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Vavra O, Damborsky J, Bednar D. Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies. Biotechnol Adv 2022; 60:108009. [PMID: 35738509 DOI: 10.1016/j.biotechadv.2022.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
Acceleration of chemical reactions by the enzymes optimized using protein engineering represents one of the key pillars of the contribution of biotechnology towards sustainability. Tunnels and channels of enzymes with buried active sites enable the exchange of ligands, ions, and water molecules between the outer environment and active site pockets. The efficient exchange of ligands is a fundamental process of biocatalysis. Therefore, enzymes have evolved a wide range of mechanisms for repetitive conformational changes that enable periodic opening and closing. Protein-ligand interactions are traditionally studied by molecular docking, whereas molecular dynamics is the method of choice for studying conformational changes and ligand transport. However, computational demands make molecular dynamics impractical for screening purposes. Thus, several approximative methods have been recently developed to study interactions between a protein and ligand during the ligand transport process. Apart from identifying the best binding modes, these methods also provide information on the energetics of the transport and identify problematic regions limiting the ligand passage. These methods use approximations to simulate binding or unbinding events rapidly (calculation times from minutes to hours) and provide energy profiles that can be used to rank ligands or pathways. Here we provide a critical comparison of available methods, showcase their results on sample systems, discuss their practical applications in molecular biotechnologies and outline possible future developments.
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Affiliation(s)
- Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic; Enantis, INBIT, Kamenice 34, 625 00 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic.
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Gusyatiner MM. Do Thiol Amino Acids Inhibit Threonine Deaminase Activity in E. coli? (Letter to the Editor). Curr Microbiol 2022; 79:42. [PMID: 34982257 DOI: 10.1007/s00284-021-02738-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/01/2021] [Indexed: 11/03/2022]
Abstract
Cysteine and homocysteine suppress the growth of Escherichia coli. It was explained by the inhibition of threonine deaminase (TD) (Harris in J Bacteriol 145(2):1031-1035, 1981). TD inhibition was detected by a decline in its product, 2-ketobutyrate (2-KB). We propose that cysteine or homocysteine may not inhibit TD activity. Instead, 2-KB binds to them forming stable cyclic adducts. This binding possibly leads to isoleucine limitation and growth inhibition.
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Szajko K, Ciekot J, Wasilewicz-Flis I, Marczewski W, Sołtys-Kalina D. Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents. BMC Plant Biol 2021; 21:60. [PMID: 33482727 PMCID: PMC7825178 DOI: 10.1186/s12870-021-02825-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Glycoalkaloids are bioactive compounds that contribute to the defence response of plants against herbivore attack and during pathogenesis. Solanaceous plants, including cultivated and wild potato species, are sources of steroidal glycoalkaloids. Solanum plants differ in the content and composition of glycoalkaloids in organs. In wild and cultivated potato species, more than 50 steroidal glycoalkaloids were recognized. Steroidal glycoalkaloids are recognized as potential allelopathic/phytotoxic compounds that may modify the growth of target plants. There are limited data on the impact of the composition of glycoalkaloids on their phytotoxic potential. RESULTS The presence of α-solasonine and α-solamargine in potato leaf extracts corresponded to the high phytotoxic potential of the extracts. Among the differentially expressed genes between potato leaf bulks with high and low phytotoxic potential, the most upregulated transcripts in sample of high phytotoxic potential were anthocyanin 5-aromatic acyltransferase-like and subtilisin-like protease SBT1.7-transcript variant X2. The most downregulated genes were carbonic anhydrase chloroplastic-like and miraculin-like. An analysis of differentially expressed proteins revealed that the most abundant group of proteins were those related to stress and defence, including glucan endo-1,3-beta-glucosidase acidic isoform, whose expression level was 47.96× higher in potato leaf extract with low phytotoxic. CONCLUSIONS The phytotoxic potential of potato leaf extract possessing low glycoalkaloid content is determined by the specific composition of these compounds in leaf extract, where α-solasonine and α-solamargine may play significant roles. Differentially expressed gene and protein profiles did not correspond to the glycoalkaloid biosynthesis pathway in the expression of phytotoxic potential. We cannot exclude the possibility that the phytotoxic potential is influenced by other compounds that act antagonistically or may diminish the glycoalkaloids effect.
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Affiliation(s)
- Katarzyna Szajko
- Plant Breeding and Acclimatization Institute, Młochów Research Centre, Platanowa 19 st, 05-831, Młochów, Poland
| | - Jarosław Ciekot
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Laboratory of Biomedical Chemistry, Rudolfa Weigla 12 st, 53-114, Wrocław, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute, Młochów Research Centre, Platanowa 19 st, 05-831, Młochów, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute, Młochów Research Centre, Platanowa 19 st, 05-831, Młochów, Poland
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute, Młochów Research Centre, Platanowa 19 st, 05-831, Młochów, Poland.
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Marinho CM, Dos Santos PT, Kallipolitis BH, Johansson J, Ignatov D, Guerreiro DN, Piveteau P, O’Byrne CP. The σ B-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in Listeria monocytogenes through a direct interaction with the ilvA transcript. RNA Biol 2019; 16:1424-1437. [PMID: 31242083 PMCID: PMC6779388 DOI: 10.1080/15476286.2019.1632776] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 12/25/2022] Open
Abstract
The facultative intracellular pathogen Listeria monocytogenes can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σB) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σB regulon in facilitating this transition are understood the role of σB-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σB-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of in silico and in vivo approaches, a binding interaction was predicted with the Shine-Dalgarno region of the ilvA mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both ilvA transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the rli47 gene. The Δrli47 mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σB. The impact of the Δrli47 on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of L. monocytogenes in niches both outside and within the mammalian host.
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Affiliation(s)
- Catarina M. Marinho
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
| | - Patrícia T. Dos Santos
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Birgitte H. Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jörgen Johansson
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS), Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Dmitriy Ignatov
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS), Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Duarte N. Guerreiro
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Conor P. O’Byrne
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
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Du Y, Hong L, Tang W, Li L, Wang X, Ma H, Wang Z, Zhang H, Zheng X, Zhang Z. Threonine deaminase MoIlv1 is important for conidiogenesis and pathogenesis in the rice blast fungus Magnaporthe oryzae. Fungal Genet Biol 2014; 73:53-60. [PMID: 25307542 DOI: 10.1016/j.fgb.2014.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 09/28/2014] [Accepted: 10/01/2014] [Indexed: 01/01/2023]
Abstract
Threonine deaminase is the first critical enzyme in the biosynthesis of branched-chain amino acids (BCAAs), which catalyzes threonine into NH2 and ketobutyrate acid. Previously, we identified and characterized two acetolactate synthases MoIlv2 and MoIlv6 that are involved in the second step of BCAA biosynthesis. Deletion of MoILV2 and MoILV6 resulted in auxotrophy for leucine, isoleucine, and valine and defects in conidiation, appressorial penetration, and pathogenicity. Here, we identified a threonine dehydratase, named MoIlv1, from Magnaporthe oryzae. MoIlv1 is a homolog of Saccharomyces cerevisiae Ilv1p, which has an important role in the biosynthesis of isoleucine. To characterize the function of MoIlv1, a ΔMoilv1 knock-out mutant was generated and analyzed. Disruption of MoILV1 resulted in abnormal conidial morphology, reduced conidiation, limited appressorium-mediated penetration, and attenuated virulence on both barley and rice seedlings. Further analysis by domain-specific deletion revealed that the PALP domain is indispensable for MoIlv1 function. Our study indicates that MoIlv1 is a protein involved in isoleucine biosynthesis that underlies the complex process governing morphogenesis, appressorium formation, invasive hyphae growth, and pathogenicity.
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Affiliation(s)
- Yan Du
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Li Hong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Wei Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Lianwei Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Xiaoli Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Hongyu Ma
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Zhengyi Wang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China.
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
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Kang JH, Baldwin IT. Isolation and characterization of the threonine deaminase promoter in Nicotiana attenuata. Plant Sci 2006; 171:435-40. [PMID: 25193640 DOI: 10.1016/j.plantsci.2006.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 04/16/2006] [Accepted: 05/04/2006] [Indexed: 05/08/2023]
Abstract
The enzyme encoded by the threonine deaminase (TD) gene catalyzes the conversion of threonine to α-keto butyrate in the biosynthesis of isoleucine (Ile). In Nicotiana attenuata, TD transcripts accumulate constitutively in cotyledons and flowers and are elicited in leaves by wounding, herbivore attack, and methyl jasmonic acid (MeJA) treatment. To understand TD's unique pattern of expression, we isolated a genomic clone of the TD gene from N. attenuata and characterized its promoter. T2 transgenic plants, each harboring single copies of fusions of different parts of the 5' non-coding region to the β-glucuronidase reporter gene, demonstrated that the promoter was constitutively expressed in seedlings and flowers, and elicited in leaves by wounding or by MeJA treatment. Promoter deletion analysis defined the promoter regions capable of directing minimal expression in cotyledons and anthers as -142 to -31bp, and in stigmas as -289 to -231bp. Regions from -142 to -31bp were found to be important for basal elicitation in leaves by both wounding and MeJA treatment. These promoter elements may prove valuable in biotechnological applications.
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Affiliation(s)
- Jin-Ho Kang
- Department of Molecular Ecology, Max-Planck Institute of Chemical Ecology, Hans Knöll Str. 8, D-07745 Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max-Planck Institute of Chemical Ecology, Hans Knöll Str. 8, D-07745 Jena, Germany.
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