1
|
LeBlanc A, Wuest WM. Siderophores: A Case Study in Translational Chemical Biology. Biochemistry 2024; 63:1877-1891. [PMID: 39041827 PMCID: PMC11308372 DOI: 10.1021/acs.biochem.4c00276] [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: 05/22/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
Siderophores are metal-binding secondary metabolites that assist in iron homeostasis and have been of interest to the scientific community for the last half century. Foundational siderophore research has enabled several translational applications including siderophore-antibiotic and siderophore-peptide conjugates, identification of new antimicrobial targets, advances in disease imaging, and novel therapeutics. This review aims to connect the basic science research (biosynthesis, cellular uptake, gene regulation, and effects on homeostasis) of well-known siderophores with the successive translational application that results. Intertwined throughout are connections to the career of Christopher T. Walsh, his impact on the field of chemical biology, and the legacy of his trainees who continue to innovate.
Collapse
Affiliation(s)
- Andrew
R. LeBlanc
- Department of Chemistry, Emory
University, Atlanta, Georgia 30322, United States
| | - William M. Wuest
- Department of Chemistry, Emory
University, Atlanta, Georgia 30322, United States
| |
Collapse
|
2
|
Reitz ZL. Predicting metallophore structure and function through genome mining. Methods Enzymol 2024; 702:371-401. [PMID: 39155119 DOI: 10.1016/bs.mie.2024.06.007] [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] [Indexed: 08/20/2024]
Abstract
Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.
Collapse
Affiliation(s)
- Zachary L Reitz
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, United States.
| |
Collapse
|
3
|
Sakata S, Li J, Yasuno Y, Shinada T, Shin-Ya K, Katsuyama Y, Ohnishi Y. Identification of the Cirratiomycin Biosynthesis Gene Cluster in Streptomyces Cirratus: Elucidation of the Biosynthetic Pathways for 2,3-Diaminobutyric Acid and Hydroxymethylserine. Chemistry 2024; 30:e202400271. [PMID: 38456538 DOI: 10.1002/chem.202400271] [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: 02/22/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Cirratiomycin, a heptapeptide with antibacterial activity, was isolated and characterized in 1981; however, its biosynthetic pathway has not been elucidated. It contains several interesting nonproteinogenic amino acids, such as (2S,3S)-2,3-diaminobutyric acid ((2S,3S)-DABA) and α-(hydroxymethyl)serine, as building blocks. Here, we report the identification of a cirratiomycin biosynthetic gene cluster in Streptomyces cirratus. Bioinformatic analysis revealed that several Streptomyces viridifaciens and Kitasatospora aureofaciens strains also have this cluster. One S. viridifaciens strain was confirmed to produce cirratiomycin. The biosynthetic gene cluster was shown to be responsible for cirratiomycin biosynthesis in S. cirratus in a gene inactivation experiment using CRISPR-cBEST. Interestingly, this cluster encodes a nonribosomal peptide synthetase (NRPS) composed of 12 proteins, including those with an unusual domain organization: a stand-alone adenylation domain, two stand-alone condensation domains, two type II thioesterases, and two NRPS modules that have no adenylation domain. Using heterologous expression and in vitro analysis of recombinant enzymes, we revealed the biosynthetic pathway of (2S,3S)-DABA: (2S,3S)-DABA is synthesized from l-threonine by four enzymes, CirR, CirS, CirQ, and CirB. In addition, CirH, a glycine/serine hydroxymethyltransferase homolog, was shown to synthesize α-(hydroxymethyl)serine from d-serine in vitro. These findings broaden our knowledge of nonproteinogenic amino acid biosynthesis.
Collapse
Affiliation(s)
- Shunki Sakata
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jiafeng Li
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
4
|
Singh RP, Sinha A, Deb S, Kumari K. First report on in-depth genome and comparative genome analysis of a metal-resistant bacterium Acinetobacter pittii S-30, isolated from environmental sample. Front Microbiol 2024; 15:1351161. [PMID: 38741743 PMCID: PMC11089254 DOI: 10.3389/fmicb.2024.1351161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
A newly isolated bacterium Acinetobacter pittii S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO4. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of A. pittii S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in A. pittii strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.
Collapse
Affiliation(s)
- Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Ayushi Sinha
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| |
Collapse
|
5
|
Long Q, Zhou W, Zhou H, Tang Y, Chen W, Liu Q, Bian X. Polyamine-containing natural products: structure, bioactivity, and biosynthesis. Nat Prod Rep 2024; 41:525-564. [PMID: 37873660 DOI: 10.1039/d2np00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Covering: 2005 to August, 2023Polyamine-containing natural products (NPs) have been isolated from a wide range of terrestrial and marine organisms and most of them exhibit remarkable and diverse activities, including antimicrobial, antiprotozoal, antiangiogenic, antitumor, antiviral, iron-chelating, anti-depressive, anti-inflammatory, insecticidal, antiobesity, and antioxidant properties. Their extraordinary activities and potential applications in human health and agriculture attract increasing numbers of studies on polyamine-containing NPs. In this review, we summarized the source, structure, classification, bioactivities and biosynthesis of polyamine-containing NPs, focusing on the biosynthetic mechanism of polyamine itself and representative polyamine alkaloids, polyamine-containing siderophores with catechol/hydroxamate/hydroxycarboxylate groups, nonribosomal peptide-(polyketide)-polyamine (NRP-(PK)-PA), and NRP-PK-long chain poly-fatty amine (lcPFAN) hybrid molecules.
Collapse
Affiliation(s)
- Qingshan Long
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wen Zhou
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural, Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ying Tang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Qingshu Liu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Microbiology Application, Hunan Institute of Microbiology, Changsha, 410009, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
6
|
Li R, Lichstrahl MS, Zandi TA, Kahlert L, Townsend CA. The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for ( 2S, 3R)-diaminobutyrate production. iScience 2024; 27:109202. [PMID: 38433893 PMCID: PMC10906522 DOI: 10.1016/j.isci.2024.109202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) assemble metabolites of medicinal and commercial value. Both serine and threonine figure prominently in these processes and separately can be converted to the additional NRPS building blocks 2,3-diaminopropionate (Dap) and 2,3-diaminobutyrate (Dab). Here we bring extensive bioinformatics, in vivo and in vitro experimentation to compose a unified view of the biosynthesis of these widely distributed non-canonical amino acids that both derive by pyridoxal-mediated β-elimination of the activated O-phosphorylated substrates followed by β-addition of an amine donor. By examining monobactam biosynthesis in Pseudomonas and in Burkholderia species where it is silent, we show that (2S,3R)-Dab synthesis depends on an l-threonine kinase (DabA), a β-replacement reaction with l-aspartate (DabB) and an argininosuccinate lyase-like protein (DabC). The growing clinical importance of monobactams to both withstand Ambler Class B metallo-β-lactamases and retain their antibiotic activity make reprogrammed precursor and NRPS synthesis of modified monobactams a feasible and attractive goal.
Collapse
Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Michael S. Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Trevor A. Zandi
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, MD, USA
| | - Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| |
Collapse
|
7
|
Chakma V, Barman DN, Das SC, Hossain A, Momin MB, Tasneem M, Gupta SD. In silico analysis of a novel hypothetical protein (YP_498675.1) from Staphylococcus aureus unravels the protein of tryptophan synthase beta superfamily (Try-synth-beta_ II). J Genet Eng Biotechnol 2023; 21:135. [PMID: 37995054 PMCID: PMC10667181 DOI: 10.1186/s43141-023-00613-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Staphylococcus aureus is a gram-positive spherical bacteria and the most common cause of nosocomial infections in the world. Given its clinical significance, the genome sequence of S. aureus has been elucidated to enhance our comprehension of its lifestyle and pathogenicity. The research aimed to summarize a potential hypothetical protein that may play an important role in S. aureus virulence and pathogenicity, covering its anticipated structure, probable biological functions, and importance in this context. RESULTS A hypothetical protein, YP_498675.1 with 281 amino acid residues of S. aureus, was chosen for analysis and modeling by several bioinformatics tools and databases in this work. According to primary and secondary structure analyses, YP_498675.1 is a stable hydrophilic protein with a significant proportion of α-helices. Subcellular localization predictions by CELLO, PSORTb, and SOSUI server indicate that it is a cytoplasmic protein. NCBI-CDD, Pfam, and InterProScan functional genomics research revealed that the hypothetical protein may include the pyridoxal phosphate (PLP)-dependent 2, 3-diaminopropionate biosynthesis protein SbnA domain. In the homology modeling method, the HHpred server was employed to create its 3D structure using the template structure of a Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP (PDB ID: 5D84_A), an X-ray diffraction model having 100% sequence identity with the hypothetical protein. After energy minimization, several quality assessments and validation factors determined that the generated protein model was reliable and of reasonable quality. CONCLUSION The present study has characterized and functionally annotated the hypothetical protein YP_498675.1 of S. aureus. Further experimental validation would aid in determining the actual function of YP_498675.1 as well as confirm the protein's value as a therapeutic target.
Collapse
Affiliation(s)
- Vivian Chakma
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Dhirendra Nath Barman
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Shuvo Chandra Das
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Anwar Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Monira Binte Momin
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Maisha Tasneem
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Shipan Das Gupta
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| |
Collapse
|
8
|
Huang D, Wang X, Liu WB, Ye BC. Remodeling metabolism of Corynebacterium glutamicum for high-level dencichine production. BIORESOURCE TECHNOLOGY 2023; 388:129800. [PMID: 37748563 DOI: 10.1016/j.biortech.2023.129800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Dencichine, a sought-after compound in the medical industry, requires a more efficient and sustainable production method than the current plant extraction process. This study successfully remodeled the metabolic pathway of Corynebacterium glutamicum to produce dencichine from the precursors of L-2,3-diaminopropionate (L-DAP) and oxalyl-coenzyme A. Firstly, a synthetic pathway for L-DAP was established by introducing exogenous enzymes ZmaU/ZmaV. This resulted in a production of 628 mg/L by overexpressing key genes and reducing the endogenous competitive pathway. Secondly, an oxalyl-CoA synthetic pathway was created through the enzymatic conversion of glyoxylate by introducing heterologous enzymes. Finally, with the integration of the exogenous enzyme BAHD, de novo synthesis of dencichine in C. glutamicum was achieved, and production reached 31.75 mg/L within 48-hour fermentation. This achievement represents the first successful biosynthesis of dencichine in C. glutamicum, offering a promising approach for natural product through microbial fermentation.
Collapse
Affiliation(s)
- Dan Huang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xin Wang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei-Bing Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
9
|
Toh SI, Lo CL, Chang CY. Crystal structure of CmnB involved in the biosynthesis of the nonproteinogenic amino acid L-2,3-diaminopropionic acid. Acta Crystallogr F Struct Biol Commun 2023; 79:193-199. [PMID: 37405487 PMCID: PMC10327575 DOI: 10.1107/s2053230x23005769] [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: 03/03/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
L-2,3-Diaminopropionic acid (L-Dap) is a nonproteinogenic amino acid that plays as an important role as a building block in the biosynthesis of several natural products, including capreomycin, viomycin, zwittermicin, staphyloferrin and dapdiamide. A previous study reported that CmnB and CmnK are two enzymes that are involved in the formation of L-Dap in the biosynthesis of capreomycin. CmnB catalyzes the condensation reaction of O-phospho-L-serine and L-glutamic acid to generate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid, which subsequently undergoes oxidative hydrolysis via CmnK to generate the product L-Dap. Here, the crystal structure of CmnB in complex with the reaction intermediate PLP-α-aminoacrylate is reported at 2.2 Å resolution. Notably, CmnB is the second known example of a PLP-dependent enzyme that forms a monomeric structure in crystal packing. The crystal structure of CmnB also provides insights into the catalytic mechanism of the enzyme and supports the biosynthetic pathway of L-Dap reported in previous studies.
Collapse
Affiliation(s)
- Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Chieh-Ling Lo
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| |
Collapse
|
10
|
Edwards A, Njaci I, Sarkar A, Jiang Z, Kaithakottil GG, Moore C, Cheema J, Stevenson CEM, Rejzek M, Novák P, Vigouroux M, Vickers M, Wouters RHM, Paajanen P, Steuernagel B, Moore JD, Higgins J, Swarbreck D, Martens S, Kim CY, Weng JK, Mundree S, Kilian B, Kumar S, Loose M, Yant L, Macas J, Wang TL, Martin C, Emmrich PMF. Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nat Commun 2023; 14:876. [PMID: 36797319 PMCID: PMC9935904 DOI: 10.1038/s41467-023-36503-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.
Collapse
Affiliation(s)
- Anne Edwards
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Isaac Njaci
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Abhimanyu Sarkar
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- National Institute of Agricultural Botany, 93 Laurence Weaver Road, Cambridge, CB3 0LE, UK
| | - Zhouqian Jiang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- School of Traditional Chinese Medicine, Capital Medical University, You An Men, Beijing, 100069, PR China
| | | | - Christopher Moore
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Martin Rejzek
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Marielle Vigouroux
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Martin Vickers
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Roland H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Pirita Paajanen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Jonathan D Moore
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Stefan Martens
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098, San Michele all' Adige (TN), Italy
| | - Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sagadevan Mundree
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Avenue Hafiane Cherkaoui, Rabat, Morocco
| | - Matt Loose
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, NG7 2RD, Nottingham, UK
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Trevor L Wang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Peter M F Emmrich
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya.
- Norwich Institute for Sustainable Development, School of International Development, University of East Anglia, Norwich, NR4 7TJ, UK.
| |
Collapse
|
11
|
Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022; 61:e202208573. [PMID: 35903822 PMCID: PMC9489664 DOI: 10.1002/anie.202208573] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Indexed: 08/27/2023]
Abstract
Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.
Collapse
Affiliation(s)
- Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 (USA)
| |
Collapse
|
12
|
Mantas MJQ, Nunn PB, Codd GA, Barker D. Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 3-N-methyl-2,3-diaminopropanoic acid (BMAA). PHYTOCHEMISTRY 2022; 200:113198. [PMID: 35447107 DOI: 10.1016/j.phytochem.2022.113198] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an ancient clade of photosynthetic prokaryotes, present in many habitats throughout the world, including water resources. They can present health hazards to humans and animals due to the production of a wide range of toxins (cyanotoxins), including the diaminoacid neurotoxin, 3-N-methyl-2,3-diaminopropanoic acid (β-N-methylaminoalanine, BMAA). Knowledge of the biosynthetic pathway for BMAA, and its role in cyanobacteria, is lacking. Present evidence suggests that BMAA is derived by 3-N methylation of 2,3-diaminopropanoic acid (2,3-DAP) and, although the latter has never been reported in cyanobacteria, there are multiple pathways to its biosynthesis known in other bacteria and in plants. Here, we used bioinformatics analyses to investigate hypotheses concerning 2,3-DAP and BMAA biosynthesis in cyanobacteria. We assessed the potential presence or absence of each enzyme in candidate biosynthetic routes known in Albizia julibrissin, Lathyrus sativus seedlings, Streptomyces, Clostridium, Staphylococcus aureus, Pantoea agglomerans, and Paenibacillus larvae, in 130 cyanobacterial genomes using sequence alignment, profile hidden Markov models, substrate specificity/active site identification and the reconstruction of gene phylogenies. Most enzymes involved in pathways leading to 2,3-DAP in other species were not found in the cyanobacteria analysed. Nevertheless, two species appear to have the genes sbnA and sbnB, responsible for forming the 2,3-DAP constituent in staphyloferrin B, a siderophore from Staphylococcus aureus. It is currently undetermined whether these species are also capable of biosynthesising BMAA. It is possible that, in some cyanobacteria, the formation of 2,3-DAP and/or BMAA is associated with environmental iron-scavenging. The pam gene cluster, responsible for the biosynthesis of the BMAA-containing peptide, paenilamicin, so far appears to be restricted to Paenibacillus larvae. It was not detected in any of the cyanobacterial genomes analysed, nor was it found in 93 other Paenibacillus genomes or in the genomes of two BMAA-producing diatom species. We hypothesise that the presence, in some cyanobacterial species, of the enzymes 2,3-diaminopropionate ammonia-lyase (DAPAL) and reactive intermediate deaminase A (RidA) may explain the failure to detect 2,3-DAP in analytical studies. Overall, the taxonomic distribution of 2,3-DAP and BMAA in cyanobacteria is unclear; there may be multiple and additional routes, and roles, for the biosynthesis of 2,3-DAP and BMAA in these organisms.
Collapse
Affiliation(s)
- Maria José Q Mantas
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
| | - Peter B Nunn
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom.
| | - Geoffrey A Codd
- School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom; School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom.
| | - Daniel Barker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
| |
Collapse
|
13
|
Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuchen Li
- Princeton University Chemistry UNITED STATES
| | | | | | - Mohammad R. Seyedsayamdost
- Princeton University Chemistry Washington UniversityFrick Chemistry Lab, Room 333 08544 Princeton UNITED STATES
| |
Collapse
|
14
|
Zhang H, Zhang C, Li Q, Ma J, Ju J. Metabolic Blockade-Based Genome Mining Reveals Lipochain-Linked Dihydro-β-alanine Synthetases Involved in Autucedine Biosynthesis. Org Lett 2022; 24:5535-5540. [PMID: 35876054 DOI: 10.1021/acs.orglett.2c01957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Chunyan Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Rd., Nansha District, Guangzhou 511458, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| |
Collapse
|
15
|
Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. Sci Rep 2022; 12:10857. [PMID: 35760985 PMCID: PMC9237127 DOI: 10.1038/s41598-022-14913-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 12/30/2022] Open
Abstract
The rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between beneficial and pathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here we used the Genome properties (GP) common biological pathways annotation system and Machine Learning (ML) to establish the relationship between the genome wide GP composition and the plant-associated lifestyle of 91 Pseudomonas strains isolated from the rhizosphere and the phyllosphere representing both plant-associated phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A test set of 75 new strains confirmed the importance of the selected features for classification. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated lifestyle.
Collapse
|
16
|
Oliveira F, Lima T, Correia A, Silva AM, Soares C, Morais S, Weißelberg S, Vilanova M, Rohde H, Cerca N. Involvement of the Iron-Regulated Loci hts and fhuC in Biofilm Formation and Survival of Staphylococcus epidermidis within the Host. Microbiol Spectr 2022; 10:e0216821. [PMID: 35019768 PMCID: PMC8754135 DOI: 10.1128/spectrum.02168-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/05/2021] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus epidermidis is a major nosocomial pathogen with a remarkable ability to persist on indwelling medical devices through biofilm formation. Nevertheless, it remains intriguing how this process is efficiently achieved under the host's harsh conditions, where the availability of nutrients, such as essential metals, is scarce. Following our previous identification of two iron-regulated loci putatively involved in iron transport, hts and fhuC, we assessed here their individual contribution to both bacterial physiology and interaction with host immune cells. Single deletions of the hts and fhuC loci led to marked changes in the cell iron content, which were partly detrimental for planktonic growth and strongly affected biofilm formation under iron-restricted conditions. Deletion of each of these two loci did not lead to major changes in S. epidermidis survival within human macrophages or in an ex vivo human blood model of bloodstream infection. However, the lack of either hts or fhuC loci significantly impaired bacterial survival in vivo in a murine model of bacteremia. Collectively, this study establishes, for the first time, the pivotal role of the iron-regulated loci hts and fhuC in S. epidermidis biofilm formation and survival within the host, providing relevant information for the development of new targeted therapeutics against this pathogen. IMPORTANCE Staphylococcus epidermidis is one of the most important nosocomial pathogens and a major cause of central line-associated bloodstream infections. Once in the bloodstream, this bacterium must surpass severe iron restriction in order to survive and establish infection. Surprisingly, very little is known about the iron acquisition mechanisms in this species. This study represents the first report on the involvement of the S. epidermidis iron-regulated loci hts and fhuC in biofilm formation under host relevant conditions and, most importantly, in survival within the host. Ultimately, these findings highlight iron acquisition and these loci in particular, as potential targets for future therapeutic strategies against biofilm-associated S. epidermidis infections.
Collapse
Affiliation(s)
- Fernando Oliveira
- Centre of Biological Engineering, LIBRO – Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Tânia Lima
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Alexandra Correia
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana Margarida Silva
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Cristina Soares
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Simone Morais
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Samira Weißelberg
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Manuel Vilanova
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS-UP, Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Nuno Cerca
- Centre of Biological Engineering, LIBRO – Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| |
Collapse
|
17
|
M VNUM, Faidh MA, Chadha A. The ornithine cyclodeaminase/µ-crystallin superfamily of proteins: A novel family of oxidoreductases for the biocatalytic synthesis of chiral amines. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
|
18
|
Colibrimycins, novel halogenated hybrid PKS-NRPS compounds produced by Streptomyces sp. CS147. Appl Environ Microbiol 2021; 88:e0183921. [PMID: 34669429 DOI: 10.1128/aem.01839-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The improvement on genome sequencing techniques has brought to light the biosynthetic potential of actinomycetes due to the high number of gene clusters they present compared to the number of known compounds. Genome mining is a recent strategy in the search for novel bioactive compounds, which involves the analysis of sequenced genomes to identify uncharacterized natural product biosynthetic gene clusters, many of which are cryptic or silent under laboratory conditions, and to develop experimental approaches to identify their products. Owing to the importance of halogenation in terms of structural diversity, bioavailability and bioactivity, searching for new halogenated bioactive compounds has become an interesting issue in the field of natural product discovery. Following this purpose, a screening for halogenase coding genes was performed on twelve Streptomyces strains isolated from fungus growing ants of the Attini tribe. Using the bioinformatics tools antiSMASH and BLAST, six halogenase coding genes were identified. Some of these genes were located within biosynthetic gene clusters (BGCs), which were studied by construction of several mutants for the identification of the putative halogenated compounds produced. The comparison of the metabolite production profile of wild type strains and their corresponding mutants by UPLC-UV and HPLC-MS allowed us the identification of a novel family of halogenated compounds in Streptomyces sp. CS147, designated as colibrimycins. Importance Genome mining has proven its usefulness in the search for novel bioactive compounds produced by microorganisms, and halogenases comprise an interesting starting point. In this work, we have identified a new halogenase coding gene, which led to the discovery of novel lipopetide NRPS/PKS-derived natural products, the colibrimycins, produced by Streptomyces sp. CS147, isolated from Attini ant niche. Some colibrimycins display an unusual α-ketoamide moiety in the peptide structure. Although its biosynthetic origin remains unknown, its presence might be related with a hypothetical inhibition of virus proteases and, together with the presence of the halogenase, it represents a feature to be incorporated in the arsenal of structural modifications available for combinatorial biosynthesis.
Collapse
|
19
|
Uma Mahesh VNM, Chadha A. Imine reduction by an Ornithine cyclodeaminase/μ-crystallin homolog purified from Candida parapsilosis ATCC 7330. ACTA ACUST UNITED AC 2021; 31:e00664. [PMID: 34557391 PMCID: PMC8446579 DOI: 10.1016/j.btre.2021.e00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 11/26/2022]
Abstract
Novel imine reductase from yeast Candida parapsilosis purified and characterized. CpIM1 belongs to unexplored Ornithine cyclodeaminase/Mu crystallin protein family CpIM1 catalyzed stereospecific alkylamination of α-ketoacids/ketoesters. CpIM1 also reduced cyclic and aryl imines. First report on enzymatic alkylamination of α-ketoesters and reduction of arylimines.
We report a stereospecific imine reductase from Candida parapsilosis ATCC 7330 (CpIM1), a versatile biocatalyst and a rich source of highly stereospecific oxidoreductases. The recombinant gene was overexpressed in Escherichia coli and the protein CpIM1 was purified to homogeneity. This protein belongs to the Ornithine cyclodeaminase/ μ-crystallin (OCD-Mu) family of proteins which has only a few characterized members. CpIM1 catalyzed the alkylamination of α-keto acids/esters producing exclusively (S)-N-alkyl amino acids/esters e.g. N-methyl-l-alanine with > 90% conversion and > 99% enantiomeric excess (ee). The enzyme showed the highest activity for the alkylamination of pyruvate and methylamine leading to N-methyl-l-alanine with an apparent KM of 15.04 ± 2.8 mM and Vmax of 13.75 ± 1.07 μmol/min/mg. CpIM1 also catalyzed (i) the reduction of imines e.g. 2-methyl-1-pyrroline to (S)-2-methylpyrrolidine with ∼30% conversion and 75% ee and (ii) the dehydrogenation of cyclic amino acids e.g. l-Proline (as monitered by reduction of cofactor NADP+ spectrophotometrically).
Collapse
Affiliation(s)
- V N M Uma Mahesh
- Laboratory of Bioorganic Chemistry, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Anju Chadha
- Laboratory of Bioorganic Chemistry, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India.,National Center for Catalysis Research, Indian Institute of Technology Madras, Chennai 600 036, India
| |
Collapse
|
20
|
Abstract
![]()
The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
Collapse
Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
21
|
Takehara M, Saimura M, Inaba H, Kato Y, Muro S, Matsunaga T, Yamanaka K. Characterization of an L-α,β-diaminopropionic acid polymer with comb-like structure isolated from a poly(ε-L-lysine)-producing Streptomyces sp. Appl Microbiol Biotechnol 2021; 105:3145-3157. [PMID: 33846822 DOI: 10.1007/s00253-021-11257-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
Polymers of basic amino acids function as polycationic compounds under physiological conditions and exhibit intriguing biological properties, such as antimicrobial and antiviral activities, immunopotentiating ability, and DNA-binding activity. Poly(ε-L-lysine) (ε-PL) produced by some strains of Streptomyces spp. is a cationic homopolymer of L-lysine linking between ε-amino and α-carboxylic acid functional groups and has been used as a food preservative based on its biocompatibility and biodegradability. An ε-PL-producing strain of Streptomyces sp. USE-33 was found to secrete a novel polycationic substance into its culture broth along with ε-PL. High-performance liquid chromatography analyses and one- and two-dimensional 1H and 13C nuclear magnetic resonance (NMR) experiments, accompanied by NMR titration studies, revealed that the secreted substance was poly[β-(L-diaminopropionyl-L-diaminopropionic acid)], PAP, characterized by an isopeptide backbone linking between the β-amino and α-carboxylic acid groups of L-α,β-diaminopropionic acid (L-Dpr) with pendent L-Dpr residues. PAP had a molecular weight of 500 to 1400, and copolymers composed of the two amino acids L-Dpr and L-lysine were not detected in the producer strain USE-33. The strain coproduced high levels of the two poly(amino acid)s in the presence of glycerol, citrate, and ammonium sulfate at pH 4.0 in a two-stage cultivation procedure. PAP exhibited strong inhibitory activities against several yeasts and weaker activities against bacteria than ε-PL. PAP may share a number of biological functions with ε-PL, and the use of PAP along with ε-PL has potential as a specific and advanced material for technical applications in various fields.Key points• Novel cationic poly(amino acid) was found in an ε-PL-producing Streptomyces species.• The l-α,β-diaminopropionic acid polymer was characterized by a comb-like structure.• The novel poly(amino acid), PAP, exhibited antibacterial and antifungal activities.
Collapse
Affiliation(s)
- Munenori Takehara
- Department of Materials Science, School of Engineering, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan.
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Haruka Inaba
- Department of Materials Science, School of Engineering, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Yoshinao Kato
- Department of Materials Science, School of Engineering, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Shogo Muro
- Department of Materials Science, School of Engineering, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Tatsuki Matsunaga
- Department of Materials Science, School of Engineering, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Kazuya Yamanaka
- Department of Life Science and Biotechnology, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, 564-8680, Japan
| |
Collapse
|
22
|
Panter F, Bader CD, Müller R. The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*. Angew Chem Int Ed Engl 2021; 60:8081-8088. [PMID: 33534143 PMCID: PMC8048970 DOI: 10.1002/anie.202014671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins.
Collapse
Affiliation(s)
- Fabian Panter
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
| | - Chantal D. Bader
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
| |
Collapse
|
23
|
Panter F, Bader CD, Müller R. Die Sandarazole sind kryptische und strukturell einzigartige, Plasmid‐codierte Toxine aus einem seltenen Myxobakterium**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Panter
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
| | - Chantal D. Bader
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
| |
Collapse
|
24
|
Shin YH, Ban YH, Kim TH, Bae ES, Shin J, Lee SK, Jang J, Yoon YJ, Oh DC. Structures and Biosynthetic Pathway of Coprisamides C and D, 2-Alkenylcinnamic Acid-Containing Peptides from the Gut Bacterium of the Carrion Beetle Silpha perforata. JOURNAL OF NATURAL PRODUCTS 2021; 84:239-246. [PMID: 33497210 DOI: 10.1021/acs.jnatprod.0c00864] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Coprisamides C and D (1 and 2) were isolated from a gut bacterium, Micromonospora sp. UTJ3, of the carrion beetle Silpha perforata. Based on the combined analysis of UV, MS, and NMR spectral data, the planar structures of 1 and 2 were elucidated to be unreported derivatives of coprisamides A and B, cyclic depsipeptides bearing a 2-alkenylcinnamic acid unit and the unusual amino acids β-methylaspartic acid and 2,3-diaminopropanoic acid. The absolute configuration of 1 was determined using the advanced Marfey's method, phenylglycine methyl ester derivatization, and J-based configuration analysis. The biosynthetic gene clusters for the coprisamides were investigated based on genomic data from coprisamide-producing strains Micromonospora sp. UTJ3 and Streptomyces sp. SNU533. Coprisamide C (1) was active against the Mycobacterium tuberculosis mc2 6230 strain.
Collapse
Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| |
Collapse
|
25
|
Hsu SH, Zhang S, Huang SC, Wu TK, Xu Z, Chang CY. Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis. Biochemistry 2020; 60:77-84. [PMID: 33356147 DOI: 10.1021/acs.biochem.0c00808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capreomycin (CMN) and viomycin (VIO) are nonribosomal peptide antituberculosis antibiotics, the structures of which contain four nonproteinogenic amino acids, including l-2,3-diaminopropionic acid (l-Dap), β-ureidodehydroalanine, l-capreomycidine, and β-lysine. Previous bioinformatics analysis suggested that CmnB/VioB and CmnK/VioK participate in the formation of l-Dap; however, the real substrates of these enzymes are yet to be confirmed. We herein show that starting from O-phospho-l-Ser (OPS) and l-Glu precursors, CmnB catalyzes the condensation reaction to generate a metabolite intermediate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid (ACEGA), which undergoes NAD+-dependent oxidative hydrolysis by CmnK to generate l-Dap. Furthermore, the binding site of ACEGA and the catalytic mechanism of CmnK were elucidated with the assistance of three crystal structures, including those of apo-CmnK, the NAD+-CmnK complex, and CmnK in an alternative conformation. The CmnK-ACEGA docking model revealed that the glutamate α-hydrogen points toward the nicotinamide moiety. It provides evidence that the reaction is dependent on hydride transfer to form an imine intermediate, which is subsequently hydrolyzed by a water molecule to produce l-Dap. These findings modify the original proposed pathway and provide insights into l-Dap formation in the biosynthesis of other related natural products.
Collapse
Affiliation(s)
- Sheng-Hsin Hsu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Shouqi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Sheng-Cih Huang
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Tung-Kung Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC.,Center for Intelligent Drug Systems and Smart Bio-devices, National Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| |
Collapse
|
26
|
Covas C, Almeida B, Esteves AC, Lourenço J, Domingues P, Caetano T, Mendo S. Peptone from casein, an antagonist of nonribosomal peptide synthesis: a case study of pedopeptins produced by Pedobacter lusitanus NL19. N Biotechnol 2020; 60:62-71. [PMID: 32891869 DOI: 10.1016/j.nbt.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 01/30/2023]
Abstract
Novel natural products are urgently needed to address the worldwide incidence of bacterial resistance to antibiotics. Extreme environments are a major source of novel compounds with unusual chemical structures. Pedobacter lusitanus NL19 is a new bacterial species that was isolated from one such environment and which produces compounds with potent activity against relevant microorganisms in the clinical, food, veterinary and aquaculture areas. The production of antimicrobials by P. lusitanus NL19 was identified in tryptic soy agar (TSA), but not in its equivalent broth (TSB). It was observed that in TSB medium a high concentration of casein peptone (PC) repressed the production of antibacterial compounds. HPLC, MS and MS/MS spectra with de novo sequencing revealed that the bioactivity of P. lusitanus NL19 was due to the production of pedopeptins. Hence, biosynthesis of pedopeptins is inhibited by high concentrations of PC in the broth medium. Furthermore, a nonribosomal peptide synthetase (NRPS) gene cluster was identified in the genome of NL19 encoding the biosynthesis of the peptides. qPCR analysis confirmed that the transcription of these genes is repressed in cells cultivated in high concentrations of PC. It is shown that pedopeptins are nonribosomal peptides with a broad-spectrum activity, including against Gram-positive and Gram-negative bacteria and yeasts.
Collapse
Affiliation(s)
- Cláudia Covas
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Beatriz Almeida
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Cristina Esteves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal; Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Portugal
| | - Joana Lourenço
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre and LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| |
Collapse
|
27
|
Guo Q, Wu D, Gao L, Bai Y, Liu Y, Guo N, Du X, Yang J, Wang X, Lei X. Identification of the AMA Synthase from the Aspergillomarasmine A Biosynthesis and Evaluation of Its Biocatalytic Potential. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Qianqian Guo
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, No.5 Yi he yuan Road, Beijing 100871, People’s Republic of China
| | - Dongshan Wu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Yingjie Bai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Yuan Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Nianxin Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Xiaoxia Du
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Jun Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| | - Xiaoming Wang
- Jiangsu JITRI Molecular Engineering Inst. Co., Ltd., Jiangsu 215500, People’s Republic of China
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, No.5 Yi he yuan Road, Beijing 100871, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, People’s Republic of China
| |
Collapse
|
28
|
Ferrario E, Miggiano R, Rizzi M, Ferraris DM. Structure of Thermococcus litoralis Δ 1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:496-505. [PMID: 32355045 DOI: 10.1107/s2059798320004866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/05/2020] [Indexed: 11/10/2022]
Abstract
L-Hydroxyproline (L-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. L-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-L-proline (T3LHyp) and trans-4-hydroxy-L-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and L-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.
Collapse
Affiliation(s)
- Eugenio Ferrario
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Riccardo Miggiano
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| |
Collapse
|
29
|
Marchetti M, De Bei O, Bettati S, Campanini B, Kovachka S, Gianquinto E, Spyrakis F, Ronda L. Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development. Int J Mol Sci 2020; 21:E2145. [PMID: 32245010 PMCID: PMC7139808 DOI: 10.3390/ijms21062145] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 02/08/2023] Open
Abstract
Nutritional immunity is a form of innate immunity widespread in both vertebrates and invertebrates. The term refers to a rich repertoire of mechanisms set up by the host to inhibit bacterial proliferation by sequestering trace minerals (mainly iron, but also zinc and manganese). This strategy, selected by evolution, represents an effective front-line defense against pathogens and has thus inspired the exploitation of iron restriction in the development of innovative antimicrobials or enhancers of antimicrobial therapy. This review focuses on the mechanisms of nutritional immunity, the strategies adopted by opportunistic human pathogen Staphylococcus aureus to circumvent it, and the impact of deletion mutants on the fitness, infectivity, and persistence inside the host. This information finally converges in an overview of the current development of inhibitors targeting the different stages of iron uptake, an as-yet unexploited target in the field of antistaphylococcal drug discovery.
Collapse
Affiliation(s)
- Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
| | - Omar De Bei
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
| |
Collapse
|
30
|
Temperini A, Aiello D, Mazzotti F, Athanassopoulos CM, De Luca P, Siciliano C. 2,3-Diaminopropanols Obtained from d-Serine as Intermediates in the Synthesis of Protected 2,3-l-Diaminopropanoic Acid (l-Dap) Methyl Esters. Molecules 2020; 25:E1313. [PMID: 32183079 PMCID: PMC7145313 DOI: 10.3390/molecules25061313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 11/16/2022] Open
Abstract
A synthetic strategy for the preparation of two orthogonally protected methyl esters of the non-proteinogenic amino acid 2,3-l-diaminopropanoic acid (l-Dap) was developed. In these structures, the base-labile protecting group 9-fluorenylmethyloxycarbonyl (Fmoc) was paired to the p-toluensulfonyl (tosyl, Ts) or acid-labile tert-butyloxycarbonyl (Boc) moieties. The synthetic approach to protected l-Dap methyl esters uses appropriately masked 2,3-diaminopropanols, which are obtained via reductive amination of an aldehyde prepared from the commercial amino acid Nα-Fmoc-O-tert-butyl-d-serine, used as the starting material. Reductive amination is carried out with primary amines and sulfonamides, and the process is assisted by the Lewis acid Ti(OiPr)4. The required carboxyl group is installed by oxidizing the alcoholic function of 2,3-diaminopropanols bearing the tosyl or benzyl protecting group on the 3-NH2 site. The procedure can easily be applied using the crude product obtained after each step, minimizing the need for chromatographic purifications. Chirality of the carbon atom of the starting d-serine template is preserved throughout all synthetic steps.
Collapse
Affiliation(s)
- Andrea Temperini
- Dipartimento di Scienze Farmaceutiche, Università di Perugia, Via del Liceo 1, 06123 Perugia, Italy;
| | - Donatella Aiello
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Via Ponte P. Bucci, Cubo 12D, Università della Calabria, I-87036 Arcavacata di Rende (CS), Italy; (D.A.); (F.M.)
| | - Fabio Mazzotti
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Via Ponte P. Bucci, Cubo 12D, Università della Calabria, I-87036 Arcavacata di Rende (CS), Italy; (D.A.); (F.M.)
| | | | - Pierantonio De Luca
- Dipartimento di Ingegneria Meccanica, Energetica e Gestionale, Università della Calabria, I-87036 Arcavacata di Rende (CS), Italy;
| | - Carlo Siciliano
- Dipartimento di Farmacia e Scienze della Salute e della Nutrizione, Edificio Polifunzionale, Università della Calabria, I-87036 Arcavacata di Rende (CS), Italy
| |
Collapse
|
31
|
Navo CD, Mazo N, Oroz P, Gutiérrez-Jiménez MI, Marín J, Asenjo J, Avenoza A, Busto JH, Corzana F, Zurbano MM, Jiménez-Osés G, Peregrina JM. Synthesis of Nβ-Substituted α,β-Diamino Acids via Stereoselective N-Michael Additions to a Chiral Bicyclic Dehydroalanine. J Org Chem 2020; 85:3134-3145. [PMID: 32040912 DOI: 10.1021/acs.joc.9b03020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The highly diastereoselective 1,4-conjugate additions of several nitrogen nucleophiles to chiral bicyclic dehydroalanines have been assessed effectively at room temperature in good to excellent yields without needing any catalyst or additional base. This methodology is general, simple, oxygen and moisture tolerant, high-yielding, totally chemo- and stereoselective. This procedure offers an efficient and practical approach for the synthesis of Nβ-substituted α,β-diamino acids, such as 1-isohistidine, τ-histidinoalanine, β-benzylaminoalanine, β-(piperidin-1-yl)alanine, β-(azepan-1-yl)alanine, and fluorescent and ciprofloxacin-containing amino acid derivatives.
Collapse
Affiliation(s)
- Claudio D Navo
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain.,CIC bioGUNE, Bizkaia Technology Park, Building 800, 48170 Derio, Spain
| | - Nuria Mazo
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Paula Oroz
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Marta I Gutiérrez-Jiménez
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Javier Marín
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Juan Asenjo
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Alberto Avenoza
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Jesús H Busto
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - María M Zurbano
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain.,CIC bioGUNE, Bizkaia Technology Park, Building 800, 48170 Derio, Spain
| | - Jesús M Peregrina
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| |
Collapse
|
32
|
Wang M, Niikura H, He H, Daniel‐Ivad P, Ryan KS. Biosynthesis of the N–N‐Bond‐Containing Compound
l
‐Alanosine. Angew Chem Int Ed Engl 2020; 59:3881-3885. [DOI: 10.1002/anie.201913458] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Menghua Wang
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Haruka Niikura
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Hai‐Yan He
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Phillip Daniel‐Ivad
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| |
Collapse
|
33
|
Wang M, Niikura H, He H, Daniel‐Ivad P, Ryan KS. Biosynthesis of the N–N‐Bond‐Containing Compound
l
‐Alanosine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Menghua Wang
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Haruka Niikura
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Hai‐Yan He
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Phillip Daniel‐Ivad
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry The University of British Columbia Vancouver British Columbia Canada
| |
Collapse
|
34
|
Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
Collapse
Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
35
|
Ng TL, McCallum ME, Zheng CR, Wang JX, Wu KJY, Balskus EP. The l-Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis. Chembiochem 2019; 21:1155-1160. [PMID: 31643127 DOI: 10.1002/cbic.201900565] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Indexed: 12/29/2022]
Abstract
N-Nitroso-containing natural products are bioactive metabolites with antibacterial and anticancer properties. In particular, compounds containing the diazeniumdiolate (N-nitrosohydroxylamine) group display a wide range of bioactivities ranging from cytotoxicity to metal chelation. Despite the importance of this structural motif, knowledge of its biosynthesis is limited. Herein we describe the discovery of a biosynthetic gene cluster in Streptomyces alanosinicus ATCC 15710 responsible for producing the diazeniumdiolate natural product l-alanosine. Gene disruption and stable isotope feeding experiments identified essential biosynthetic genes and revealed the source of the N-nitroso group. Additional biochemical characterization of the biosynthetic enzymes revealed that the non-proteinogenic amino acid l-2,3-diaminopropionic acid (l-Dap) is synthesized and loaded onto a free-standing peptidyl carrier protein (PCP) domain in l-alanosine biosynthesis, which we propose may be a mechanism of handling unstable intermediates generated en route to the diazeniumdiolate. These discoveries will facilitate efforts to determine the biochemistry of diazeniumdiolate formation.
Collapse
Affiliation(s)
- Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Monica E McCallum
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Christine R Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Jennifer X Wang
- Small Molecule Mass Spectrometry Facility, Faculty of Arts and Sciences Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| |
Collapse
|
36
|
Verstraete MM, Morales LD, Kobylarz MJ, Loutet SA, Laakso HA, Pinter TB, Stillman MJ, Heinrichs DE, Murphy MEP. The heme-sensitive regulator SbnI has a bifunctional role in staphyloferrin B production by Staphylococcus aureus. J Biol Chem 2019; 294:11622-11636. [PMID: 31197035 DOI: 10.1074/jbc.ra119.007757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/12/2019] [Indexed: 01/30/2023] Open
Abstract
Staphylococcus aureus infection relies on iron acquisition from its host. S. aureus takes up iron through heme uptake by the iron-responsive surface determinant (Isd) system and by the production of iron-scavenging siderophores. Staphyloferrin B (SB) is a siderophore produced by the 9-gene sbn gene cluster for SB biosynthesis and efflux. Recently, the ninth gene product, SbnI, was determined to be a free l-serine kinase that produces O-phospho-l-serine (OPS), a substrate for SB biosynthesis. Previous studies have also characterized SbnI as a DNA-binding regulatory protein that senses heme to control sbn gene expression for SB synthesis. Here, we present crystal structures at 1.9-2.1 Å resolution of a SbnI homolog from Staphylococcus pseudintermedius (SpSbnI) in both apo form and in complex with ADP, a product of the kinase reaction; the latter confirmed the active-site location. The structures revealed that SpSbnI forms a dimer through C-terminal domain swapping and a dimer of dimers through intermolecular disulfide formation. Heme binding had only a modest effect on SbnI enzymatic activity, suggesting that its two functions are independent and structurally distinct. We identified a heme-binding site and observed catalytic heme transfer between a heme-degrading protein of the Isd system, IsdI, and SbnI. These findings support the notion that SbnI has a bifunctional role contributing precursor OPS to SB synthesis and directly sensing heme to control expression of the sbn locus. We propose that heme transfer from IsdI to SbnI enables S. aureus to control iron source preference according to the sources available in the environment.
Collapse
Affiliation(s)
- Meghan M Verstraete
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - L Daniela Morales
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Marek J Kobylarz
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Slade A Loutet
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Holly A Laakso
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Tyler B Pinter
- Department of Chemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Martin J Stillman
- Department of Chemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
37
|
Conroy BS, Grigg JC, Kolesnikov M, Morales LD, Murphy MEP. Staphylococcus aureus heme and siderophore-iron acquisition pathways. Biometals 2019; 32:409-424. [PMID: 30911924 DOI: 10.1007/s10534-019-00188-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/18/2019] [Indexed: 11/24/2022]
Abstract
Staphylococcus aureus is a versatile opportunistic human pathogen. Infection by this bacterium requires uptake of iron from the human host, but iron is highly restricted in this environment. Staphylococcus aureus iron sufficiency is achieved primarily through uptake of heme and high-affinity iron chelators, known as siderophores. Two siderophores (staphyloferrins) are produced and secreted by S. aureus into the extracellular environment to capture iron. Staphylococcus aureus expresses specific uptake systems for staphyloferrins and more general uptake systems for siderophores produced by other microorganisms. The S. aureus heme uptake system uses highly-specific cell surface receptors to extract heme from hemoglobin and hemoglobin-haptoglobin complexes for transport into the cytoplasm where it is degraded to liberate iron. Initially thought to be independent systems, recent findings indicate that these iron uptake pathways intersect. IruO is a reductase that releases iron from heme and some ferric-siderophores. Moreover, multifunctional SbnI produces a precursor for staphyloferrin B biosynthesis, and also binds heme to regulate expression of the staphyloferrin B biosynthesis pathway. Intersection of the S. aureus iron uptake pathways is hypothesized to be important for rapid adaptation to available iron sources. Components of the heme and siderophore uptake systems are currently being targeted in the development of therapeutics against S. aureus.
Collapse
Affiliation(s)
- Brigid S Conroy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - L Daniela Morales
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada.
| |
Collapse
|
38
|
Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
Collapse
Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| |
Collapse
|
39
|
Law BJC, Zhuo Y, Winn M, Francis D, Zhang Y, Samborskyy M, Murphy A, Ren L, Leadlay PF, Micklefield J. A vitamin K-dependent carboxylase orthologue is involved in antibiotic biosynthesis. Nat Catal 2018. [DOI: 10.1038/s41929-018-0178-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
40
|
Verstraete MM, Perez-Borrajero C, Brown KL, Heinrichs DE, Murphy MEP. SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus. J Biol Chem 2018; 293:6147-6160. [PMID: 29483190 DOI: 10.1074/jbc.ra118.001875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/15/2018] [Indexed: 12/22/2022] Open
Abstract
Staphyloferrin B (SB) is an iron-chelating siderophore produced by Staphylococcus aureus in invasive infections. Proteins for SB biosynthesis and export are encoded by the sbnABCDEFGHI gene cluster, in which SbnI, a member of the ParB/Srx superfamily, acts as a heme-dependent transcriptional regulator of the sbn locus. However, no structural or functional information about SbnI is available. Here, a crystal structure of SbnI revealed striking structural similarity to an ADP-dependent free serine kinase, SerK, from the archaea Thermococcus kodakarensis We found that features of the active sites are conserved, and biochemical assays and 31P NMR and HPLC analyses indicated that SbnI is also a free serine kinase but uses ATP rather than ADP as phosphate donor to generate the SB precursor O-phospho-l-serine (OPS). SbnI consists of two domains, and elevated B-factors in domain II were consistent with the open-close reaction mechanism previously reported for SerK. Mutagenesis of Glu20 and Asp58 in SbnI disclosed that they are required for kinase activity. The only known OPS source in bacteria is through the phosphoserine aminotransferase activity of SerC within the serine biosynthesis pathway, and we demonstrate that an S. aureus serC mutant is a serine auxotroph, consistent with a function in l-serine biosynthesis. However, the serC mutant strain could produce SB when provided l-serine, suggesting that SbnI produces OPS for SB biosynthesis in vivo These findings indicate that besides transcriptionally regulating the sbn locus, SbnI also has an enzymatic role in the SB biosynthetic pathway.
Collapse
Affiliation(s)
| | - Cecilia Perez-Borrajero
- the Genome Sciences and Technology Program Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | | | - David E Heinrichs
- the Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | | |
Collapse
|
41
|
Batoon P, Oomens J, Berden G, Ren J. Conformations of Protonated AlaDap and DapAla Characterized by IRMPD Spectroscopy and Molecular Modeling. J Phys Chem B 2018; 122:2191-2202. [DOI: 10.1021/acs.jpcb.7b10435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Batoon
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jianhua Ren
- Department
of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
| |
Collapse
|
42
|
Oliver RA, Li R, Townsend CA. Monobactam formation in sulfazecin by a nonribosomal peptide synthetase thioesterase. Nat Chem Biol 2018; 14:5-7. [PMID: 29155429 PMCID: PMC5726899 DOI: 10.1038/nchembio.2526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/20/2017] [Indexed: 11/25/2022]
Abstract
The N-sulfonated monocyclic β-lactam ring characteristic of the monobactams confers resistance to zinc metallo-β-lactamases and affords the most effective class to combat carbapenem-resistant enterobacteria (CRE). Here we report unprecedented nonribosomal peptide synthetase activities, wherein an assembled tripeptide is N-sulfonated in trans before direct synthesis of the β-lactam ring in a noncanonical, cysteine-containing thioesterase domain. This means of azetidinone synthesis is distinct from the three others known in nature.
Collapse
Affiliation(s)
- Ryan A. Oliver
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| |
Collapse
|
43
|
Nunn PB, Codd GA. Metabolic solutions to the biosynthesis of some diaminomonocarboxylic acids in nature: Formation in cyanobacteria of the neurotoxins 3-N-methyl-2,3-diaminopropanoic acid (BMAA) and 2,4-diaminobutanoic acid (2,4-DAB). PHYTOCHEMISTRY 2017; 144:253-270. [PMID: 29059579 DOI: 10.1016/j.phytochem.2017.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown. This review considers possible metabolic routes, by analogy with reactions used in other species, by which these amino acids might be biosynthesised by cyanobacteria, which are a widespread potential environmental source of these neurotoxins. Where possible, the gene expression that might be implicated in these biosyntheses is discussed.
Collapse
Affiliation(s)
- Peter B Nunn
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, PO1 2DT, UK.
| | - Geoffrey A Codd
- School of Life Sciences, University of Dundee, DD1 5EH, UK; School of Natural Sciences, University of Stirling, FK9 4LA, UK.
| |
Collapse
|
44
|
Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance. mBio 2017; 8:mBio.00225-17. [PMID: 28292982 PMCID: PMC5350466 DOI: 10.1128/mbio.00225-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential for microbes to overcome antibiotics of different classes before they reach bacterial cells is largely unexplored. Here we show that a soluble bacterial lipocalin produced by Burkholderia cenocepacia upon exposure to sublethal antibiotic concentrations increases resistance to diverse antibiotics in vitro and in vivo These phenotypes were recapitulated by heterologous expression in B. cenocepacia of lipocalin genes from Pseudomonas aeruginosa, Mycobacterium tuberculosis, and methicillin-resistant Staphylococcus aureus Purified lipocalin bound different classes of bactericidal antibiotics and contributed to bacterial survival in vivo Experimental and X-ray crystal structure-guided computational studies revealed that lipocalins counteract antibiotic action by capturing antibiotics in the extracellular space. We also demonstrated that fat-soluble vitamins prevent antibiotic capture by binding bacterial lipocalin with higher affinity than antibiotics. Therefore, bacterial lipocalins contribute to antimicrobial resistance by capturing diverse antibiotics in the extracellular space at the site of infection, which can be counteracted by known vitamins.IMPORTANCE Current research on antibiotic action and resistance focuses on targeting essential functions within bacterial cells. We discovered a previously unrecognized mode of general bacterial antibiotic resistance operating in the extracellular space, which depends on bacterial protein molecules called lipocalins. These molecules are highly conserved in most bacteria and have the ability to capture different classes of antibiotics outside bacterial cells. We also discovered that liposoluble vitamins, such as vitamin E, overcome in vitro and in vivo antibiotic resistance mediated by bacterial lipocalins, providing an unexpected new alternative to combat resistance by using this vitamin or its derivatives as antibiotic adjuvants.
Collapse
|
45
|
Kumari M, Shukla S, Pandey S, Giri VP, Bhatia A, Tripathi T, Kakkar P, Nautiyal CS, Mishra A. Enhanced Cellular Internalization: A Bactericidal Mechanism More Relative to Biogenic Nanoparticles than Chemical Counterparts. ACS APPLIED MATERIALS & INTERFACES 2017; 9:4519-4533. [PMID: 28051856 DOI: 10.1021/acsami.6b15473] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Biogenic synthesis of silver nanoparticles for enhanced antimicrobial activity has gained a lot of momentum making it an urgent need to search for a suitable biocandidate which could be utilized for efficient capping and shaping of silver nanoparticles with enhanced bactericidal activity utilizing its secondary metabolites. Current work illustrates the enhancement of antimicrobial efficacy of silver nanoparticles by reducing and modifying their surface with antimicrobial metabolites of cell free filtrate of Trichoderma viride (MTCC 5661) in comparison to citrate stabilized silver nanoparticles. Nanoparticles were characterized by visual observations, UV-visible spectroscopy, zetasizer, and transmission electron microscopy (TEM). Synthesized particles were monodispersed, spherical in shape and 10-20 nm in size. Presence of metabolites on surface of biosynthesized silver nanoparticles was observed by gas chromatography-mass spectroscopy (GC-MS), energy dispersive X-ray analysis (EDAX), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The antimicrobial activity of both silver nanoparticles was tested against Shigella sonnei, Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) by growth inhibition curve analysis and colony formation unit assay. Further, it was noted that internalization of biosynthesized nanoparticles inside the bacterial cell was much higher as compared to citrate stabilized particles which in turn lead to higher production of reactive oxygen species. Increase in oxidative stress caused severe damage to bacterial membrane enhancing further uptake of particles and revoking other pathways for bacterial disintegration resulting in complete and rapid death of pathogens as evidenced by fluorescein diacetate/propidium iodide dual staining and TEM. Thus, study reveals that biologically synthesized silver nanoarchitecture coated with antimicrobial metabolites of T. viride was more potent than their chemical counterpart in killing of pathogenic bacteria.
Collapse
Affiliation(s)
- Madhuree Kumari
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Shatrunajay Shukla
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Shipra Pandey
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Ved P Giri
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Anil Bhatia
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Tusha Tripathi
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Poonam Kakkar
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Chandra S Nautiyal
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Aradhana Mishra
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| |
Collapse
|
46
|
Li R, Oliver RA, Townsend CA. Identification and Characterization of the Sulfazecin Monobactam Biosynthetic Gene Cluster. Cell Chem Biol 2017; 24:24-34. [PMID: 28017601 PMCID: PMC5286544 DOI: 10.1016/j.chembiol.2016.11.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/18/2016] [Accepted: 11/17/2016] [Indexed: 11/16/2022]
Abstract
The monobactams, exemplified by the natural product sulfazecin, are the only class of β-lactam antibiotics not inactivated by metallo-β-lactamases, which confer bacteria with extended-spectrum β-lactam resistance. We screened a transposon mutagenesis library from Pseudomonas acidophila ATCC 31363 and isolated a sulfazecin-deficient mutant that revealed a gene cluster encoding two non-ribosomal peptide synthetases (NRPSs), a methyltransferase, a sulfotransferase, and a dioxygenase. Three modules and an aberrant C-terminal thioesterase (TE) domain are distributed across the two NRPSs. Biochemical examination of the adenylation (A) domains provided evidence that L-2,3-diaminopropionate, not L-serine as previously thought, is the direct source of the β-lactam ring of sulfazecin. ATP/PPi exchange assay also revealed an unusual substrate selectivity shift of one A domain when expressed with or without the immediately upstream condensation domain. Gene inactivation analysis defined a cluster of 13 open reading frames sufficient for sulfazecin production, precursor synthesis, self-resistance, and regulation. The identification of a key intermediate supported a proposed NRPS-mediated mechanism of sulfazecin biosynthesis and β-lactam ring formation distinct from the nocardicins, another NRPS-derived subclass of monocyclic β-lactam. These findings will serve as the basis for further biosynthetic research and potential engineering of these important antibiotics.
Collapse
Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Ryan A Oliver
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
| |
Collapse
|
47
|
Batoon P, Ren J. Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues. J Phys Chem B 2016; 120:7783-94. [DOI: 10.1021/acs.jpcb.6b03776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Batoon
- Department of Chemistry, University of the Pacific, 3601 Pacific
Avenue, Stockton, California 95211, United States
| | - Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific
Avenue, Stockton, California 95211, United States
| |
Collapse
|
48
|
Ernst DC, Anderson ME, Downs DM. L-2,3-diaminopropionate generates diverse metabolic stresses in Salmonella enterica. Mol Microbiol 2016; 101:210-23. [PMID: 27010356 DOI: 10.1111/mmi.13384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2016] [Indexed: 12/28/2022]
Abstract
Unchecked amino acid accumulation in living cells has the potential to cause stress by disrupting normal metabolic processes. Thus, many organisms have evolved degradation strategies that prevent endogenous accumulation of amino acids. L-2,3-diaminopropionate (Dap) is a non-protein amino acid produced in nature where it serves as a precursor to siderophores, neurotoxins and antibiotics. Dap accumulation in Salmonella enterica was previously shown to inhibit growth by unknown mechanisms. The production of diaminopropionate ammonia-lyase (DpaL) alleviated Dap toxicity in S. enterica by catalyzing the degradation of Dap to pyruvate and ammonia. Here, we demonstrate that Dap accumulation in S. enterica elicits a proline requirement for growth and specifically inhibits coenzyme A and isoleucine biosynthesis. Additionally, we establish that the DpaL-dependent degradation of Dap to pyruvate proceeds through an unbound 2-aminoacrylate (2AA) intermediate, thus contributing to 2AA stress inside the cell. The reactive intermediate deaminase, RidA, is shown to prevent 2AA damage caused by DpaL-dependent Dap degradation by enhancing the rate of 2AA hydrolysis. The results presented herein inform our understanding of the effects Dap has on metabolism in S. enterica, and likely other organisms, and highlight the critical role played by RidA in preventing 2AA stress stemming from Dap detoxification.
Collapse
Affiliation(s)
- Dustin C Ernst
- Department of Microbiology, University of Georgia, Athens, GA, 30602-2605, USA
| | - Mary E Anderson
- Department of Microbiology, University of Georgia, Athens, GA, 30602-2605, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, 30602-2605, USA
| |
Collapse
|
49
|
Kobylarz MJ, Grigg JC, Liu Y, Lee MSF, Heinrichs DE, Murphy MEP. Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis. Biochemistry 2016; 55:927-39. [PMID: 26794841 PMCID: PMC5084695 DOI: 10.1021/acs.biochem.5b01045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Staphylococcus aureus assembles the siderophore,
staphyloferrin B, from l-2,3-diaminopropionic acid (l-Dap), α-ketoglutarate, and citrate. Recently, SbnA and SbnB
were shown to produce l-Dap and α-ketoglutarate from O-phospho-l-serine (OPS) and l-glutamate.
SbnA is a pyridoxal 5′-phosphate (PLP)-dependent enzyme with
homology to O-acetyl-l-serine sulfhydrylases;
however, SbnA utilizes OPS instead of O-acetyl-l-serine (OAS), and l-glutamate serves as a nitrogen
donor instead of a sulfide. In this work, we examined how SbnA dictates
substrate specificity for OPS and l-glutamate using a combination
of X-ray crystallography, enzyme kinetics, and site-directed mutagenesis.
Analysis of SbnA crystals incubated with OPS revealed the structure
of the PLP-α-aminoacrylate intermediate. Formation of the intermediate
induced closure of the active site pocket by narrowing the channel
leading to the active site and forming a second substrate binding
pocket that likely binds l-glutamate. Three active site residues
were identified: Arg132, Tyr152, Ser185 that were essential for OPS
recognition and turnover. The Y152F/S185G SbnA double mutant was completely
inactive, and its crystal structure revealed that the mutations induced
a closed form of the enzyme in the absence of the α-aminoacrylate
intermediate. Lastly, l-cysteine was shown to be a competitive
inhibitor of SbnA by forming a nonproductive external aldimine with
the PLP cofactor. These results suggest a regulatory link between
siderophore and l-cysteine biosynthesis, revealing a potential
mechanism to reduce iron uptake under oxidative stress.
Collapse
Affiliation(s)
- Marek J Kobylarz
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| | - Yunan Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| | - Mathew S F Lee
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3
| |
Collapse
|
50
|
Spohn M, Wohlleben W, Stegmann E. Elucidation of the zinc-dependent regulation inAmycolatopsis japonicumenabled the identification of the ethylenediamine-disuccinate ([S,S]-EDDS) genes. Environ Microbiol 2016; 18:1249-63. [DOI: 10.1111/1462-2920.13159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/13/2015] [Accepted: 11/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
- Partner Site Tuebingen; German Centre for Infection Research (DZIF); Tuebingen Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology; University of Tuebingen; 72076 Tuebingen Germany
- Partner Site Tuebingen; German Centre for Infection Research (DZIF); Tuebingen Germany
| |
Collapse
|