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Soong CL, Deguchi K, Takeuchi M, Kozono S, Horinouchi N, Si D, Hibi M, Shimizu S, Ogawa J. Gene identification and enzymatic characterization of the initial enzyme in pyrimidine oxidative metabolism, uracil-thymine dehydrogenase. J Biosci Bioeng 2024; 137:413-419. [PMID: 38485553 DOI: 10.1016/j.jbiosc.2024.02.004] [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: 01/29/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 05/20/2024]
Abstract
Uracil-thymine dehydrogenase (UTDH), which catalyzes the irreversible oxidation of uracil to barbituric acid in oxidative pyrimidine metabolism, was purified from Rhodococcus erythropolis JCM 3132. The finding of unusual stabilizing conditions (pH 11, in the presence of NADP+ or NADPH) enabled the enzyme purification. The purified enzyme was a heteromer consisting of three different subunits. The enzyme catalyzed oxidation of uracil to barbituric acid with artificial electron acceptors such as methylene blue, phenazine methosulfate, benzoquinone, and α-naphthoquinone; however, NAD+, NADP+, flavin adenine dinucleotide, and flavin mononucleotide did not serve as electron acceptors. The enzyme acted not only on uracil and thymine but also on 5-halogen-substituted uracil and hydroxypyrimidine (pyrimidone), while dihydropyrimidine, which is an intermediate in reductive pyrimidine metabolism, and purine did not serve as substrates. The activity of UTDH was enhanced by cerium ions, and this activation was observed with all combinations of substrates and electron acceptors.
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Affiliation(s)
- Chee-Leong Soong
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kengo Deguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Michiki Takeuchi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Syoko Kozono
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nobuyuki Horinouchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Dayong Si
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science & Technology, China Agricultural University, Beijing 100193, China
| | - Makoto Hibi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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2
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Singh AK, Bilal M, Iqbal HMN, Raj A. Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144561. [PMID: 33736422 DOI: 10.1016/j.scitotenv.2020.144561] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 02/05/2023]
Abstract
The feasibility of in-silico techniques, together with the computational framework, has been applied to predictive bioremediation aiming to clean-up contaminants, toxicity evaluation, and possibilities for the degradation of complex recalcitrant compounds. Emerging contaminants from different industries have posed a significant hazard to the environment and public health. Given current bioremediation strategies, it is often a failure or inadequate for sustainable mitigation of hazardous pollutants. However, clear-cut vital information about biodegradation is quite incomplete from a conventional remediation techniques perspective. Lacking complete information on bio-transformed compounds leads to seeking alternative methods. Only scarce information about the transformed products and toxicity profile is available in the published literature. To fulfill this literature gap, various computational or in-silico technologies have emerged as alternating techniques, which are being recognized as in-silico approaches for bioremediation. Molecular docking, molecular dynamics simulation, and biodegradation pathways predictions are the vital part of predictive biodegradation, including the Quantitative Structure-Activity Relationship (QSAR), Quantitative structure-biodegradation relationship (QSBR) model system. Furthermore, machine learning (ML), artificial neural network (ANN), genetic algorithm (GA) based programs offer simultaneous biodegradation prediction along with toxicity and environmental fate prediction. Herein, we spotlight the feasibility of in-silico remediation approaches for various persistent, recalcitrant contaminants while traditional bioremediation fails to mitigate such pollutants. Such could be addressed by exploiting described model systems and algorithm-based programs. Furthermore, recent advances in QSAR modeling, algorithm, and dedicated biodegradation prediction system have been summarized with unique attributes.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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4
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Koziel JA, Ahn H, Glanville TD, Frana TS, van Leeuwen JH, Nguyen LT. Lab-scale evaluation of aerated burial concept for treatment and emergency disposal of infectious animal carcasses. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 76:715-726. [PMID: 29548829 DOI: 10.1016/j.wasman.2018.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
Nearly 55,000 outbreaks of animal disease were reported to the World Animal Health Information Database between 2005 and 2016. To suppress the spread of disease, large numbers of animal mortalities often must be disposed of quickly and are frequently buried on the farm where they were raised. While this method of emergency disposal is fast and relatively inexpensive, it also can have undesirable and lasting impacts (slow decay, concerns about groundwater contamination, pathogens re-emergence, and odor). Following the 2010 foot-and-mouth disease outbreak, the Republic of Korea's National Institute of Animal Science funded research on selected burial alternatives or modifications believed to have potential to reduce undesirable impacts of burial. One such modification involves the injection of air into the liquid degradation products from the 60-70% water from decomposing carcasses in lined burial trenches. Prior to prototype development in the field, a laboratory-scale study of aerated decomposition (AeD) of poultry carcasses was conducted to quantify improvements in time of carcass decomposition, reduction of potential groundwater pollutants in the liquid products of decomposition (since trench liners may ultimately leak), and reduction of odorous VOCs emitted during decomposition. Headspace gases also were monitored to determine the potential for using gaseous biomarkers in the aerated burial trench exhaust stream to monitor completion of the decomposition. Results of the lab-scale experiments show that the mass of chicken carcasses was reduced by 95.0 ± 0.9% within 3 months at mesophilic temperatures (vs. negligible reduction via mesophilic anaerobic digestion typical of trench burial) with concomitant reduction of biochemical oxygen demand (BOD; 99%), volatile suspended solids (VSS; 99%), total suspended solids (TSS; 99%), and total ammonia nitrogen (TAN; 98%) in the liquid digestate. At week #7 BOD and TSS in digestate met the U.S. EPA standards for treated wastewater discharge to surface water. Salmonella and Staphylococcus were inactivated by the AeD process after week #1 and #3, respectively. Five gaseous biomarkers: pyrimidine; p-cresol; phenol; dimethyl disulfide; and dimethyl trisulfide; were identified and correlated with digestate quality. Phenol was the best predictor of TAN (R = 0.96), BOD (R = 0.92), and dissolved oxygen (DO) (R = -0.91). Phenol was also the best predictor populations of Salmonella (R = 0.95) and aerobes (R = 0.88). P-cresol was the best predictor for anaerobes (R = 0.88). The off-gas from AeD will require biofiltration or other odor control measures for a much shorter time than anaerobic decomposition. The lab-scale studies indicate that AeD burial has the potential to make burial a faster, safer, and more environmentally friendly method for emergency disposal and treatment of infectious animal carcasses and that this method should be further developed via prototype-scale field studies.
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Affiliation(s)
- Jacek A Koziel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA; Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA 50011, USA; Department of Food Science and Human Nutrition, Iowa State University, Iowa State University, Ames, IA 50011, USA.
| | - Heekwon Ahn
- Department of Animal Biosystems Science, Chungnam National University, Daejeon, Republic of Korea.
| | - Thomas D Glanville
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - Timothy S Frana
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA.
| | - J Hans van Leeuwen
- Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA 50011, USA; Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA; Department of Food Science and Human Nutrition, Iowa State University, Iowa State University, Ames, IA 50011, USA.
| | - Lam T Nguyen
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
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5
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Han Y, Xiong L, Xu Y, Tian T, Wang T. The β-alanine transporter BalaT is required for visual neurotransmission in Drosophila. eLife 2017; 6. [PMID: 28806173 PMCID: PMC5555718 DOI: 10.7554/elife.29146] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/17/2017] [Indexed: 02/06/2023] Open
Abstract
The recycling of neurotransmitters is essential for sustained synaptic transmission. In Drosophila, histamine recycling is required for visual synaptic transmission. Synaptic histamine is rapidly taken up by laminar glia, and is converted to carcinine. After delivered back to photoreceptors, carcinine is hydrolyzed to release histamine and β-alanine. This histamine is repackaged into synaptic vesicles, but it is unclear how the β-alanine is returned to the laminar glial cells. Here, we identified a new β-alanine transporter, which we named BalaT (Beta-alanine Transporter). Null balat mutants exhibited lower levels of β-alanine, as well as less β-alanine accumulation in the retina. Moreover, BalaT is expressed and required in retinal pigment cells for maintaining visual synaptic transmission and phototaxis behavior. These results provide the first genetic evidence that retinal pigment cells play a critical role in visual neurotransmission, and suggest that a BalaT-dependent β-alanine trafficking pathway is required for histamine homeostasis and visual neurotransmission. DOI:http://dx.doi.org/10.7554/eLife.29146.001 Neurons transmit information around the body in the form of electrical signals, but these signals cannot cross the gaps between neurons. To send a message to its neighbor, a neuron releases a molecule known as a neurotransmitter into the gap between the cells. The neurotransmitter binds to proteins on the recipient neuron and triggers new electrical signals inside that cell. When the message has been received, the neurotransmitter molecules are returned to the first neuron so that they can be reused. This recycling is particularly important in the visual system, where neurons communicate via rapid-fire signaling. In fruit flies, for example, light-sensitive neurons in the eye known as photoreceptors release a neurotransmitter called histamine when they detect light. Supporting cells called laminar glia take up any leftover histamine and combine it with another molecule known as β-alanine to form a larger molecule. The photoreceptors absorb this larger molecule and break it back down into histamine and β-alanine. However, it is not clear how the β-alanine returns to the glia to allow this cycle to continue. Many molecules rely on so-called “transporter” proteins to help them move into or out of cells. To identify transporters that might help to move β-alanine, Han, Xiong et al. prepared a list of fruit fly genes that encode transporter proteins found inside the insect’s head. Testing the resulting proteins in a cultured cell system revealed that one of them was able to transport β-alanine. This protein, named BalaT, is found in another type of support cell called retinal pigment cells. Mutant flies that cannot produce BalaT are blind because their photoreceptors have problems in transmitting information to other neurons. Han, Xiong et al. propose that BalaT transports β-alanine from photoreceptors to retinal pigment cells, which then pass β-alanine on to the laminar glia. Follow-up studies are required to find out exactly how the laminar glia take up histamine. DOI:http://dx.doi.org/10.7554/eLife.29146.002
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Affiliation(s)
- Yongchao Han
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Liangyao Xiong
- National Institute of Biological Sciences, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China
| | - Ying Xu
- National Institute of Biological Sciences, Beijing, China.,School of Life Sciences, Beijing Normal University, Beijing, China
| | - Tian Tian
- National Institute of Biological Sciences, Beijing, China
| | - Tao Wang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
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6
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Clough JM, Dale RP, Elsdon B, Hawkes TR, Hogg BV, Howell A, Kloer DP, Lecoq K, McLachlan MM, Milnes PJ, O'Riordan TJ, Ranasinghe S, Shanahan SE, Sumner KD, Tayab S. Synthesis and evaluation of hydroxyazolopyrimidines as herbicides; the generation of amitrole in planta. PEST MANAGEMENT SCIENCE 2016; 72:2254-2272. [PMID: 26918632 DOI: 10.1002/ps.4264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Exploiting novel herbicidal modes of action is an important method to overcome the challenges faced by increasing resistance and regulatory pressure on existing commercial herbicides. Recent reports of inhibitors of enzymes in the non-mevalonate pathway of isoprenoid biosynthesis led to the design of a novel class of azolopyrimidines which were assessed for their herbicidal activity. Studies were also undertaken to determine the mode of action responsible for the observed herbicidal activity. RESULTS In total, 30 novel azolopyrimidines were synthesised and their structures were unambiguously determined by 1 H NMR, mass spectroscopy and X-ray crystallographic analysis. The herbicidal activity of this new chemical class was assessed against six common weed species, with compounds from this series displaying bleaching symptomology in post-emergence tests. A structure-activity relationship for the novel compounds was determined, which showed that only those belonging to the hydroxytriazolopyrimidine subclass displayed significant herbicidal activity. Observed similarities between the bleaching symptomology displayed by these herbicides and amitrole suggested that hydroxytriazolopyrimidines could be acting as elaborate propesticides of amitrole, and this was subsequently demonstrated in plant metabolism studies using Amaranthus retroflexus. It was shown that selected hydroxytriazolopyrimidines that displayed promising herbicidal activity generated amitrole, with peak concentrations of amitrole generally being observed 1 day after application. Additionally, the herbicidal activity of selected compounds was profiled against tobacco plants engineered to overexpress 4-diphosphocytidyl-2C-methyl-d-erythritol synthase (IspD) or lycopene β-cyclase, and the results suggested that, where significant herbicidal activity was observed, inhibition of IspD was not responsible for the activity. Tobacco plants overexpressing lycopene β-cyclase showed tolerance to amitrole and the two most herbicidally active triazolopyrimidines. CONCLUSIONS Inhibition of IspD leading to herbicidal activity has been ruled out as the mode of action for the hydroxytriazolopyrimidine class of herbicides. Additionally, tobacco plants overexpressing lycopene β-cyclase showed tolerance to amitrole, which indicates that this is the main herbicidal mode of action for amitrole. Results from the metabolic fate study of selected hydroxytriazolopyrimidines suggested that the herbicidal activity displayed by these compounds is due to amitrole production, which was confirmed when tobacco plants overexpressing lycopene β-cyclase also showed tolerance towards two triazolopyrimidines from this study. © 2016 Society of Chemical Industry.
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Affiliation(s)
- John M Clough
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Richard P Dale
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Barry Elsdon
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Timothy R Hawkes
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Bridget V Hogg
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Anushka Howell
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Daniel P Kloer
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Karine Lecoq
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | | | - Phillip J Milnes
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | | | - Saranga Ranasinghe
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Stephen E Shanahan
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Karen D Sumner
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
| | - Shanaaz Tayab
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berks, UK
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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8
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Metabolic Engineering for Production of Small Molecule Drugs: Challenges and Solutions. FERMENTATION-BASEL 2016. [DOI: 10.3390/fermentation2010004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Huang X, Poelchau MF, Armbruster PA. Global transcriptional dynamics of diapause induction in non-blood-fed and blood-fed Aedes albopictus. PLoS Negl Trop Dis 2015; 9:e0003724. [PMID: 25897664 PMCID: PMC4405372 DOI: 10.1371/journal.pntd.0003724] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Aedes albopictus is a vector of increasing public health concern due to its rapid global range expansion and ability to transmit Dengue virus, Chikungunya virus and a wide range of additional arboviruses. Traditional vector control strategies have been largely ineffective against Ae. albopictus and novel approaches are urgently needed. Photoperiodic diapause is a crucial ecological adaptation in a wide range of temperate insects. Therefore, targeting the molecular regulation of photoperiodic diapause or diapause-associated physiological processes could provide the basis of novel approaches to vector control. METHODOLOGY/PRINCIPAL FINDINGS We investigated the global transcriptional profiles of diapause induction in Ae. albopictus by performing paired-end RNA-Seq of biologically replicated libraries. We sequenced RNA from whole bodies of adult females reared under diapause-inducing and non-diapause-inducing photoperiods either with or without a blood meal. We constructed a comprehensive transcriptome assembly that incorporated previous assemblies and represents over 14,000 annotated dipteran gene models. Mapping of sequence reads to the transcriptome identified differential expression of 2,251 genes in response to diapause-inducing short-day photoperiods. In non-blood-fed females, potential regulatory elements of diapause induction were transcriptionally up-regulated, including two of the canonical circadian clock genes, timeless and cryptochrome 1. In blood-fed females, genes in metabolic pathways related to energy production and offspring provisioning were differentially expressed under diapause-inducing conditions, including the oxidative phosphorylation pathway and lipid metabolism genes. CONCLUSIONS/SIGNIFICANCE This study is the first to utilize powerful RNA-Seq technologies to elucidate the transcriptional basis of diapause induction in any insect. We identified candidate genes and pathways regulating diapause induction, including a conserved set of genes that are differentially expressed as part of the diapause program in a diverse group of insects. These genes provide candidates whose diapause-associated function can be further interrogated using functional genomics approaches in Ae. albopictus and other insects.
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Affiliation(s)
- Xin Huang
- Department of Biology, Georgetown University, Washington, D.C., United States of America
| | - Monica F. Poelchau
- Department of Biology, Georgetown University, Washington, D.C., United States of America
| | - Peter A. Armbruster
- Department of Biology, Georgetown University, Washington, D.C., United States of America
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10
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Ippolito DL, Lewis JA, Yu C, Leon LR, Stallings JD. Alteration in circulating metabolites during and after heat stress in the conscious rat: potential biomarkers of exposure and organ-specific injury. BMC PHYSIOLOGY 2014; 14:14. [PMID: 25623799 PMCID: PMC4306243 DOI: 10.1186/s12899-014-0014-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 12/11/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Heat illness is a debilitating and potentially life-threatening condition. Limited data are available to identify individuals with heat illness at greatest risk for organ damage. We recently described the transcriptomic and proteomic responses to heat injury and recovery in multiple organs in an in vivo model of conscious rats heated to a maximum core temperature of 41.8°C (Tc,Max). In this study, we examined changes in plasma metabolic networks at Tc,Max, 24, or 48 hours after the heat stress stimulus. RESULTS Circulating metabolites were identified by gas chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry. Bioinformatics analysis of the metabolomic data corroborated proteomics and transcriptomics data in the tissue at the pathway level, supporting modulations in metabolic networks including cell death or catabolism (pyrimidine and purine degradation, acetylation, sulfation, redox alterations and glutathione metabolism, and the urea cycle/creatinine metabolism), energetics (stasis in glycolysis and tricarboxylic acid cycle, β-oxidation), cholesterol and nitric oxide metabolism, and bile acids. Hierarchical clustering identified 15 biochemicals that differentiated animals with histopathological evidence of cardiac injury at 48 hours from uninjured animals. The metabolic networks perturbed in the plasma corroborated the tissue proteomics and transcriptomics pathway data, supporting a model of irreversible cell death and decrements in energetics as key indicators of cardiac damage in response to heat stress. CONCLUSIONS Integrating plasma metabolomics with tissue proteomics and transcriptomics supports a diagnostic approach to assessing individual susceptibility to organ injury and predicting recovery after heat stress.
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Affiliation(s)
- Danielle L Ippolito
- />The United States Army Center for Environmental Health Research, Environmental Health Program, Bldg. 568 Doughten Drive, Fort Detrick, Frederick, MD 21702-5010 USA
| | - John A Lewis
- />The United States Army Center for Environmental Health Research, Environmental Health Program, Bldg. 568 Doughten Drive, Fort Detrick, Frederick, MD 21702-5010 USA
| | - Chenggang Yu
- />Biotechnology High Performance Computing Software Applications Institute, Frederick, MD 21702-5010 USA
| | - Lisa R Leon
- />Thermal Mountain Medicine Division, US Army Research Institute of Environmental Medicine, Natick, MA 01760-5007 USA
| | - Jonathan D Stallings
- />The United States Army Center for Environmental Health Research, Environmental Health Program, Bldg. 568 Doughten Drive, Fort Detrick, Frederick, MD 21702-5010 USA
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11
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Price DRG, Wilson ACC. A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont. BMC Biol 2014; 12:110. [PMID: 25527092 PMCID: PMC4306246 DOI: 10.1186/s12915-014-0110-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/11/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genome evolution in intracellular microbial symbionts is characterized by gene loss, generating some of the smallest and most gene-poor genomes known. As a result of gene loss these genomes commonly contain metabolic pathways that are fragmented relative to their free-living relatives. The evolutionary retention of fragmented metabolic pathways in the gene-poor genomes of endosymbionts suggests that they are functional. However, it is not always clear how they maintain functionality. To date, the fragmented metabolic pathways of endosymbionts have been shown to maintain functionality through complementation by host genes, complementation by genes of another endosymbiont and complementation by genes in host genomes that have been horizontally acquired from a microbial source that is not the endosymbiont. Here, we demonstrate a fourth mechanism. RESULTS We investigate the evolutionary retention of a fragmented pathway for the essential nutrient pantothenate (vitamin B5) in the pea aphid, Acyrthosiphon pisum endosymbiosis with Buchnera aphidicola. Using quantitative analysis of gene expression we present evidence for complementation of the Buchnera pantothenate biosynthesis pathway by host genes. Further, using complementation assays in an Escherichia coli mutant we demonstrate functional replacement of a pantothenate biosynthesis enzyme, 2-dehydropantoate 2-reductase (E.C. 1.1.1.169), by an endosymbiont gene, ilvC, encoding a substrate ambiguous enzyme. CONCLUSIONS Earlier studies have speculated that missing enzyme steps in fragmented endosymbiont metabolic pathways are completed by adaptable endosymbiont enzymes from other pathways. Here, we experimentally demonstrate completion of a fragmented endosymbiont vitamin biosynthesis pathway by recruitment of a substrate ambiguous enzyme from another pathway. In addition, this work extends host/symbiont metabolic collaboration in the aphid/Buchnera symbiosis from amino acid metabolism to include vitamin biosynthesis.
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Affiliation(s)
- Daniel R G Price
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
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12
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Arora PK, Bae H. Integration of bioinformatics to biodegradation. Biol Proced Online 2014; 16:8. [PMID: 24808763 PMCID: PMC4012781 DOI: 10.1186/1480-9222-16-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/19/2014] [Indexed: 12/22/2022] Open
Abstract
Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.
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Affiliation(s)
- Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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13
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Barba M, Glansdorff N, Labedan B. Evolution of Cyclic Amidohydrolases: A Highly Diversified Superfamily. J Mol Evol 2013; 77:70-80. [DOI: 10.1007/s00239-013-9580-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/16/2013] [Indexed: 11/29/2022]
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14
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Borycz J, Borycz JA, Edwards TN, Boulianne GL, Meinertzhagen IA. The metabolism of histamine in the Drosophila optic lobe involves an ommatidial pathway: β-alanine recycles through the retina. ACTA ACUST UNITED AC 2012; 215:1399-411. [PMID: 22442379 DOI: 10.1242/jeb.060699] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Flies recycle the photoreceptor neurotransmitter histamine by conjugating it to β-alanine to form β-alanyl-histamine (carcinine). The conjugation is regulated by Ebony, while Tan hydrolyses carcinine, releasing histamine and β-alanine. In Drosophila, β-alanine synthesis occurs either from uracil or from the decarboxylation of aspartate but detailed roles for the enzymes responsible remain unclear. Immunohistochemically detected β-alanine is present throughout the fly's entire brain, and is enhanced in the retina especially in the pseudocone, pigment and photoreceptor cells of the ommatidia. HPLC determinations reveal 10.7 ng of β-alanine in the wild-type head, roughly five times more than histamine. When wild-type flies drink uracil their head β-alanine increases more than after drinking l-aspartic acid, indicating the effectiveness of the uracil pathway. Mutants of black, which lack aspartate decarboxylase, cannot synthesize β-alanine from l-aspartate but can still synthesize it efficiently from uracil. Our findings demonstrate a novel function for pigment cells, which not only screen ommatidia from stray light but also store and transport β-alanine and carcinine. This role is consistent with a β-alanine-dependent histamine recycling pathway occurring not only in the photoreceptor terminals in the lamina neuropile, where carcinine occurs in marginal glia, but vertically via a long pathway that involves the retina. The lamina's marginal glia are also a hub involved in the storage and/or disposal of carcinine and β-alanine.
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Affiliation(s)
- Janusz Borycz
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Canada, B3H 4J1
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15
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van Kuilenburg ABP, Dobritzsch D, Meijer J, Krumpel M, Selim LA, Rashed MS, Assmann B, Meinsma R, Lohkamp B, Ito T, Abeling NGGM, Saito K, Eto K, Smitka M, Engvall M, Zhang C, Xu W, Zoetekouw L, Hennekam RCM. ß-ureidopropionase deficiency: phenotype, genotype and protein structural consequences in 16 patients. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1096-108. [PMID: 22525402 DOI: 10.1016/j.bbadis.2012.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 03/29/2012] [Accepted: 04/09/2012] [Indexed: 12/26/2022]
Abstract
ß-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid to ß-alanine and ß-aminoisobutyric acid, ammonia and CO(2). To date, only five genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 11 newly identified ß-ureidopropionase deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological abnormalities (intellectual disabilities, seizures, abnormal tonus regulation, microcephaly, and malformations on neuro-imaging) and markedly elevated levels of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid in urine and plasma. Analysis of UPB1, encoding ß-ureidopropionase, showed 6 novel missense mutations and one novel splice-site mutation. Heterologous expression of the 6 mutant enzymes in Escherichia coli showed that all mutations yielded mutant ß-ureidopropionase proteins with significantly decreased activity. Analysis of a homology model of human ß-ureidopropionase generated using the crystal structure of the enzyme from Drosophila melanogaster indicated that the point mutations p.G235R, p.R236W and p.S264R lead to amino acid exchanges in the active site and therefore affect substrate binding and catalysis. The mutations L13S, R326Q and T359M resulted most likely in folding defects and oligomer assembly impairment. Two mutations were identified in several unrelated ß-ureidopropionase patients, indicating that ß-ureidopropionase deficiency may be more common than anticipated.
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Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, Emma Children's Hospital, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105 AZ Amsterdam, The Netherlands.
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Cornelius S, Witz S, Rolletschek H, Möhlmann T. Pyrimidine degradation influences germination seedling growth and production of Arabidopsis seeds. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:5623-32. [PMID: 21865177 PMCID: PMC3223058 DOI: 10.1093/jxb/err251] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/30/2011] [Accepted: 07/18/2011] [Indexed: 05/20/2023]
Abstract
PYD1 (dihydropyrimidine dehydogenase) initiates the degradation of pyrimidine nucleobases and is located in plastids. In this study, a physiological analysis of PYD1 employing T-DNA knockout mutants and overexpressors was carried out. PYD1 knockout mutants were restricted in degradation of exogenously provided uracil and accumulated high uracil levels in plant organs throughout development, especially in dry seeds. Moreover, PYD1 knockout mutants showed delayed germination which was accompanied by low invertase activity and decreased monosaccharide levels. Abscisic acid (ABA) is an important regulator of seed germination, and ABA-responsive genes were deregulated in PYD1 knockout mutants. Together with an observed increased PYD1 expression in wild-type seedlings upon ABA treatment, an interference of PYD1 with ABA signalling can be assumed. Constitutive PYD1 overexpression mutants showed increased growth and higher seed number compared with wild-type and knockout mutant plants. During senescence PYD1 expression increased to allow uracil catabolism. From this it is concluded that early in development and during seed production PYD1 is needed to balance pyrimidine catabolism versus salvage.
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Affiliation(s)
- Stefanie Cornelius
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Sandra Witz
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Hardy Rolletschek
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Technische Universität Kaiserslautern, Corrensstraße 3, D-06466 Gatersleben, Germany
| | - Torsten Möhlmann
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
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17
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Chen XZ, Shen W, Fan Y, Wang ZX. [Genomics and metabolic engineering of filamentous fungi in the post-genomics era]. YI CHUAN = HEREDITAS 2011; 33:1067-78. [PMID: 21993281 DOI: 10.3724/sp.j.1005.2011.01067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Filamentous fungi are used in a variety of industrial processes including the production of primary metabolites (e.g., organic acid, vitamins, and extracellular enzymes) and secondary metabolites (e.g., antibiotics, alkaloids, and gibberellins). Moreover, filamentous fungi have become preferred cell factories for production of foreign (heterologous) proteins in biotechnology in recent years. Compared to bacterial and yeast hosts, filamentous fungi showed predominant features such as the ability of growing on rather simple and inexpensive substrates, producing and secreting exceptionally large amounts of proteins, post-translational modifications, and GRAS (generally regarded as safe) approval. Therefore, the exploration of filamentous fungi has been attractive recently. This review summarizes the recent development in genomics, comparative genomics, transcriptomics, proteomics and metabolomics of filamentous fungi, and describes their applications and functions in reconstruction of metabolic network, discovery of novel proteins and genes, investigation of cell physiological and biochemical reactions, and strain breeding. This review also analyzes the bottlenecks of heterologous protein expression in filamentous fungi. Furthermore, special emphasis is given on the strategies for improving the protein production, including fusion expression of heterologous proteins, RNAi technology, manipulations of secretion pathways, codon optimization of foreign genes, and screening of protease mutants. Lastly, this review proposes the future direction of metabolic engineering of filamentous fungi.
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18
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DREAMS of metabolism. Trends Biotechnol 2010; 28:501-8. [DOI: 10.1016/j.tibtech.2010.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 06/29/2010] [Accepted: 07/01/2010] [Indexed: 01/11/2023]
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19
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Björnberg O, Vodnala M, Domkin V, Hofer A, Rasmussen A, Andersen G, Piskur J. Ribosylurea accumulates in yeast urc4 mutants. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 29:433-7. [PMID: 20544532 DOI: 10.1080/15257771003741265] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Yeast Saccharomyces (Lachancea) kluyveri urc4 mutants, unable to grow on uracil, biotransformed (14)C(2)-uracil into two labeled compounds, as detected by high performance liquid chromatography (HPLC). These two compounds could also be obtained following organic synthesis of ribosylurea. This finding demonstrates that in the URC pyrimidine degradation pathway, the opening of the uracil ring takes place when uracil is attached to the ribose moiety. Ribosylurea has not been reported in the cell metabolism before and the two observed compounds likely represent an equilibrium mixture of the pyranosyl and furanosyl forms.
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Affiliation(s)
- O Björnberg
- Department of Cell and Organism Biology, Lund University, Lund, Sweden
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20
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Zhu Y, Zhang Y, Li Y. Understanding the industrial application potential of lactic acid bacteria through genomics. Appl Microbiol Biotechnol 2009; 83:597-610. [DOI: 10.1007/s00253-009-2034-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 05/04/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
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21
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Zrenner R, Riegler H, Marquard CR, Lange PR, Geserick C, Bartosz CE, Chen CT, Slocum RD. A functional analysis of the pyrimidine catabolic pathway in Arabidopsis. THE NEW PHYTOLOGIST 2009; 183:117-132. [PMID: 19413687 PMCID: PMC2713857 DOI: 10.1111/j.1469-8137.2009.02843.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/19/2009] [Indexed: 05/04/2023]
Abstract
* Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.
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Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops14979 Großbeeren, Germany
| | - Heike Riegler
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Cathleen R Marquard
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Peter R Lange
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Claudia Geserick
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Caren E Bartosz
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Celine T Chen
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Robert D Slocum
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
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22
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Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol 2009; 191:3437-44. [PMID: 19363119 DOI: 10.1128/jb.00034-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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23
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Schnackerz KD, Andersen G, Dobritzsch D, Piskur J. Degradation of pyrimidines in Saccharomyces kluyveri: transamination of beta-alanine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:794-9. [PMID: 18600542 DOI: 10.1080/15257770802145983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Beta-alanine is an intermediate in the reductive degradation of uracil. Recently we have identified and characterized the Saccharomyces kluyveri PYD4 gene and the corresponding enzyme beta -alanine aminotransferase ((Sk)Pyd4p), highly homologous to eukaryotic gamma-aminobutyrate aminotransferase (GABA-AT). S. kluyveri has two aminotransferases, GABA aminotransferase ((Sk)Uga1p) with 80% and (Sk)Pyd4p with 55% identity to S. cerevisiae GABA-AT. (Sk)Pyd4p is a typical pyridoxal phosphate-dependent aminotransferase, specific for alpha-ketoglutarate (alpha KG), beta-alanine (BAL) and gamma-aminobutyrate (GABA), showing a ping-pong kinetic mechanism involving two half-reactions and substrate inhibition. (Sk)Uga1p accepts only alpha KG and GABA but not BAL, thus only (Sk)Pydy4p belongs to the uracil degradative pathway.
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Affiliation(s)
- K D Schnackerz
- Cell- and Organism Biology, Lund University, Lund, Sweden.
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24
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Andersen G, Björnberg O, Polakova S, Pynyaha Y, Rasmussen A, Møller K, Hofer A, Moritz T, Sandrini MPB, Merico AM, Compagno C, Akerlund HE, Gojković Z, Piskur J. A second pathway to degrade pyrimidine nucleic acid precursors in eukaryotes. J Mol Biol 2008; 380:656-66. [PMID: 18550080 DOI: 10.1016/j.jmb.2008.05.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 05/09/2008] [Accepted: 05/10/2008] [Indexed: 11/16/2022]
Abstract
Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyveri, we show that during degradation, uracil is not reduced to dihydrouracil. Six loci, named URC1-6 (for uracil catabolism), are involved in the novel catabolic pathway. Four of them, URC3,5, URC6, and URC2 encode urea amidolyase, uracil phosphoribosyltransferase, and a putative transcription factor, respectively. The gene products of URC1 and URC4 are highly conserved proteins with so far unknown functions and they are present in a variety of prokaryotes and fungi. In bacteria and in some fungi, URC1 and URC4 are linked on the genome together with the gene for uracil phosphoribosyltransferase (URC6). Urc1p and Urc4p are therefore likely the core components of this novel biochemical pathway. A combination of genetic and analytical chemistry methods demonstrates that uridine monophosphate and urea are intermediates, and 3-hydroxypropionic acid, ammonia and carbon dioxide the final products of degradation. The URC pathway does not require the presence of an active respiratory chain and is therefore different from the oxidative and rut pathways described in prokaryotes, although the latter also gives 3-hydroxypropionic acid as the end product. The genes of the URC pathway are not homologous to any of the eukaryotic or prokaryotic genes involved in pyrimidine degradation described to date.
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Affiliation(s)
- Gorm Andersen
- Department of Cell and Organism Biology, Lund University, 223 62 Lund, Sweden
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Andersen B, Lundgren S, Dobritzsch D, Piškur J. A Recruited Protease is Involved in Catabolism of Pyrimidines. J Mol Biol 2008; 379:243-50. [DOI: 10.1016/j.jmb.2008.03.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/11/2008] [Accepted: 03/31/2008] [Indexed: 11/25/2022]
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26
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Lundgren S, Lohkamp B, Andersen B, Piskur J, Dobritzsch D. The crystal structure of beta-alanine synthase from Drosophila melanogaster reveals a homooctameric helical turn-like assembly. J Mol Biol 2008; 377:1544-59. [PMID: 18336837 DOI: 10.1016/j.jmb.2008.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Revised: 02/06/2008] [Accepted: 02/07/2008] [Indexed: 11/29/2022]
Abstract
Beta-alanine synthase (betaAS) is the third enzyme in the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of the nucleotide bases uracil and thymine in higher organisms. It catalyzes the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate to the corresponding beta-amino acids. betaASs are grouped into two phylogenetically unrelated subfamilies, a general eukaryote one and a fungal one. To reveal the molecular architecture and understand the catalytic mechanism of the general eukaryote betaAS subfamily, we determined the crystal structure of Drosophila melanogaster betaAS to 2.8 A resolution. It shows a homooctameric assembly of the enzyme in the shape of a left-handed helical turn, in which tightly packed dimeric units are related by 2-fold symmetry. Such an assembly would allow formation of higher oligomers by attachment of additional dimers on both ends. The subunit has a nitrilase-like fold and consists of a central beta-sandwich with a layer of alpha-helices packed against both sides. However, the core fold of the nitrilase superfamily enzymes is extended in D. melanogaster betaAS by addition of several secondary structure elements at the N-terminus. The active site can be accessed from the solvent by a narrow channel and contains the triad of catalytic residues (Cys, Glu, and Lys) conserved in nitrilase-like enzymes.
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Affiliation(s)
- Stina Lundgren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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27
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Lundgren S, Andersen B, Piškur J, Dobritzsch D. Crystallization and preliminary X-ray data analysis of beta-alanine synthase from Drosophila melanogaster. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:874-7. [PMID: 17909293 PMCID: PMC2339735 DOI: 10.1107/s1744309107042984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Accepted: 09/03/2007] [Indexed: 11/11/2022]
Abstract
Beta-alanine synthase catalyzes the last step in the reductive degradation pathway for uracil and thymine, which represents the main clearance route for the widely used anticancer drug 5-fluorouracil. Crystals of the recombinant enzyme from Drosophila melanogaster, which is closely related to the human enzyme, were obtained by the hanging-drop vapour-diffusion method. They diffracted to 3.3 A at a synchrotron-radiation source, belong to space group C2 (unit-cell parameters a = 278.9, b = 95.0, c = 199.3 A, beta = 125.8 degrees) and contain 8-10 molecules per asymmetric unit.
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Affiliation(s)
- Stina Lundgren
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Birgit Andersen
- Department of Organism and Cell Biology, Lund University, Lund, Sweden
| | - Jure Piškur
- Department of Organism and Cell Biology, Lund University, Lund, Sweden
| | - Doreen Dobritzsch
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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