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Ledermann R, Bourdès A, Schuller M, Jorrin B, Ahel I, Poole PS. Aspartate aminotransferase of Rhizobium leguminosarum has extended substrate specificity and metabolizes aspartate to enable N 2 fixation in pea nodules. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073398 DOI: 10.1099/mic.0.001471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Rhizobium leguminosarum aspartate aminotransferase (AatA) mutants show drastically reduced symbiotic nitrogen fixation in legume nodules. Whilst AatA reversibly transaminates the two major amino-donor compounds aspartate and glutamate, the reason for the lack of N2 fixation in the mutant has remained unclear. During our investigations into the role of AatA, we found that it catalyses an additional transamination reaction between aspartate and pyruvate, forming alanine. This secondary reaction runs at around 60 % of the canonical aspartate transaminase reaction rate and connects alanine biosynthesis to glutamate via aspartate. This may explain the lack of any glutamate-pyruvate transaminase activity in R. leguminosarum, which is common in eukaryotic and many prokaryotic genomes. However, the aspartate-to-pyruvate transaminase reaction is not needed for N2 fixation in legume nodules. Consequently, we show that aspartate degradation is required for N2 fixation, rather than biosynthetic transamination to form an amino acid. Hence, the enzyme aspartase, which catalyses the breakdown of aspartate to fumarate and ammonia, suppressed an AatA mutant and restored N2 fixation in pea nodules.
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Affiliation(s)
| | - Alexandre Bourdès
- John Innes Centre, NR4 7UH, Norwich, UK
- School of Animal and Microbial Sciences, University of Reading, RG6 6AJ, Reading, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Beatriz Jorrin
- Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Philip Simon Poole
- Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
- John Innes Centre, NR4 7UH, Norwich, UK
- School of Animal and Microbial Sciences, University of Reading, RG6 6AJ, Reading, UK
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2
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Bisello G, Saris CG, Franchini R, Verbeek MM, Willemsen MA, Perduca M, Bertoldi M. An attenuated, adult case of AADC deficiency demonstrated by protein characterization. Mol Genet Metab Rep 2024; 39:101071. [PMID: 38524666 PMCID: PMC10958467 DOI: 10.1016/j.ymgmr.2024.101071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/10/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
A case of an adult with borderline AADC deficiency symptoms is presented here. Genetic analysis revealed that the patient carries two AADC variants (NM_000790.3: c.1040G > A and c.679G > C) in compound heterozygosis, resulting in p.Arg347Gln and p.Glu227Gln amino acid alterations. While p.Arg347Gln is a known pathogenic variant, p.Glu227Gln is unknown. Combining clinical features to bioinformatic and molecular characterization of the AADC protein population of the patient (p.Arg347Gln/p.Arg347Gln homodimer, p.Glu227Gln/p.Glu227Gln homodimer, and p.Glu227Gln/p.Arg347Gln heterodimer), we determined that: i) the p.Arg347Gln/p.Arg347Gln homodimer is inactive since the alteration affects a catalytically essential structural element at the active site, ii) the p.Glu227Gln/p.Glu227Gln homodimer is as active as the wild-type AADC since the alteration occurs at the surface and does not change the chemical nature of the amino acid, and iii) the p.Glu227Gln/p.Arg347Gln heterodimer has a catalytic efficiency 75% that of the wild-type since only one of the two active sites is compromised, thus demonstrating a positive complementation. By this approach, the molecular basis for the mild presentation of the disease is provided, and the experience made can also be useful for personalized therapeutic decisions in other mild AADC deficiency patients. Interestingly, in the last few years, many previously undiagnosed or misdiagnosed patients have been identified as mild cases of AADC deficiency, expanding the phenotype of this neurotransmitter disease.
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Affiliation(s)
- Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Christiaan G.J. Saris
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands
| | - Rossella Franchini
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Marcel M. Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands
- Translational Metabolic Laboratory, Department of Human Gentics, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands
| | - Michel A.A.P. Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands
| | - Massimiliano Perduca
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
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Murakami Y, Ikuta S, Fukuda W, Akasaka N, Maruyama JI, Shinma S, Fukusaki E, Fujiwara S. Identification and enzymatic properties of arginine decarboxylase from Aspergillus oryzae. Appl Environ Microbiol 2024; 90:e0029424. [PMID: 38624200 PMCID: PMC11107147 DOI: 10.1128/aem.00294-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
Aspergillus oryzae spores, when sprinkled onto steamed rice and allowed to propagate, are referred to as rice "koji." Agmatine, a natural polyamine derived from arginine through the action of arginine decarboxylase (ADC), is abundantly produced by solid state-cultivated rice koji of A. oryzae RIB40 under low pH conditions, despite the apparent absence of ADC orthologs in its genome. Mass spectrometry imaging revealed that agmatine was accumulated inside rice koji at low pH conditions, where arginine was distributed. ADC activity was predominantly observed in substrate mycelia and minimally in aerial mycelia. Natural ADC was isolated from solid state-cultivated A. oryzae rice koji containing substrate mycelia, using ammonium sulfate fractionation, ion exchange, and gel-filtration chromatography. The purified protein was subjected to sodium dodecyl sulfate poly-acrylamide gel electrophoresis (SDS-PAGE), and the detected peptide band was digested for identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The gene AO090102000327 of strain RIB40 was identified, previously annotated as phosphatidylserine decarboxylase (PSD), and encoded a 483-amino acid peptide. Recombinant protein encoded by AO090102000327 was expressed in Escherichia coli cells cultivated at 20°C, resulting in the detection of 49 kDa and 5 kDa peptides. The protein exhibited pyruvoyl-dependent decarboxylase activity, favoring arginine over ornithine and showing no activity with phosphatidylserine. The gene was designated Ao-adc1. Ao-ADC1 expression in rice koji at pH 4-6 was confirmed through western blotting using the anti-Ao-ADC1 serum. These findings indicate that Ao-adc1 encodes arginine decarboxylase involved in agmatine production.IMPORTANCEGene AO090102000327 in A. oryzae RIB40, previously annotated as a PSD, falls into a distinct clade when examining the phylogenetic distribution of PSDs. Contrary to the initial PSD annotation, our analysis indicates that the protein encoded by AO090102000327 is expressed in the substrate mycelia area of solid state-cultivated A. oryzae rice koji and functions as an arginine decarboxylase (ADC). The clade to which Ao-ADC1 belongs includes three other Ao-ADC1 paralogs (AO090103000445, AO090701000800, and AO090701000802) that presumably encode ADC rather than PSDs. Regarding PSD, AO090012000733 and AO090005001124 were speculated to be nonmitochondrial and mitochondrial PSDs in A. oryzae RIB40, respectively.
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Affiliation(s)
- Yui Murakami
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Soichiro Ikuta
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Naoki Akasaka
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
- Laboratory for Circular Bioeconomy Development, Office of Society-Academia Collaboration for Innovation, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shuichi Shinma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, Suita,, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, Suita,, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
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Bisello G, Rossignoli G, Choi S, Phillips RS, Bertoldi M. Active site serine-193 modulates activity of human aromatic amino acid decarboxylase. Biochem Biophys Res Commun 2023; 679:6-14. [PMID: 37651872 DOI: 10.1016/j.bbrc.2023.08.049] [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: 06/29/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Aromatic amino acid decarboxylase is a pyridoxal 5'-phosphate-dependent enzyme responsible for the synthesis of the neurotransmitters, dopamine and serotonin. Here, by a combination of bioinformatic predictions and analyses, phosphorylation assays, spectroscopic investigations and activity measurements, we determined that Ser-193, a conserved residue located at the active site, can be phosphorylated, increasing catalytic efficiency. In order to determine the molecular basis for this functional improvement, we determined the structural and kinetic properties of the site-directed variants S193A, S193D and S193E. While S193A retains 27% of the catalytic efficiency of wild-type, the two acidic side chain variants are impaired in catalysis with efficiencies of about 0.15% with respect to the wild-type. Thus, even if located at the active site, Ser-193 is not essential for enzyme activity. We advance the idea that this residue is fundamental for the correct architecture of the active site in terms of network of interactions triggering catalysis. This role has been compared with the properties of the Ser-194 of the highly homologous enzyme histidine decarboxylase whose catalytic loop is visible in the spatial structure, allowing us to propose the validation for the effect of the phosphorylation. The effect could be interesting for AADC deficiency, a rare monogenic disease, whose broad clinical phenotype could be also related to post translational AADC modifications.
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Affiliation(s)
- Giovanni Bisello
- Section of Biochemistry, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, 8, Verona, Italy
| | - Giada Rossignoli
- Section of Biochemistry, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, 8, Verona, Italy
| | - Sarah Choi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Mariarita Bertoldi
- Section of Biochemistry, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, 8, Verona, Italy.
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5
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Jevtovic V, Alhar MSO, Milenković D, Marković Z, Dimitrić Marković J, Dimić D. Synthesis, Structural Characterization, Cytotoxicity, and Protein/DNA Binding Properties of Pyridoxylidene-Aminoguanidine-Metal (Fe, Co, Zn, Cu) Complexes. Int J Mol Sci 2023; 24:14745. [PMID: 37834192 PMCID: PMC10573062 DOI: 10.3390/ijms241914745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Pyridoxylidene-aminoguanidine (PLAG) and its transition metal complexes are biologically active compounds with interesting properties. In this contribution, three new metal-PLAG complexes, Zn(PLAG)(SO4)(H2O)].∙H2O (Zn-PLAG), [Co(PLAG)2]SO4∙2H2O (Co-PLAG), and [Fe(PLAG)2]SO4∙2H2O) (Fe-PLAG), were synthetized and characterized by the X-ray crystallography. The intermolecular interactions governing the stability of crystal structure were compared to those of Cu(PLAG)(NCS)2 (Cu-PLAG) within Hirshfeld surface analysis. The structures were optimized at B3LYP/6-31+G(d,p)(H,C,N,O,S)/LanL2DZ (Fe,Co,Zn,Cu), and stability was assessed through Natural Bond Orbital Theory and Quantum Theory of Atoms in Molecules. Special emphasis was put on investigating the ligand's stability and reactivity. The binding of these compounds to Bovine and Human serum albumin was investigated by spectrofluorometric titration. The importance of complex geometry and various ligands for protein binding was shown. These results were complemented by the molecular docking study to elucidate the most important interactions. The thermodynamic parameters of the binding process were determined. The binding to DNA, as one of the main pathways in the cell death cycle, was analyzed by molecular docking. The cytotoxicity was determined towards HCT116, A375, MCF-7, and A2780 cell lines. The most active compound was Cu-PLAG due to the presence of PLAG and two thiocyanate ligands.
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Affiliation(s)
- Violeta Jevtovic
- Department of Chemistry, College of Science, University Ha’il, Ha’il 81451, Saudi Arabia
| | | | - Dejan Milenković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Zoran Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | | | - Dušan Dimić
- Faculty of Physical Chemistry, University of Belgrade, Studentski Trg 12–16, 11000 Belgrade, Serbia
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6
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Ueno K, Ushimaru R, Abe I. Photoinduced Reductive Dehalogenation of Phenacyl Bromides with Pyridoxal 5'-Phosphate. Chem Pharm Bull (Tokyo) 2023; 71:675-677. [PMID: 37394629 DOI: 10.1248/cpb.c23-00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We describe the photoinduced reductive debromination of phenacyl bromides using pyridoxal 5'-phosphate (PLP). The reaction requires irradiation with cyan or blue light in an anaerobic atmosphere. Mechanistic analysis reveals the formation of the phenacyl radical as an intermediate in the reaction, implying a single electron transfer to phenacyl bromides from a PLP-derived species resulting from excitation by illumination.
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Affiliation(s)
- Koki Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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Cronan JE. How an overlooked gene in coenzyme a synthesis solved an enzyme mechanism predicament. Mol Microbiol 2023; 119:687-694. [PMID: 37140060 PMCID: PMC10330860 DOI: 10.1111/mmi.15070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Coenzyme A (CoA) is an essential cofactor throughout biology. The first committed step in the CoA synthetic pathway is synthesis of β-alanine from aspartate. In Escherichia coli and Salmonella enterica panD encodes the responsible enzyme, aspartate-1-decarboxylase, as a proenzyme. To become active, the E. coli and S. enterica PanD proenzymes must undergo an autocatalytic cleavage to form the pyruvyl cofactor that catalyzes decarboxylation. A problem was that the autocatalytic cleavage was too slow to support growth. A long-neglected gene (now called panZ) was belatedly found to encode the protein that increases autocatalytic cleavage of the PanD proenzyme to a physiologically relevant rate. PanZ must bind CoA or acetyl-CoA to interact with the PanD proenzyme and accelerate cleavage. The CoA/acetyl-CoA dependence has led to proposals that the PanD-PanZ CoA/acetyl-CoA interaction regulates CoA synthesis. Unfortunately, regulation of β-alanine synthesis is very weak or absent. However, the PanD-PanZ interaction provides an explanation for the toxicity of the CoA anti-metabolite, N5-pentyl pantothenamide.
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Affiliation(s)
- John E. Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana 61801, USA
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Jang J, Chang JH. Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065139. [PMID: 36982214 PMCID: PMC10049462 DOI: 10.3390/ijms24065139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.
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Affiliation(s)
- Jiyeon Jang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5913; Fax: +82-53-950-6809
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Aithal A, Dagar S, Rajamani S. Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins. ACS OMEGA 2023; 8:5197-5208. [PMID: 36816708 PMCID: PMC9933472 DOI: 10.1021/acsomega.2c07635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 06/07/2023]
Abstract
Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.
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Affiliation(s)
- Anuraag Aithal
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Shikha Dagar
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
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Xie MJ, Cromie GA, Owens K, Timour MS, Tang M, Kutz JN, El-Hattab AW, McLaughlin RN, Dudley AM. Predicting the functional effect of compound heterozygous genotypes from large scale variant effect maps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523651. [PMID: 36711904 PMCID: PMC9882023 DOI: 10.1101/2023.01.11.523651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Pathogenic variants in PHGDH, PSAT1 , and PSPH cause a set of rare, autosomal recessive diseases known as serine biosynthesis defects. Serine biosynthesis defects present in a broad phenotypic spectrum that includes, at the severe end, Neu-Laxova syndrome, a lethal multiple congenital anomaly disease, intermediately in the form of infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end, as childhood disease with intellectual disability. However, because L-serine supplementation, especially if started early, can ameliorate and in some cases even prevent symptoms, knowledge of pathogenic variants is highly actionable. Methods Recently, our laboratory established a yeast-based assay for human PSAT1 function. We have now applied it at scale to assay the functional impact of 1,914 SNV-accessible amino acid substitutions. In addition to assaying the functional impact of individual variants in yeast haploid cells, we can assay pairwise combinations of PSAT1 alleles that recapitulate human genotypes, including compound heterozygotes, in yeast diploids. Results Results of our assays of individual variants (in haploid yeast cells) agree well with clinical interpretations and protein structure-function relationships, supporting the use of our data as functional evidence under the ACMG interpretation guidelines. Results from our diploid assay successfully distinguish patient genotypes from those of healthy carriers and agree well with disease severity. Finally, we present a linear model that uses individual allele measurements (in haploid yeast cells) to accurately predict the biallelic function (in diploid yeast cells) of ~ 1.8 million allele combinations corresponding to potential human genotypes. Conclusions Taken together, our work provides an example of how large-scale functional assays in model systems can be powerfully applied to the study of a rare disease.
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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12
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Ngo HPT, Nguyen DQ, Park H, Park YS, Kwak K, Kim T, Lee JH, Cho KS, Kang LW. Conformational change of organic cofactor PLP is essential for catalysis in PLP-dependent enzymes. BMB Rep 2022; 55:439-446. [PMID: 36104257 PMCID: PMC9537024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 03/08/2024] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are ubiquitous, catalyzing various biochemical reactions of approximately 4% of all classified enzymatic activities. They transform amines and amino acids into important metabolites or signaling molecules and are important drug targets in many diseases. In the crystal structures of PLP-dependent enzymes, organic cofactor PLP showed diverse conformations depending on the catalytic step. The conformational change of PLP is essential in the catalytic mechanism. In the study, we review the sophisticated catalytic mechanism of PLP, especially in transaldimination reactions. Most drugs targeting PLP-dependent enzymes make a covalent bond to PLP with the transaldimination reaction. A detailed understanding of organic cofactor PLP will help develop a new drug against PLP-dependent enzymes. [BMB Reports 2022; 55(9): 439-446].
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Affiliation(s)
- Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Kiwoong Kwak
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Taejoon Kim
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Jang Ho Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 05029, Korea
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13
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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14
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Perchat N, Dubois C, Mor-Gautier R, Duquesne S, Lechaplais C, Roche D, Fouteau S, Darii E, Perret A. Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes. J Biol Chem 2022; 298:102067. [PMID: 35623386 PMCID: PMC9213253 DOI: 10.1016/j.jbc.2022.102067] [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: 12/16/2021] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/28/2022] Open
Abstract
Bacteria adapt to utilize the nutrients available in their environment through a sophisticated metabolic system composed of highly specialized enzymes. Although these enzymes can metabolize molecules other than those for which they evolved, their efficiency toward promiscuous substrates is considered too low to be of physiological relevance. Herein, we investigated the possibility that these promiscuous enzymes are actually efficient enough at metabolizing secondary substrates to modify the phenotype of the cell. For example, in the bacterium Acinetobacter baylyi ADP1 (ADP1), panD (coding for l-aspartate decarboxylase) encodes the only protein known to catalyze the synthesis of β-alanine, an obligate intermediate in CoA synthesis. However, we show that the ADP1 ΔpanD mutant could also form this molecule through an unknown metabolic pathway arising from promiscuous enzymes and grow as efficiently as the wildtype strain. Using metabolomic analyses, we identified 1,3-diaminopropane and 3-aminopropanal as intermediates in this novel pathway. We also conducted activity screening and enzyme kinetics to elucidate candidate enzymes involved in this pathway, including 2,4-diaminobutyrate aminotransferase (Dat) and 2,4-diaminobutyrate decarboxylase (Ddc) and validated this pathway in vivo by analyzing the phenotype of mutant bacterial strains. Finally, we experimentally demonstrate that this novel metabolic route is not restricted to ADP1. We propose that the occurrence of conserved genes in hundreds of genomes across many phyla suggests that this previously undescribed pathway is widespread in prokaryotes.
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Affiliation(s)
- Nadia Perchat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christelle Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Rémi Mor-Gautier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Sophie Duquesne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
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15
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Zhang Y, Li D, Feng X, Wang X, Wang M, Han W, Manzoor MA, Li G, Chen T, Wang H, Cai Y. Whole-genome analysis of CGS, SAHH, SAMS gene families in five Rosaceae species and their expression analysis in Pyrus bretschneideri. PeerJ 2022; 10:e13086. [PMID: 35313526 PMCID: PMC8934043 DOI: 10.7717/peerj.13086] [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: 11/04/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
Cystathionine γ-synthase (CGS), S-adenosyl-L-homocysteine hydrolase (SAHH), and S-adenosy-L-methionine synthetase (SAMS) play an important role in the regulation of plant growth, development, and secondary metabolism. In this study, a total of 6 CGS, 6 SAHH, and 28 SAMS genes were identified from five Rosaceae species (Pyrus bretschneideri, Prunus persica, Prunus mume, Fragaria vesca, and Malus domestica). The evolutionary relationship and microsynteny analysis in five Rosaceae species revealed that duplicated regions were conserved between three gene families (CGS, SAHH, SAMS). Moreover, the chromosomal locations, gene structures, conserved motifs, cis-elements, physicochemical properties, and Ka/Ks analysis were performed by using numerous bioinformatics tools. The expression of different organs showed that the CGS, SAHH and SAMS genes of pear have relatively high expression patterns in flowers and stems, except for PbCGS1. RNA-seq and qRT-PCR combined analysis showed that PbSAMS1 may be involved in the regulation of pear stone cell development. In summary, this study provides the basic information of CGS, SAHH and SAMS genes in five Rosaceae species, further revealing the expression patterns in the pear fruit, which provides the theoretical basis for the regulation of pear stone cells.
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Affiliation(s)
- Yang Zhang
- Anhui Agricultural University, Hefei, China
| | - Decong Li
- Anhui Agricultural University, Hefei, China
| | | | - Xinya Wang
- Anhui Agricultural University, Hefei, China
| | | | | | | | | | | | - Han Wang
- Anhui Agricultural University, Hefei, China
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16
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Saxena VK, Vedamurthy G, Singh R. A novel concept of Pyridoxal 5'-phosphate permeability in E.coli for modulating the heterologous expression of PLP dependent proteins. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.12.016] [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: 10/19/2022]
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17
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Liu G, Cheng G, Zhang Y, Gao S, Sun H, Bai L, Li S, Zhu Y, Wang C, Li F. Pyridoxine regulates hair follicle development via the PI3K/Akt, Wnt and Notch signalling pathways in rex rabbits. ACTA ACUST UNITED AC 2021; 7:1162-1172. [PMID: 34754958 PMCID: PMC8556489 DOI: 10.1016/j.aninu.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 08/19/2021] [Accepted: 09/08/2021] [Indexed: 11/26/2022]
Abstract
This study was conducted to evaluate the effect of pyridoxine on the development of hair follicles in Rex rabbits and the underlying molecular mechanism. Two hundred 3-month-old Rex rabbits were randomly divided into 5 groups and fed diets supplemented with 0, 5, 10, 20, or 40 mg/kg pyridoxine. The hair follicle density on the dorsal skin and the gene and protein expression levels of components of the phosphoinositide 3-kinase (PI3K)/protein kinase B (PKB or Akt), Wnt, Notch and bone morphogenetic protein (BMP) signalling pathways were measured. In addition, free hair follicles were isolated from Rex rabbits and cultured with pyridoxine in vitro to measure hair shaft growth. Furthermore, dermal papilla cells (DPC) were isolated from the skin of Rex rabbits and cultured with pyridoxine in vitro to measure the gene and protein expression levels of components of the PI3K/Akt, Wnt, Notch and BMP signalling pathways. The results showed that the addition of dietary pyridoxine significantly increased the total follicle density, secondary follicle density, and secondary-to-primary ratio (S/P, P < 0.05), that the growth ratio of hair stems was promoted by pyridoxine in basic culture medium, and that the growth length of tentacle hair follicles cultured in the pyridoxine group was longer than that in the control group (P < 0.05). In addition, pyridoxine changed the DPC cycle progression and promoted cell proliferation, and appropriate concentrations of pyridoxine (10 and 20 μmol/L) significantly inhibited cell apoptosis (P < 0.05). Pyridoxine significantly affected the gene expression of components of the PI3K/Akt, Wnt and Notch signalling pathways in the skin and DPC of Rex rabbits (P < 0.05), increased the levels of phosphorylated catenin beta 1 (CTNNB1) and Akt, and decreased the level of phosphorylated glycogen synthase kinase 3 beta (GSK-3β) (P < 0.05). Therefore, the molecular mechanism by which pyridoxine promotes hair follicle density in Rex rabbits probably occurs through activation of the PI3K/Akt, Wnt and Notch signalling pathways, prolonging hair follicle growth and delaying the onset of telogen.
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Affiliation(s)
- Gongyan Liu
- College of Animal Science and Technology, Shandong Agricultural University; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Institute of Animal Husbandry and Veterinary, Shandong Academy of Agricultural Sciences; Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan 251000, China
| | - Guangmin Cheng
- Shandong Vocational Animal Science and Veterinary College, Weifang 261061, China
| | - Yongcui Zhang
- Shandong Vocational Animal Science and Veterinary College, Weifang 261061, China
| | - Shuxia Gao
- Institute of Animal Husbandry and Veterinary, Shandong Academy of Agricultural Sciences; Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan 251000, China
| | - Haitao Sun
- Institute of Animal Husbandry and Veterinary, Shandong Academy of Agricultural Sciences; Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan 251000, China
| | - Liya Bai
- Institute of Animal Husbandry and Veterinary, Shandong Academy of Agricultural Sciences; Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan 251000, China
| | - Shu Li
- College of Animal Science and Technology, Shandong Agricultural University; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China
| | - Yanli Zhu
- College of Animal Science and Technology, Shandong Agricultural University; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China
| | - Chunyang Wang
- College of Animal Science and Technology, Shandong Agricultural University; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China
| | - Fuchang Li
- College of Animal Science and Technology, Shandong Agricultural University; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China
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18
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A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases. Proc Natl Acad Sci U S A 2021; 118:2012591118. [PMID: 34580201 DOI: 10.1073/pnas.2012591118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 01/02/2023] Open
Abstract
The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.
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19
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He M, Ma J, Chen Q, Zhang Q, Yu P. Engineered production of pyridoxal 5'-phosphate in Escherichia coli BL21. Prep Biochem Biotechnol 2021; 52:498-507. [PMID: 34431758 DOI: 10.1080/10826068.2021.1966801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is the coenzyme of more than 140 enzymes and is widely used in various fields. In this study, to enhance the production of PLP in Escherichia coli BL21, the recombinant strain E. coli BL21/pETDuet-1-pdxj-zwf-dxs was constructed. The concentration of PLP in this strain was 82.69 mg/L, which was increased by 1.38-fold as compared to that in E. coli BL21. Glucose, yeast extract, and pH had an obvious impact on the concentration of PLP, and their optimal levels were 34.89 g/L, 31.17 g/L, and 10.07, respectively. The concentration of PLP under the optimal condition reached 2.23 g/L. The time-course analysis showed that the highest concentration of PLP was 2.32 g/L in recombinant strain after the induction for 12 h by 0.1 mM IPTG in a 1 L shake flask, which was increased by 38.76-fold as compared to that in E. coli BL21. This study provides a good basis for the efficient production of PLP in E. coli BL21.
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Affiliation(s)
- Min He
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Jian Ma
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Qingwei Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Qili Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
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20
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Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput Biol 2021; 17:e1007817. [PMID: 34161321 PMCID: PMC8259983 DOI: 10.1371/journal.pcbi.1007817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/06/2021] [Accepted: 05/31/2021] [Indexed: 11/21/2022] Open
Abstract
Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles. Escherichia coli is capable of growing in many environments, each of which requires a different collection of enzymes to metabolize the nutrients within that environment. Each individual enzyme requires its own set of amino acids and oftentimes cofactors, which are accessory molecules essential for the enzyme to function. Thus, the composition of the micronutrients (amino acids, cofactors, etc.) within a cell will differ depending on its metabolic needs. The presented work is the first effort to employ metabolic models to probe the connection between E. coli’s diverse growth environments and its biomass composition. We first show how differences in model-predicted enzyme use for aerobic or anaerobic growth results in distinct amino acid and cofactor usage. Alternatively, we show that the metabolic models can predict how modifying the cell’s biomass composition will affect growth. For example, by modeling the exposure of E. coli to trimethoprim or sulfamethoxazole—two antibiotics that target folate (vitamin B9) synthesis—we predicted how E. coli could adapt to grow under folate-limited conditions. This work demonstrates how models can be used to study antibiotic resistance of drugs that target amino acid or cofactor synthesis.
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Affiliation(s)
- Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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21
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Zhu W, Doubleday PF, Butrin A, Weerawarna PM, Melani R, Catlin DS, Dwight TA, Liu D, Kelleher NL, Silverman RB. Remarkable and Unexpected Mechanism for ( S)-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8193-8207. [PMID: 34014654 PMCID: PMC8369387 DOI: 10.1021/jacs.1c03572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that was recently found to play an important role in the metabolic reprogramming of hepatocellular carcinoma (HCC) via the proline and glutamine metabolic pathways. The selective inhibition of hOAT by compound 10 exhibited potent in vivo antitumor activity. Inspired by the discovery of the aminotransferase inactivator (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid (5), we rationally designed, synthesized, and evaluated a series of six-membered-ring analogs. Among them, 14 was identified as a new selective hOAT inactivator, which demonstrated a potency 22× greater than that of 10. Three different types of protein mass spectrometry approaches and two crystallographic approaches were employed to identify the structure of hOAT-14 and the formation of a remarkable final adduct (32') in the active site. These spectral studies reveal an enzyme complex heretofore not observed in a PLP-dependent enzyme, which has covalent bonds to two nearby residues. Crystal soaking experiments and molecular dynamics simulations were carried out to identify the structure of the active-site intermediate 27' and elucidate the order of the two covalent bonds that formed, leading to 32'. The initial covalent reaction of the activated warhead occurs with *Thr322 from the second subunit, followed by a subsequent nucleophilic attack by the catalytic residue Lys292. The turnover mechanism of 14 by hOAT was supported by a mass spectrometric analysis of metabolites and fluoride ion release experiments. This novel mechanism for hOAT with 14 will contribute to the further rational design of selective inactivators and an understanding of potential inactivation mechanisms by aminotransferases.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Pathum M. Weerawarna
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel S. Catlin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Timothy A. Dwight
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Neil L. Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois 60611, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
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22
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Evers MS, Roullier-Gall C, Morge C, Sparrow C, Gobert A, Alexandre H. Vitamins in wine: Which, what for, and how much? Compr Rev Food Sci Food Saf 2021; 20:2991-3035. [PMID: 33884746 DOI: 10.1111/1541-4337.12743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/11/2021] [Accepted: 03/01/2021] [Indexed: 12/01/2022]
Abstract
Vitamins are essential compounds to yeasts, and notably in winemaking contexts. Vitamins are involved in numerous yeast metabolic pathways, including those of amino acids, fatty acids, and alcohols, which suggests their notable implication in fermentation courses, as well as in the development of aromatic compounds in wines. Although they are major components in the course of those microbial processes, their significance and impact have not been extensively studied in the context of winemaking and wine products, as most of the studies focusing on the subject in the past decades have relied on relatively insensitive and imprecise analytical methods. Therefore, this review provides an extensive overview of the current knowledge regarding the impacts of vitamins on grape must fermentations, wine-related yeast metabolisms, and requirements, as well as on the profile of wine sensory characteristics. We also highlight the methodologies and techniques developed over time to perform vitamin analysis in wines, and assess the importance of precisely defining the role played by vitamins in winemaking processes, to ensure finer control of the fermentation courses and product characteristics in a highly complex matrix.
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Affiliation(s)
- Marie Sarah Evers
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France.,SAS Sofralab, Magenta, France
| | - Chloé Roullier-Gall
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
| | | | | | | | - Hervé Alexandre
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
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23
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Abstract
Vitamin B6 is an ensemble of six interconvertible vitamers: pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL), and their 5'-phosphate derivatives, PNP, PMP, and PLP. Pyridoxal 5'-phosphate is a coenzyme in a variety of enzyme reactions concerning transformations of amino and amino acid compounds. This review summarizes all known and putative PLP-binding proteins found in the Escherichia coli MG1655 proteome. PLP can have toxic effects since it contains a very reactive aldehyde group at its 4' position that easily forms aldimines with primary and secondary amines and reacts with thiols. Most PLP is bound either to the enzymes that use it as a cofactor or to PLP carrier proteins, protected from the cellular environment but at the same time readily transferable to PLP-dependent apoenzymes. E. coli and its relatives synthesize PLP through the seven-step deoxyxylulose-5-phosphate (DXP)-dependent pathway. Other bacteria synthesize PLP in a single step, through a so-called DXP-independent pathway. Although the DXP-dependent pathway was the first to be revealed, the discovery of the widespread DXP-independent pathway determined a decline of interest in E. coli vitamin B6 metabolism. In E. coli, as in most organisms, PLP can also be obtained from PL, PN, and PM, imported from the environment or recycled from protein turnover, via a salvage pathway. Our review deals with all aspects of vitamin B6 metabolism in E. coli, from transcriptional to posttranslational regulation. A critical interpretation of results is presented, in particular, concerning the most obscure aspects of PLP homeostasis and delivery to PLP-dependent enzymes.
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Singh RK, Kumar D, Gourinath S. Phosphoserine aminotransferase has conserved active site from microbes to higher eukaryotes with minor deviations. Protein Pept Lett 2021; 28:996-1008. [PMID: 33588715 DOI: 10.2174/0929866528666210215140231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
Serine is ubiquitously synthesized in all living organisms from the glycolysis intermediate 3-phosphoglycerate (PGA) by phosphoserine biosynthetic pathway, consisting of three different enzymes, namely: 3-phosphoglycerate dehydrogenase (PGDH), phosphoserine aminotransferase (PSAT), and phosphoserine phosphatase (PSP). Any functional defect or mutation in these enzymes may cause deliberating conditions, such as colon cancer progression and chemoresistance in humans. Phosphoserine aminotransferase (PSAT) is the second enzyme in this pathway that converts phosphohydroxypyruvate (PHP) to O-phospho-L-serine (OPLS). Humans encode two isoforms of this enzyme: PSAT1 and PSAT2. PSAT1 exists as a functional dimer, where each protomer has a large and a small domain; each large domain contains a Lys residue that covalently binds PLP. The PLP-binding site of human PSAT1 and most of its active site residues are highly conserved in all known PSAT structures except for Cys-80. Interestingly, Two PSAT structures from different organisms show halide binding near their active site. While the human PSAT1 shows a water molecule at this site with different interacting residues, suggesting the inability of halide binding in the human enzyme. Analysis of the human PSAT1 structure showed a big patch of positive charge around the active site, in contrast to the bacterial PSATs. Compared to human PSAT1, the PSAT2 isoform lacks 46 residues at its C-terminal tail. This tail region is present at the opening of the active site as observed in the other PSAT structures. Further structural work on human PSAT2 may reveal the functional importance of these 46 residues.
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Affiliation(s)
- Rohit Kumar Singh
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
| | - Devbrat Kumar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
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25
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Gonzalez-Rodriguez J, Sevilla J, Pineda T, Blazquez M, López-Guerrero M. A study on the electrooxidation of vitamin B6 compounds on glassy carbon and polycrystalline gold electrodes. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Yuan Z, Liao J, Jiang H, Cao P, Li Y. Aldehyde catalysis - from simple aldehydes to artificial enzymes. RSC Adv 2020; 10:35433-35448. [PMID: 35515689 PMCID: PMC9056934 DOI: 10.1039/d0ra06651f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/16/2020] [Indexed: 12/22/2022] Open
Abstract
Chemists have been learning and mimicking enzymatic catalysis in various aspects of organic synthesis. One of the major goals is to develop versatile catalysts that inherit the high catalytic efficiency of enzymatic processes, while being effective for a broad scope of substrates. In this field, the study of aldehyde catalysts has achieved significant progress. This review summarizes the application of aldehydes as sustainable and effective catalysts in different reactions. The fields, in which the aldehydes successfully mimic enzymatic systems, include light energy absorption/transfer, intramolecularity introduction through tether formation, metal binding for activation/orientation and substrate activation via aldimine formation. Enantioselective aldehyde catalysis has been achieved with the development of chiral aldehyde catalysts. Direct simplification of aldehyde-dependent enzymes has also been investigated for the synthesis of noncanonical chiral amino acids. Further development in aldehyde catalysis is expected, which might also promote exploration in fields related to prebiotic chemistry, early enzyme evolution, etc.
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Affiliation(s)
- Zeqin Yuan
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Jun Liao
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Hao Jiang
- Undisclosed Pharmaceutical Company Copenhagen Denmark
| | - Peng Cao
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Yang Li
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
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27
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Oxygen reactivity with pyridoxal 5'-phosphate enzymes: biochemical implications and functional relevance. Amino Acids 2020; 52:1089-1105. [PMID: 32844248 PMCID: PMC7497351 DOI: 10.1007/s00726-020-02885-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022]
Abstract
The versatility of reactions catalyzed by pyridoxal 5'-phosphate (PLP) enzymes is largely due to the chemistry of their extraordinary catalyst. PLP is necessary for many reactions involving amino acids. Reaction specificity is controlled by the orientation of the external aldimine intermediate that is formed upon addition of the amino acidic substrate to the coenzyme. The breakage of a specific bond of the external aldimine gives rise to a carbanionic intermediate. From this point, the different reaction pathways diverge leading to multiple activities: transamination, decarboxylation, racemization, elimination, and synthesis. A significant novelty appeared approximately 30 years ago when it was reported that some PLP-dependent decarboxylases are able to consume molecular oxygen transforming an amino acid into a carbonyl compound. These side paracatalytic reactions could be particularly relevant for human health, also considering that some of these enzymes are responsible for the synthesis of important neurotransmitters such as γ-aminobutyric acid, dopamine, and serotonin, whose dysregulation under oxidative conditions could have important implications in neurodegenerative states. However, the reactivity of PLP enzymes with dioxygen is not confined to mammals/animals. In fact, some plant PLP decarboxylases have been reported to catalyze oxidative reactions producing carbonyl compounds. Moreover, other recent reports revealed the existence of new oxidase activities catalyzed by new PLP enzymes, MppP, RohP, Ind4, CcbF, PvdN, Cap15, and CuaB. These PLP enzymes belong to the bacterial and fungal kingdoms and are present in organisms synthesizing bioactive compounds. These new PLP activities are not paracatalytic and could only scratch the surface on a wider and unexpected catalytic capability of PLP enzymes.
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28
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Abdelfattah F, Kariminejad A, Kahlert AK, Morrison PJ, Gumus E, Mathews KD, Darbro BW, Amor DJ, Walsh M, Sznajer Y, Weiß L, Weidensee S, Chitayat D, Shannon P, Bermejo-Sánchez E, Riaño-Galán I, Hayes I, Poke G, Rooryck C, Pennamen P, Khung-Savatovsky S, Toutain A, Vuillaume ML, Ghaderi-Sohi S, Kariminejad MH, Weinert S, Sticht H, Zenker M, Schanze D. Expanding the genotypic and phenotypic spectrum of severe serine biosynthesis disorders. Hum Mutat 2020; 41:1615-1628. [PMID: 32579715 DOI: 10.1002/humu.24067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu-Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre- or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease-causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.
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Affiliation(s)
- Fatima Abdelfattah
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | | | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Patrick J Morrison
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Evren Gumus
- Division of Medical Genetics, School of Medicine, Harran University, Sanliurfa, Turkey
| | | | | | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Maie Walsh
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Luisa Weiß
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - David Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for SickKids, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Eva Bermejo-Sánchez
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies (UIAC), Institute of Rare Diseases Research (IIER), Institute of Health Carlos III, Ministry of Science and Innovation, Madrid, Spain
| | - Isolina Riaño-Galán
- AGC de Pediatría, Hospital Universitario Central de Asturias, Oviedo, Spain.,IUOPA-Departamento de Medicina-ISPA, Universidad de Oviedo, Oviedo, Spain.,CIBER de Epidemiologia y Salud Pública, Madrid, Spain
| | - Ian Hayes
- Genetic Health Service New Zealand, Auckland Hospital, Auckland, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington Regional Hospital, Wellington, New Zealand
| | - Caroline Rooryck
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | - Perrine Pennamen
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | | | | | - Sönke Weinert
- Department of Cardiology and Angiology, Internal Medicine, University Hospital Magdeburg, Magdeburg, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
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29
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Cao J, Hyster TK. Pyridoxal-Catalyzed Racemization of α-Aminoketones Enables the Stereodivergent Synthesis of 1,2-Amino Alcohols Using Ketoreductases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01502] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jingzhe Cao
- Department of Chemistry, Princeton University, Frick Chemical
Laboratory, Princeton, New Jersey 08544, United States
| | - Todd K. Hyster
- Department of Chemistry, Princeton University, Frick Chemical
Laboratory, Princeton, New Jersey 08544, United States
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30
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Koivulehto M, Battchikova N, Korpela S, Khalikova E, Zavialov A, Korpela T. Comparison of kinetic and enzymatic properties of intracellular phosphoserine aminotransferases from alkaliphilic and neutralophilic bacteria. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIntracellular pyridoxal 5´-phosphate (PLP) -dependent recombinant phosphoserine aminotransferases (PSATs; EC 2.6.1.52) from two alkaliphilicBacillusstrains were overproduced inEscherichia coli, purified to homogeneity and their enzymological characteristics were compared to PSAT from neutralophilicE. coli. Some of the enzymatic characteristics of the PSATs from the alkaliphiles were unique, showing high and sharp pH optimal of the activity related to putative internal pH inside the microbes. The specific activities of all of the studied enzymes were similar (42-44 U/mg) as measured at the pH optima of the enzymes. The spectrophotometric acid-base titration of the PLP chromophore of the enzymes from the alkaliphiles showed that the pH optimum of the activity appeared at the pH wherein the active sites were half-protonated. Detachment of PLP from holoenzymes did not take place even at pH up to 11. The kinetics of the activity loss at acid and alkaline pHs were similar in all three enzymes and followed similar kinetics. The available 3-D structural data is discussed as well as the role of protons at the active site of aminotransferases.
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Affiliation(s)
- Marianne Koivulehto
- International Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Tykistökatu 6A, Turku, FIN-20520, Finland
| | - Natalia Battchikova
- International Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Tykistökatu 6A, Turku, FIN-20520, Finland
| | - Saara Korpela
- International Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Tykistökatu 6A, Turku, FIN-20520, Finland
| | - Elvira Khalikova
- International Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Tykistökatu 6A, Turku, FIN-20520, Finland
| | - Anton Zavialov
- International Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Tykistökatu 6A, Turku, FIN-20520, Finland
| | - Timo Korpela
- Department of Future Technologies, University of Turku, FI 20014, TurkuFinland
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31
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Hillier HT, Altermark B, Leiros I. The crystal structure of the tetrameric DABA-aminotransferase EctB, a rate-limiting enzyme in the ectoine biosynthesis pathway. FEBS J 2020; 287:4641-4658. [PMID: 32112674 DOI: 10.1111/febs.15265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023]
Abstract
l-2,4-diaminobutyric acid (DABA) aminotransferases can catalyze the formation of amines at the distal ω-position of substrates, and is the intial and rate-limiting enzyme in the biosynthesis pathway of the cytoprotecting molecule (S)-2-methyl-1,4,5,6-tetrahydro-4-pyrimidine carboxylic acid (ectoine). Although there is an industrial interest in the biosynthesis of ectoine, the DABA aminotransferases remain poorly characterized. Herein, we present the crystal structure of EctB (2.45 Å), a DABA aminotransferase from Chromohalobacter salexigens DSM 3043, a well-studied organism with respect to osmoadaptation by ectoine biosynthesis. We investigate the enzyme's oligomeric state to show that EctB from C. salexigens is a tetramer of two functional dimers, and suggest conserved recognition sites for dimerization that also includes the characteristic gating loop that helps shape the active site of the neighboring monomer. Although ω-transaminases are known to have two binding pockets to accommodate for their dual substrate specificity, we herein provide the first description of two binding pockets in the active site that may account for the catalytic character of DABA aminotransferases. Furthermore, our biochemical data reveal that the EctB enzyme from C. salexigens is a thermostable, halotolerant enzyme with a broad pH tolerance which may be linked to its tetrameric state. Put together, this study creates a solid foundation for a deeper structural understanding of DABA aminotransferases and opening up for future downstream studies of EctB's catalytic character and its redesign as a better catalyst for ectoine biosynthesis. In summary, we believe that the EctB enzyme from C. salexigens can serve as a benchmark enzyme for characterization of DABA aminotransferases. DATABASE: Structural data are available in PDB database under the accession number 6RL5.
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Affiliation(s)
- Heidi Therese Hillier
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
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32
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Pérez-Burgos M, García-Romero I, Valvano MA, Søgaard Andersen L. Identification of the Wzx flippase, Wzy polymerase and sugar-modifying enzymes for spore coat polysaccharide biosynthesis in Myxococcus xanthus. Mol Microbiol 2020; 113:1189-1208. [PMID: 32064693 DOI: 10.1111/mmi.14486] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/11/2020] [Indexed: 12/28/2022]
Abstract
The rod-shaped cells of Myxococcus xanthus, a Gram-negative deltaproteobacterium, differentiate to environmentally resistant spores upon starvation or chemical stress. The environmental resistance depends on a spore coat polysaccharide that is synthesised by the ExoA-I proteins, some of which are part of a Wzx/Wzy-dependent pathway for polysaccharide synthesis and export; however, key components of this pathway have remained unidentified. Here, we identify and characterise two additional loci encoding proteins with homology to enzymes involved in polysaccharide synthesis and export, as well as sugar modification and show that six of the proteins encoded by these loci are essential for the formation of environmentally resistant spores. Our data support that MXAN_3260, renamed ExoM and MXAN_3026, renamed ExoJ, are the Wzx flippase and Wzy polymerase, respectively, responsible for translocation and polymerisation of the repeat unit of the spore coat polysaccharide. Moreover, we provide evidence that three glycosyltransferases (MXAN_3027/ExoK, MXAN_3262/ExoO and MXAN_3263/ExoP) and a polysaccharide deacetylase (MXAN_3259/ExoL) are important for formation of the intact spore coat, while ExoE is the polyisoprenyl-phosphate hexose-1-phosphate transferase responsible for initiating repeat unit synthesis, likely by transferring N-acetylgalactosamine-1-P to undecaprenyl-phosphate. Together, our data generate a more complete model of the Exo pathway for spore coat polysaccharide biosynthesis and export.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Lotte Søgaard Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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33
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Kardon JR, Moroco JA, Engen JR, Baker TA. Mitochondrial ClpX activates an essential biosynthetic enzyme through partial unfolding. eLife 2020; 9:54387. [PMID: 32091391 PMCID: PMC7077987 DOI: 10.7554/elife.54387] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/19/2020] [Indexed: 01/28/2023] Open
Abstract
Mitochondria control the activity, quality, and lifetime of their proteins with an autonomous system of chaperones, but the signals that direct substrate-chaperone interactions and outcomes are poorly understood. We previously discovered that the mitochondrial AAA+ protein unfoldase ClpX (mtClpX) activates the initiating enzyme for heme biosynthesis, 5-aminolevulinic acid synthase (ALAS), by promoting cofactor incorporation. Here, we ask how mtClpX accomplishes this activation. Using S. cerevisiae proteins, we identified sequence and structural features within ALAS that position mtClpX and provide it with a grip for acting on ALAS. Observation of ALAS undergoing remodeling by mtClpX revealed that unfolding is limited to a region extending from the mtClpX-binding site to the active site. Unfolding along this path is required for mtClpX to gate cofactor binding to ALAS. This targeted unfolding contrasts with the global unfolding canonically executed by ClpX homologs and provides insight into how substrate-chaperone interactions direct the outcome of remodeling.
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Affiliation(s)
- Julia R Kardon
- Department of Biochemistry, Brandeis University, Waltham, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jamie A Moroco
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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34
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Li Z, Zhao Y, Zhou H, Luo HB, Zhan CG. Catalytic Roles of Coenzyme Pyridoxal-5'-phosphate (PLP) in PLP-dependent Enzymes: Reaction Pathway for Methionine-γ-lyase-catalyzed L-methionine Depletion. ACS Catal 2020; 10:2198-2210. [PMID: 33344000 DOI: 10.1021/acscatal.9b03907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), the active form of vitamin B6, is an important and versatile coenzyme involved in a variety of enzymatic reactions, accounting for about 4% of all classified activities. However, the detailed catalytic reaction pathways for PLP-dependent enzymes remain to be explored. Methionine-γ-lyase (MGL), a promising alternative anti-tumor agent to conventional chemotherapies whose catalytic mechanism is highly desired for guiding further development of re-engineered enzymes, was used as a representative PLP-dependent enzyme, and the catalytic mechanism for L-Met elimination by MGL was explored at the first-principles quantum mechanical/molecular mechanical (QM/MM) level with umbrella sampling. The QM/MM calculations revealed that the enzymatic reaction pathway consists of 4 stages for a total of 19 reaction steps with five intermediates captured in available crystal structures. Furthermore, the more comprehensive role of PLP was revealed. Besides the commonly known role of "electron sink", coenzyme PLP can also assist proton transfer and temporarily store the excess proton generated in some intermediate states by using its hydroxyl group and phosphate group. Thus, PLP is participated in most of the 19 steps. This study not only provided a theoretical basis for further development and re-engineering MGL as a potential anti-tumor agent, but also revealed the comprehensive role of PLP which could be used to explore the mechanisms of other PLP-dependent enzymes.
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Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Yunsong Zhao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Huifang Zhou
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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35
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Bezsudnova EY, Popov VO, Boyko KM. Structural insight into the substrate specificity of PLP fold type IV transaminases. Appl Microbiol Biotechnol 2020; 104:2343-2357. [PMID: 31989227 DOI: 10.1007/s00253-020-10369-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/04/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023]
Abstract
Pyridoxal-5'-phosphate-dependent transaminases of fold type IV (class IV) are promising enzymes for (R)-selective amination of organic compounds. Transaminases of fold type IV exhibit either strict (R)-selectivity or (S)-selectivity that is implemented within geometrically similar active sites of different amino acid compositions. Based on substrate specificity, class IV comprises three large families of transaminases: (S)-selective branched-chain L-amino acid aminotransferases and (R)-selective D-amino acid aminotransferases and (R)-amine:pyruvate transaminases. In this review, we aim to analyze the substrate profiles and correlations between the substrate specificity and organization of the active site in transaminases from these structurally related families. New transaminases with an expanded substrate specificity are also discussed. An analysis of the structural features of substrate binding and comparisons of structural determinants of chiral discrimination between members of the class IV transaminases could be helpful in identifying new biocatalytically relevant enzymes as well as rational protein engineering.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.,Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, Moscow, Russian Federation, 123182
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071
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36
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Johnstone DL, Al-Shekaili HH, Tarailo-Graovac M, Wolf NI, Ivy AS, Demarest S, Roussel Y, Ciapaite J, van Roermund CWT, Kernohan KD, Kosuta C, Ban K, Ito Y, McBride S, Al-Thihli K, Abdelrahim RA, Koul R, Al Futaisi A, Haaxma CA, Olson H, Sigurdardottir LY, Arnold GL, Gerkes EH, Boon M, Heiner-Fokkema MR, Noble S, Bosma M, Jans J, Koolen DA, Kamsteeg EJ, Drögemöller B, Ross CJ, Majewski J, Cho MT, Begtrup A, Wasserman WW, Bui T, Brimble E, Violante S, Houten SM, Wevers RA, van Faassen M, Kema IP, Lepage N, Lines MA, Dyment DA, Wanders RJA, Verhoeven-Duif N, Ekker M, Boycott KM, Friedman JM, Pena IA, van Karnebeek CDM. PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights. Brain 2020; 142:542-559. [PMID: 30668673 DOI: 10.1093/brain/awy346] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/30/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.
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Affiliation(s)
- Devon L Johnstone
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Hilal H Al-Shekaili
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Maja Tarailo-Graovac
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Institute of Physiology and Biochemistry, Faculty of Biology, The University of Belgrade, Belgrade, Serbia.,Departments of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam University Medical Centres, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Autumn S Ivy
- Division of Child Neurology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, CA, USA
| | - Scott Demarest
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Children's Hospital Colorado, CO, USA
| | - Yann Roussel
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jolita Ciapaite
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Carlo W T van Roermund
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Ceres Kosuta
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kevin Ban
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Skye McBride
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Khalid Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Rana A Abdelrahim
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Roshan Koul
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al Futaisi
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute of Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Heather Olson
- Department of Neurology, Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, MA, USA
| | - Laufey Yr Sigurdardottir
- Department of Neurology, University of Central Florida, Nemours Children's Hospital, Orlando, FL, USA
| | - Georgianne L Arnold
- Department of Pediatrics, University of Pittsburgh Medical Center, Pittsburg, PA, USA
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Boon
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandra Noble
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Marjolein Bosma
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Judith Jans
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Britt Drögemöller
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | | | - Wyeth W Wasserman
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tuan Bui
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron A Wevers
- United for Metabolic Diseases, The Netherlands.,Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nathalie Lepage
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Matthew A Lines
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Ronald J A Wanders
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Nanda Verhoeven-Duif
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Clara D M van Karnebeek
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,United for Metabolic Diseases, The Netherlands.,Departments of Pediatrics and Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,Centre for Molecular Medicine and Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, Canada
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d-Phenylglycine aminotransferase ( d-PhgAT) – substrate scope and structural insights of a stereo-inverting biocatalyst used in the preparation of aromatic amino acids. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01391a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the crystal structure and substrate scope of a versatile aminotransferase biocatalyst.
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38
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Thairu MW, Hansen AK. Changes in Aphid Host Plant Diet Influence the Small-RNA Expression Profiles of Its Obligate Nutritional Symbiont, Buchnera. mBio 2019; 10:e01733-19. [PMID: 31744912 PMCID: PMC6867890 DOI: 10.1128/mbio.01733-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/08/2019] [Indexed: 12/31/2022] Open
Abstract
Plants are a difficult food resource to use, and herbivorous insects have evolved a variety of mechanisms that allow them to fully exploit this poor nutritional resource. One such mechanism is the maintenance of bacterial symbionts that aid in host plant feeding and development. The majority of these intracellular symbionts have highly eroded genomes that lack many key regulatory genes; consequently, it is unclear if these symbionts can respond to changes in the insect's diet to facilitate host plant use. There is emerging evidence that symbionts with highly eroded genomes express small RNAs (sRNAs), some of which potentially regulate gene expression. In this study, we sought to determine if the reduced genome of the nutritional symbiont (Buchnera) in the pea aphid responds to changes in the aphid's host plant diet. Using transcriptome sequencing (RNA-seq), Buchnera sRNA expression profiles were characterized within two Buchnera life stages when pea aphids fed on either alfalfa or fava bean. Overall, this study demonstrates that Buchnera sRNA expression changes not only with life stage but also with changes in aphid host plant diet. Of the 321 sRNAs characterized in this study, 47% were previously identified and 22% showed evidence of conservation in two or more Buchnera taxa. Functionally, 13 differentially expressed sRNAs were predicted to target genes related to pathways involved in essential amino acid biosynthesis. Overall, results from this study reveal that host plant diet influences the expression of conserved and lineage-specific sRNAs in Buchnera and that these sRNAs display distinct host plant-specific expression profiles among biological replicates.IMPORTANCE In general, the genomes of intracellular bacterial symbionts are reduced compared to those of free-living relatives and lack many key regulatory genes. Many of these reduced genomes belong to obligate mutualists of insects that feed on a diet that is deficient in essential nutrients, such as essential amino acids. It is unclear if these symbionts respond with their host to changes in insect diet, because of their reduced regulatory capacity. Emerging evidence suggests that these symbionts express small RNAs (sRNAs) that regulate gene expression at the posttranscriptional level. Therefore, in this study, we sought to determine if the reduced genome of the nutritional symbiont Buchnera in the pea aphid responds to changes in the aphid's host plant diet. This study demonstrates for the first time that Buchnera sRNAs, some conserved in two or more Buchnera lineages, are differentially expressed when aphids feed on different plant species and potentially target genes within essential amino acid biosynthesis pathways.
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Affiliation(s)
- Margaret W Thairu
- Department of Entomology, University of California, Riverside, Riverside, California, USA
- Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin, USA
| | - Allison K Hansen
- Department of Entomology, University of California, Riverside, Riverside, California, USA
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39
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Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc Natl Acad Sci U S A 2019; 116:24164-24173. [PMID: 31712440 PMCID: PMC6883840 DOI: 10.1073/pnas.1915569116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The evolution of new metabolic pathways has been a driver of diversification from the last universal common ancestor 3.8 billion y ago to the present. Bioinformatic evidence suggests that many pathways were assembled by recruiting promiscuous enzymes to serve new functions. However, the processes by which new pathways have emerged are lost in time. We have little information about the environmental conditions that fostered emergence of new pathways, the genome context in which new pathways emerged, and the types of mutations that elevated flux through inefficient new pathways. Experimental laboratory evolution has allowed us to evolve a new pathway and identify mechanisms by which mutations increase fitness when an inefficient new pathway becomes important for survival. PdxB (erythronate 4-phosphate dehydrogenase) is expected to be required for synthesis of the essential cofactor pyridoxal 5′-phosphate (PLP) in Escherichia coli. Surprisingly, incubation of the ∆pdxB strain in medium containing glucose as a sole carbon source for 10 d resulted in visible turbidity, suggesting that PLP is being produced by some alternative pathway. Continued evolution of parallel lineages for 110 to 150 generations produced several strains that grow robustly in glucose. We identified a 4-step bypass pathway patched together from promiscuous enzymes that restores PLP synthesis in strain JK1. None of the mutations in JK1 occurs in a gene encoding an enzyme in the new pathway. Two mutations indirectly enhance the ability of SerA (3-phosphoglycerate dehydrogenase) to perform a new function in the bypass pathway. Another disrupts a gene encoding a PLP phosphatase, thus preserving PLP levels. These results demonstrate that a functional pathway can be patched together from promiscuous enzymes in the proteome, even without mutations in the genes encoding those enzymes.
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40
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Simon E, Andrews P. The use of hydrolytic enzymes and multi-stage tandem mass spectrometry to analyze pyridoxal phosphate-modified peptides. Anal Biochem 2019; 581:113341. [PMID: 31233711 DOI: 10.1016/j.ab.2019.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 04/25/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
Abstract
A previous approach was established that allowed direct identification of pyridoxal-5'-phosphate (PLP) bonding sites in proteins using mass spectrometry after tryptic proteolysis. The approach required peptide mass fingerprinting owing to suppressed amide backbone fragmentation in favor of side-chain elimination of diagnostic product ions from PLP-derivatized lysyl residues. While sufficient for purified proteins, unambiguous sequence determination is needed to assign PLP bonding sites in unknown proteins in complex mixtures. Here, we describe the use of hydrolytic enzymes and multi-stage tandem mass spectrometry to elucidate the amino acid sequence and PLP bonding site in PLP-modified peptides.
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Affiliation(s)
- Eric Simon
- University of Michigan, Department of Biological Chemistry, USA.
| | - Phil Andrews
- University of Michigan, Department of Biological Chemistry, Department of Chemistry, Department of Computational Medicine and Bioinformatics, USA
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41
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Keller S, Wetterhorn KM, Vecellio A, Seeger M, Rayment I, Schubert T. Structural and functional analysis of an l-serine O-phosphate decarboxylase involved in norcobamide biosynthesis. FEBS Lett 2019; 593:3040-3053. [PMID: 31325159 DOI: 10.1002/1873-3468.13543] [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: 05/22/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 11/11/2022]
Abstract
Structural diversity of natural cobamides (Cbas, B12 vitamers) is limited to the nucleotide loop. The loop is connected to the cobalt-containing corrin ring via an (R)-1-aminopropan-2-ol O-2-phosphate (AP-P) linker moiety. AP-P is produced by the l-threonine O-3-phosphate (l-Thr-P) decarboxylase CobD. Here, the CobD homolog SMUL_1544 of the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans was characterized as a decarboxylase that produces ethanolamine O-phosphate (EA-P) from l-serine O-phosphate (l-Ser-P). EA-P is assumed to serve as precursor of the linker moiety of norcobamides that function as cofactors in the respiratory reductive dehalogenase. SMUL_1544 (SmCobD) is a pyridoxal-5'-phosphate (PLP)-containing enzyme. The structural analysis of the SmCobD apoprotein combined with the characterization of truncated mutant proteins uncovered a role of the SmCobD N-terminus in efficient l-Ser-P conversion.
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Affiliation(s)
- Sebastian Keller
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Karl M Wetterhorn
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, WI, USA
| | - Alison Vecellio
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, WI, USA
| | - Mark Seeger
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, WI, USA
| | - Ivan Rayment
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, WI, USA
| | - Torsten Schubert
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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Abstract
There is a lot of controversy in the origin and early evolution of life field, but most people agree that at the advent of genetically coded protein synthesis, cells must have had access to ribonucleotides, amino acids, lipids and some sort of energy source. However, the provenance of these materials is a contentious issue — did early life obtain its building blocks prefabricated from the environment, or did it synthesise them from feedstocks such as CO2 and N2? In the first case, synthesis conditions need not have been compatible with life and any kind of reaction network that furnished the building blocks — and not much else — could have provisioned the subsequent origin and early evolution of life. In the second case, synthesis must have been under life-compatible conditions, with the reaction network either along the same lines as extant biology or along different ones. On the basis of experimental evidence, we will argue in favour of prefabrication and against synthesis by life in its nascent state, especially synthesis that resembles extant biosynthesis, which we suggest would have been well-nigh impossible without biological catalysts.
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Nogueira TCM, dos Santos Cruz L, Lourenço MC, de Souza MVN. Design, Synthesis and Anti-tuberculosis Activity of Hydrazones and N-acylhydrazones Containing Vitamin B6 and Different Heteroaromatic Nucleus. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180627122055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The term vitamin B6 refers to a set of six compounds, pyridoxine,pyridoxal
,and pyridoxamine and their phosphorylated forms, among which pyridoxal 5´-phosphate (PLP) is
the most important and active form acting as a critical cofactor. These compounds are very useful
in medicinal chemistry because of their structure and functionalities and are also used in bioinorganic
chemistry as ligands for complexation with metals.
Methods:
In this study, a series of hydrazones 1a-g and N-acylhydrazones 2a-f containing vitamin
B6 have been synthesized from commercial pyridoxal hydrochloride and the appropriate aromatic or
heteroaromatic hydrazine or N-acylhydrazine. All synthesized compounds have been fully characterized
and tested against Mycobacterium tuberculosis.
Results:
Among the N-acylhydrazones derivatives 2a-f, 2d (para- pyridine substituted Nacylhydrazone;
MIC = 10.90 µM) exhibited the best activity. The ortho-pyridine derivative 2b exhibited
intermediate activity (MIC = 87.32 µM), and the meta-pyridine derivative 2c was inactive.
In case of the hydrazone series 1a-g, 7-chloroquinoxaline derivative 1f (MIC = 72.72 µM) showed
the best result, indicating that the number of nitrogen and chlorine atoms in the radical moiety play an
important role in the anti-tuberculosis activity of the quinoxaline derivatives (1f and 1g).
Conclusion:
The data reported herein indicates that the isoniazid derivative 2d (MIC = 10.90 µM)
exhibited the best activity in the N-acylhydrazone series and; the quinoxaline nucleus derivative 1f
(MIC = 72.72 µM) was the most active compound in the hydrazone series.
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Affiliation(s)
- Thais Cristina Mendonça Nogueira
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
| | - Lucas dos Santos Cruz
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
| | - Maria Cristina Lourenço
- Fundacao Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Departamento de Bacteriologia, 21045-900, Manguinhos, Rio de Janeiro, Brazil
| | - Marcus Vinicius Nora de Souza
- Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos-Far-Manguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, Brazil
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44
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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45
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Lu JB, Zhang MQ, Li LC, Zhang CX. DDC plays vital roles in the wing spot formation, egg production, and chorion tanning in the brown planthopper. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 101:e21552. [PMID: 31033045 DOI: 10.1002/arch.21552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
The gene dopa decarboxylase (Nlddc) of the brown planthopper (BPH, Nilaparvata lugens) was identified in the genome and transcriptome of the insect. The open reading frame of Nlddc is 1,434 bp in length and, it has the potential to encode a protein of 477 amino acid with a conserved pyridoxal-dependent decarboxylase domain and a typical motif, NFNPHKW. Real-time quantification polymerase chain reaction analyses revealed that this gene was highly expressed in the integument and brain, and transcript level peaked in the late stages of egg period and each nymph instar with periodicity. RNA interference results revealed that Nlddc played essential roles in pigment synthesis, formation of wing spot, egg production, and tanning of the chorion. A rapid accumulation of Nlddc transcripts was detected, and it coincided with the injection of the hormone 20-hydroxyecdysone (20E), suggesting that Nlddc transcription was regulated by 20E.
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Affiliation(s)
- Jia-Bao Lu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Meng-Qiu Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Ling-Chen Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, Hangzhou, China
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46
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Dobrynin AB, Kibardina LK, Trifonov AV, Pudovik MA. Short contacts with P = S-bond in crystals of substituted phosphorus-containing furopyridines on basis of pyridoxal. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2018.1550492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- A. B. Dobrynin
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences, Kazan, Russia
| | - L. K. Kibardina
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences, Kazan, Russia
| | - A. V. Trifonov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences, Kazan, Russia
| | - M. A. Pudovik
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences, Kazan, Russia
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica. Int J Biol Macromol 2019; 132:1012-1023. [PMID: 30959130 DOI: 10.1016/j.ijbiomac.2019.04.027] [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: 01/30/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/24/2022]
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the second reversible step in the phosphoserine biosynthetic pathway producing serine. The crystal structure of E. histolytica PSAT (EhPSAT) complexed with PLP was elucidated at 3.0 Å resolution and the structures of its mutants, EhPSAT_Δ45 and EhPSAT_Δ4, at 1.8 and 2.4 Å resolution respectively. Deletion of 45 N-terminal residues (EhPSAT_Δ45) resulted in an inactive protein, the structure showed a dimeric arrangement drastically different from that of the wild-type protein, with the two monomers translated and rotated by almost 180° with respect to each other; causing a rearrangement of the active site to which PLP was unable to bind. Deletion of first N-terminal 15 (EhPSAT_Δ15) and four 11th to 14th residues (EhPSAT_Δ4) yielded up to 98% and 90% decrease in the activity respectively. Absence of aldimine linkage between PLP-Lys in the crystal structure of EhPSAT_Δ4 mutant explains for such decrease in activity and describes the importance of these N-terminal residues. Furthermore, a halide-binding site was found in close proximity to the active site. A stretch of six amino acids (146-NNTIYG-151) only conserved in the Entamoeba genus, contributes to halide binding may explain that the halide inhibition could be specific to Entamoeba.
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Han X, Sun R, Sandalova T, Achour A. Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae. Open Biol 2019; 8:rsob.170248. [PMID: 29669826 PMCID: PMC5936713 DOI: 10.1098/rsob.170248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/23/2018] [Indexed: 11/28/2022] Open
Abstract
Spr1654 from Streptococcus pneumoniae plays a key role in the production of unusual sugars, presumably functioning as a pyridoxal-5′-phosphate (PLP)-dependent aminotransferase. Spr1654 was predicted to catalyse the transferring of amino group to form the amino sugar 2-acetamido-4-amino-2, 4, 6-trideoxygalactose moiety (AATGal), representing a crucial step in biosynthesis of teichoic acids in S. pneumoniae. We have determined the crystal structures of the apo-, PLP- and PMP-bound forms of Spr1654. Spr1654 forms a homodimer, in which each monomer contains one active site. Using spectrophotometry and based on absorbance profiles of PLP- and PMP-formed enzymes, our results indicate that l-glutamate is most likely the preferred amino donor. Structural superposition of the crystal structures of Spr1654 on previously determined structures of other sugar aminotransferases in complex with glutamate and/or UDP-activated sugar allowed us to identify key Spr1654 residues for ligand binding and catalysis. The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae.
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Affiliation(s)
- Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden .,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
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Pudovik MA, Kibardina L, Trifonov A, Dobrynin A, Katsyuba S, Burilov A. Phosphorylation of pyridoxal azomethines. Synthesis of phosphorus containing azomethines and furopyridines. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2018.1513516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Michael A. Pudovik
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
| | - Lyudmila Kibardina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
| | - Alexey Trifonov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
- Kazan National Research Technological University. Karl Marx str. 68, Kazan, Russia
| | - Alexey Dobrynin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
| | - Sergei Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
| | - Alexander Burilov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences A.E. Arbuzov str. 8, Kazan, Russia
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