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Li X, Cao Y, Liu C, Tan J, Zhou X. l-Proline and GelMA hydrogel complex:An efficient antifreeze system for cell cryopreservation. Cryobiology 2024; 116:104942. [PMID: 39032528 DOI: 10.1016/j.cryobiol.2024.104942] [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: 01/05/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Cryopreservation of biological samples is an important technology for expanding their applications in the biomedical field. However, the quality and functionality of samples after rewarming are limited by the toxicity of commonly used cryoprotectant agents (CPAs). Here, we developed a novel preservation system by combining the natural amino acid l-proline (L-Pro) with gelatin methacryloyl (GelMA) hydrogels. Compared with dimethyl sulfoxide (DMSO), L-Pro and GelMA demonstrated excellent biocompatibility when co-culturing with cells. Cryopreservation procedures were optimized using 3T3 as model cells. The results showed that rapid cooling was the most suitable cooling procedure for L-Pro and GelMA among the three cooling procedures. Co-culturing with cells for 3 h before cryopreservation, 6 % L-Pro +7 % GelMA had the highest survival rate, reaching up to 80 %. Differential Scanning Calorimetry (DSC) analysis showed that 6 % L-Pro + 7 % GelMA lowered the freezing point of the solution to -4.2 °C and increased the unfrozen water content to 20 %. To the best of our knowledge, this is the first report of cell cryopreservation using a combination of L-Pro and GelMA hydrogels, which provides a new strategy for improving cell cryopreservation.
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Affiliation(s)
- Xin Li
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China; Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, 200093, China; Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, 200093, China
| | - Yukun Cao
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China; Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, 200093, China; Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, 200093, China
| | - Chenxi Liu
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China; Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, 200093, China; Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, 200093, China
| | - Jia Tan
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China; Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, 200093, China; Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, 200093, China
| | - Xinli Zhou
- Institute of Biothermal Science & Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China; Shanghai Co-innovation Center for Energy Therapy of Tumors, Shanghai, 200093, China; Shanghai Technical Service Platform for Cryopreservation of Biological Resources, Shanghai, 200093, China.
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2
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Masand VH, Al-Hussain S, Alzahrani AY, Al-Mutairi AA, Sultan Alqahtani A, Samad A, Alafeefy AM, Jawarkar RD, Zaki MEA. Unveiling dynamics of nitrogen content and selected nitrogen heterocycles in thrombin inhibitors: a ceteris paribus approach. Expert Opin Drug Discov 2024; 19:991-1009. [PMID: 38898679 DOI: 10.1080/17460441.2024.2368743] [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: 01/26/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Despite the progress in comprehending molecular design principles and biochemical processes associated with thrombin inhibition, there is a crucial need to optimize efforts and curtail the recurrence of synthesis-testing cycles. Nitrogen and N-heterocycles are key features of many anti-thrombin drugs. Hence, a pragmatic analysis of nitrogen and N-heterocycles in thrombin inhibitors is important throughout the drug discovery pipeline. In the present work, the authors present an analysis with a specific focus on understanding the occurrence and distribution of nitrogen and selected N-heterocycles in the realm of thrombin inhibitors. RESEARCH DESIGN AND METHODS A dataset comprising 4359 thrombin inhibitors is used to scrutinize various categories of nitrogen atoms such as ring, non-ring, aromatic, and non-aromatic. In addition, selected aromatic and aliphatic N-heterocycles have been analyzed. RESULTS The analysis indicates that ~62% of thrombin inhibitors possess five or fewer nitrogen atoms. Substituted N-heterocycles have a high occurrence, like pyrrolidine (23.24%), pyridine (20.56%), piperidine (16.10%), thiazole (9.61%), imidazole (7.36%), etc. in thrombin inhibitors. CONCLUSIONS The majority of active thrombin inhibitors contain nitrogen atoms close to 5 and a combination of N-heterocycles like pyrrolidine, pyridine, piperidine, etc. This analysis provides crucial insights to optimize the transformation of lead compounds into potential anti-thrombin inhibitors.
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Affiliation(s)
- Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, India
| | - Sami Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail Asser, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Arwa Sultan Alqahtani
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Iraq
| | - Ahmed M Alafeefy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Universiti Teknologi MARA [UiTM], Bandar Puncak Alam, Selangor, Malaysia
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, Amravati, India
| | - Magdi E A Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
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3
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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4
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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5
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Guo H, Wang N, Ding T, Zheng B, Guo L, Huang C, Zhang W, Sun L, Ma X, Huo YX. A tRNAModification-based strategy for Identifying amiNo acid Overproducers (AMINO). Metab Eng 2023; 78:11-25. [PMID: 37149082 DOI: 10.1016/j.ymben.2023.04.012] [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: 01/17/2023] [Revised: 04/05/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and marker genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries of Escherichia coli and Corynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.
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Affiliation(s)
- Hao Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China; Beijing Institute of Technology (Tangshan) Translational Research Center, Tangshan Port Economic Development Zone, Tangshan, 063611, PR China
| | - Ning Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Tingting Ding
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Bo Zheng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Wuyuan Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Lichao Sun
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China; Beijing Institute of Technology (Tangshan) Translational Research Center, Tangshan Port Economic Development Zone, Tangshan, 063611, PR China.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, PR China; Beijing Institute of Technology (Tangshan) Translational Research Center, Tangshan Port Economic Development Zone, Tangshan, 063611, PR China.
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6
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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 PMCID: PMC10296201 DOI: 10.3390/biom13060981] [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: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G. Castro
- CEB—Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (T.G.C.); (A.C.-P.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Cristina E. A. Sousa
- BioMark Sensor Research—School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal;
| | - Artur Cavaco-Paulo
- CEB—Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (T.G.C.); (A.C.-P.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - João C. Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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7
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Mahmood MS, Afzal M, Batool H, Saif A, Aqdas T, Ashraf NM, Saleem M. Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach. Bioinform Biol Insights 2022; 16:11779322221115547. [PMID: 35966807 PMCID: PMC9373111 DOI: 10.1177/11779322221115547] [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: 03/14/2022] [Accepted: 06/11/2022] [Indexed: 11/15/2022] Open
Abstract
LHPP gene encodes a phospholysine phosphohistidine inorganic pyrophosphate phosphatase, which functions as a tumor-suppressor protein. The tumor suppression by this protein has been confirmed in various cancers, including hepatocellular carcinoma (HCC). LHPP downregulation promotes cell growth and proliferation by modulating the PI3K/AKT signaling pathway. This study identifies potentially deleterious missense single nucleotide variants (SNVs) associated with the LHPP gene using multiple computational tools based on different algorithms. A total of 4 destabilizing mutants are identified as L22P, I212T, G227R, and G236R, from the conserved region of the phosphatase. The 3-dimensional (3D) modeling and structural comparison of variants with the native protein reveals significant structural and conformational variations after mutations, suggesting disruption in the function of phospholysine phosphohistidine inorganic pyrophosphate phosphatase. The identified mutations might, therefore, participate in the cause of HCC.
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Affiliation(s)
- Malik Siddique Mahmood
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan.,Department of Biochemistry, NUR International University, Lahore, Pakistan
| | - Maryam Afzal
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hina Batool
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Amara Saif
- Department of Life Sciences, University of Management and Technology, Lahore, Pakistan
| | - Tahreem Aqdas
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry & Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
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8
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Sobel RA, Albertelli M, Hinojoza JR, Eaton MJ, Grimes KV, Rubenstein E. Azetidine-2-Carboxylic Acid-Induced Oligodendrogliopathy: Relevance to the Pathogenesis of Multiple Sclerosis. J Neuropathol Exp Neurol 2022; 81:414-433. [PMID: 35521963 PMCID: PMC9123080 DOI: 10.1093/jnen/nlac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The naturally occurring imino acid azetidine-2-carboxylic acid (Aze) is consumed by humans and can be misincorporated in place of proline in myelin basic protein (MBP) in vitro. To determine Aze effects on the mammalian CNS in vivo, adult CD1 mice were given Aze orally or intraperitoneally. Clinical signs reminiscent of MBP-mutant mice occurred with 600 mg/kg Aze exposure. Aze induced oligodendrocyte (OL) nucleomegaly and nucleoplasm clearing, dilated endoplasmic reticulum, cytoplasmic vacuolation, abnormal mitochondria, and Aze dose-dependent apoptosis. Immunohistochemistry demonstrated myelin blistering and nuclear translocation of unfolded protein response (UPR)/proinflammatory molecules (ATF3, ATF4, ATF6, eIF2α, GADD153, NFκB, PERK, XBP1), MHC I expression, and MBP cytoplasmic aggregation in OL. There were scattered microglial nodules in CNS white matter (WM); other CNS cells appeared unaffected. Mice given Aze in utero and postnatally showed more marked effects than their dams. These OL, myelin, and microglial alterations are found in normal-appearing WM (NAWM) in multiple sclerosis (MS) patients. Thus, Aze induces a distinct oligodendrogliopathy in mice that recapitulates MS NAWM pathology without leukocyte infiltration. Because myelin proteins are relatively stable throughout life, we hypothesize that Aze misincorporation in myelin proteins during myelinogenesis in humans results in a progressive UPR that may be a primary process in MS pathogenesis.
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Affiliation(s)
- Raymond A Sobel
- From the Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Megan Albertelli
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Julian R Hinojoza
- From the Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Mary Jane Eaton
- From the Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Kevin V Grimes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Edward Rubenstein
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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9
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Liu C, Wang Y, Wang A, Su F, Wang H. Structures, spectral and photodynamic properties of two nitrosylruthenium (II) isomer complexes containing 8-quinolinolate and L-proline ligands. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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10
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Chiral secondary amino acids, their importance, and methods of analysis. Amino Acids 2022; 54:687-719. [PMID: 35192062 DOI: 10.1007/s00726-022-03136-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
Abstract
Naturally occurring secondary amino acids, with proline as the main representative, contain an alpha-imino group in a cycle that is typically four-, five-, and six-membered. The unique ring structure exhibits exceptional properties-conformational rigidity, chemical stability, and specific roles in protein structure and folding. Many proline analogues have been used as valuable compounds for the study of metabolism of both prokaryotic and eukaryotic cells and for the synthesis of compounds with desired biological, pharmaceutical, or industrial properties. The D-forms of secondary amino acids play different roles in living organisms than the L-forms. They have different metabolic pathways, biological, physiological, and pharmacological effects, they can be indicators of changes and also serve as biomarkers of diseases. In the scientific literature, the number of articles examining D-amino acids in biological samples is increasing. The review summarises information on the occurrence and importance of D- and L-secondary amino acids-azetidic acid, proline, hydroxyprolines, pipecolic, nipecotic, hydroxypipecolic acids and related peptides containing these D-AAs, as well as the main analytical methods (mostly chromatographic) used for their enantiomeric determination in different matrices (biological samples, plants, food, water, and soil).
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11
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Kwiatkowski S, Bozko M, Zarod M, Witecka A, Kocdemir K, Jagielski AK, Drozak J. Recharacterization of the Mammalian Cytosolic Type 2 (R)-β-Hydroxybutyrate Dehydrogenase (BDH2) as 4-Oxo-L-Proline Reductase (EC 1.1.1.104). J Biol Chem 2022; 298:101708. [PMID: 35150746 PMCID: PMC8914325 DOI: 10.1016/j.jbc.2022.101708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Early studies revealed that chicken embryos incubated with a rare analog of l-proline, 4-oxo-l-proline, showed increased levels of the metabolite 4-hydroxy-l-proline. In 1962, 4-oxo-l-proline reductase, an enzyme responsible for the reduction of 4-oxo-l-proline, was partially purified from rabbit kidneys and characterized biochemically. However, only recently was the molecular identity of this enzyme solved. Here, we report the purification from rat kidneys, identification, and biochemical characterization of 4-oxo-l-proline reductase. Following mass spectrometry analysis of the purified protein preparation, the previously annotated mammalian cytosolic type 2 (R)-β-hydroxybutyrate dehydrogenase (BDH2) emerged as the only candidate for the reductase. We subsequently expressed rat and human BDH2 in Escherichia coli, then purified it, and showed that it catalyzed the reversible reduction of 4-oxo-l-proline to cis-4-hydroxy-l-proline via chromatographic and tandem mass spectrometry analysis. Specificity studies with an array of compounds carried out on both enzymes showed that 4-oxo-l-proline was the best substrate, and the human enzyme acted with 12,500-fold higher catalytic efficiency on 4-oxo-l-proline than on (R)-β-hydroxybutyrate. In addition, human embryonic kidney 293T (HEK293T) cells efficiently metabolized 4-oxo-l-proline to cis-4-hydroxy-l-proline, whereas HEK293T BDH2 KO cells were incapable of producing cis-4-hydroxy-l-proline. Both WT and KO HEK293T cells also produced trans-4-hydroxy-l-proline in the presence of 4-oxo-l-proline, suggesting that the latter compound might interfere with the trans-4-hydroxy-l-proline breakdown in human cells. We conclude that BDH2 is a mammalian 4-oxo-l-proline reductase that converts 4-oxo-l-proline to cis-4-hydroxy-l-proline and not to trans-4-hydroxy-l-proline, as originally thought. We also hypothesize that this enzyme may be a potential source of cis-4-hydroxy-l-proline in mammalian tissues.
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Affiliation(s)
- Sebastian Kwiatkowski
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Maria Bozko
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Michal Zarod
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Kubra Kocdemir
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Adam K Jagielski
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Warsaw, Poland.
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12
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Sheng Q, Wu XY, Xu X, Tan X, Li Z, Zhang B. Production of l-glutamate family amino acids in Corynebacterium glutamicum: Physiological mechanism, genetic modulation, and prospects. Synth Syst Biotechnol 2021; 6:302-325. [PMID: 34632124 PMCID: PMC8484045 DOI: 10.1016/j.synbio.2021.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/19/2022] Open
Abstract
l-glutamate family amino acids (GFAAs), consisting of l-glutamate, l-arginine, l-citrulline, l-ornithine, l-proline, l-hydroxyproline, γ-aminobutyric acid, and 5-aminolevulinic acid, are widely applied in the food, pharmaceutical, cosmetic, and animal feed industries, accounting for billions of dollars of market activity. These GFAAs have many functions, including being protein constituents, maintaining the urea cycle, and providing precursors for the biosynthesis of pharmaceuticals. Currently, the production of GFAAs mainly depends on microbial fermentation using Corynebacterium glutamicum (including its related subspecies Corynebacterium crenatum), which is substantially engineered through multistep metabolic engineering strategies. This review systematically summarizes recent advances in the metabolic pathways, regulatory mechanisms, and metabolic engineering strategies for GFAA accumulation in C. glutamicum and C. crenatum, which provides insights into the recent progress in l-glutamate-derived chemical production.
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Affiliation(s)
- Qi Sheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinyi Xu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Zhimin Li
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Corresponding author. Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
- Corresponding author. Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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13
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Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Heinilä LMP, Fewer DP, Jokela JK, Wahlsten M, Ouyang X, Permi P, Jortikka A, Sivonen K. The structure and biosynthesis of heinamides A1-A3 and B1-B5, antifungal members of the laxaphycin lipopeptide family. Org Biomol Chem 2021; 19:5577-5588. [PMID: 34085692 DOI: 10.1039/d1ob00772f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Laxaphycins are a family of cyclic lipopeptides with synergistic antifungal and antiproliferative activities. They are produced by multiple cyanobacterial genera and comprise two sets of structurally unrelated 11- and 12-residue macrocyclic lipopeptides. Here, we report the discovery of new antifungal laxaphycins from Nostoc sp. UHCC 0702, which we name heinamides, through antimicrobial bioactivity screening. We characterized the chemical structures of eight heinamide structural variants A1-A3 and B1-B5. These variants contain the rare non-proteinogenic amino acids 3-hydroxy-4-methylproline, 4-hydroxyproline, 3-hydroxy-d-leucine, dehydrobutyrine, 5-hydroxyl β-amino octanoic acid, and O-carbamoyl-homoserine. We obtained an 8.6-Mb complete genome sequence from Nostoc sp. UHCC 0702 and identified the 93 kb heinamide biosynthetic gene cluster. The structurally distinct heinamides A1-A3 and B1-B5 variants are synthesized using an unusual branching biosynthetic pathway. The heinamide biosynthetic pathway also encodes several enzymes that supply non-proteinogenic amino acids to the heinamide synthetase. Through heterologous expression, we showed that (2S,4R)-4-hydroxy-l-proline is supplied through the action of a novel enzyme LxaN, which hydroxylates l-proline. 11- and 12-residue heinamides have the characteristic synergistic activity of laxaphycins against Aspergillus flavus FBCC 2467. Structural and genetic information of heinamides may prove useful in future discovery of natural products and drug development.
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Affiliation(s)
| | - David Peter Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Jouni Kalevi Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Xiaodan Ouyang
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland and Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Anna Jortikka
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
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15
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Biratsi A, Athanasopoulos A, Kouvelis VN, Gournas C, Sophianopoulou V. A highly conserved mechanism for the detoxification and assimilation of the toxic phytoproduct L-azetidine-2-carboxylic acid in Aspergillus nidulans. Sci Rep 2021; 11:7391. [PMID: 33795709 PMCID: PMC8016842 DOI: 10.1038/s41598-021-86622-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Plants produce toxic secondary metabolites as defense mechanisms against phytopathogenic microorganisms and predators. L-azetidine-2-carboxylic acid (AZC), a toxic proline analogue produced by members of the Liliaceae and Agavaciae families, is part of such a mechanism. AZC causes a broad range of toxic, inflammatory and degenerative abnormalities in human and animal cells, while it is known that some microorganisms have evolved specialized strategies for AZC resistance. However, the mechanisms underlying these processes are poorly understood. Here, we identify a widespread mechanism for AZC resistance in fungi. We show that the filamentous ascomycete Aspergillus nidulans is able to not only resist AZC toxicity but also utilize it as a nitrogen source via GABA catabolism and the action of the AzhA hydrolase, a member of a large superfamily of detoxifying enzymes, the haloacid dehalogenase-like hydrolase (HAD) superfamily. This detoxification process is further assisted by the NgnA acetyltransferase, orthologue of Mpr1 of Saccharomyces cerevisiae. We additionally show that heterologous expression of AzhA protein can complement the AZC sensitivity of S. cerevisiae. Furthermore, a detailed phylogenetic analysis of AzhA homologues in Fungi, Archaea and Bacteria is provided. Overall, our results unravel a widespread mechanism for AZC resistance among microorganisms, including important human and plant pathogens.
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Affiliation(s)
- Ada Biratsi
- grid.6083.d0000 0004 0635 6999Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Alexandros Athanasopoulos
- grid.6083.d0000 0004 0635 6999Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research, Demokritos (NCSRD), Athens, Greece ,grid.6083.d0000 0004 0635 6999Light Microscopy Unit, Institute of Biosciences and Applications, National Centre for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Vassili N. Kouvelis
- grid.5216.00000 0001 2155 0800Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Gournas
- grid.6083.d0000 0004 0635 6999Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Vicky Sophianopoulou
- grid.6083.d0000 0004 0635 6999Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research, Demokritos (NCSRD), Athens, Greece
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16
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A chiral GC-MS method for analysis of secondary amino acids after heptafluorobutyl chloroformate & methylamine derivatization. Amino Acids 2021; 53:347-358. [PMID: 33586043 DOI: 10.1007/s00726-021-02949-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
L-amino acids (L-AAs) play different important roles in the physiology of all living organisms. Their chiral counterparts, D-amino acids (D-AAs) are increasingly being recognized as essential molecules in many biological systems. Secondary amino acids with cyclic structures, such as prolines, exhibit conformational rigidity and thus unique properties in the structural and protein folding. Despite their widespread occurrence, much less attention was paid to their chiral analysis, particularly when the minor, typically D-enantiomer, is present in low amounts in a complex biological matrix. In this paper, a cost-effective, chiral GC-MS method is described for capillary Chirasil-L-Val separation of nine cyclic secondary amino acid enantiomers with four-, five-, and six-membered rings, involving azetidine-2-carboxylic acid, pipecolic acid, nipecotic acid, proline, isomeric cis/trans 3-hydroxy, 4-hydroxyproline, and cis/trans-5-hydroxy-L-pipecolic acid in the excess of its enantiomeric antipode. The sample preparation involves in-situ derivatization with heptafluorobutyl chloroformate, simultaneous liquid-liquid micro-extraction into isooctane followed by amidation of the arising low-polar derivatives with methylamine, an evaporation step, re-dissolution, and final GC-MS analysis. The developed method was used for analyses of human biofluids, biologically active peptides containing chiral proline constituents, and collagen.
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17
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Morgante P, Guruge C, Ouedraogo YP, Nesnas N, Peverati R. Competition between cyclization and unusual Norrish type I and type II nitro-acyl migration pathways in the photouncaging of 1-acyl-7-nitroindoline revealed by computations. Sci Rep 2021; 11:1396. [PMID: 33446751 DOI: 10.26434/chemrxiv.11991651.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 05/21/2023] Open
Abstract
The 7-nitroindolinyl family of caging chromophores has received much attention in the past two decades. However, its uncaging mechanism is still not clearly understood. In this study, we performed state-of-the-art density functional theory calculations to unravel the photo-uncaging mechanism in its entirety, and we compared the probabilities of all plausible pathways. We found competition between a classical cyclization and an acyl migration pathway, and here we explain the electronic and steric reasons behind such competition. The migration mechanism possesses the characteristics of a combined Norrish type I and a 1,6-nitro-acyl variation of a Norrish type II mechanism, which is reported here for the first time. We also found negligible energetic differences in the uncaging mechanisms of the 4-methoxy-5,7-dinitroindolinyl (MDNI) cages and their mononitro analogues (MNI). We traced the experimentally observed improved quantum yields of MDNI to a higher population of the reactants in the triplet surface. This fact is supported by a more favorable intersystem crossing due to the availability of a higher number of triplet excited states with the correct symmetry in MDNI than in MNI. Our findings may pave the way for improved cage designs that possess higher quantum yields and a more efficient agonist release.
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Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL, 32901, USA
| | - Charitha Guruge
- Chemistry Program, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL, 32901, USA
| | - Yannick P Ouedraogo
- Chemistry Program, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL, 32901, USA
| | - Nasri Nesnas
- Chemistry Program, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL, 32901, USA.
| | - Roberto Peverati
- Chemistry Program, Florida Institute of Technology, 150 W. University Blvd, Melbourne, FL, 32901, USA.
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18
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Competition between cyclization and unusual Norrish type I and type II nitro-acyl migration pathways in the photouncaging of 1-acyl-7-nitroindoline revealed by computations. Sci Rep 2021; 11:1396. [PMID: 33446751 PMCID: PMC7809399 DOI: 10.1038/s41598-020-79701-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022] Open
Abstract
The 7-nitroindolinyl family of caging chromophores has received much attention in the past two decades. However, its uncaging mechanism is still not clearly understood. In this study, we performed state-of-the-art density functional theory calculations to unravel the photo-uncaging mechanism in its entirety, and we compared the probabilities of all plausible pathways. We found competition between a classical cyclization and an acyl migration pathway, and here we explain the electronic and steric reasons behind such competition. The migration mechanism possesses the characteristics of a combined Norrish type I and a 1,6-nitro-acyl variation of a Norrish type II mechanism, which is reported here for the first time. We also found negligible energetic differences in the uncaging mechanisms of the 4-methoxy-5,7-dinitroindolinyl (MDNI) cages and their mononitro analogues (MNI). We traced the experimentally observed improved quantum yields of MDNI to a higher population of the reactants in the triplet surface. This fact is supported by a more favorable intersystem crossing due to the availability of a higher number of triplet excited states with the correct symmetry in MDNI than in MNI. Our findings may pave the way for improved cage designs that possess higher quantum yields and a more efficient agonist release.
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19
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Chen X, Yi J, Liu J, Luo Q, Liu L. Enzymatic production of trans-4-hydroxy-l-proline by proline 4-hydroxylase. Microb Biotechnol 2020; 14:479-487. [PMID: 32618422 PMCID: PMC7936316 DOI: 10.1111/1751-7915.13616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/23/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Trans-4-hydroxy-l-proline (Hyp) is a useful chiral building block for production of many nutritional supplements and pharmaceuticals. However, it is still challenging for industrial production of Hyp due to heavy environmental pollution and low production efficiency. To establish a green and efficient process for Hyp production, the proline 4-hydroxylase (DsP4H) from Dactylosporangium sp. RH1 was overexpressed and functionally characterized in Escherichia coli BL21(DE3). The recombinant DsP4H with l-proline as a substrate exhibited Km , kcat and kcat /Km values up to 0.80 mM, 0.52 s-1 and 0.65 s-1 ·mM-1 respectively. Furthermore, DsP4H showed the highest activity at 35°C and pH 6.5 towards l-proline. The highest enzyme activity of 175.6 U mg-1 was achieved by optimizing culture parameters. Under the optimal transformation conditions in a 5-l fermenter, Hyp titre, conversion rate and productivity were up to 99.9 g l-1 , 99.9% and 2.77 g l-1 h-1 respectively. This strategy described here provides an efficient method for production of Hyp and thus has a great potential in industrial application.
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Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Juyang Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Shaoxing Baiyin Biotechnology Co. Ltd, Shaoxing, 312000, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
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20
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Mat Nanyan NSB, Takagi H. Proline Homeostasis in Saccharomyces cerevisiae: How Does the Stress-Responsive Transcription Factor Msn2 Play a Role? Front Genet 2020; 11:438. [PMID: 32411186 PMCID: PMC7198862 DOI: 10.3389/fgene.2020.00438] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Overexpression of MSN2, which is the transcription factor gene in response to stress, is well-known to increase the tolerance of the yeast Saccharomyces cerevisiae cells to a wide variety of environmental stresses. Recent studies have found that the Msn2 is a feasible potential mediator of proline homeostasis in yeast. This result is based on the finding that overexpression of the MSN2 gene exacerbates the cytotoxicity of yeast to various amino acid analogs whose uptake is increased by the active amino acid permeases localized on the plasma membrane as a result of a dysfunctional deubiquitination process. Increased understanding of the cellular responses induced by the Msn2-mediated proline incorporation will provide better comprehension of how cells respond to and counteract to different kinds of stimuli and will also contribute to the breeding of industrial yeast strains with increased productivity.
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Affiliation(s)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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21
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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22
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Guruge C, Rfaish SY, Byrd C, Yang S, Starrett AK, Guisbert E, Nesnas N. Caged Proline in Photoinitiated Organocatalysis. J Org Chem 2019; 84:5236-5244. [PMID: 30908906 DOI: 10.1021/acs.joc.9b00220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Organocatalysis is an emerging field, in which small metal-free organic structures catalyze a diversity of reactions with a remarkable stereoselectivity. The ability to selectively switch on such pathways upon demand has proven to be a valuable tool in biological systems. Light as a trigger provides the ultimate spatial and temporal control of activation. However, there have been limited examples of phototriggered catalytic systems. Herein, we describe the synthesis and application of a caged proline system that can initiate organocatalysis upon irradiation. The caged proline was generated using the highly efficient 4-carboxy-5,7-dinitroindolinyl (CDNI) photocleavable protecting group in a four-step synthesis. Advantages of this system include water solubility, biocompatibility, high quantum yield for catalyst release, and responsiveness to two-photon excitation. We showed the light-triggered catalysis of a crossed aldol reaction, a Mannich reaction, and a self-aldol condensation reaction. We also demonstrated light-initiated catalysis, leading to the formation of a biocide in situ, which resulted in the growth inhibition of E. coli, with as little as 3 min of irradiation. This technique can be broadly applied to other systems, by which the formation of active forms of drugs can be catalytically assembled remotely via two-photon irradiation.
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Affiliation(s)
- Charitha Guruge
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Saad Y Rfaish
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Chanel Byrd
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Shukun Yang
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Anthony K Starrett
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Nasri Nesnas
- Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
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23
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Yan F, Müller R. Class I Methyltransferase VioH Catalyzes Unusual S-Adenosyl-l-methionine Cyclization Leading to 4-Methylazetidinecarboxylic Acid Formation during Vioprolide Biosynthesis. ACS Chem Biol 2019; 14:99-105. [PMID: 30540188 DOI: 10.1021/acschembio.8b00958] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-Adenosyl-l-methionine (SAM)-dependent methyltransferases are intensely studied because they play important roles in the methylation of biomolecules in all domains of life. In this study, we describe that the methyltransferase VioH from Cysotobacter violaceus catalyzes a so far unknown cyclization of SAM to azetidine-2-carboxylic acid (AZE), which is proposed to be the precursor of the unusual 4-methylazetidinecarboxylic acid (MAZ) moiety of vioprolides. In vitro biochemical investigations reveal that SAM is converted to AZE in the presence of VioH while MAZ is generated by coexpression of VioH and the radical SAM enzyme VioG in Myxococcus xanthus or by combination of VioH and the cell lysate of M. xanthus expressing VioG. Thus, our findings unveil a novel function of SAM-dependent methyltransferases and shed light on the biosynthetic mechanism of MAZ formation.
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Affiliation(s)
- Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
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24
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Roest G, Hesemans E, Welkenhuyzen K, Luyten T, Engedal N, Bultynck G, Parys JB. The ER Stress Inducer l-Azetidine-2-Carboxylic Acid Elevates the Levels of Phospho-eIF2α and of LC3-II in a Ca 2+-Dependent Manner. Cells 2018; 7:E239. [PMID: 30513588 PMCID: PMC6316609 DOI: 10.3390/cells7120239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Accumulation of misfolded proteins in the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) to reduce protein load and restore homeostasis, including via induction of autophagy. We used the proline analogue l-azetidine-2-carboxylic acid (AZC) to induce ER stress, and assessed its effect on autophagy and Ca2+ homeostasis. Treatment with 5 mM AZC did not induce poly adenosine diphosphate ribose polymerase (PARP) cleavage while levels of binding immunoglobulin protein (BiP) and phosphorylated eukaryotic translation initiation factor 2α (eIF2α) increased and those of activating transcription factor 6 (ATF6) decreased, indicating activation of the protein kinase RNA-like ER kinase (PERK) and the ATF6 arms of the UPR but not of apoptosis. AZC treatment in combination with bafilomycin A1 (Baf A1) led to elevated levels of the lipidated form of the autophagy marker microtubule-associated protein light chain 3 (LC3), pointing to activation of autophagy. Using the specific PERK inhibitor AMG PERK 44, we could deduce that activation of the PERK branch is required for the AZC-induced lipidation of LC3. Moreover, both the levels of phospho-eIF2α and of lipidated LC3 were strongly reduced when cells were co-treated with the intracellular Ca2+ chelator 1,2-bis(O-aminophenoxy)ethane-N,N,N',N'-tetraaceticacid tetra(acetoxy-methyl) ester (BAPTA-AM) but not when co-treated with the Na⁺/K⁺ ATPase inhibitor ouabain, suggesting an essential role of Ca2+ in AZC-induced activation of the PERK arm of the UPR and LC3 lipidation. Finally, AZC did not trigger Ca2+ release from the ER though appeared to decrease the cytosolic Ca2+ rise induced by thapsigargin while also decreasing the time constant for Ca2+ clearance. The ER Ca2+ store content and mitochondrial Ca2+ uptake however remained unaffected.
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Affiliation(s)
- Gemma Roest
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Evelien Hesemans
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Kirsten Welkenhuyzen
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Tomas Luyten
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Nikolai Engedal
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership for Molecular Medicine, University of Oslo, P.O. Box 1137 Blindern, N-0318 Oslo, Norway.
| | - Geert Bultynck
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Jan B Parys
- Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine & Leuven Kanker Instituut, KU Leuven, Campus Gasthuisberg O/N-1 B-802, Herestraat 49, BE-3000 Leuven, Belgium.
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25
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Zhang Y, Zhang Y, Shang X, Wang B, Hu Q, Liu S, Wen T. Reconstruction of tricarboxylic acid cycle in Corynebacterium glutamicum with a genome-scale metabolic network model for trans-4-hydroxyproline production. Biotechnol Bioeng 2018; 116:99-109. [PMID: 30102770 DOI: 10.1002/bit.26818] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 07/25/2018] [Accepted: 08/08/2018] [Indexed: 11/09/2022]
Abstract
trans-4-Hydroxy- l-proline (Hyp) is an abundant component of mammalian collagen and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l-proline to Hyp; however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp. strain RH1. In silico model-based simulation showed that α-ketoglutarate was redirected from the TCA cycle toward Hyp synthetic pathway driven by P4H when the carbon flux from succinyl-CoA to succinate descended to zero. The interruption of the TCA cycle by the deletion of sucCD-encoding the succinyl-CoA synthetase (SUCOAS) led to a 60% increase in Hyp production and had no obvious impact on the growth rate. Fine-tuning of plasmid-borne ProB* and P4H abundances led to a significant increase in the yield of Hyp on glucose. The final engineered Hyp-7 strain produced up to 21.72 g/L Hyp with a yield of 0.27 mol/mol (Hyp/glucose) and a volumetric productivity of 0.36 g·L -1 ·hr -1 in the shake flask fermentation. To our knowledge, this is the highest yield and productivity achieved by microbial fermentation in a glucose-minimal medium for Hyp production. This strategy provides new insights into engineering C. glutamicum by flux coupling for the fermentative production of Hyp and related products.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qitiao Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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26
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Cho H, Shin JE, Lee S, Jeon H, Park S, Kim S. Asymmetric Cα-Alkylation of Proline via Chirality Transfers of Conformationally Restricted Proline Derivative: Application to the Total Synthesis of (-)-Amathaspiramide F. Org Lett 2018; 20:6121-6125. [PMID: 30234312 DOI: 10.1021/acs.orglett.8b02568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient strategy for the asymmetric synthesis of Cα-tetrasubstituted proline derivatives from proline has been established. A nitrogen-fused bicyclic system was devised to control the stereodynamics of proline. Through N-quaternizations with allylic electrophiles followed by [2,3]-rearrangements, the bicyclic proline system delivered enantioenriched Cα-tetrasubstituted prolines. This strategy was applied to the concise total synthesis of (-)-amathaspiramide F.
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Affiliation(s)
- Hyunkyung Cho
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
| | - Jae Eui Shin
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
| | - Seokwoo Lee
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
| | - Hongjun Jeon
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
| | - Soojun Park
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
| | - Sanghee Kim
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Korea
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27
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Zheng B, Ma X, Wang N, Ding T, Guo L, Zhang X, Yang Y, Li C, Huo YX. Utilization of rare codon-rich markers for screening amino acid overproducers. Nat Commun 2018; 9:3616. [PMID: 30190534 PMCID: PMC6127279 DOI: 10.1038/s41467-018-05830-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 07/27/2018] [Indexed: 11/24/2022] Open
Abstract
The translation of rare codons relies on their corresponding rare tRNAs, which could not be fully charged under amino acid starvation. Theoretically, disrupted or retarded translation caused by the lack of charged rare tRNAs can be partially restored by feeding or intracellular synthesis of the corresponding amino acids. Inspired by this assumption, we develop a screening or selection system for obtaining overproducers of a target amino acid by replacing its common codons with the corresponding synonymous rare alternative in the coding sequence of selected reporter proteins or antibiotic-resistant markers. Results show that integration of rare codons can inhibit gene translations in a frequency-dependent manner. As a proof-of-concept, Escherichia coli strains overproducing L-leucine, L-arginine or L-serine are successfully selected from random mutation libraries. The system is also applied to Corynebacterium glutamicum to screen out L-arginine overproducers. This strategy sheds new light on obtaining and understanding amino acid overproduction strains.
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Affiliation(s)
- Bo Zheng
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xiaoyan Ma
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Ning Wang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tingting Ding
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Liwei Guo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
- UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China
| | - Xiaorong Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, 100101, Beijing, China
| | - Yu Yang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Chun Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
- UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China.
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28
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Yang H, Male M, Li Y, Wang N, Zhao C, Jin S, Hu J, Chen Z, Ye Z, Xu H. Efficacy of Hydroxy-L-proline (HYP) analogs in the treatment of primary hyperoxaluria in Drosophila Melanogaster. BMC Nephrol 2018; 19:167. [PMID: 29980178 PMCID: PMC6035412 DOI: 10.1186/s12882-018-0980-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Background Substrate reduction therapy with analogs reduces the accumulation of substrates by inhibiting the metabolic pathways involved in their biosynthesis, providing new treatment options for patients with primary hyperoxalurias (PHs) that often progress to end-stage renal disease (ESRD). This research aims to evaluate the inhibition efficacy of Hydroxy-L-proline (HYP) analogs against calcium oxalate (CaOx) crystal formation in the Drosophila Melanogaster (D. Melanogaster) by comparing them with Pyridoxine (Vitamin B6). Methods Three stocks of Drosophila Melanogaster (W118, CG3926 RNAi, and Act5C-GAL4/CyO) were utilized. Two stocks (CG3926 RNAi and Act5C-GAL4 /CyO) were crossed to generate the Act5C > dAGXT RNAi recombinant line (F1 generation) of D. Melanogaster which was used to compare the efficacy of Hydroxy-L-proline (HYP) analogs inhibiting CaOx crystal formation with Vitamin B6 as the traditional therapy for primary hyperoxaluria. Results Nephrolithiasis model was successfully constructed by downregulating the function of the dAGXT gene in D. Melanogaster (P-Value = 0.0045). Furthermore, the efficacy of Hydroxy-L-proline (HYP) analogs against CaOx crystal formation was demonstrated in vivo using D. Melanogaster model; the results showed that these L-Proline analogs were better in inhibiting stone formation at very low concentrations than Vitamin B6 (IC50 = 0.6 and 1.8% for standard and dietary salt growth medium respectively) compared to N-acetyl-L-Hydroxyproline (IC50 = 0.1% for both standard and dietary salt growth medium) and Baclofen (IC50 = 0.06 and 0.1% for standard and dietary salt growth medium respectively). Analysis of variance (ANOVA) also showed that Hydroxy-L-proline (HYP) analogs were better alternatives for CaOx inhibition at very low concentration especially when both genetics and environmental factors are intertwined (p < 0.0008) for the dietary salt growth medium and (P < 0.063) for standard growth medium. Conclusion Addition of Hydroxy-L-Proline analogs to growth medium resulted in the reduction of CaOx crystals formation. These analogs show promise as potential inhibitors for oxalate reduction in Primary Hyperoxaluria.
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Affiliation(s)
- Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Musa Male
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- College of Life Sciences, Hubei University, Wuhan, China
| | - Ning Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenming Zhao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Jin
- College of Life Sciences, Hubei University, Wuhan, China
| | - Juncheng Hu
- College of Life Sciences, Hubei University, Wuhan, China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China. .,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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29
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Castro TG, Micaêlo NM, Melle-Franco M. Modeling the secondary structures of the peptaibols antiamoebin I and zervamicin II modified with D-amino acids and proline analogues. J Mol Model 2017; 23:313. [DOI: 10.1007/s00894-017-3479-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022]
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30
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Watanabe K, Fujii K. Isolation of high-level-CO 2 -preferring Picochlorum sp. strains and their biotechnological potential. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Yokoo T, Takata R, Yan J, Matsumoto F, Teraishi M, Okumoto Y, Jander G, Mori N. Identification of β-phenylalanine as a non-protein amino acid in cultivated rice, Oryza sativa. Commun Integr Biol 2016; 8:e1086045. [PMID: 27066169 PMCID: PMC4802750 DOI: 10.1080/19420889.2015.1086045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 10/31/2022] Open
Abstract
Non-protein amino acids, often analogs of the standard 20 protein amino acids, have been discovered in many plant species. Recent research with cultivated rice (Oryza sativa) identified (3R)-β-tyrosine, as well as a tyrosine amino mutase that synthesizes (3R)-β-tyrosine from the protein amino acid (2S)-α-tyrosine. Gas chromatography-mass spectrometry (GC-MS) assays and comparison to an authentic standard showed that β-phenylalanine is also a relatively abundant non-protein amino acid in rice leaves and that its biosynthesis occurs independently from that of β-tyrosine.
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Affiliation(s)
- Takayuki Yokoo
- Graduate School of Agriculture, Kyoto University ; Kyoto, Japan
| | - Ryo Takata
- Graduate School of Agriculture, Kyoto University ; Kyoto, Japan
| | - Jian Yan
- Boyce Thompson Institute for Plant Research; Ithaca, NY USA; Present address: South China Agricultural University; Guangzhou, China
| | - Fuka Matsumoto
- Graduate School of Agriculture, Kyoto University ; Kyoto, Japan
| | | | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University ; Kyoto, Japan
| | - Georg Jander
- Boyce Thompson Institute for Plant Research ; Ithaca, NY USA
| | - Naoki Mori
- Graduate School of Agriculture, Kyoto University ; Kyoto, Japan
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32
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Wei X, Liu D, An Q, Zhang W. Hydrogen-Bond Directed Regioselective Pd-Catalyzed Asymmetric Allylic Alkylation: The Construction of Chiral α-Amino Acids with Vicinal Tertiary and Quaternary Stereocenters. Org Lett 2015; 17:5768-71. [DOI: 10.1021/acs.orglett.5b02868] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xuan Wei
- School
of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Delong Liu
- School
of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Qianjin An
- School
of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wanbin Zhang
- School
of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
- School
of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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33
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Kubyshkin V, Kheylik Y, Mykhailiuk PK. Synthesis and studies on gem-fluorinated 2-azabicyclo[n.1.0]alkanes. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2015.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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34
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Roy J, Mitra S, Sengupta K, Mandal AK. Hsp70 clears misfolded kinases that partitioned into distinct quality-control compartments. Mol Biol Cell 2015; 26:1583-600. [PMID: 25739454 PMCID: PMC4436772 DOI: 10.1091/mbc.e14-08-1262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/26/2015] [Indexed: 01/13/2023] Open
Abstract
Hsp70 facilitates maturation of newly synthesized kinases and assists degradation of kinases under normal and stressed conditions. Hsp70 degrades misfolded kinases that partition into different quality-control compartments by promoting their ubiquitination, thus protecting cells from proteotoxic stress. Hsp70 aids in protein folding and directs misfolded proteins to the cellular degradation machinery. We describe discrete roles of Hsp70,SSA1 as an important quality-control machinery that switches functions to ameliorate the cellular environment. SSA1 facilitates folding/maturation of newly synthesized protein kinases by aiding their phosphorylation process and also stimulates ubiquitylation and degradation of kinases in regular protein turnover or during stress when kinases are denatured or improperly folded. Significantly, while kinases accumulate as insoluble inclusions upon SSA1 inhibition, they form soluble inclusions upon Hsp90 inhibition or stress foci during heat stress. This suggests formation of inclusion-specific quality-control compartments under various stress conditions. Up-regulation of SSA1 results in complete removal of these inclusions by the proteasome. Elevation of the cellular SSA1 level accelerates kinase turnover and protects cells from proteotoxic stress. Upon overexpression, SSA1 targets heat-denatured kinases toward degradation, which could enable them to recover their functional state under physiological conditions. Thus active participation of SSA1 in the degradation of misfolded proteins establishes an essential role of Hsp70 in deciding client fate during stress.
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Affiliation(s)
- Joydeep Roy
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Sahana Mitra
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Kaushik Sengupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
| | - Atin K Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
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35
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Lu H, Guan X, Wang J, Zhou J, Zhang H. Enhanced bio-decolorization of 1-amino-4-bromoanthraquinone-2-sulfonic acid by Sphingomonas xenophaga with nutrient amendment. J Environ Sci (China) 2015; 27:124-130. [PMID: 25597670 DOI: 10.1016/j.jes.2014.05.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/11/2014] [Accepted: 05/11/2014] [Indexed: 06/04/2023]
Abstract
Bacterial decolorization of anthraquinone dye intermediates is a slow process under aerobic conditions. To speed up the process, in the present study, effects of various nutrients on 1-amino-4-bromoanthraquinone-2-sulfonic acid (ABAS) decolorization by Sphingomonas xenophaga QYY were investigated. The results showed that peptone, yeast extract and casamino acid amendments promoted ABAS bio-decolorization. In particular, the addition of peptone and casamino acids could improve the decolorization activity of strain QYY. Further experiments showed that l-proline had a more significant accelerating effect on ABAS decolorization compared with other amino acids. l-Proline not only supported cell growth, but also significantly increased the decolorization activity of strain QYY. Membrane proteins of strain QYY exhibited ABAS decolorization activities in the presence of l-proline or reduced nicotinamide adenine dinucleotide, while this behavior was not observed in the presence of other amino acids. Moreover, the positive correlation between l-proline concentration and the decolorization activity of membrane proteins was observed, indicating that l-proline plays an important role in ABAS decolorization. The above findings provide us not only a novel insight into bacterial ABAS decolorization, but also an l-proline-supplemented bioaugmentation strategy for enhancing ABAS bio-decolorization.
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Affiliation(s)
- Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Xiaofan Guan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Haikun Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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36
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Houwaart S, Youssar L, Hüttel W. Pneumocandin biosynthesis: involvement of a trans-selective proline hydroxylase. Chembiochem 2014; 15:2365-9. [PMID: 25270390 DOI: 10.1002/cbic.201402175] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 11/09/2022]
Abstract
Echinocandins are cyclic nonribosomal hexapeptides based mostly on nonproteinogenic amino acids and displaying strong antifungal activity. Despite previous studies on their biosynthesis by fungi, the origin of three amino acids, trans-4- and trans-3-hydroxyproline, as well as trans-3-hydroxy-4-methylproline, is still unknown. Here we describe the identification, overexpression, and characterization of GloF, the first eukaryotic α-ketoglutarate/Fe(II) -dependent proline hydroxylase from the pneumocandin biosynthesis cluster of the fungus Glarea lozoyensis ATCC 74030. In in vitro transformations with L-proline, GloF generates trans-4- and trans-3-hydroxyproline simultaneously in a ratio of 8:1; the latter reaction was previously unknown for proline hydroxylase catalysis. trans-4-Methyl-L-proline is converted into the corresponding trans-3-hydroxyproline. All three hydroxyprolines required for the biosynthesis of the echinocandins pneumocandins A0 and B0 in G. lozoyensis are thus provided by GloF. Sequence analyses revealed that GloF is not related to bacterial proline hydroxylases, and none of the putative proteins with high sequence similarity in the databases has been characterized so far.
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Affiliation(s)
- Stefanie Houwaart
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg (Germany)
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37
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Johnston HJ, McWhinnie FS, Landi F, Hulme AN. Flexible, Phase-Transfer Catalyzed Approaches to 4-Substituted Prolines. Org Lett 2014; 16:4778-81. [PMID: 25191962 DOI: 10.1021/ol502239g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Heather J. Johnston
- EaStCHEM School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, U.K
| | - Fergus S. McWhinnie
- EaStCHEM School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, U.K
| | - Felicetta Landi
- EaStCHEM School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, U.K
| | - Alison N. Hulme
- EaStCHEM School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, U.K
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38
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Zajkoska P, Rosenberg M, Heath R, Malone KJ, Stloukal R, Turner NJ, Rebroš M. Immobilised whole-cell recombinant monoamine oxidase biocatalysis. Appl Microbiol Biotechnol 2014; 99:1229-36. [DOI: 10.1007/s00253-014-5983-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022]
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39
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Würdemann M, Christoffers J. Investigations on intramolecular 1,3-dipolar cycloadditions for the synthesis of isoxazolo-annulated pyrrolidines, piperidines and azepanes. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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40
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The γ-aminobutyrate permease GabP serves as the third proline transporter of Bacillus subtilis. J Bacteriol 2013; 196:515-26. [PMID: 24142252 DOI: 10.1128/jb.01128-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PutP and OpuE serve as proline transporters when this imino acid is used by Bacillus subtilis as a nutrient or as an osmostress protectant, respectively. The simultaneous inactivation of the PutP and OpuE systems still allows the utilization of proline as a nutrient. This growth phenotype pointed to the presence of a third proline transport system in B. subtilis. We took advantage of the sensitivity of a putP opuE double mutant to the toxic proline analog 3,4-dehydro-dl-proline (DHP) to identify this additional proline uptake system. DHP-resistant mutants were selected and found to be defective in the use of proline as a nutrient. Whole-genome resequencing of one of these strains provided the lead that the inactivation of the γ-aminobutyrate (GABA) transporter GabP was responsible for these phenotypes. DNA sequencing of the gabP gene in 14 additionally analyzed DHP-resistant strains confirmed this finding. Consistently, each of the DHP-resistant mutants was defective not only in the use of proline as a nutrient but also in the use of GABA as a nitrogen source. The same phenotype resulted from the targeted deletion of the gabP gene in a putP opuE mutant strain. Hence, the GabP carrier not only serves as an uptake system for GABA but also functions as the third proline transporter of B. subtilis. Uptake studies with radiolabeled GABA and proline confirmed this conclusion and provided information on the kinetic parameters of the GabP carrier for both of these substrates.
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