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Schulz S, Schall C, Stehle T, Breitmeyer C, Krysenko S, Mitulski A, Wohlleben W. Optimization of the precursor supply for an enhanced FK506 production in Streptomyces tsukubaensis. Front Bioeng Biotechnol 2022; 10:1067467. [DOI: 10.3389/fbioe.2022.1067467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
Tacrolimus (FK506) is a macrolide widely used as immunosuppressant to prevent transplant rejection. Synthetic production of FK506 is not efficient and costly, whereas the biosynthesis of FK506 is complex and the level produced by the wild type strain, Streptomyces tsukubaensis, is very low. We therefore engineered FK506 biosynthesis and the supply of the precursor L-lysine to generate strains with improved FK506 yield. To increase FK506 production, first the intracellular supply of the essential precursor lysine was improved in the native host S. tsukubaensis NRRL 18488 by engineering the lysine biosynthetic pathway. Therefore, a feedback deregulated aspartate kinase AskSt* of S. tsukubaensis was generated by site directed mutagenesis. Whereas overexpression of AskSt* resulted only in a 17% increase in FK506 yield, heterologous overexpression of a feedback deregulated AskCg* from Corynebacterium glutamicum was proven to be more efficient. Combined overexpression of AskCg* and DapASt, showed a strong enhancement of the intracellular lysine pool following increase in the yield by approximately 73% compared to the wild type. Lysine is coverted into the FK506 building block pipecolate by the lysine cyclodeaminase FkbL. Construction of a ∆fkbL mutant led to a complete abolishment of the FK506 production, confirming the indispensability of this enzyme for FK506 production. Chemical complementation of the ∆fkbL mutant by feeding pipecolic acid and genetic complementation with fkbL as well as with other lysine cyclodeaminase genes (pipAf, pipASt, originating from Actinoplanes friuliensis and Streptomyces pristinaespiralis, respectively) completely restored FK506 production. Subsequently, FK506 production was enchanced by heterologous overexpression of PipAf and PipASp in S. tsukubaensis. This resulted in a yield increase by 65% compared to the WT in the presence of PipAf from A. friuliensis. For further rational yield improvement, the crystal structure of PipAf from A. friuliensis was determined at 1.3 Å resolution with the cofactor NADH bound and at 1.4 Å with its substrate lysine. Based on the structure the Ile91 residue was replaced by Val91 in PipAf, which resulted in an overall increase of FK506 production by approx. 100% compared to the WT.
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Wang Y, Lu Y, Lu J, Yang ZN, Yang Z. Research Progress on the Biosynthesis and Bioproduction of the Biodegradable Chelating Agent (S,S)-EDDS. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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M VNUM, Faidh MA, Chadha A. The ornithine cyclodeaminase/µ-crystallin superfamily of proteins: A novel family of oxidoreductases for the biocatalytic synthesis of chiral amines. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Uma Mahesh VNM, Chadha A. Imine reduction by an Ornithine cyclodeaminase/μ-crystallin homolog purified from Candida parapsilosis ATCC 7330. ACTA ACUST UNITED AC 2021; 31:e00664. [PMID: 34557391 PMCID: PMC8446579 DOI: 10.1016/j.btre.2021.e00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 11/26/2022]
Abstract
Novel imine reductase from yeast Candida parapsilosis purified and characterized. CpIM1 belongs to unexplored Ornithine cyclodeaminase/Mu crystallin protein family CpIM1 catalyzed stereospecific alkylamination of α-ketoacids/ketoesters. CpIM1 also reduced cyclic and aryl imines. First report on enzymatic alkylamination of α-ketoesters and reduction of arylimines.
We report a stereospecific imine reductase from Candida parapsilosis ATCC 7330 (CpIM1), a versatile biocatalyst and a rich source of highly stereospecific oxidoreductases. The recombinant gene was overexpressed in Escherichia coli and the protein CpIM1 was purified to homogeneity. This protein belongs to the Ornithine cyclodeaminase/ μ-crystallin (OCD-Mu) family of proteins which has only a few characterized members. CpIM1 catalyzed the alkylamination of α-keto acids/esters producing exclusively (S)-N-alkyl amino acids/esters e.g. N-methyl-l-alanine with > 90% conversion and > 99% enantiomeric excess (ee). The enzyme showed the highest activity for the alkylamination of pyruvate and methylamine leading to N-methyl-l-alanine with an apparent KM of 15.04 ± 2.8 mM and Vmax of 13.75 ± 1.07 μmol/min/mg. CpIM1 also catalyzed (i) the reduction of imines e.g. 2-methyl-1-pyrroline to (S)-2-methylpyrrolidine with ∼30% conversion and 75% ee and (ii) the dehydrogenation of cyclic amino acids e.g. l-Proline (as monitered by reduction of cofactor NADP+ spectrophotometrically).
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Affiliation(s)
- V N M Uma Mahesh
- Laboratory of Bioorganic Chemistry, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Anju Chadha
- Laboratory of Bioorganic Chemistry, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India.,National Center for Catalysis Research, Indian Institute of Technology Madras, Chennai 600 036, India
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Hooykaas MJG, Hooykaas PJJ. The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid. Microbiologyopen 2021; 10:e1180. [PMID: 33970547 PMCID: PMC8087989 DOI: 10.1002/mbo3.1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.
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Ferrario E, Miggiano R, Rizzi M, Ferraris DM. Structure of Thermococcus litoralis Δ 1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:496-505. [PMID: 32355045 DOI: 10.1107/s2059798320004866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/05/2020] [Indexed: 11/10/2022]
Abstract
L-Hydroxyproline (L-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. L-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-L-proline (T3LHyp) and trans-4-hydroxy-L-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and L-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.
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Affiliation(s)
- Eugenio Ferrario
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Riccardo Miggiano
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
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Structure of Thermococcus litoralis trans-3-hydroxy-l-proline dehydratase in the free and substrate-complexed form. Biochem Biophys Res Commun 2019; 516:189-195. [DOI: 10.1016/j.bbrc.2019.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023]
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Watanabe Y, Watanabe S, Itoh Y, Watanabe Y. Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon. Biochem Biophys Res Commun 2019; 511:135-140. [PMID: 30773259 DOI: 10.1016/j.bbrc.2019.01.141] [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: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/30/2022]
Abstract
The hypothetical OCC_00372 protein from Thermococcus litoralis is a member of the ProR superfamily from hyperthermophilic archaea and exhibits unique bifunctional proline racemase/hydroxyproline 2-epimerase activity. However, the molecular mechanism of the broad substrate specificity and extreme thermostability of this enzyme (TlProR) remains unclear. Here we determined the crystal structure of TlProR at 2.7 Å resolution. Of note, a substrate proline molecule, derived from expression host Escherichia coli cells, was tightly bound in the active site of TlProR. The substrate bound structure and mutational analyses suggested that Trp241 is involved in hydroxyproline recognition by making a hydrogen bond between the indole group of Trp241 and the hydroxyl group of hydroxyproline. Additionally, Tyr171 may contribute to the thermostability by making hydrogen bonds between the hydroxyl group of Tyr171 and catalytic residues. Our structural and functional analyses provide a structural basis for understanding the molecular mechanism of substrate specificity and thermostability of ProR superfamily proteins.
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Affiliation(s)
- Yasunori Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Yoshika Itoh
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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Characterization of a Novel cis-3-Hydroxy-l-Proline Dehydratase and a trans-3-Hydroxy-l-Proline Dehydratase from Bacteria. J Bacteriol 2017; 199:JB.00255-17. [PMID: 28559297 DOI: 10.1128/jb.00255-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/21/2017] [Indexed: 11/20/2022] Open
Abstract
Hydroxyprolines, such as trans-4-hydroxy-l-proline (T4LHyp), trans-3-hydroxy-l-proline (T3LHyp), and cis-3-hydroxy-l-proline (C3LHyp), are present in some proteins including collagen, plant cell wall, and several peptide antibiotics. In bacteria, genes involved in the degradation of hydroxyproline are often clustered on the genome (l-Hyp gene cluster). We recently reported that an aconitase X (AcnX)-like hypI gene from an l-Hyp gene cluster functions as a monomeric C3LHyp dehydratase (AcnXType I). However, the physiological role of C3LHyp dehydratase remained unclear. We here demonstrate that Azospirillum brasilense NBRC 102289, an aerobic nitrogen-fixing bacterium, robustly grows using not only T4LHyp and T3LHyp but also C3LHyp as the sole carbon source. The small and large subunits of the hypI gene (hypIS and hypIL, respectively) from A. brasilense NBRC 102289 are located separately from the l-Hyp gene cluster and encode a C3LHyp dehydratase with a novel heterodimeric structure (AcnXType IIa). A strain disrupted in the hypIS gene did not grow on C3LHyp, suggesting its involvement in C3LHyp metabolism. Furthermore, C3LHyp induced transcription of not only the hypI genes but also the hypK gene encoding Δ1-pyrroline-2-carboxylate reductase, which is involved in T3LHyp, d-proline, and d-lysine metabolism. On the other hand, the l-Hyp gene cluster of some other bacteria contained not only the AcnXType IIa gene but also two putative proline racemase-like genes (hypA1 and hypA2). Despite having the same active sites (a pair of Cys/Cys) as hydroxyproline 2-epimerase, which is involved in the metabolism of T4LHyp, the dominant reaction by HypA2 was clearly the dehydration of T3LHyp, a novel type of T3LHyp dehydratase that differed from the known enzyme (Cys/Thr).IMPORTANCE More than 50 years after the discovery of trans-4-hydroxy-l-proline (generally called l-hydroxyproline) degradation in aerobic bacteria, its genetic and molecular information has only recently been elucidated. l-Hydroxyproline metabolic genes are often clustered on bacterial genomes. These loci frequently contain a hypothetical gene(s), whose novel enzyme functions are related to the metabolism of trans-3-hydroxyl-proline and/or cis-3-hydroxyl-proline, a relatively rare l-hydroxyproline in nature. Several l-hydroxyproline metabolic enzymes show no sequential similarities, suggesting their emergence by convergent evolution. Furthermore, transcriptional regulation by trans-4-hydroxy-l-proline, trans-3-hydroxy-l-proline, and/or cis-3-hydroxy-l-proline significantly differs between bacteria. The results of the present study show that several l-hydroxyprolines are available for bacteria as carbon and energy sources and may contribute to the discovery of potential metabolic pathways of another hydroxyproline(s).
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Reciprocal Control of Thyroid Binding and the Pipecolate Pathway in the Brain. Neurochem Res 2016; 42:217-243. [DOI: 10.1007/s11064-016-2015-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/15/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
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Watanabe S, Hiraoka Y, Endo S, Tanimoto Y, Tozawa Y, Watanabe Y. An enzymatic method to estimate the content of L-hydroxyproline. J Biotechnol 2015; 199:9-16. [DOI: 10.1016/j.jbiotec.2015.01.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/27/2015] [Accepted: 01/31/2015] [Indexed: 11/27/2022]
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Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution. PLoS One 2015; 10:e0120349. [PMID: 25786142 PMCID: PMC4364671 DOI: 10.1371/journal.pone.0120349] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
Proline racemase (ProR) is a member of the pyridoxal 5’-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.
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