1
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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2
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Hauth F, Funck D, Hartig JS. A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins. Nucleic Acids Res 2023; 51:2001-2010. [PMID: 36626933 PMCID: PMC10018355 DOI: 10.1093/nar/gkac1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Error-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dietmar Funck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- To whom correspondence should be addressed. Tel: +49 7531 88 4575;
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3
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Vasilev NA, Voronin AP, Surov AO, Perlovich GL. Influence of Co-amorphization on the Physical Stability and Dissolution Performance of an Anthelmintic Drug Flubendazole. Mol Pharm 2023; 20:1657-1669. [PMID: 36732935 DOI: 10.1021/acs.molpharmaceut.2c00873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this work, the co-amorphization approach was applied to flubendazole (FluBZ), resulting in the formation of two novel solid forms of FluBZ with l-phenylalanine (Phe) and l-tryptophan (Trp). A variety of physicochemical techniques have been used to describe new systems, including powder X-ray diffraction, thermal methods, infrared spectroscopy, and scanning electron microscopy. Co-amorphization has been shown to suppress crystallization tendency and considerably increase the shelf-life storage of amorphous flubendazole solid across a wide range of relative humidities. The dissolution behavior of the amorphous forms in biorelevant media at pH = 1.6, pH = 6.5, and 37 °C has been studied in terms of Cmax (maximum FluBZ concentration), Tmax (time to attain peak drug concentration), and AUC (concentration area under the curve during dissolution). At pH = 6.5, a continuous supersaturation and the highest AUC value of all examined systems were observed for the FluBZ-Phe (1:1) system. The phase solubility diagrams revealed that the reason for the better dissolution performance of FluBZ-Phe (1:1) at pH = 6.5 is a complexation between the components in a solution. This work highlights the applicability of co-amorphous systems in improving the physical stability and dissolution performance of drug compounds with poor biopharmaceutical characteristics.
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Affiliation(s)
- Nikita A Vasilev
- G.A. Krestov Institute of Solution Chemistry RAS, 153045Ivanovo, Russia
| | | | - Artem O Surov
- G.A. Krestov Institute of Solution Chemistry RAS, 153045Ivanovo, Russia
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4
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Zhou D, Huang G, Xu G, Xiang L, Huang S, Chen X, Zhang Y, Wang D. CRISPRi-Mediated Gene Suppression Reveals Putative Reverse Transcriptase Gene PA0715 to Be a Global Regulator of Pseudomonas aeruginosa. Infect Drug Resist 2022; 15:7577-7599. [PMID: 36579125 PMCID: PMC9792118 DOI: 10.2147/idr.s384980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Pseudomonas aeruginosa is a common pathogen of infection in burn and trauma patients, and multi-drug resistant P. aeruginosa has become an increasingly important pathogen. Essential genes are key to the development of novel antibiotics. The PA0715 gene is a novel unidentified essential gene that has attracted our interest as a potential antibiotic target. Our study aims to determine the exact role of PA0715 in cell physiology and bacterial pathogenicity, providing important clues for antibiotic development. Patients and Methods The shuttle vector pHERD20T containing an arabinose inducible promoter was used to construct the CRISPRi system. Alterations in cellular physiology and bacterial pathogenicity of P. aeruginosa PAO1 after PA0715 inhibition were characterized. High-throughput RNA-seq was performed to gain more insight into the mechanisms by which PA0715 regulates the vital activity of P. aeruginosa. Results We found that down-regulation of PA0715 significantly reduced PAO1 growth rate, motility and chemotaxis, antibiotic resistance, pyocyanin and biofilm production. In addition, PA0715 inhibition reduced the pathogenicity of PAO1 to the greater galleria mellonella larvae. Transcriptional profiling identified 1757 genes including those related to amino acid, carbohydrate, ketone body and organic salt metabolism, whose expression was directly or indirectly controlled by PA0715. Unexpectedly, genes involved in oxidative phosphorylation also varied with PA0715 levels, and these findings support a hitherto unrecognized critical role for PA0715 in oxidative respiration in P. aeruginosa. Conclusion We identified PA0715 as a global regulator of the metabolic network that is indispensable for the survival and reproduction of P. aeruginosa. Our results provide a basis for future studies of potential antibiotic targets for P. aeruginosa and offer new ideas for P. aeruginosa infection control.
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Affiliation(s)
- Dapeng Zhou
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
| | - Guangtao Huang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
- Department of Burn and Plastic Surgery, Department of Wound Repair, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Guangchao Xu
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
| | - Lijuan Xiang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China
| | - Siyi Huang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
| | - Xinchong Chen
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
| | - Yixin Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Dali Wang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, People’s Republic of China
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5
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Levitskiy OA, Aglamazova OI, Grishin YK, Magdesieva TV. Reductive opening of a cyclopropane ring in the Ni(II) coordination environment: a route to functionalized dehydroalanine and cysteine derivatives. Beilstein J Org Chem 2022; 18:1166-1176. [PMID: 36128429 PMCID: PMC9475196 DOI: 10.3762/bjoc.18.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
The involvement of an α,α-cyclopropanated amino acid in the chiral Ni(II) coordination environment in the form of a Schiff base is considered as a route to electrochemical broadening of the donor-acceptor cyclopropane concept in combination with chirality induction in the targeted products. A tendency to the reductive ring-opening and the follow-up reaction paths of thus formed radical anions influenced by substituents in the cyclopropane ring are discussed. Optimization of the reaction conditions opens a route to the non-proteinogenic amino acid derivatives containing an α-β or β-γ double C=C bond in the side chain; the regioselectivity can be tuned by the addition of Lewis acids. One-pot combination of the reductive ring opening and subsequent addition of thiols allows obtaining the cysteine derivatives in practical yields and with high stereoselectivity at the removed β-stereocenter.
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Affiliation(s)
- Oleg A Levitskiy
- Lomonosov Moscow State University, Dept. of Chemistry, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Olga I Aglamazova
- Lomonosov Moscow State University, Dept. of Chemistry, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Yuri K Grishin
- Lomonosov Moscow State University, Dept. of Chemistry, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Tatiana V Magdesieva
- Lomonosov Moscow State University, Dept. of Chemistry, Leninskie Gory 1/3, Moscow 119991, Russian Federation
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6
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Pellegrino R, Blasi F, Angelini P, Ianni F, Alabed HBR, Emiliani C, Venanzoni R, Cossignani L. LC/MS Q-TOF Metabolomic Investigation of Amino Acids and Dipeptides in Pleurotus ostreatus Grown on Different Substrates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10371-10382. [PMID: 35944091 PMCID: PMC9413224 DOI: 10.1021/acs.jafc.2c04197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The well-established correlation between diet and health arouses great interest in seeking new health-promoting functional foods that may contribute to improving health and well-being. Herein, the metabolomic investigation of Pleurotus ostreatus samples grown on two different substrates (black poplar wood logs, WS, and lignocellulosic byproducts, LcS) revealed the high potential of such a mushroom as a source of bioactive species. The liquid chromatography/mass spectrometry combined with quadrupole time-of-flight (LC/MS Q-TOF) analysis allowed the identification of essential and nonessential amino acids along with the outstanding presence of dipeptides. Multivariate statistical models highlighted important differences in the expression of both classes of compounds arising from the growth of P. ostreatus strains on WS and LcS. The former, in particular, was correlated to an increased expression of carnitine-based amino acid derivatives and proline-based dipeptides. This finding may represent a potential strategy to drive the expression of bioactive compounds of interest to obtain enriched mushrooms or useful functional ingredients from them.
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Affiliation(s)
| | - Francesca Blasi
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
| | - Paola Angelini
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Federica Ianni
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
- . Tel.: +075 5857955
| | - Husam B. R. Alabed
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Carla Emiliani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Roberto Venanzoni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Lina Cossignani
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
- Center
for Perinatal and Reproductive Medicine, Santa Maria della Misericordia University Hospital, University of
Perugia, Sant’Andrea
delle Fratte, 06132 Perugia, Italy
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7
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Koksharova OA, Safronov NA. The effects of secondary bacterial metabolites on photosynthesis in microalgae cells. Biophys Rev 2022; 14:843-856. [PMID: 36124259 PMCID: PMC9481811 DOI: 10.1007/s12551-022-00981-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2022] [Indexed: 12/26/2022] Open
Abstract
Secondary metabolites of bacteria are regulatory molecules that act as "info-chemicals" that control some metabolic processes in the cells of microorganisms. These molecules provide the function of bacteria communication in microbial communities. As primary producers of organic matter in the biosphere, microalgae play a central ecological role in various ecosystems. Photosynthesis is a central process in microalgae cells, and it is exposed to various biotic and abiotic factors. Various secondary metabolites of bacteria confer a noticeable regulatory effect on photosynthesis in microalgae cells. The main purpose of this review is to highlight recent experimental results that demonstrate the impact of several types of common bacterial metabolites (volatile organic compounds, non-protein amino acids, and peptides) on photosynthetic activity in cells of microalgae. The use of these molecules as herbicides can be of great importance both for practical applications and for basic research.
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Affiliation(s)
- O. A. Koksharova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-40, 119991 Moscow, Russia
- Institute of Molecular Genetics of National Research Center, Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia
| | - N. A. Safronov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-40, 119991 Moscow, Russia
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8
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Ramírez-Guerrero S, Guardo-Maya S, Medina-Rincón GJ, Orrego-González EE, Cabezas-Pérez R, González-Reyes RE. Taurine and Astrocytes: A Homeostatic and Neuroprotective Relationship. Front Mol Neurosci 2022; 15:937789. [PMID: 35866158 PMCID: PMC9294388 DOI: 10.3389/fnmol.2022.937789] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/17/2022] [Indexed: 12/20/2022] Open
Abstract
Taurine is considered the most abundant free amino acid in the brain. Even though there are endogenous mechanisms for taurine production in neural cells, an exogenous supply of taurine is required to meet physiological needs. Taurine is required for optimal postnatal brain development; however, its brain concentration decreases with age. Synthesis of taurine in the central nervous system (CNS) occurs predominantly in astrocytes. A metabolic coupling between astrocytes and neurons has been reported, in which astrocytes provide neurons with hypotaurine as a substrate for taurine production. Taurine has antioxidative, osmoregulatory, and anti-inflammatory functions, among other cytoprotective properties. Astrocytes release taurine as a gliotransmitter, promoting both extracellular and intracellular effects in neurons. The extracellular effects include binding to neuronal GABAA and glycine receptors, with subsequent cellular hyperpolarization, and attenuation of N-methyl-D-aspartic acid (NMDA)-mediated glutamate excitotoxicity. Taurine intracellular effects are directed toward calcium homeostatic pathway, reducing calcium overload and thus preventing excitotoxicity, mitochondrial stress, and apoptosis. However, several physiological aspects of taurine remain unclear, such as the existence or not of a specific taurine receptor. Therefore, further research is needed not only in astrocytes and neurons, but also in other glial cells in order to fully comprehend taurine metabolism and function in the brain. Nonetheless, astrocyte’s role in taurine-induced neuroprotective functions should be considered as a promising therapeutic target of several neuroinflammatory, neurodegenerative and psychiatric diseases in the near future. This review provides an overview of the significant relationship between taurine and astrocytes, as well as its homeostatic and neuroprotective role in the nervous system.
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Affiliation(s)
- Sofía Ramírez-Guerrero
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Santiago Guardo-Maya
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Germán J. Medina-Rincón
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Eduardo E. Orrego-González
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Ricardo Cabezas-Pérez
- Grupo de Investigación en Ciencias Biomédicas GRINCIBIO, Facultad de Medicina, Universidad Antonio Nariño, Bogotá, Colombia
| | - Rodrigo E. González-Reyes
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencias Neurovitae-UR, Instituto de Medicina Traslacional (IMT), Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
- *Correspondence: Rodrigo E. González-Reyes,
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9
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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10
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Kazemi Shariat Panahi H, Dehhaghi M, Heng B, Lane DJR, Bush AI, Guillemin GJ, Tan VX. Neuropathological Mechanisms of β-N-Methylamino-L-Alanine (BMAA) with a Focus on Iron Overload and Ferroptosis. Neurotox Res 2022; 40:614-635. [PMID: 35023054 DOI: 10.1007/s12640-021-00455-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023]
Abstract
The incidence of neurodegenerative diseases and cyanobacterial blooms is concomitantly increasing worldwide. The cyanotoxin β-N-methylamino-L-alanine (BMAA) is produced by most of the Cyanobacteria spp. This cyanotoxin is described as a potential environmental etiology factor for some sporadic neurodegenerative diseases. Climate change and eutrophication significantly increase the frequency and intensity of cyanobacterial bloom in water bodies. This review evaluates different neuropathological mechanisms of BMAA at molecular and cellular levels and compares the related studies to provide some useful recommendations. Additionally, the structure and properties of BMAA as well as its microbial origin, especially by gut bacteria, are also briefly covered. Unlike previous reviews, we hypothesize the possible neurotoxic mechanism of BMAA through iron overload. We also discuss the involvement of BMAA in excitotoxicity, TAR DNA-binding protein 43 (TDP-43) translocation and accumulation, tauopathy, and other protein misincorporation and misfolding.
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Affiliation(s)
- Hamed Kazemi Shariat Panahi
- Neuroinflammation Group, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mona Dehhaghi
- Neuroinflammation Group, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- PANDIS.Org, Bendigo, Australia
- Department of Microbial Biotechnology, School of Biology and Centre of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Benjamin Heng
- Neuroinflammation Group, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Darius J R Lane
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Gilles J Guillemin
- Neuroinflammation Group, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
- PANDIS.Org, Bendigo, Australia.
| | - Vanessa X Tan
- Neuroinflammation Group, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- PANDIS.Org, Bendigo, Australia
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11
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Hauth F, Buck H, Stanoppi M, Hartig JS. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chem Biol 2022; 3:1240-1250. [PMID: 36320885 PMCID: PMC9533460 DOI: 10.1039/d2cb00128d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Canavanine, the δ-oxa-analogue of arginine, is produced as one of the main nitrogen storage compounds in legume seeds and has repellent properties. Its toxicity originates from incorporation into proteins as well as arginase-mediated hydrolysis to canaline that forms stable oximes with carbonyls. So far no pathway or enzyme has been identified acting specifically on canavanine. Here we report the characterization of a novel PLP-dependent enzyme, canavanine-γ-lyase, that catalyzes the elimination of hydroxyguanidine from canavanine to subsequently yield homoserine. Homoserine-dehydrogenase, aspartate–semialdehyde–dehydrogenase and ammonium–aspartate–lyase activities are also induced for facilitating canavanine utilization. We demonstrate that this novel pathway is found in certain Pseudomonas species and the Rhizobiales symbionts of legumes. The findings broaden the diverse reactions that the versatile class of PLP-dependent enzymes is able to catalyze. Since canavanine utilization is found prominently in root-associated bacteria, it could have important implications for the establishment and maintenance of the legume rhizosphere. A novel degradation pathway enables rhizosphere-associated bacteria to utilize canavanine.![]()
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Hiltrun Buck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Marco Stanoppi
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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12
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Moosmann B, Schindeldecker M, Hajieva P. Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation. Biol Chem 2021; 401:213-231. [PMID: 31318686 DOI: 10.1515/hsz-2019-0232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.
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Affiliation(s)
- Bernd Moosmann
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Mario Schindeldecker
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Parvana Hajieva
- Cellular Adaptation Group, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
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13
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Then A, Mácha K, Ibrahim B, Schuster S. A novel method for achieving an optimal classification of the proteinogenic amino acids. Sci Rep 2020; 10:15321. [PMID: 32948819 PMCID: PMC7501307 DOI: 10.1038/s41598-020-72174-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
The classification of proteinogenic amino acids is crucial for understanding their commonalities as well as their differences to provide a hint for why life settled on the usage of precisely those amino acids. It is also crucial for predicting electrostatic, hydrophobic, stacking and other interactions, for assessing conservation in multiple alignments and many other applications. While several methods have been proposed to find "the" optimal classification, they have several shortcomings, such as the lack of efficiency and interpretability or an unnecessarily high number of discriminating features. In this study, we propose a novel method involving a repeated binary separation via a minimum amount of five features (such as hydrophobicity or volume) expressed by numerical values for amino acid characteristics. The features are extracted from the AAindex database. By simple separation at the medians, we successfully derive the five properties volume, electron-ion-interaction potential, hydrophobicity, α-helix propensity, and π-helix propensity. We extend our analysis to separations other than by the median. We further score our combinations based on how natural the separations are.
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Affiliation(s)
- Andre Then
- Chair of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Karel Mácha
- Chair of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.,Westernacher Solutions, Columbiadamm 37, 10965, Berlin, Germany
| | - Bashar Ibrahim
- Chair of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany. .,Department of Mathematics and Natural Sciences, Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, 32093, Hawally, Kuwait.
| | - Stefan Schuster
- Chair of Bioinformatics, Matthias Schleiden Institute, University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
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14
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Ding Y, Ting JP, Liu J, Al-Azzam S, Pandya P, Afshar S. Impact of non-proteinogenic amino acids in the discovery and development of peptide therapeutics. Amino Acids 2020; 52:1207-1226. [PMID: 32945974 PMCID: PMC7544725 DOI: 10.1007/s00726-020-02890-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
With the development of modern chemistry and biology, non-proteinogenic amino acids (NPAAs) have become a powerful tool for developing peptide-based drug candidates. Drug-like properties of peptidic medicines, due to the smaller size and simpler structure compared to large proteins, can be changed fundamentally by introducing NPAAs in its sequence. While peptides composed of natural amino acids can be used as drug candidates, the majority have shown to be less stable in biological conditions. The impact of NPAA incorporation can be extremely beneficial in improving the stability, potency, permeability, and bioavailability of peptide-based therapies. Conversely, undesired effects such as toxicity or immunogenicity should also be considered. The impact of NPAAs in the development of peptide-based therapeutics is reviewed in this article. Further, numerous examples of peptides containing NPAAs are presented to highlight the ongoing development in peptide-based therapeutics.
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Affiliation(s)
- Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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15
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Danchin A. Isobiology: A Variational Principle for Exploring Synthetic Life. Chembiochem 2020; 21:1781-1792. [DOI: 10.1002/cbic.202000060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Antoine Danchin
- Stellate TherapeuticsInstitut Cochin 24 rue du Faubourg Saint-Jacques 75014 Paris France
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16
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J. Ayon N. Features, roles and chiral analyses of proteinogenic amino acids. AIMS MOLECULAR SCIENCE 2020. [DOI: 10.3934/molsci.2020011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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17
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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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18
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Fichtner M, Schuster S, Stark H. Determination of scoring functions for protein damage susceptibility. Biosystems 2019; 187:104035. [PMID: 31614190 DOI: 10.1016/j.biosystems.2019.104035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022]
Abstract
Protein damage (partly followed by protein aggregation) plays a significant role in ageing, cancer and in neurodegenerative and other diseases. It is known that the proteinogenic amino acids differ in their susceptibility to non-enzymatic modification, such as hydroxylation, peroxidation, chlorination etc. In a novel bioinformatics approach, we introduce measures to quantify the susceptibility of the 20 standard proteinogenic amino acids to such modification. Based on these amino acid scores, we calculated different susceptibilities for 116,387 proteins, testing various scoring approaches. These approaches are based on review articles, text mining and a combination of both. We also show an application by combining the score information with a tool for visualization.
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Affiliation(s)
- Maximilian Fichtner
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Stefan Schuster
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Heiko Stark
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany; Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Erbertstraße 1, 07743 Jena, Germany
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19
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Xi B, Tao J, Liu X, Xu X, He P, Dai Q. RaaMLab: A MATLAB toolbox that generates amino acid groups and reduced amino acid modes. Biosystems 2019; 180:38-45. [PMID: 30904554 DOI: 10.1016/j.biosystems.2019.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/25/2018] [Accepted: 03/06/2019] [Indexed: 01/31/2023]
Abstract
Amino acid (AA) classification and its different biophysical and chemical characteristics have been widely applied to analyze and predict the structural, functional, expression and interaction profiles of proteins and peptides. We present RaaMLab, a free and open-source MATLAB toolbox, to facilitate studies on proteins and peptides, to generate AA groups and to extract the structural and physicochemical features of reduced AAs (RedAA). This toolbox offers 4 kinds of databases, including the physicochemical properties of AAs and their groupings, 49 AA classification methods and 5 types of biophysicochemical features of RedAAs. These factors can be easily computed based on user-defined alphabet size and AA properties of AA groupings. RaaMLab is an open source freely available at https://github.com/bioinfo0706/RaaMLab. This website also contains a tutorial, extensive documentation and examples.
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Affiliation(s)
- Baohang Xi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Jin Tao
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Xiaoqing Liu
- College of Sciences, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Xinnan Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Pingan He
- College of Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Qi Dai
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.
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20
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Nunn PB, Codd GA. Metabolic solutions to the biosynthesis of some diaminomonocarboxylic acids in nature: Formation in cyanobacteria of the neurotoxins 3-N-methyl-2,3-diaminopropanoic acid (BMAA) and 2,4-diaminobutanoic acid (2,4-DAB). PHYTOCHEMISTRY 2017; 144:253-270. [PMID: 29059579 DOI: 10.1016/j.phytochem.2017.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown. This review considers possible metabolic routes, by analogy with reactions used in other species, by which these amino acids might be biosynthesised by cyanobacteria, which are a widespread potential environmental source of these neurotoxins. Where possible, the gene expression that might be implicated in these biosyntheses is discussed.
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Affiliation(s)
- Peter B Nunn
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, PO1 2DT, UK.
| | - Geoffrey A Codd
- School of Life Sciences, University of Dundee, DD1 5EH, UK; School of Natural Sciences, University of Stirling, FK9 4LA, UK.
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21
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Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids. Sci Rep 2017; 7:39821. [PMID: 28071669 PMCID: PMC5223158 DOI: 10.1038/srep39821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 11/28/2016] [Indexed: 12/21/2022] Open
Abstract
In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when cis/trans isomerism is neglected. Since the ratio of two consecutive Fibonacci numbers tends to the Golden section, 1.618, organisms can increase fatty acid variability approximately by that factor per carbon atom invested. Moreover, we show that, under consideration of cis/trans isomerism and/or of modification by hydroxy and/or oxo groups, diversity can be described by generalized Fibonacci numbers (e.g. Pell numbers). For the sake of easy comprehension, we deliberately build the proof on the recursive definitions of these number series. Our results should be of interest for mass spectrometry, combinatorial chemistry, synthetic biology, patent applications, use of fatty acids as biomarkers and the theory of evolution. The recursive definition of Fibonacci numbers paves the way to construct all structural formulas of fatty acids in an automated way.
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