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Liu Y, Wang S, Wang L, Lu H, Zhang T, Zeng W. Characterization of Genomic, Physiological, and Probiotic Features of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui. Foods 2024; 13:1082. [PMID: 38611386 PMCID: PMC11011416 DOI: 10.3390/foods13071082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as "Jiangshui" in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden-Meyerhof-Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement.
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Affiliation(s)
- Yang Liu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
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Yetiman A, Horzum M, Bahar D, Akbulut M. Assessment of Genomic and Metabolic Characteristics of Cholesterol-Reducing and GABA Producer Limosilactobacillus fermentum AGA52 Isolated from Lactic Acid Fermented Shalgam Based on "In Silico" and "In Vitro" Approaches. Probiotics Antimicrob Proteins 2024; 16:334-351. [PMID: 36735220 DOI: 10.1007/s12602-022-10038-2] [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] [Accepted: 12/19/2022] [Indexed: 02/04/2023]
Abstract
This study aimed to characterize the genomic and metabolic properties of a novel Lb. fermentum strain AGA52 which was isolated from a lactic acid fermented beverage called "shalgam." The genome size of AGA52 was 2,001,184 bp, which is predicted to carry 2024 genes, including 50 tRNAs, 3 rRNAs, 3 ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases, and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analyzed by comparison with the other Lb. fermentum strains. The detected resistome on the genome of AGA52 was found to be intrinsic originated. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Furthermore, the strain is found to have a better antioxidant capacity and to be tolerant to gastrointestinal simulated conditions. It was also observed that the AGA52 has antimicrobial activity against Yersinia enterocolitica ATCC9610, Bacillus cereus ATCC33019, Salmonella enterica sv. Typhimurium, Escherichia coli O157:h7 ATCC43897, Listeria monocytogenes ATCC7644, Klebsiella pneumoniae ATCC13883, and Proteus vulgaris ATCC8427. Additionally, AGA52 exhibited 42.74 ± 4.82% adherence to HT29 cells. Cholesterol assimilation (33.9 ± 0.005%) and GABA production capacities were also confirmed by "in silico" and "in vitro." Overall, the investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.
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Affiliation(s)
- Ahmet Yetiman
- Food Engineering Department, Faculty of Engineering, Erciyes University, 38030, Kayseri, Turkey.
| | - Mehmet Horzum
- Food Engineering Department, Graduate School of Natural and Applied Sciences, Erciyes University, 38030, Kayseri, Turkey
| | - Dilek Bahar
- Genkök Genome and Stem Cell Center, Erciyes University, 38030, Kayseri, Turkey
| | - Mikail Akbulut
- Department of Biology, Faculty of Science, Erciyes University, 38030, Kayseri, Turkey
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Nguyen VH, Wemheuer B, Song W, Bennett H, Webster N, Thomas T. Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species. Syst Appl Microbiol 2023; 46:126426. [PMID: 37141831 DOI: 10.1016/j.syapm.2023.126426] [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: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.
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Affiliation(s)
- Viet Hung Nguyen
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia; Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Im H, Pearson ML, Martinez E, Cichos KH, Song X, Kruckow KL, Andrews RM, Ghanem ES, Orihuela CJ. Targeting NAD+ regeneration enhances antibiotic susceptibility of Streptococcus pneumoniae during invasive disease. PLoS Biol 2023; 21:e3002020. [PMID: 36928033 PMCID: PMC10019625 DOI: 10.1371/journal.pbio.3002020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/02/2023] [Indexed: 03/18/2023] Open
Abstract
Anaerobic bacteria are responsible for half of all pulmonary infections. One such pathogen is Streptococcus pneumoniae (Spn), a leading cause of community-acquired pneumonia, bacteremia/sepsis, and meningitis. Using a panel of isogenic mutants deficient in lactate, acetyl-CoA, and ethanol fermentation, as well as pharmacological inhibition, we observed that NAD(H) redox balance during fermentation was vital for Spn energy generation, capsule production, and in vivo fitness. Redox balance disruption in fermentation pathway-specific fashion substantially enhanced susceptibility to killing in antimicrobial class-specific manner. Blocking of alcohol dehydrogenase activity with 4-methylpyrazole (fomepizole), an FDA-approved drug used as an antidote for toxic alcohol ingestion, enhanced susceptibility of multidrug-resistant Spn to erythromycin and reduced bacterial burden in the lungs of mice with pneumonia and prevented the development of invasive disease. Our results indicate fermentation enzymes are de novo targets for antibiotic development and a novel strategy to combat multidrug-resistant pathogens.
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Affiliation(s)
- Hansol Im
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Madison L. Pearson
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eriel Martinez
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Kyle H. Cichos
- Department of Orthopaedic Surgery Arthroplasty Section, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Xiuhong Song
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Katherine L. Kruckow
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rachel M. Andrews
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elie S. Ghanem
- Department of Orthopaedic Surgery Arthroplasty Section, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Carlos J. Orihuela
- Department of Microbiology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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5
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Zheng Y, Zhang B, Xie Y, Lin J, Wei D. Using a novel data-driven combinatorial mutagenesis strategy to engineer an alcohol dehydrogenase for efficient geraniol synthesis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Kummer M, Lee YS, Yuan M, Alkotaini B, Zhao J, Blumenthal E, Minteer SD. Substrate Channeling by a Rationally Designed Fusion Protein in a Biocatalytic Cascade. JACS AU 2021; 1:1187-1197. [PMID: 34467357 PMCID: PMC8397353 DOI: 10.1021/jacsau.1c00180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/31/2023]
Abstract
Substrate channeling, where an intermediate in a multistep reaction is directed toward a reaction center rather than freely diffusing, offers several advantages when employed in catalytic cascades. Here we present a fusion enzyme comprised of an alcohol and aldehyde dehydrogenase, that is computationally designed to facilitate electrostatic substrate channeling using a cationic linker bridging the two structures. Rosetta protein folding software was utilized to determine an optimal linker placement, added to the truncated termini of the proteins, which is as close as possible to the active sites of the enzymes without disrupting critical catalytic residues. With improvements in stability, product selectivity (90%), and catalyst turnover frequency, representing 500-fold increased activity compared to the unbound enzymes and nearly 140-fold for a neutral-linked fusion enzyme, this design strategy holds promise for making other multistep catalytic processes more sustainable and efficient.
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Affiliation(s)
- Matthew
J. Kummer
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - Yoo Seok Lee
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - Mengwei Yuan
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - Bassam Alkotaini
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - John Zhao
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - Emmy Blumenthal
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University
of Utah, 315 S 1400 E, Salt Lake
City, Utah 84112, United States
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7
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Guntupalli SR, Li Z, Chang L, Plapp BV, Subramanian R. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry 2021; 60:663-677. [PMID: 33620215 DOI: 10.1021/acs.biochem.0c00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD+ and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have D2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism.
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Affiliation(s)
- Sai Rohit Guntupalli
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal University, Manipal, India.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bryce V Plapp
- Department of Biochemistry, Bowen Science Building, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Ramaswamy Subramanian
- Department of Biological Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle. Appl Environ Microbiol 2020; 86:AEM.02038-20. [PMID: 33097507 DOI: 10.1128/aem.02038-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022] Open
Abstract
Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings.IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.
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Petratos K, Gessmann R, Daskalakis V, Papadovasilaki M, Papanikolau Y, Tsigos I, Bouriotis V. Structure and Dynamics of a Thermostable Alcohol Dehydrogenase from the Antarctic Psychrophile Moraxella sp. TAE123. ACS OMEGA 2020; 5:14523-14534. [PMID: 32596590 PMCID: PMC7315583 DOI: 10.1021/acsomega.0c01210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
The structure of a recombinant (His-tagged at C-terminus) alcohol dehydrogenase (MoADH) from the cold-adapted bacterium Moraxella sp. TAE123 has been refined with X-ray diffraction data extending to 1.9 Å resolution. The enzyme assumes a homo-tetrameric structure. Each subunit comprises two distinct structural domains: the catalytic domain (residues 1-150 and 288-340/345) and the nucleotide-binding domain (residues 151-287). There are two Zn2+ ions in each protein subunit. Two additional zinc ions have been found in the crystal structure between symmetry-related subunits. The structure has been compared with those of homologous enzymes from Geobacillus stearothermophilus (GsADH), Escherichia coli (EcADH), and Thermus sp. ATN1 (ThADH) that thrive in environments of diverse temperatures. Unexpectedly, MoADH has been found active from 10 to at least 53 °C and unfolds at 89 °C according to circular dichroism spectropolarimetry data. MoADH with substrate ethanol exhibits a small value of activation enthalpy ΔH ‡ of 30 kJ mol-1. Molecular dynamics simulations for single subunits of the closely homologous enzymes MoADH and GsADH performed at 280, 310, and 340 K showed enhanced wide-ranging mobility of MoADH at high temperatures and generally lower but more distinct and localized mobility for GsADH. Principal component analysis of the fluctuations of both ADHs resulted in a prominent open-close transition of the structural domains mainly at 280 K for MoADH and 340 K for GsADH. In conclusion, MoADH is a very thermostable, cold-adapted enzyme and the small value of activation enthalpy allows the enzyme to function adequately at low temperatures.
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Affiliation(s)
- Kyriacos Petratos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Renate Gessmann
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Vangelis Daskalakis
- Department
of Chemical Engineering, Cyprus University
of Technology, 3603 Limassol, Cyprus
| | - Maria Papadovasilaki
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Yannis Papanikolau
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Iason Tsigos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
| | - Vassilis Bouriotis
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, 70013 Heraklion, Greece
- Department
of Biology, University of Crete, 70013 Heraklion, Greece
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10
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Nguyen GT, Kim YG, Ahn JW, Chang JH. Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli. Molecules 2020; 25:molecules25102404. [PMID: 32455802 PMCID: PMC7287880 DOI: 10.3390/molecules25102404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 12/02/2022] Open
Abstract
In metabolic engineering and synthetic biology fields, there have been efforts to produce variable bioalcohol fuels, such as isobutanol and 2-phenylethanol, in order to meet industrial demands. YjgB is an aldehyde dehydrogenase from Escherichia coli that shows nicotinamide adenine dinucleotide phosphate (NADP)-dependent broad selectivity for aldehyde derivatives with an aromatic ring or small aliphatic chain. This could contribute to the design of industrial synthetic pathways. We determined the crystal structures of YjgB for both its apo-form and NADP-complexed form at resolutions of 1.55 and 2.00 Å, respectively, in order to understand the mechanism of broad substrate selectivity. The hydrophobic pocket of the active site and the nicotinamide ring of NADP(H) are both involved in conferring its broad specificity toward aldehyde substrates. In addition, based on docking-simulation data, we inferred that π–π stacking between substrates and aromatic side chains might play a crucial role in recognizing substrates. Our structural analysis of YjgB might provide insights into establishing frameworks to understand its broad substrate specificity and develop engineered enzymes for industrial biofuel synthesis.
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Affiliation(s)
- Giang Thu Nguyen
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea;
| | - Yeon-Gil Kim
- Beamline Science Division, Pohang Accelerator Laboratory, 127 Jigok-ro, Nam-Gu, Pohang, Gyoungbuk 37673, Korea;
| | - Jae-Woo Ahn
- Postech Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-Gu, Pohang, Gyoungbuk 37673, Korea
- Correspondence: (J.-W.A.); (J.H.C.); Tel.: +82-54-279-8648 (J.-W.A.); +82-53-950-5913 (J.H.C.); Fax: +82-54-279-8379 (J.-W.A.); +82-53-950-6809 (J.H.C.); M.P.: +82-10-9578-1734 (J.-W.A.); +82-10-4765-1107 (J.H.C.)
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea;
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea
- Correspondence: (J.-W.A.); (J.H.C.); Tel.: +82-54-279-8648 (J.-W.A.); +82-53-950-5913 (J.H.C.); Fax: +82-54-279-8379 (J.-W.A.); +82-53-950-6809 (J.H.C.); M.P.: +82-10-9578-1734 (J.-W.A.); +82-10-4765-1107 (J.H.C.)
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11
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Sun T, Zhang B, Lin J, Ren Y. Reversible photocontrol of oxidase activity by inserting a photosensitive domain into the oxidase. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0263-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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High-yield production of D-1,2,4-butanetriol from lignocellulose-derived xylose by using a synthetic enzyme cascade in a cell-free system. J Biotechnol 2019; 292:76-83. [PMID: 30703470 DOI: 10.1016/j.jbiotec.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/17/2018] [Accepted: 01/03/2019] [Indexed: 11/21/2022]
Abstract
Approaches using metabolic engineering to produce D-1, 2, 4-butanetriol (BT) from renewable biomass in microbial systems have achieved initial success. However, due to the lack of incomplete understanding of the complex branch pathway, the efficient fermentation system for BT production was difficult to develop. Here we reconstituted a cell-free system in vitro using purified enzymes to produce BT from d-xylose. The factors that influencing the efficiency of cell-free system, including enzyme concentration, reaction buffer, pH, temperature, metal ion additives and cofactors were first identified to define optimal reaction conditions and essential components for the cascade reaction. Meanwhile, a natural cofactor recycling system was found in cell-free system. Finally, we were able to convert 18 g/L xylose to 6.1 g/L BT within 40 h with a yield of 48.0%. The feasibility of cell-free system to produce BT in corncob hydrolysates was also determined.
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Behiry EM, Ruiz-Pernia JJ, Luk L, Tuñón I, Moliner V, Allemann RK. Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Enas M. Behiry
- School of Chemistry; Cardiff University; Park Place Cardiff CF10 3AT UK
| | | | - Louis Luk
- School of Chemistry; Cardiff University; Park Place Cardiff CF10 3AT UK
| | - Iñaki Tuñón
- Departament de Química Física; Universitat de València; 46100 Burjassot Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I; 12071 Castelló Spain
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Behiry EM, Ruiz‐Pernia JJ, Luk L, Tuñón I, Moliner V, Allemann RK. Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State. Angew Chem Int Ed Engl 2018; 57:3128-3131. [PMID: 29341402 PMCID: PMC5861672 DOI: 10.1002/anie.201712826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 11/10/2022]
Abstract
The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate-dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohols. BsADH prefers smaller substrates, which cause less protein friction along the reaction coordinate and reduced frequencies of dynamic recrossing. This hypothesis allows a prediction of the trend of enzyme isotope effects for a wide variety of substrates.
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Affiliation(s)
- Enas M. Behiry
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
| | | | - Louis Luk
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
| | - Iñaki Tuñón
- Departament de Química FísicaUniversitat de València46100BurjassotSpain
| | - Vicent Moliner
- Departament de Química Física i AnalíticaUniversitat Jaume I12071CastellóSpain
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15
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Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry 2017. [PMID: 28640600 PMCID: PMC5518280 DOI: 10.1021/acs.biochem.7b00446] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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During catalysis
by liver alcohol dehydrogenase (ADH), a water
bound to the catalytic zinc is replaced by the oxygen of the substrates.
The mechanism might involve a pentacoordinated zinc or a double-displacement
reaction with participation by a nearby glutamate residue, as suggested
by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs.
Zinc coordination and participation of water in the enzyme mechanism
were investigated by X-ray crystallography. The apoenzyme and its
complex with adenosine 5′-diphosphoribose have an open protein
conformation with the catalytic zinc in one position, tetracoordinated
by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators
2,2′-bipyridine and 1,10-phenanthroline displace the water
and form a pentacoordinated zinc. The enzyme–NADH complex has
a closed conformation similar to that of ternary complexes with coenzyme
and substrate analogues; the coordination of the catalytic zinc is
similar to that found in the apoenzyme, except that a minor, alternative
position for the catalytic zinc is ∼1.3 Å from the major
position and closer to Glu-68, which could form the alternative coordination
to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide
or N-benzylformamide (or with NAD+ and
fluoro alcohols) have the classical tetracoordinated zinc, and no
water is bound to the zinc or the nicotinamide rings. The major forms
of the enzyme in the mechanism have a tetracoordinated zinc, where
the carboxylate group of Glu-68 could participate in the exchange
of water and substrates on the zinc. Hydride transfer in the Michaelis
complexes does not involve a nearby water.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Baskar Raj Savarimuthu
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Daniel J Ferraro
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Jon K Rubach
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Eric N Brown
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - S Ramaswamy
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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16
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Metabolic pathway optimization for biosynthesis of 1,2,4-butanetriol from xylose by engineered Escherichia coli. Enzyme Microb Technol 2016; 93-94:51-58. [DOI: 10.1016/j.enzmictec.2016.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022]
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17
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Cahn JKB, Baumschlager A, Brinkmann-Chen S, Arnold FH. Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes. Protein Eng Des Sel 2016; 29:31-8. [PMID: 26512129 PMCID: PMC4678007 DOI: 10.1093/protein/gzv057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 11/14/2022] Open
Abstract
NAD(P)H-dependent enzymes are ubiquitous in metabolism and cellular processes and are also of great interest for pharmaceutical and industrial applications. Here, we present a structure-guided enzyme engineering strategy for improving catalytic properties of NAD(P)H-dependent enzymes toward native or native-like reactions using mutations to the enzyme's adenine-binding pocket, distal to the site of catalysis. Screening single-site saturation mutagenesis libraries identified mutations that increased catalytic efficiency up to 10-fold in 7 out of 10 enzymes. The enzymes improved in this study represent three different cofactor-binding folds (Rossmann, DHQS-like, and FAD/NAD binding) and utilize both NADH and NADPH. Structural and biochemical analyses show that the improved activities are accompanied by minimal changes in other properties (cooperativity, thermostability, pH optimum, uncoupling), and initial tests on two enzymes (ScADH6 and EcFucO) show improved functionality in Escherichia coli.
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Affiliation(s)
- J K B Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - A Baumschlager
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - S Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - F H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
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18
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Radivojevic J, Minovska G, Senerovic L, O'Connor K, Jovanovic P, Savic V, Tokic-Vujosevic Z, Nikodinovic-Runic J, Maslak V. Synthesis of γ-nitroaldehydes containing quaternary carbon in the α-position using a 4-oxalocrotonate tautomerase whole-cell biocatalyst. RSC Adv 2014. [DOI: 10.1039/c4ra05517a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthetically valuable quaternary carbon containing γ-nitroaldehydes were obtained from branched chain aldehydes and a range of α,β-unsaturated nitroalkenes by a whole-cell biocatalytic reaction using 4-oxalocrotonate tautomerase as catalyst.
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Affiliation(s)
- Jelena Radivojevic
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
| | - Gordana Minovska
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
| | - Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
| | - Kevin O'Connor
- School of Biomolecular and Biomedical Sciences
- Centre for Synthesis and Chemical Biology
- University College Dublin
- Dublin 4, Ireland
| | - Predrag Jovanovic
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Belgrade
- 11221 Belgrade, Serbia
| | - Vladimir Savic
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Belgrade
- 11221 Belgrade, Serbia
| | - Zorana Tokic-Vujosevic
- Department of Organic Chemistry
- Faculty of Pharmacy
- University of Belgrade
- 11221 Belgrade, Serbia
| | | | - Veselin Maslak
- Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
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