1
|
Frantsuzova E, Bogun A, Solomentsev V, Vetrova A, Streletskii R, Solyanikova I, Delegan Y. Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds. BIOLOGY 2023; 12:biology12050721. [PMID: 37237534 DOI: 10.3390/biology12050721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023]
Abstract
The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.
Collapse
Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Viktor Solomentsev
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| |
Collapse
|
2
|
Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
Collapse
Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|
3
|
Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence. Appl Microbiol Biotechnol 2022; 106:3153-3171. [PMID: 35396956 DOI: 10.1007/s00253-022-11906-1] [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: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 11/02/2022]
Abstract
The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.
Collapse
|
4
|
Qin X, Xue B, Tian H, Fang C, Yu J, Chen C, Xue Q, Jones J, Wang X. An unconventionally secreted effector from the root knot nematode Meloidogyne incognita, Mi-ISC-1, promotes parasitism by disrupting salicylic acid biosynthesis in host plants. MOLECULAR PLANT PATHOLOGY 2022; 23:516-529. [PMID: 34923729 PMCID: PMC8916211 DOI: 10.1111/mpp.13175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 05/14/2023]
Abstract
Plant-parasitic nematodes need to deliver effectors that suppress host immunity for successful parasitism. We have characterized a novel isochorismatase effector from the root-knot nematode Meloidogyne incognita, named Mi-ISC-1. The Mi-isc-1 gene is expressed in the subventral oesophageal glands and is up-regulated in parasitic-stage juveniles. Tobacco rattle virus-induced gene silencing targeting Mi-isc-1 attenuated M. incognita parasitism. Enzyme activity assays confirmed that Mi-ISC-1 can catalyse hydrolysis of isochorismate into 2,3-dihydro-2,3-dihydroxybenzoate in vitro. Although Mi-ISC-1 lacks a classical signal peptide for secretion at its N-terminus, a yeast invertase secretion assay showed that this protein can be secreted from eukaryotic cells. However, the subcellular localization and plasmolysis assay revealed that the unconventional secretory signal present on the Mi-ISC-1 is not recognized by the plant secretory pathway and that the effector was localized within the cytoplasm of plant cells, but not apoplast, when transiently expressed in Nicotiana benthamiana leaves by agroinfiltration. Ectopic expression of Mi-ISC-1 in N. benthamiana reduced expression of the PR1 gene and levels of salicylic acid (SA), and promoted infection by Phytophthora capsici. The cytoplasmic localization of Mi-ISC-1 is required for its function. Moreover, Mi-ISC-1 suppresses the production of SA following the reconstitution of the de novo SA biosynthesis via the isochorismate pathway in the cytoplasm of N. benthamiana leaves. These results demonstrate that M. incognita deploys a functional isochorismatase that suppresses SA-mediated plant defences by disrupting the isochorismate synthase pathway for SA biosynthesis to promote parasitism.
Collapse
Affiliation(s)
- Xin Qin
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Bowen Xue
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Haiyang Tian
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Chenjie Fang
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Jiarong Yu
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Cong Chen
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Qing Xue
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - John Jones
- School of BiologyBiomedical Sciences Research ComplexUniversity of St AndrewsSt AndrewsUK
- Cell & Molecular Sciences DepartmentThe James Hutton InstituteDundeeUK
| | - Xuan Wang
- Key Laboratory of Integrated Management of Crop Disease and PestsMinistry of EducationNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| |
Collapse
|
5
|
Converting the E. coli Isochorismatase Nicotinamidase into γ-Lactamase. Microbiol Spectr 2022; 10:e0098521. [PMID: 35171012 PMCID: PMC8849098 DOI: 10.1128/spectrum.00985-21] [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] [Indexed: 11/20/2022] Open
Abstract
Nicotinamidase (Nic) (E.C.3.5.1.19) is a representative protein of the isochorismatase superfamily from Escherichia coli. Despite showing no (+) γ-lactamase activity, its active site constellations (ASCs) are very similar to those of two other known (+) γ-lactamases (Mhpg and RutB), indicating that it could be a latent (+) γ-lactamase. In this study, the primary sequences of the five representative proteins of the isochorismatase superfamily from E. coli were aligned, and a "lid"-like unit of a six-residue loop (112GENPLV117) was established. The Nic protein was converted to a (+) γ-lactamase by eliminating the loop. A conversion mechanism was proposed in which a more compact binding pocket is formed after lid deletion. In addition, the "shrunk" binding pocket stabilized the small substrate and the catalysis intermediate, which triggered catalysis. Moreover, we identified another latent (+) γ-lactamase in the E. coli isochorismatase superfamily and successfully converted it into an active (+) γ-lactamase. In summary, the isochorismatase superfamily is potentially a good candidate for obtaining novel (+) γ-lactamases. IMPORTANCE γ-Lactamases are important enzymatic catalysts in preparing optically pure γ-lactam enantiomers, which are high-value chiral intermediates. Different studies have presumed that the isochorismatase superfamily is a candidate to obtain novel (+) γ-lactamases. By engineering its substrate entrance tunnel, Nic, a representative protein of the isochorismatase superfamily, is converted to a (+) γ-lactamase. Tunnel engineering has proven effective in enhancing enzyme promiscuity. Therefore, the latent or active γ-lactamase activities of the isochorismatase superfamily members indicate their evolutionary path positions.
Collapse
|
6
|
Tassoulas LJ, Elias MH, Wackett LP. Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway. J Biol Chem 2020; 296:100055. [PMID: 33172891 PMCID: PMC7948467 DOI: 10.1074/jbc.ra120.015631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022] Open
Abstract
Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition (trtA) in bacterial genomes, clustered with biuH, which encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase (IHL) protein family, similarly to BiuH, and has a catalytic efficiency (kcat/KM) of 6 x 105 M−1s−1, a KM for triuret of 20 μM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared with the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity, and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1–2%), but is largely found in plant-associated, nodulating, and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism
Collapse
Affiliation(s)
- Lambros J Tassoulas
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA
| | - Mikael H Elias
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA
| | - Lawrence P Wackett
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA.
| |
Collapse
|
7
|
Bauters L, Kyndt T, De Meyer T, Morreel K, Boerjan W, Lefevere H, Gheysen G. Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae, increase host susceptibility by manipulating secondary metabolite content of rice. MOLECULAR PLANT PATHOLOGY 2020; 21:1634-1646. [PMID: 33084136 PMCID: PMC7694671 DOI: 10.1111/mpp.13003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 05/11/2023]
Abstract
Hirschmanniella oryzae is one of the most devastating nematodes on rice, leading to substantial yield losses. Effector proteins aid the nematode during the infection process by subduing plant defence responses. In this research we characterized two potential H. oryzae effector proteins, chorismate mutase (HoCM) and isochorismatase (HoICM), and investigated their enzymatic activity and their role in plant immunity. Both HoCM and HoICM proved to be enzymatically active in complementation tests in mutant Escherichia coli strains. Infection success by the migratory nematode H. oryzae was significantly higher in transgenic rice lines constitutively expressing HoCM or HoICM. Expression of HoCM, but not HoICM, increased rice susceptibility against the sedentary nematode Meloidogyne graminicola also. Transcriptome and metabolome analyses indicated reductions in secondary metabolites in the transgenic rice plants expressing the potential nematode effectors. The results presented here demonstrate that both HoCM and HoICM suppress the host immune system and that this may be accomplished by lowering secondary metabolite levels in the plant.
Collapse
Affiliation(s)
- Lander Bauters
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical ModellingFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Kris Morreel
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Department of Plant Biotechnology and BioinformaticsFaculty of SciencesGhent UniversityGhentBelgium
| | - Wout Boerjan
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Department of Plant Biotechnology and BioinformaticsFaculty of SciencesGhent UniversityGhentBelgium
| | - Hannes Lefevere
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Godelieve Gheysen
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| |
Collapse
|
8
|
Li H, Gao S, Qiu Y, Liang C, Zhu S, Zheng G. Genome mining integrating semi-rational protein engineering and nanoreactor design: roadmap for a robust biocatalyst for industrial resolution of Vince lactam. Appl Microbiol Biotechnol 2019; 104:1109-1123. [PMID: 31828408 DOI: 10.1007/s00253-019-10275-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 11/23/2019] [Indexed: 11/25/2022]
Abstract
Biomanufacturing of chemicals using biocatalysts is an attractive strategy for the production of valuable pharmaceuticals since it is usually more economical and has a much-reduced environmental impact. However, there are often challenges such as their thermal instability that should be overcome before a newly discovered enzyme is eventually translated into industrial processes. In this work, we describe a roadmap for the development of a robust catalyst for industrial resolution of Vince lactam, a key intermediate for the synthesis of carbocyclic-nucleoside-related pharmaceuticals. By a genome mining strategy, a new (+)-γ-lactamase (MiteL) from Microbacterium testaceum was successfully discovered and biochemically characterized. In vitro studies showed that the enzyme exhibited high activity but poor enantioselectivity (E = 6.3 ± 0.2) toward racemic Vince lactam, and thus, it is not suitable for industrial applications. Based on structural modeling and docking studies, a semi-rational engineering strategy combined with an efficient screening method was then applied to improve the enantioselectivity of MiteL. Several mutants with significant shifting stereoselectivity toward (-)-γ-lactam were obtained by site-saturation mutagenesis. Synergy effects led to the final mutant F14D/Q114R/M117L, which enabled efficient acquisition of (-)-γ-lactam with a high E value (> 200). The mutant was biochemically characterized, and the docking studies suggested a plausible mechanism for its improved selectivity. Finally, a sunflower-like nanoreactor was successfully constructed to improve the mutant's robustness via protein supramolecular self-assembly. Thus, the synergism between semi-rational protein engineering and self-assembling immobilization enabled construction of a nanoreactor with superior properties, which can be used for resolution of Vince lactam in large scale.
Collapse
Affiliation(s)
- Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shuaihua Gao
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yan Qiu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Chaoqun Liang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| |
Collapse
|
9
|
Robinson SL, Badalamenti JP, Dodge AG, Tassoulas LJ, Wackett LP. Microbial biodegradation of biuret: defining biuret hydrolases within the isochorismatase superfamily. Environ Microbiol 2018. [PMID: 29528550 DOI: 10.1111/1462-2920.14094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here, we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla. The BH enzymes reacted exclusively with biuret in the range of 2-11 µmol min-1 mg-1 protein. We then constructed a global protein superfamily network to map structure-function relationships in the BH subfamily and used this to mine > 7000 genomes. High-confidence BH sequences were detected in Actinobacteria, Alpha- and Beta-proteobacteria, and some fungi, archaea and green algae, but not animals or land plants. Unexpectedly, no cyanuric acid hydrolase homologs were detected in > 90% of genomes with BH homologs, suggesting BHs may have arisen independently of s-triazine ring metabolism. This work links genotype to phenotype by enabling accurate genome-mining to predict microbial utilization of biuret. Importantly, it advances understanding of the microbial capacity for biuret biodegradation in agricultural systems.
Collapse
Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Jonathan P Badalamenti
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Anthony G Dodge
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Lambros J Tassoulas
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Lawrence P Wackett
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| |
Collapse
|
10
|
Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
Collapse
|
11
|
Dong L, Liu Y. Comparative studies of the catalytic mechanisms of two chorismatases: CH-fkbo and CH-Hyg5. Proteins 2017; 85:1146-1158. [DOI: 10.1002/prot.25279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Lihua Dong
- School of Chemistry and Chemical Engineering; Shandong University; Jinan Shandong 250100 China
- School of Chemistry and Chemical Engineering; Qilu Normal University; Jinan Shandong 250013 China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering; Shandong University; Jinan Shandong 250100 China
| |
Collapse
|
12
|
Structural insights into the γ-lactamase activity and substrate enantioselectivity of an isochorismatase-like hydrolase from Microbacterium hydrocarbonoxydans. Sci Rep 2017; 7:44542. [PMID: 28295028 PMCID: PMC5353710 DOI: 10.1038/srep44542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/24/2017] [Indexed: 11/29/2022] Open
Abstract
(+)-γ-lactamase catalyzes the specific hydrolysis of (+)-γ-lactam out of the racemic γ-lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one) to leave optically pure (−)-γ-lactam, which is the key building block of antiviral drugs such as carbovir and abacavir. However, no structural data has been reported on how the enzymes bind the γ-lactams and achieve their enantioselectivities. We previously identified an isochorismatase-like hydrolase (IHL, Mh33H4-5540) with (+)-γ-lactamase activity, which constitutes a novel family of γ-lactamase. Here, we first discovered that this enzyme actually hydrolyzed both (+)- and (−)-γ-lactam, but with apparently different specificities. We determined the crystal structures of the apo-form, (+)-γ-lactam bound, and (−)-γ-lactam bound forms of the enzyme. The structures showed that the binding sites of both (+) and (−)-γ-lactam resemble those of IHLs, but the “cover” loop conserved in IHLs is lacking in the enzyme, probably resulting in its incomplete enantioselectivity. Structural, biochemical, and molecular dynamics simulation studies demonstrated that the steric clash caused by the binding-site residues, especially the side-chain of Cys111 would reduce the binding affinity of (−)-γ-lactam and possibly the catalytic efficiency, which might explain the different catalytic specificities of the enantiomers of γ-lactam. Our results would facilitate the directed evolution and application of Mh33H4-5540 in antiviral drug synthesis.
Collapse
|
13
|
Wang Y, Zhang K, Shi X, Wang C, Wang F, Fan J, Shen F, Xu J, Bao W, Liu M, Yu L. Critical role of bacterial isochorismatase in the autophagic process induced by Acinetobacter baumannii in mammalian cells. FASEB J 2016; 30:3563-3577. [PMID: 27432399 PMCID: PMC5024702 DOI: 10.1096/fj.201500019r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 07/05/2016] [Indexed: 12/21/2022]
Abstract
A recent study reported that Acinetobacter baumannii could induce
autophagy, but the recognition and clearance mechanism of intracytosolic A.
baumannii in the autophagic process and the molecular mechanism of
autophagy induced by the pathogen remains unknown. In this study, we first
demonstrated that invading A. baumannii induced a complete,
ubiquitin-mediated autophagic response that is dependent upon septins SEPT2 and SEPT9
in mammalian cells. We also demonstrated that autophagy induced by A.
baumannii was Beclin-1 dependent via the
AMPK/ERK/mammalian target of rapamycin pathway. Of interest, we found that the
isochorismatase mutant strain had significantly decreased siderophore-mediated ferric
iron acquisition ability and had a reduced the ability to induce autophagy. We
verified that isochorismatase was required for the recognition of intracytosolic
A. baumannii mediated by septin cages, ubiquitinated proteins,
and ubiquitin-binding adaptor proteins p62 and NDP52 in autophagic response. We also
confirmed that isochorismatase was required for the clearance of invading A.
baumannii by autophagy in vitro and in the mouse model
of infection. Together, these findings provide insight into the distinctive
recognition and clearance of intracytosolic A. baumannii by
autophagy in host cells, and that isochorismatase plays a critical role in the
A. baumannii–induced autophagic process.—Wang, Y.,
Zhang, K., Shi, X., Wang, C., Wang, F., Fan, J., Shen, F., Xu, J., Bao, W., Liu, M.,
Yu, L. Critical role of bacterial isochorismatase in the autophagic process induced
by Acinetobacter baumannii in mammalian cells.
Collapse
Affiliation(s)
- Yang Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Kaiyu Zhang
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Xiaochen Shi
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Chao Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Feng Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Junwen Fan
- Laboratory Animal Center, Academy of Military Medical Sciences, Beijing, China
| | - Fengge Shen
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Jiancheng Xu
- College of Veterinary Medicine and Animal Science, Jilin University, Changchun, China
| | - Wanguo Bao
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China
| | - Mingyuan Liu
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China; Department of Clinical Laboratory, First Hospital of Jilin University, Changchun, China; and
| | - Lu Yu
- Department of Infectious Diseases, First Hospital of Jilin University, Key Laboratory for Zoonosis Research, Institute of Zoonosis, Ministry of Medical Sciences, Changchun, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| |
Collapse
|
14
|
Gao S, Huang R, Zhu S, Li H, Zheng G. Identification and characterization of a novel (+)-γ-lactamase from Microbacterium hydrocarbonoxydans. Appl Microbiol Biotechnol 2016; 100:9543-9553. [DOI: 10.1007/s00253-016-7643-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 11/24/2022]
|
15
|
Wang J, Zhu J, Wu S. Immobilization on macroporous resin makes E. coli RutB a robust catalyst for production of (−) Vince lactam. Appl Microbiol Biotechnol 2014; 99:4691-700. [DOI: 10.1007/s00253-014-6247-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]
|
16
|
Characterization of a recombinant (+)-γ-lactamase from Microbacterium hydrocarbonoxydans which provides evidence that two enantiocomplementary γ-lactamases are in the strain. Appl Microbiol Biotechnol 2014; 99:3069-80. [DOI: 10.1007/s00253-014-6114-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 11/25/2022]
|
17
|
Liu T, Song T, Zhang X, Yuan H, Su L, Li W, Xu J, Liu S, Chen L, Chen T, Zhang M, Gu L, Zhang B, Dou D. Unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis. Nat Commun 2014; 5:4686. [PMID: 25156390 PMCID: PMC4348438 DOI: 10.1038/ncomms5686] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/14/2014] [Indexed: 11/23/2022] Open
Abstract
Plant diseases caused by fungi and oomycetes pose an increasing threat to food security and ecosystem health worldwide. These filamentous pathogens, while taxonomically distinct, modulate host defense responses by secreting effectors, which are typically identified based on the presence of signal peptides. Here we show that Phytophthora sojae and Verticillium dahliae secrete isochorismatases (PsIsc1 and VdIsc1, respectively) that are required for full pathogenesis. PsIsc1 and VdIsc1 can suppress salicylate-mediated innate immunity in planta and hydrolyse isochorismate in vitro. A conserved triad of catalytic residues is essential for both functions. Thus, the two proteins are isochorismatase effectors that disrupt the plant salicylate metabolism pathway by suppressing its precursor. Furthermore, these proteins lack signal peptides, but exhibit characteristics that lead to unconventional secretion. Therefore, this secretion pathway is a novel mechanism for delivering effectors and might play an important role in host–pathogen interactions. Salicylate is a regulator of innate immunity to infection in plants. Here, Liu et al. show that two plant pathogens secrete enzymes that disrupt salicylate biosynthesis and plant immunity, and reveal that these effectors are secreted via an unconventional mechanism.
Collapse
Affiliation(s)
- Tingli Liu
- 1] Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China [2] Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China [3]
| | - Tianqiao Song
- 1] Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China [2]
| | - Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Hongbo Yuan
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China
| | - Liming Su
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wanlin Li
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Jing Xu
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Shiheng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Linlin Chen
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| |
Collapse
|
18
|
Juneja P, Hubrich F, Diederichs K, Welte W, Andexer JN. Mechanistic Implications for the Chorismatase FkbO Based on the Crystal Structure. J Mol Biol 2014; 426:105-15. [DOI: 10.1016/j.jmb.2013.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
|