: 10.1111/1758-2229.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Cobalamin (vitamin B12 ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.
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Affiliation(s)
- Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yaofang Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haihang Cao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
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49
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Intra-hemocoel injection of pseurotin A from Metarhizium anisopliae, induces dose-dependent reversible paralysis in the Greater Wax Moth (Galleria mellonella). Fungal Genet Biol 2022; 159:103675. [DOI: 10.1016/j.fgb.2022.103675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 11/21/2022]
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50
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Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc Natl Acad Sci U S A 2022; 119:2116022119. [PMID: 35074914 PMCID: PMC8795539 DOI: 10.1073/pnas.2116022119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
Sulfoquinovose, a sulfosugar derivative of glucose, is produced by most photosynthetic organisms and contains up to half of all sulfur in the biosphere. Several pathways for its breakdown are known, though they provide access to only half of the carbon in sulfoquinovose and none of its sulfur. Here, we describe a fundamentally different pathway within the plant pathogen Agrobacterium tumefaciens that features oxidative desulfurization of sulfoquinovose to access all carbon and sulfur within the molecule. Biochemical and structural analyses of the pathway’s key proteins provided insights how the sulfosugar is recognized and degraded. Genes encoding this sulfoquinovose monooxygenase pathway are present in many plant pathogens and symbionts, alluding to a possible role for sulfoquinovose in plant host–bacteria interactions. Catabolism of sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to support the growth of the plant pathogen Agrobacterium tumefaciens. SQ or its glycoside sulfoquinovosyl glycerol are imported into the cell by an ATP-binding cassette transporter system with an associated SQ binding protein. A sulfoquinovosidase hydrolyzes the SQ glycoside and the liberated SQ is acted on by a flavin mononucleotide-dependent sulfoquinovose monooxygenase, in concert with an NADH-dependent flavin reductase, to release sulfite and 6-oxo-glucose. An NAD(P)H-dependent oxidoreductase reduces the 6-oxo-glucose to glucose, enabling entry into primary metabolic pathways. Structural and biochemical studies provide detailed insights into the recognition of key metabolites by proteins in this pathway. Bioinformatic analyses reveal that the sulfoquinovose monooxygenase pathway is distributed across Alpha- and Betaproteobacteria and is especially prevalent within the Rhizobiales order. This strategy for SQ catabolism is distinct from previously described pathways because it enables the complete utilization of all carbons within SQ by a single organism with concomitant production of inorganic sulfite.
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