1
|
Okegawa Y, Tsuda N, Sakamoto W, Motohashi K. Maintaining the Chloroplast Redox Balance through the PGR5-Dependent Pathway and the Trx System Is Required for Light-Dependent Activation of Photosynthetic Reactions. Plant Cell Physiol 2022; 63:92-103. [PMID: 34623443 DOI: 10.1093/pcp/pcab148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Light-dependent activation of chloroplast enzymes is required for the rapid induction of photosynthesis after a shift from dark to light. The thioredoxin (Trx) system plays a central role in this process. In chloroplasts, the Trx system consists of two pathways: the ferredoxin (Fd)/Trx pathway and the nicotinamide adenine dinucleotide phosphate (NADPH)-Trx reductase C (NTRC) pathway. In Arabidopsis (Arabidopsis thaliana) mutants defective in either pathway, the photoreduction of thiol enzymes was impaired, resulting in decreased carbon fixation. The close relationship between the Fd/Trx pathway and proton gradient regulation 5 (PGR5)-dependent photosystem I cyclic electron transport (PSI CET) in the induction of photosynthesis was recently elucidated. However, how the PGR5-dependent pathway is involved in the NTRC pathway is unclear, although NTRC has been suggested to physically interact with PGR5. In this study, we analyzed Arabidopsis mutants lacking either the PGR5 or the chloroplast NADH dehydrogenase-like complex (NDH)-dependent PSI CET pathway in the ntrc mutant background. The ntrc pgr5 double mutant suppressed both the growth defects and the high non-photochemical quenching phenotype of the ntrc mutant when grown under long-day conditions. By contrast, the inactivation of NDH activity with the chlororespiratory reduction 2-2 mutant failed to suppress either phenotype. We discovered that the phenotypic rescue of ntrc by pgr5 is caused by the partial restoration of Trx-dependent reduction of thiol enzymes. These results suggest that electron partitioning to the PGR5-dependent pathway and the Trx system needs to be properly regulated for the activation of the Calvin-Benson-Bassham cycle enzymes during the induction of photosynthesis.
Collapse
Affiliation(s)
- Yuki Okegawa
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046 Japan
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, 603-8047 Japan
| | - Natsuki Tsuda
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, 603-8047 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046 Japan
| | - Ken Motohashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, 603-8047 Japan
| |
Collapse
|
2
|
Ma Y, Ma X, Gao X, Wu W, Zhou B. Light Induced Regulation Pathway of Anthocyanin Biosynthesis in Plants. Int J Mol Sci 2021; 22:ijms222011116. [PMID: 34681776 PMCID: PMC8538450 DOI: 10.3390/ijms222011116] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 01/05/2023] Open
Abstract
Anthocyanins are natural pigments with antioxidant effects that exist in various fruits and vegetables. The accumulation of anthocyanins is induced by environmental signals and regulated by transcription factors in plants. Numerous evidence has indicated that among the environmental factors, light is one of the most signal regulatory factors involved in the anthocyanin biosynthesis pathway. However, the signal transduction of light and molecular regulation of anthocyanin synthesis remains to be explored. Here, we focus on the research progress of signal transduction factors for positive and negative regulation in light-dependent and light-independent anthocyanin biosynthesis. In particular, we will discuss light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis in plants. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by transcription factors is discussed based on the significant progress.
Collapse
Affiliation(s)
- Yanyun Ma
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China; (Y.M.); (X.M.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xu Ma
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China; (Y.M.); (X.M.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China;
| | - Weilin Wu
- Agricultural College, Yanbian University, Yanji 133002, China
- Correspondence: (W.W.); (B.Z.); Tel.: +86-183-4338-8262 (W.W.); +86-0451-8219-1738 (B.Z.)
| | - Bo Zhou
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China; (Y.M.); (X.M.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (W.W.); (B.Z.); Tel.: +86-183-4338-8262 (W.W.); +86-0451-8219-1738 (B.Z.)
| |
Collapse
|
3
|
Abstract
Vitamin D plays an important role in maintaining a healthy mineralized skeleton. It is also considered an immunomodulatory agent that regulates innate and adaptive immune systems. The aim of this narrative review is to provide general concepts of vitamin D for the skeletal and immune health, and to summarize the mechanistic, epidemiological, and clinical evidence on the relationship between vitamin D and rheumatic diseases. Multiple observational studies have demonstrated the association between a low level of serum 25-hydroxyvitamin D [25(OH)D] and the presence and severity of several rheumatic diseases, such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), spondyloarthropathies, and osteoarthritis (OA). Nevertheless, the specific benefits of vitamin D supplements for the treatment and prevention of rheumatic diseases are less accepted as the results from randomized clinical trials are inconsistent, although some conceivable benefits of vitamin D for the improvement of disease activity of RA, SLE, and OA have been demonstrated in meta-analyses. It is also possible that some individuals might benefit from vitamin D differently than others, as inter-individual difference in responsiveness to vitamin D supplementation has been observed in genomic studies. Although the optimal level of serum 25(OH)D is still debatable, it is advisable it is advisable that patients with rheumatic diseases should maintain a serum 25(OH)D level of at least 30 ng/mL (75 nmol/L) to prevent osteomalacia, secondary osteoporosis, and fracture, and possibly 40–60 ng/mL (100–150 nmol/L) to achieve maximal benefit from vitamin D for immune health and overall health.
Collapse
Affiliation(s)
- Nipith Charoenngam
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, MA 02138, USA;
- Section Endocrinology, Diabetes, Nutrition and Weight Management, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| |
Collapse
|
4
|
Maher M, Ahmad H, Nishawy E, Li Y, Luo J. Novel Transcriptome Study and Detection of Metabolic Variations in UV-B-Treated Date Palm ( Phoenix dactylifera cv. Khalas). Int J Mol Sci 2021; 22:2564. [PMID: 33806362 PMCID: PMC7961990 DOI: 10.3390/ijms22052564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Date palm (Phoenix dactylifera) is one of the most widespread fruit crop species and can tolerate drastic environmental conditions that may not be suitable for other fruit species. Excess UV-B stress is one of the greatest concerns for date palm trees and can cause genotoxic effects. Date palm responds to UV-B irradiation through increased DEG expression levels and elaborates upon regulatory metabolic mechanisms that assist the plants in adjusting to this exertion. Sixty-day-old Khalas date palm seedlings (first true-leaf stage) were treated with UV-B (wavelength, 253.7 nm; intensity, 75 μW cm-2 for 72 h (16 h of UV light and 8 h of darkness). Transcriptome analysis revealed 10,249 and 12,426 genes whose expressions were upregulated and downregulated, respectively, compared to the genes in the control. Furthermore, the differentially expressed genes included transcription factor-encoding genes and chloroplast- and photosystem-related genes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to detect metabolite variations. Fifty metabolites, including amino acids and flavonoids, showed changes in levels after UV-B excess. Amino acid metabolism was changed by UV-B irradiation, and some amino acids interacted with precursors of different pathways that were used to synthesize secondary metabolites, i.e., flavonoids and phenylpropanoids. The metabolite content response to UV-B irradiation according to hierarchical clustering analysis showed changes in amino acids and flavonoids compared with those of the control. Amino acids might increase the function of scavengers of reactive oxygen species by synthesizing flavonoids that increase in response to UV-B treatment. This study enriches the annotated date palm unigene sequences and enhances the understanding of the mechanisms underlying UV-B stress through genetic manipulation. Moreover, this study provides a sequence resource for genetic, genomic and metabolic studies of date palm.
Collapse
Affiliation(s)
- Mohamed Maher
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (M.M.); (H.A.); (E.N.); (Y.L.)
- Department of Biochemistry, College of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Hasan Ahmad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (M.M.); (H.A.); (E.N.); (Y.L.)
- National Gene Bank, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Elsayed Nishawy
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (M.M.); (H.A.); (E.N.); (Y.L.)
- Desert Research Center, Genetics Resource Department, Egyptian Deserts Gene Bank, Cairo 11735, Egypt
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (M.M.); (H.A.); (E.N.); (Y.L.)
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; (M.M.); (H.A.); (E.N.); (Y.L.)
- Institute of Tropical Agriculture and Forestry of Hainan University, Haikou 570288, China
| |
Collapse
|
5
|
Fu S, Xue S, Chen J, Shang S, Xiao H, Zang Y, Tang X. Effects of Different Short-Term UV-B Radiation Intensities on Metabolic Characteristics of Porphyra haitanensis. Int J Mol Sci 2021; 22:ijms22042180. [PMID: 33671697 PMCID: PMC7927003 DOI: 10.3390/ijms22042180] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/03/2022] Open
Abstract
The effects of ultraviolet (UV) radiation, particularly UV-B on algae, have become an important issue as human-caused depletion of the protecting ozone layer has been reported. In this study, the effects of different short-term UV-B radiation on the growth, physiology, and metabolism of Porphyra haitanensis were examined. The growth of P. haitanensis decreased, and the bleaching phenomenon occurred in the thalli. The contents of total amino acids, soluble sugar, total protein, and mycosporine-like amino acids (MAAs) increased under different UV-B radiation intensities. The metabolic profiles of P. haitanensis differed between the control and UV-B radiation-treated groups. Most of the differential metabolites in P. haitanensis were significantly upregulated under UV-B exposure. Short-term enhanced UV-B irradiation significantly affected amino acid metabolism, carbohydrate metabolism, glutathione metabolism, and phenylpropane biosynthesis. The contents of phenylalanine, tyrosine, threonine, and serine were increased, suggesting that amino acid metabolism can promote the synthesis of UV-absorbing substances (such as phenols and MAAs) by providing precursor substances. The contents of sucrose, D-glucose-6-phosphate, and beta-D-fructose-6-phosphate were increased, suggesting that carbohydrate metabolism contributes to maintain energy supply for metabolic activity in response to UV-B exposure. Meanwhile, dehydroascorbic acid (DHA) was also significantly upregulated, denoting effective activation of the antioxidant system. To some extent, these results provide metabolic insights into the adaptive response mechanism of P. haitanensis to short-term enhanced UV-B radiation.
Collapse
Affiliation(s)
- Shimei Fu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou 256600, China;
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266000, China
- Correspondence: (Y.Z.); (X.T.)
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China; (S.F.); (S.X.); (J.C.); (H.X.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Correspondence: (Y.Z.); (X.T.)
| |
Collapse
|
6
|
Lovelett RJ, Zhao EM, Lalwani MA, Toettcher JE, Kevrekidis IG, L Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol 2021; 10:219-227. [PMID: 33492138 PMCID: PMC10410538 DOI: 10.1021/acssynbio.0c00372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic control of engineered microbes using light via optogenetics has been demonstrated as an effective strategy for improving the yield of biofuels, chemicals, and other products. An advantage of using light to manipulate microbial metabolism is the relative simplicity of interfacing biological and computer systems, thereby enabling in silico control of the microbe. Using this strategy for control and optimization of product yield requires an understanding of how the microbe responds in real-time to the light inputs. Toward this end, we present mechanistic models of a set of yeast optogenetic circuits. We show how these models can predict short- and long-time response to varying light inputs and how they are amenable to use with model predictive control (the industry standard among advanced control algorithms). These models reveal dynamics characterized by time-scale separation of different circuit components that affect the steady and transient levels of the protein under control of the circuit. Ultimately, this work will help enable real-time control and optimization tools for improving yield and consistency in the production of biofuels and chemicals using microbial fermentations.
Collapse
Affiliation(s)
- Robert J Lovelett
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton, New Jersey 08544, United States
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
7
|
Gawlik M, Savic V, Jovanovic M, Skibiński R. Mimicking of Phase I Metabolism Reactions of Molindone by HLM and Photocatalytic Methods with the Use of UHPLC-MS/MS. Molecules 2020; 25:E1367. [PMID: 32192164 PMCID: PMC7144366 DOI: 10.3390/molecules25061367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 01/30/2023] Open
Abstract
Establishing the metabolism pathway of the drug undergoing the hepatic biotransformation pathway is one of the most important aspects in the preclinical discovery process since the presence of toxic or reactive metabolites may result in drug withdrawal from the market. In this study, we present the structural elucidation of six, not described yet, metabolites of an antipsychotic molecule: molindone. The elucidation of metabolites was supported with a novel photocatalytical approach with the use of WO3 and WS2 assisted photochemical reactions. An UHPLC-ESI-Q-TOF combined system was used for the registration of all obtained metabolite profiles as well as to record the high resolution fragmentation spectra of the observed transformation products. As a reference in the in vitro metabolism simulation method, the incubation with human liver microsomes was used. Chemometric comparison of the obtained profiles pointed out the use of the WO3 approach as being more convenient in the field of drug metabolism studies. Moreover, the photocatalysis was used in the direction of the main drug metabolite synthesis in order to further isolation and characterization.
Collapse
Affiliation(s)
- Maciej Gawlik
- Department of Medicinal Chemistry, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 4, 20-090 Lublin, Poland;
| | - Vladimir Savic
- Department of Organic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (V.S.); (M.J.)
| | - Milos Jovanovic
- Department of Organic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (V.S.); (M.J.)
| | - Robert Skibiński
- Department of Medicinal Chemistry, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 4, 20-090 Lublin, Poland;
| |
Collapse
|
8
|
Zhu M, Geng S, Chakravorty D, Guan Q, Chen S, Assmann SM. Metabolomics of red-light-induced stomatal opening in Arabidopsis thaliana: Coupling with abscisic acid and jasmonic acid metabolism. Plant J 2020; 101:1331-1348. [PMID: 31677315 DOI: 10.1111/tpj.14594] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Environmental stimuli-triggered stomatal movement is a key physiological process that regulates CO2 uptake and water loss in plants. Stomata are defined by pairs of guard cells that perceive and transduce external signals, leading to cellular volume changes and consequent stomatal aperture change. Within the visible light spectrum, red light induces stomatal opening in intact leaves. However, there has been debate regarding the extent to which red-light-induced stomatal opening arises from direct guard cell sensing of red light versus indirect responses as a result of red light influences on mesophyll photosynthesis. Here we identify conditions that result in red-light-stimulated stomatal opening in isolated epidermal peels and enlargement of protoplasts, firmly establishing a direct guard cell response to red light. We then employ metabolomics workflows utilizing gas chromatography mass spectrometry and liquid chromatography mass spectrometry for metabolite profiling and identification of Arabidopsis guard cell metabolic signatures in response to red light in the absence of the mesophyll. We quantified 223 metabolites in Arabidopsis guard cells, with 104 found to be red light responsive. These red-light-modulated metabolites participate in the tricarboxylic acid cycle, carbon balance, phytohormone biosynthesis and redox homeostasis. We next analyzed selected Arabidopsis mutants, and discovered that stomatal opening response to red light is correlated with a decrease in guard cell abscisic acid content and an increase in jasmonic acid content. The red-light-modulated guard cell metabolome reported here provides fundamental information concerning autonomous red light signaling pathways in guard cells.
Collapse
Affiliation(s)
- Mengmeng Zhu
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sisi Geng
- The Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
| | - David Chakravorty
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Qijie Guan
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Sixue Chen
- The Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
9
|
Garmash EV, Velegzhaninov IO, Ermolina KV, Rybak AV, Malyshev RV. Altered levels of AOX1a expression result in changes in metabolic pathways in Arabidopsis thaliana plants acclimated to low dose rates of ultraviolet B radiation. Plant Sci 2020; 291:110332. [PMID: 31928662 DOI: 10.1016/j.plantsci.2019.110332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/28/2019] [Accepted: 11/02/2019] [Indexed: 05/27/2023]
Abstract
UV-B is a damaging component of solar radiation that inevitably reaches the Earth's surface. Plants have developed response mechanisms to adapt to UVB exposure. The alternative oxidase (AOX) catalyzes the ATP-uncoupling cyanide-resistant alternative pathway (AP) in plant mitochondria and is thought to be an important part of the cellular defense network under stress conditions. This study aimed to unravel the poorly understood functional significance of AOX1a induction in Arabidopsis thaliana leaves exposed to ecologically relevant doses of UVB radiation, by comparing wild-type (WT) plants with plants with modified expression of the AOX1a gene, either downregulated by antisense (AS-12) or overexpressed (XX-2). UVB exposure resulted in a phenotypic difference between lines. AOX1a overexpression resulted in the highest induction of AOX1A synthesis and MnSOD activity, and the lowest ROS level without pronounced changes in the phenotype relative to other genotypes. In AS-12 plants, expression of the majority of the genes encoding AOX was detected, other non-phosphorylating pathway components and antioxidant enzymes increased along with anthocyanin accumulation in leaves, and the ROS content was lower than in the WT. In addition to the expected AOX1 protein size (34 kDa), an AOX1 30 kDa band appeared under UVB exposure in all genotypes. However, in AS-12, the alterations in the transcript level and in the abundance of AOX1 protein isoforms induced by UVB could not fully functionally compensate for the lack of AOX1A. This was confirmed by the observed low AP capacity and increased levels of the oxidized form of ascorbate. These results highlight the importance of AOX in plant response to UVB for the control of a balanced metabolism, and indicate that AOX1a plays a key role in the regulation of the stress response.
Collapse
Affiliation(s)
- Elena V Garmash
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia.
| | - Ilya O Velegzhaninov
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Ksenia V Ermolina
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Anna V Rybak
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| | - Ruslan V Malyshev
- Institute of Biology, Komi Scientific Centre, Ural Branch, Russian Academy of Sciences, Syktyvkar, Russia
| |
Collapse
|
10
|
Sæbø Pettersen K, Sundaram AYM, Skjerdal T, Wasteson Y, Kijewski A, Lindbäck T, Aspholm M. Exposure to Broad-Spectrum Visible Light Causes Major Transcriptomic Changes in Listeria monocytogenes EGDe. Appl Environ Microbiol 2019; 85:e01462-19. [PMID: 31492665 PMCID: PMC6821972 DOI: 10.1128/aem.01462-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
Listeria monocytogenes, the causative agent of the serious foodborne disease listeriosis, can rapidly adapt to a wide range of environmental stresses, including visible light. This study shows that exposure of the L. monocytogenes EGDe strain to low-intensity, broad-spectrum visible light inhibited bacterial growth and caused altered multicellular behavior during growth on semisolid agar compared to when the bacteria were grown in complete darkness. These light-dependent changes were observed regardless of the presence of the blue light receptor (Lmo0799) and the stressosome regulator sigma B (SigB), which have been suggested to be important for the ability of L. monocytogenes to respond to blue light. A genome-wide transcriptional analysis revealed that exposure of L. monocytogenes EGDe to broad-spectrum visible light caused altered expression of 2,409 genes belonging to 18 metabolic pathways compared to bacteria grown in darkness. The light-dependent differentially expressed genes are involved in functions such as glycan metabolism, cell wall synthesis, chemotaxis, flagellar synthesis, and resistance to oxidative stress. Exposure to light conferred reduced bacterial motility in semisolid agar, which correlates well with the light-dependent reduction in transcript levels of flagellar and chemotaxis genes. Similar light-induced reduction in growth and motility was also observed in two different L. monocytogenes food isolates, suggesting that these responses are typical for L. monocytogenes Together, the results show that even relatively small doses of broad-spectrum visible light cause genome-wide transcriptional changes, reduced growth, and motility in L. monocytogenesIMPORTANCE Despite major efforts to control L. monocytogenes, this pathogen remains a major problem for the food industry, where it poses a continuous risk of food contamination. The ability of L. monocytogenes to sense and adapt to different stressors in the environment enables it to persist in many different niches, including food production facilities and in food products. The present study shows that exposure of L. monocytogenes to low-intensity broad-spectrum visible light reduces its growth and motility and alters its multicellular behavior. Light exposure also caused genome-wide changes in transcript levels, affecting multiple metabolic pathways, which are likely to influence the bacterial physiology and lifestyle. In practical terms, the data presented in this study suggest that broad-spectrum visible light is an important environmental variable to consider as a strategy to improve food safety by reducing L. monocytogenes contamination in food production environments.
Collapse
Affiliation(s)
- Kristin Sæbø Pettersen
- Norwegian Veterinary Institute, Oslo, Norway
- Norwegian University of Life Sciences, Oslo, Norway
| | - Arvind Y M Sundaram
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Intense efforts have been devoted to describe the biochemical pathway of plant sulphur (S) assimilation from sulphate. However, essential information on metabolic regulation of S assimilation is still lacking, such as possible interactions between S assimilation, photosynthesis and photorespiration. In particular, does S assimilation scale with photosynthesis thus ensuring sufficient S provision for amino acids synthesis? This lack of knowledge is problematic because optimization of photosynthesis is a common target of crop breeding and furthermore, photosynthesis is stimulated by the inexorable increase in atmospheric CO2. Here, we used high-resolution 33S and 13C tracing technology with NMR and LC-MS to access direct measurement of metabolic fluxes in S assimilation, when photosynthesis and photorespiration are varied via the gaseous composition of the atmosphere (CO2, O2). We show that S assimilation is stimulated by photorespiratory metabolism and therefore, large photosynthetic fluxes appear to be detrimental to plant cell sulphur nutrition.
Collapse
Affiliation(s)
- Cyril Abadie
- Research School of Biology, Australian National University, Canberra, ACT 2601 Australia
- Present Address: IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, 49071 Angers, Beaucouzé France
| | - Guillaume Tcherkez
- Research School of Biology, Australian National University, Canberra, ACT 2601 Australia
| |
Collapse
|
12
|
Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE. Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol 2019; 222:1364-1379. [PMID: 30636322 PMCID: PMC6594073 DOI: 10.1111/nph.15685] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/20/2018] [Indexed: 05/07/2023]
Abstract
Photoacclimation consists of short- and long-term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse-grained models to predict light-dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species-specific strategies and fitness, is not accounted for in these simple models. We incorporated photophysiology experimental data with genome-scale modeling to characterize organism-level, light-dependent metabolic changes in the model diatom Phaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition-specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities. Photorespiration, an ornithine-glutamine shunt, and branched-chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms. Our results suggest a flexible metabolic network in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.
Collapse
Affiliation(s)
- Jared T. Broddrick
- Division of Biological SciencesUC San DiegoLa JollaCA92093USA
- Department of BioengineeringUC San DiegoLa JollaCA92093USA
| | - Niu Du
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
| | | | - Yoshinori Tsuji
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | - Denis Jallet
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Maxwell A. Ware
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Graham Peers
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Yusuke Matsuda
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | | | - B. Greg Mitchell
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
| | | | - Andrew E. Allen
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
| |
Collapse
|
13
|
Ciesielska S, Bil P, Gajda K, Poterala-Hejmo A, Hudy D, Rzeszowska-Wolny J. Cell type-specific differences in redox regulation and proliferation after low UVA doses. PLoS One 2019; 14:e0205215. [PMID: 30682016 PMCID: PMC6347369 DOI: 10.1371/journal.pone.0205215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/04/2019] [Indexed: 01/09/2023] Open
Abstract
Ultraviolet A (UVA) radiation is harmful for living organisms but in low doses may stimulate cell proliferation. Our aim was to examine the relationships between exposure to different low UVA doses, cellular proliferation, and changes in cellular reactive oxygen species levels. In human colon cancer (HCT116) and melanoma (Me45) cells exposed to UVA doses comparable to environmental, the highest doses (30–50 kJ/m2) reduced clonogenic potential but some lower doses (1 and 10 kJ/m2) induced proliferation. This effect was cell type and dose specific. In both cell lines the levels of reactive oxygen species and nitric oxide fluctuated with dynamics which were influenced differently by UVA; in Me45 cells decreased proliferation accompanied the changes in the dynamics of H2O2 while in HCT116 cells those of superoxide. Genes coding for proteins engaged in redox systems were expressed differently in each cell line; transcripts for thioredoxin, peroxiredoxin and glutathione peroxidase showed higher expression in HCT116 cells whereas those for glutathione transferases and copper chaperone were more abundant in Me45 cells. We conclude that these two cell types utilize different pathways for regulating their redox status. Many mechanisms engaged in maintaining cellular redox balance have been described. Here we show that the different cellular responses to a stimulus such as a specific dose of UVA may be consequences of the use of different redox control pathways. Assays of superoxide and hydrogen peroxide level changes after exposure to UVA may clarify mechanisms of cellular redox regulation and help in understanding responses to stressing factors.
Collapse
Affiliation(s)
- Sylwia Ciesielska
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Patryk Bil
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Karolina Gajda
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Aleksandra Poterala-Hejmo
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Dorota Hudy
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Joanna Rzeszowska-Wolny
- Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
- * E-mail:
| |
Collapse
|
14
|
Ferguson DCJ, Smerdon GR, Harries LW, Dodd NJF, Murphy MP, Curnow A, Winyard PG. Altered cellular redox homeostasis and redox responses under standard oxygen cell culture conditions versus physioxia. Free Radic Biol Med 2018; 126:322-333. [PMID: 30142453 DOI: 10.1016/j.freeradbiomed.2018.08.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 08/20/2018] [Indexed: 01/16/2023]
Abstract
In vivo, mammalian cells reside in an environment of 0.5-10% O2 (depending on the tissue location within the body), whilst standard in vitro cell culture is carried out under room air. Little is known about the effects of this hyperoxic environment on treatment-induced oxidative stress, relative to a physiological oxygen environment. In the present study we investigated the effects of long-term culture under hyperoxia (air) on photodynamic treatment. Upon photodynamic irradiation, cells which had been cultured long-term under hyperoxia generated higher concentrations of mitochondrial reactive oxygen species, compared with cells in a physioxic (2% O2) environment. However, there was no significant difference in viability between hyperoxic and physioxic cells. The expression of genes encoding key redox homeostasis proteins and the activity of key antioxidant enzymes was significantly higher after the long-term culture of hyperoxic cells compared with physioxic cells. The induction of antioxidant genes and increased antioxidant enzyme activity appear to contribute to the development of a phenotype that is resistant to oxidative stress-induced cellular damage and death when using standard cell culture conditions. The results from experiments using selective inhibitors suggested that the thioredoxin antioxidant system contributes to this phenotype. To avoid artefactual results, in vitro cellular responses should be studied in mammalian cells that have been cultured under physioxia. This investigation provides new insights into the effects of physioxic cell culture on a model of a clinically relevant photodynamic treatment and the associated cellular pathways.
Collapse
Affiliation(s)
| | - Gary R Smerdon
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK; DDRC Healthcare, Plymouth Science Park, Research Way, Plymouth, Devon PL6 8BU, UK
| | - Lorna W Harries
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK
| | | | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alison Curnow
- University of Exeter Medical School, Truro, Cornwall TR1 3HD, UK
| | - Paul G Winyard
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK.
| |
Collapse
|
15
|
Laiakis EC, Mak TD, Strawn SJ, Wang YW, Moon BH, Ake P, Fornace AJ. Global metabolomic responses in urine from atm deficient mice in response to LD 50/30 gamma irradiation doses. Environ Mol Mutagen 2018; 59:576-585. [PMID: 30095186 PMCID: PMC6113093 DOI: 10.1002/em.22202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/09/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Exposures to ionizing radiation (IR) may either be accidental or intentional, for medical purposes or even through terrorist actions. As certain populations emerge to be more radiosensitive than others, it is imperative to assess those individuals and treat them accordingly. To demonstrate the feasibility of rapid identification of such cases, we utilized the highly radiosensitive mouse model Atm-/- in the C57BL/6 background, and evaluated the urinary responses in 8-10 week old male mice at early time points (4, 24, and 72 h) after exposure to their respective LD50/30 doses [4 Gy for Atm-/- , and 8 Gy for wild type (WT)]. Urinary profiles from heterozygous animals exhibited remarkably similar responses to WT before and after radiation exposure. However, genotypic differences (WT or Atm-/- ) were the primary driver to responses to radiation. Putative metabolites were validated through tandem mass spectrometry and included riboflavin, uric acid, d-ribose, d-glucose, pantothenic acid, taurine, kynurenic acid, xanthurenic acid, 2-oxoadipic acid, glutaric acid, 5'-deoxy-5'-methylthioadenosine, and hippuric acid. These metabolites mapped to several interconnected metabolic pathways which suggest that radiosensitive mouse models have underlying differences significantly impacting overall metabolism. This was further amplified by ionizing radiation at different time points. This study further emphasizes that genetically based radiosensitivity is reflected in the metabolic processes, and can be directly observed in urine. These differences in turn can potentially be used to identify individuals that may require altered medical treatment in an emergency radiological situation or modification of a regimen during a radiotherapy session. Environ. Mol. Mutagen. 59:576-585, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Evagelia C Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington DC, USA
| | - Tytus D Mak
- Mass Spectrometry Data Center, National Institute of Standards and Technology (NIST), Gaithersburg MD, USA
| | - Steven J Strawn
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington DC, USA
| | - Yi-Wen Wang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington DC, USA
| | - Bo-Hyun Moon
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | - Pelagie Ake
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | - Albert J Fornace
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington DC, USA
| |
Collapse
|
16
|
Chen R, Nemeth D, Mora J, Muvvala M, Wu D, Griko Y. Changes in Differential Expression of Genes in Normal and Metabolically Suppressed Mice in Response to Radiation. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:5826-5829. [PMID: 30441660 DOI: 10.1109/embc.2018.8513624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Differential gene expression profiles of mice in active and metabolically suppressed states were evaluated in response to a sublethal dose of gamma radiation to identify the beneficial protective effects of suspended animation. Results demonstrated that nearly 90% suppression of metabolic functions in mice lead to significant changes in gene expression profile of different metabolic pathways responsible for adaptation and maintenance of homeostasis in the new physiological state of suspended animation. This state was found sustainable during 18 hrs of experiment and can be reversed back to the normal active state without any visible effects on physiological and behavioral functions of mice. Gene expression during induced states was gathered via Illumina microarray methods. Further analysis of differential gene expressions yielded a result that a hypometabolic state may be responsible for short term and long-term radioprotection.
Collapse
|
17
|
Kitazaki K, Fukushima A, Nakabayashi R, Okazaki Y, Kobayashi M, Mori T, Nishizawa T, Reyes-Chin-Wo S, Michelmore RW, Saito K, Shoji K, Kusano M. Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs. Sci Rep 2018; 8:7914. [PMID: 29784957 PMCID: PMC5962576 DOI: 10.1038/s41598-018-25686-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m-2·s-1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.
Collapse
Affiliation(s)
- Kazuyoshi Kitazaki
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Kazuhiro Shoji
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan.
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| |
Collapse
|
18
|
Celeste Dias M, Pinto DCGA, Correia C, Moutinho-Pereira J, Oliveira H, Freitas H, Silva AMS, Santos C. UV-B radiation modulates physiology and lipophilic metabolite profile in Olea europaea. J Plant Physiol 2018; 222:39-50. [PMID: 29407548 DOI: 10.1016/j.jplph.2018.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 05/25/2023]
Abstract
Ultraviolet-B (UV-B) radiation plays an important role in plant photomorphogenesis. Whilst the morpho-functional disorders induced by excessive UV irradiation are well-known, it remains unclear how this irradiation modulates the metabolome, and which metabolic shifts improve plants' tolerance to UV-B. In this study, we use an important Mediterranean crop, Olea europaea, to decipher the impacts of enhanced UV-B radiation on the physiological performance and lipophilic metabolite profile. Young olive plants (cv. 'Galega Vulgar') were exposed for five days to UV-B biologically effective doses of 6.5 kJ m-2 d-1 and 12.4 kJ m-2 d-1. Cell cycle/ploidy, photosynthesis and oxidative stress, as well as GC-MS metabolites were assessed. Both UV-B treatments impaired net CO2 assimilation rate, transpiration rate, photosynthetic pigments, and RuBisCO activity, but 12.4 kJ m-2 d-1 also decreased the photochemical quenching (qP) and the effective efficiency of PSII (ΦPSII). UV-B treatments promoted mono/triperpene pathways, while only 12.4 kJ m-2 d-1 increased fatty acids and alkanes, and decreased geranylgeranyl-diphosphate. The interplay between physiology and metabolomics suggests some innate ability of these plants to tolerate moderate UV-B doses (6.5 kJ m-2 d-1). Also their tolerance to higher doses (12.4 kJ m-2 d-1) relies on plants' metabolic adjustments, where the accumulation of specific compounds such as long-chain alkanes, palmitic acid, oleic acid and particularly oleamide (which is described for the first time in olive leaves) play an important protective role. This is the first study demonstrating photosynthetic changes and lipophilic metabolite adjustments in olive leaves under moderate and high UV-B doses.
Collapse
Affiliation(s)
- Maria Celeste Dias
- Department of Life Sciences & CFE, Faculty of Sciences and Technologies, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Diana C G A Pinto
- Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Correia
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Apt. 1013, 5000-801 Vila Real, Portugal
| | - José Moutinho-Pereira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Apt. 1013, 5000-801 Vila Real, Portugal
| | - Helena Oliveira
- Department Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Chemistry & CICECO, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Helena Freitas
- Department of Life Sciences & CFE, Faculty of Sciences and Technologies, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Artur M S Silva
- Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Conceição Santos
- Department of Biology, LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| |
Collapse
|
19
|
Kaiser E, Morales A, Harbinson J. Fluctuating Light Takes Crop Photosynthesis on a Rollercoaster Ride. Plant Physiol 2018; 176:977-989. [PMID: 29046421 PMCID: PMC5813579 DOI: 10.1104/pp.17.01250] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/16/2017] [Indexed: 05/18/2023]
Abstract
Crops are regularly exposed to frequent irradiance fluctuations, which decrease their integrated CO2 assimilation and affect their phenotype.
Collapse
Affiliation(s)
- Elias Kaiser
- Horticulture and Product Physiology Group, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Alejandro Morales
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Jeremy Harbinson
- Horticulture and Product Physiology Group, Wageningen University, 6700 AA Wageningen, The Netherlands
| |
Collapse
|
20
|
Slattery RA, Walker BJ, Weber APM, Ort DR. The Impacts of Fluctuating Light on Crop Performance. Plant Physiol 2018; 176:990-1003. [PMID: 29192028 PMCID: PMC5813574 DOI: 10.1104/pp.17.01234] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/27/2017] [Indexed: 05/18/2023]
Abstract
Rapidly changing light conditions can reduce carbon gain and productivity in field crops because photosynthetic responses to light fluctuations are not instantaneous. Plant responses to fluctuating light occur across levels of organizational complexity from entire canopies to the biochemistry of a single reaction and across orders of magnitude of time. Although light availability and variation at the top of the canopy are largely dependent on the solar angle and degree of cloudiness, lower crop canopies rely more heavily on light in the form of sunflecks, the quantity of which depends mostly on canopy structure but also may be affected by wind. The ability of leaf photosynthesis to respond rapidly to these variations in light intensity is restricted by the relatively slow opening/closing of stomata, activation/deactivation of C3 cycle enzymes, and up-regulation/down-regulation of photoprotective processes. The metabolic complexity of C4 photosynthesis creates the apparently contradictory possibilities that C4 photosynthesis may be both more and less resilient than C3 to dynamic light regimes, depending on the frequency at which these light fluctuations occur. We review the current understanding of the underlying mechanisms of these limitations to photosynthesis in fluctuating light that have shown promise in improving the response times of photosynthesis-related processes to changes in light intensity.
Collapse
Affiliation(s)
- Rebecca A Slattery
- Global Change and Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Berkley J Walker
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Duesseldorf, Germany 40225
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Duesseldorf, Germany 40225
| | - Donald R Ort
- Global Change and Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
21
|
Jung ES, Park HM, Hyun SM, Shon JC, Singh D, Liu KH, Whon TW, Bae JW, Hwang JS, Lee CH. The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure. PLoS One 2017; 12:e0187154. [PMID: 29117187 PMCID: PMC5695601 DOI: 10.1371/journal.pone.0187154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/13/2017] [Indexed: 01/22/2023] Open
Abstract
The attenuating effects of green tea supplements (GTS) against the ultraviolet (UV) radiation induced skin damages are distinguished. However, the concomitant effects of GTS on the large intestinal microbiomes and associated metabolomes are largely unclear. Herein, we performed an integrated microbiome-metabolome analysis to uncover the esoteric links between gut microbiome and exo/endogenous metabolome maneuvered in the large intestine of UVB-exposed mice subjected to dietary GTS. In UVB-exposed mice groups (UVB), class Bacilli and order Bifidobacteriales were observed as discriminant taxa with decreased lysophospholipid levels compared to the unexposed mice groups subjected to normal diet (NOR). Conversely, in GTS fed UVB-exposed mice (U+GTS), the gut-microbiome diversity was greatly enhanced with enrichment in the classes, Clostridia and Erysipelotrichia, as well as genera, Allobaculum and Lachnoclostridium. Additionally, the gut endogenous metabolomes changed with an increase in amino acids, fatty acids, lipids, and bile acids contents coupled with a decrease in nucleobases and carbohydrate levels. The altered metabolomes exhibited high correlations with GTS enriched intestinal microflora. Intriguingly, the various conjugates of green tea catechins viz., sulfated, glucuronided, and methylated ones including their exogenous derivatives were detected from large intestinal contents and liver samples. Hence, we conjecture that the metabolic conversions for the molecular components in GTS strongly influenced the gut micro-environment in UVB-exposed mice groups, ergo modulate their gut-microbiome as well as exo/endogenous metabolomes.
Collapse
Affiliation(s)
- Eun Sung Jung
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Hye Min Park
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Hyun
- Department of Genetic Engineering & Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Jong Cheol Shon
- College of Pharmacy and Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Kwang-Hyeon Liu
- College of Pharmacy and Research Institute of Pharmaceutical Science, Kyungpook National University, Daegu, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Jae Sung Hwang
- Department of Genetic Engineering & Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- * E-mail: (JSH); (CHL)
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
- * E-mail: (JSH); (CHL)
| |
Collapse
|
22
|
Casero D, Gill K, Sridharan V, Koturbash I, Nelson G, Hauer-Jensen M, Boerma M, Braun J, Cheema AK. Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome. Microbiome 2017; 5:105. [PMID: 28821301 PMCID: PMC5563039 DOI: 10.1186/s40168-017-0325-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/08/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel. RESULTS Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the gut microbiome. These were accompanied by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the predicted metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the host's cellular damage repair processes. The observed radiation-induced changes in microbiota diversity and composition were analyzed at the functional level. A constitutive change in activity was found for several pathways dominated by microbiome-specific enzymatic reactions like carbohydrate digestion and absorption and lipopolysaccharide biosynthesis, while the activity in other radiation-responsive pathways like phosphatidylinositol signaling could be linked to dose-dependent changes in the abundance of specific taxa. CONCLUSIONS The implication of microbiome-mediated pathophysiology after low dose ionizing radiation may be an unappreciated biologic hazard of space travel and deserves experimental validation. This study provides a conceptual and analytical basis of further investigations to increase our understanding of the chronic effects of space radiation on human health, and points to potential new targets for intervention in adverse radiation effects.
Collapse
Affiliation(s)
- David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kirandeep Gill
- Department of Oncology, Georgetown University Medical Center, Washington DC, 20057, USA
| | - Vijayalakshmi Sridharan
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gregory Nelson
- Department of Radiation Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Martin Hauer-Jensen
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Marjan Boerma
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Amrita K Cheema
- Department of Oncology, Georgetown University Medical Center, Washington DC, 20057, USA.
- Department of Biochemistry and Molecular and & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA.
- GCD-7N Pre-Clinical Science Building, 3900 Reservoir Road NW, Washington DC, 20057, USA.
| |
Collapse
|
23
|
Zhang Q, Liu M, Ruan J. Metabolomics analysis reveals the metabolic and functional roles of flavonoids in light-sensitive tea leaves. BMC Plant Biol 2017; 17:64. [PMID: 28320327 PMCID: PMC5359985 DOI: 10.1186/s12870-017-1012-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/09/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND As the predominant secondary metabolic pathway in tea plants, flavonoid biosynthesis increases with increasing temperature and illumination. However, the concentration of most flavonoids decreases greatly in light-sensitive tea leaves when they are exposed to light, which further improves tea quality. To reveal the metabolism and potential functions of flavonoids in tea leaves, a natural light-sensitive tea mutant (Huangjinya) cultivated under different light conditions was subjected to metabolomics analysis. RESULTS The results showed that chlorotic tea leaves accumulated large amounts of flavonoids with ortho-dihydroxylated B-rings (e.g., catechin gallate, quercetin and its glycosides etc.), whereas total flavonoids (e.g., myricetrin glycoside, epigallocatechin gallate etc.) were considerably reduced, suggesting that the flavonoid components generated from different metabolic branches played different roles in tea leaves. Furthermore, the intracellular localization of flavonoids and the expression pattern of genes involved in secondary metabolic pathways indicate a potential photoprotective function of dihydroxylated flavonoids in light-sensitive tea leaves. CONCLUSIONS Our results suggest that reactive oxygen species (ROS) scavenging and the antioxidation effects of flavonoids help chlorotic tea plants survive under high light stress, providing new evidence to clarify the functional roles of flavonoids, which accumulate to high levels in tea plants. Moreover, flavonoids with ortho-dihydroxylated B-rings played a greater role in photo-protection to improve the acclimatization of tea plants.
Collapse
Affiliation(s)
- Qunfeng Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058 China
- Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, South Meiling Road 9, Hangzhou, Zhejiang 310008 China
| | - Meiya Liu
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058 China
- Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, South Meiling Road 9, Hangzhou, Zhejiang 310008 China
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310058 China
- Key Laboratory for Plant Biology and Resource Application of Tea, the Ministry of Agriculture, South Meiling Road 9, Hangzhou, Zhejiang 310008 China
| |
Collapse
|
24
|
Roś-Mazurczyk M, Wojakowska A, Marczak Ł, Polański K, Pietrowska M, Jelonek K, Domińczyk I, Hajduk A, Rutkowski T, Składowski K, Widłak P. Ionizing radiation affects profile of serum metabolites: increased level of 3-hydroxybutyric acid in serum of cancer patients treated with radiotherapy. Acta Biochim Pol 2016; 64:189-193. [PMID: 27815965 DOI: 10.18388/abp.2016_1301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/06/2016] [Accepted: 07/14/2016] [Indexed: 11/10/2022]
Abstract
Radiotherapy causes molecular changes observed at the level of body fluids, which are potential biomarker candidates for assessment of radiation exposure. Here we analyzed radiotherapy-induced changes in a profile of small metabolites detected in sera of head and neck cancer patients using the gas chromatography coupled with mass spectrometry approach. There were about 20 compounds, including carboxylic acids, sugars, amines and amino acids, whose levels significantly differed between pre-treatment and post-treatment samples. Among metabolites upregulated by radiotherapy there was 3-hydroxybutyric acid, whose level increased about three times in post-treatment samples. Moreover, compounds affected by irradiation were associated with several metabolic pathways, including protein biosynthesis and amino acid metabolism.
Collapse
Affiliation(s)
| | - Anna Wojakowska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
| | - Krzysztof Polański
- Warwick Systems Biology Centre, University of Warwick, Warwick, United Kingdom
| | - Monika Pietrowska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Karol Jelonek
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Iwona Domińczyk
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Agata Hajduk
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Tomasz Rutkowski
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Krzysztof Składowski
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Piotr Widłak
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
| |
Collapse
|
25
|
Danchenko M, Klubicova K, Krivohizha MV, Berezhna VV, Sakada VI, Hajduch M, Rashydov NM. [Not Available]. Tsitol Genet 2016; 50:60-79. [PMID: 30484603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The paper discusses different methodological approaches to the study of transgenerational alterations of metabolic pathways in soybean and flax seeds in the process of adaptation to chronic irradiation in the Chernobyl alienation zone. A combination of general biological methods and novel approaches, such as genomics, proteomics, cytogenetics, and mutagenesis, allows researchers to analyze an organism’s systemic response and identify the latent chronic irradiation effects in plants from the Chernobyl zone. The proteomic approaches are especially efficient, since they range from the identification of changes in abundance and folding of individual proteins to the characterization of posttranslational modifications, trends of qualitative changes during seed maturation, or protein-protein interactions during plant growth and development under permanent impacts of stress factors. The application of proteomics opens new horizons in the understanding of the hidden mechanisms behind the impact of chronic low-dose radiation on living cells and makes it possible to visualize metabolic network alterations regardless of their transcriptional, translational, or epigenetic nature.
Collapse
|
26
|
Wu C, Liu D, Yang X, Wu R, Zhang J, Huang J, He H. Improving Production of Protease from Pseudoalteromonas sp. CSN423 by Random Mutagenesis. Mar Biotechnol (NY) 2016; 18:610-618. [PMID: 27752851 DOI: 10.1007/s10126-016-9721-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/25/2016] [Indexed: 06/06/2023]
Abstract
Pseudoalteromonas sp. CSN423, a marine strain, can express a major protease designated as E423 and it was secreted into the supernatant. To improve the protease E423 yield, Pseudoalteromonas sp. CSN423 was subjected to mutagenesis using UV irradiation. Mutant strain with 5.1-fold higher protease yield was isolated and named as Pseudoalteromonas sp. CSN423-M. Three protease bands were detected by zymography with casein as substrate, and results of mass spectrometry (MS) showed that two lower molecular weight protein bands were the same protease but with different mature forms. The entire protease operon was sequenced and no mutation was found. Mutant strain-associated changes of expression levels of protease synthesis and secretion-related genes were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Mutant strain had higher expression of e423 than wild-type strain. Such result was consistent with protease activity profiles. Moreover, the mutant strain had higher transcriptional levels of citrate synthase (cs), α-ketoglutarate decarboxylase (kgd), cytochrome c oxidase subunit I (coxI), tolC, hlyD (membrane protein), luxR3, luxO, and luxT (transcriptional regulator). However, hexokinase (hk), pyruvate dehydrogenase E1 (pd-e1), epsD (membrane protein), and luxR1 remained unchanged, and luxR2 decreased sharply in the mutant. These results suggested that the redox pathway was promoted in the mutant strain, and LuxR family transcriptional regulators in Pseudoalteromonas spp. may play some role in regulating protease expression. Meanwhile, the secretion of extracellular protease was closely related to ABC transport system. These results may shed some light on the molecular mechanism underlying higher yield of protease E423 from Pseudoalteromonas sp. CSN423-M.
Collapse
Affiliation(s)
- Cuiling Wu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
- Department of Biochemistry, Changzhi Medical College, Changzhi, 046000, China
| | - Dan Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
| | - Xinghao Yang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
| | - Ribang Wu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
| | - Jiang Zhang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
| | - Jiafeng Huang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China
| | - Hailun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, 410013, China.
| |
Collapse
|
27
|
Brooks AL, Hoel DG, Preston RJ. The role of dose rate in radiation cancer risk: evaluating the effect of dose rate at the molecular, cellular and tissue levels using key events in critical pathways following exposure to low LET radiation. Int J Radiat Biol 2016; 92:405-26. [PMID: 27266588 PMCID: PMC4975094 DOI: 10.1080/09553002.2016.1186301] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/14/2016] [Accepted: 05/02/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE This review evaluates the role of dose rate on cell and molecular responses. It focuses on the influence of dose rate on key events in critical pathways in the development of cancer. This approach is similar to that used by the U.S. EPA and others to evaluate risk from chemicals. It provides a mechanistic method to account for the influence of the dose rate from low-LET radiation, especially in the low-dose region on cancer risk assessment. Molecular, cellular, and tissues changes are observed in many key events and change as a function of dose rate. The magnitude and direction of change can be used to help establish an appropriate dose rate effectiveness factor (DREF). CONCLUSIONS Extensive data on key events suggest that exposure to low dose-rates are less effective in producing changes than high dose rates. Most of these data at the molecular and cellular level support a large (2-30) DREF. In addition, some evidence suggests that doses delivered at a low dose rate decrease damage to levels below that observed in the controls. However, there are some data human and mechanistic data that support a dose-rate effectiveness factor of 1. In summary, a review of the available molecular, cellular and tissue data indicates that not only is dose rate an important variable in understanding radiation risk but it also supports the selection of a DREF greater than one as currently recommended by ICRP ( 2007 ) and BEIR VII (NRC/NAS 2006 ).
Collapse
Affiliation(s)
- Antone L. Brooks
- Retired Professor, Environmental Science, Washington State University,
Richland,
Washington,
USA
| | - David G. Hoel
- Medical University of South Carolina, Epidemiology,
Charleston South Carolina,
USA
| | - R. Julian Preston
- US Environmental Protection Agency, National Health and Environmental Effects Research Laboratory (NHEERL) (MD B105-01), RTP,
USA
| |
Collapse
|
28
|
Boeing S, Williamson L, Encheva V, Gori I, Saunders RE, Instrell R, Aygün O, Rodriguez-Martinez M, Weems JC, Kelly GP, Conaway JW, Conaway RC, Stewart A, Howell M, Snijders AP, Svejstrup JQ. Multiomic Analysis of the UV-Induced DNA Damage Response. Cell Rep 2016; 15:1597-1610. [PMID: 27184836 PMCID: PMC4893159 DOI: 10.1016/j.celrep.2016.04.047] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/25/2016] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining. Besides uncovering roles in the DNA damage response for numerous proteins and complexes, including Integrator, Cohesin, PHF3, ASC-1, SCAF4, SCAF8, and SCAF11, we uncovered a role for the poorly studied, melanoma-associated serine/threonine kinase 19 (STK19). Besides effectively uncovering relevant factors, the multiomic approach also provides a systems-wide overview of the diverse cellular processes connected to the transcription-related DNA damage response.
Collapse
Affiliation(s)
- Stefan Boeing
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK; Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Laura Williamson
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Ilaria Gori
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rebecca E Saunders
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rachael Instrell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ozan Aygün
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Marta Rodriguez-Martinez
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Juston C Weems
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gavin P Kelly
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Aengus Stewart
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Michael Howell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK.
| |
Collapse
|
29
|
Jang WG, Park JY, Lee J, Bang E, Kim SR, Lee EK, Yun HJ, Kang CM, Hwang GS. Investigation of relative metabolic changes in the organs and plasma of rats exposed to X-ray radiation using HR-MAS (1)H NMR and solution (1)H NMR. NMR Biomed 2016; 29:507-518. [PMID: 26871685 DOI: 10.1002/nbm.3485] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
Excess exposure to ionizing radiation generates reactive oxygen species and increases the cellular inflammatory response by modifying various metabolic pathways. However, an investigation of metabolic perturbations and organ-specific responses based on the amount of radiation during the acute phase has not been conducted. In this study, high-resolution magic-angle-spinning (HR-MAS) NMR and solution NMR-based metabolic profiling were used to investigate dose-dependent metabolic changes in multiple organs and tissues--including the jejunum, spleen, liver, and plasma--of rats exposed to X-ray radiation. The organs, tissues, and blood samples were obtained 24, 48, and 72 h after exposure to low-dose (2 Gy) and high-dose (6 Gy) X-ray radiation and subjected to metabolite profiling and multivariate analyses. The results showed the time course of the metabolic responses, and many significant changes were detected in the high-dose compared with the low-dose group. Metabolites with antioxidant properties showed acute responses in the jejunum and spleen after radiation exposure. The levels of metabolites related to lipid and protein metabolism were decreased in the jejunum. In addition, amino acid levels increased consistently at all post-irradiation time points as a consequence of activated protein breakdown. Consistent with these changes, plasma levels of tricarboxylic acid cycle intermediate metabolites decreased. The liver did not appear to undergo remarkable metabolic changes after radiation exposure. These results may provide insight into the major metabolic perturbations and mechanisms of the biological systems in response to pathophysiological damage caused by X-ray radiation.
Collapse
Affiliation(s)
- Won Gyo Jang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Ju Yeon Park
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Jueun Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
- Department of Chemistry, Sungkyunkwan University, Suwon, Republic of Korea
| | - Eunjung Bang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - So Ra Kim
- Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Eun Kyeong Lee
- Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Hyun Jin Yun
- Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Chang-Mo Kang
- Division of Radiation Effect, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| |
Collapse
|
30
|
He H, Willems LAJ, Batushansky A, Fait A, Hanson J, Nijveen H, Hilhorst HWM, Bentsink L. Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways. Plant Cell Physiol 2016; 57:473-87. [PMID: 26738545 DOI: 10.1093/pcp/pcv207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/22/2015] [Indexed: 05/20/2023]
Abstract
Seed performance is affected by the seed maturation environment, and previously we have shown that temperature, nitrate and light intensity were the most influential environmental factors affecting seed performance. Seeds developed in these environments were selected to assess the underlying metabolic pathways, using a combination of transcriptomics and metabolomics. These analyses revealed that the effects of the parental temperature and nitrate environments were reflected by partly overlapping genetic and metabolic networks, as indicated by similar changes in the expression levels of metabolites and transcripts. Nitrogen metabolism-related metabolites (asparagine, γ-aminobutyric acid and allantoin) were significantly decreased in both low temperature (15 °C) and low nitrate (N0) maturation environments. Correspondingly, nitrogen metabolism genes (ALLANTOINASE, NITRATE REDUCTASE 1, NITRITE REDUCTASE 1 and NITRILASE 4) were differentially regulated in the low temperature and nitrate maturation environments, as compared with control conditions. High light intensity during seed maturation increased galactinol content, and displayed a high correlation with seed longevity. Low light had a genotype-specific effect on cell surface-encoding genes in the DELAY OF GERMINATION 6-near isogenic line (NILDOG6). Overall, the integration of phenotypes, metabolites and transcripts led to new insights into the regulation of seed performance.
Collapse
Affiliation(s)
- Hanzi He
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Albert Batushansky
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben-Gurion, Israel
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben-Gurion, Israel
| | - Johannes Hanson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden Department of Molecular Plant Physiology, Utrecht University, NL-3584 CH Utrecht, The Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Leónie Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands Department of Molecular Plant Physiology, Utrecht University, NL-3584 CH Utrecht, The Netherlands
| |
Collapse
|
31
|
Gil-Lozano M, Hunter PM, Behan LA, Gladanac B, Casper RF, Brubaker PL. Short-term sleep deprivation with nocturnal light exposure alters time-dependent glucagon-like peptide-1 and insulin secretion in male volunteers. Am J Physiol Endocrinol Metab 2016; 310:E41-50. [PMID: 26530153 DOI: 10.1152/ajpendo.00298.2015] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/26/2015] [Indexed: 01/30/2023]
Abstract
The intestinal L cell is the principal source of glucagon-like peptide-1 (GLP-1), a major determinant of insulin release. Because GLP-1 secretion is regulated in a circadian manner in rodents, we investigated whether the activity of the human L cell is also time sensitive. Rhythmic fluctuations in the mRNA levels of canonical clock genes were found in the human NCI-H716 L cell model, which also showed a time-dependent pattern in their response to well-established secretagogues. A diurnal variation in GLP-1 responses to identical meals (850 kcal), served 12 h apart in the normal dark (2300) and light (1100) periods, was also observed in male volunteers maintained under standard sleep and light conditions. These findings suggest the existence of a daily pattern of activity in the human L cell. Moreover, we separately tested the short-term effects of sleep deprivation and nocturnal light exposure on basal and postprandial GLP-1, insulin, and glucose levels in the same volunteers. Sleep deprivation with nocturnal light exposure disrupted the melatonin and cortisol profiles and increased insulin resistance. Moreover, it also induced profound derangements in GLP-1 and insulin responses such that postprandial GLP-1 and insulin levels were markedly elevated and the normal variation in GLP-1 responses was abrogated. These alterations were not observed in sleep-deprived participants maintained under dark conditions, indicating a direct effect of light on the mechanisms that regulate glucose homeostasis. Accordingly, the metabolic abnormalities known to occur in shift workers may be related to the effects of irregular light-dark cycles on these glucoregulatory pathways.
Collapse
Affiliation(s)
| | | | - Lucy-Ann Behan
- Department of Obstetrics and Gynecology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Bojana Gladanac
- Institute of Medical Science, and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Robert F Casper
- Department of Physiology, Department of Obstetrics and Gynecology, Institute of Medical Science, and Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Patricia L Brubaker
- Department of Physiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada; and
| |
Collapse
|
32
|
Niinemets Ü, Sun Z, Talts E. Controls of the quantum yield and saturation light of isoprene emission in different-aged aspen leaves. Plant Cell Environ 2015; 38:2707-20. [PMID: 26037962 PMCID: PMC5798581 DOI: 10.1111/pce.12582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 05/11/2023]
Abstract
Leaf age alters the balance between the use of end-product of plastidic isoprenoid synthesis pathway, dimethylallyl diphosphate (DMADP), in prenyltransferase reactions leading to synthesis of pigments of photosynthetic machinery and in isoprene synthesis, but the implications of such changes on environmental responses of isoprene emission have not been studied. Because under light-limited conditions, isoprene emission rate is controlled by DMADP pool size (SDMADP ), shifts in the share of different processes are expected to particularly strongly alter the light dependency of isoprene emission. We examined light responses of isoprene emission in young fully expanded, mature and old non-senescent leaves of hybrid aspen (Populus tremula x P. tremuloides) and estimated in vivo SDMADP and isoprene synthase activity from post-illumination isoprene release. Isoprene emission capacity was 1.5-fold larger in mature than in young and old leaves. The initial quantum yield of isoprene emission (αI ) increased by 2.5-fold with increasing leaf age primarily as the result of increasing SDMADP . The saturating light intensity (QI90 ) decreased by 2.3-fold with increasing leaf age, and this mainly reflected limited light-dependent increase of SDMADP possibly due to feedback inhibition by DMADP. These major age-dependent changes in the shape of the light response need consideration in modelling canopy isoprene emission.
Collapse
Affiliation(s)
- Ülo Niinemets
- Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia
- Corresponding author,
| | - Zhihong Sun
- Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
- Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Eero Talts
- Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
| |
Collapse
|
33
|
Hwang SG, Kim DS, Hwang JE, Park HM, Jang CS. Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis. Genetica 2015; 143:635-44. [PMID: 26361777 DOI: 10.1007/s10709-015-9861-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 09/07/2015] [Indexed: 11/25/2022]
Abstract
In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.
Collapse
Affiliation(s)
- Sun-Goo Hwang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea
| | - Dong Sub Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, South Korea
| | - Jung Eun Hwang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, South Korea
| | - Hyeon Mi Park
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea
| | - Cheol Seong Jang
- Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea.
| |
Collapse
|
34
|
Karki HS, Ham JH. The roles of the shikimate pathway genes, aroA and aroB, in virulence, growth and UV tolerance of Burkholderia glumae strain 411gr-6. Mol Plant Pathol 2014; 15:940-7. [PMID: 24754446 PMCID: PMC6638700 DOI: 10.1111/mpp.12147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, which is a growing disease problem for rice growers worldwide. In our previous study, some B. glumae strains showed pigmentation phenotypes producing at least two (yellow-green and purple) pigment compounds in casein-peptone-glucose agar medium. The B. glumae strains LSUPB114 and LSUPB116 are pigment-deficient mutant derivatives of the virulent and pigment-proficient strain 411gr-6, having mini-Tn5gus insertions in aroA encoding 3-phosphoshikimate 1-carboxyvinyltransferase and aroB encoding 3-dehydroquinate synthase, respectively. Both enzymes are known to be involved in the shikimate pathway, which leads to the synthesis of aromatic amino acids. Here, we demonstrate that aroA and aroB are required for normal virulence in rice and onion, growth in M9 minimal medium and tolerance to UV light, but are dispensable for the production of the phytotoxin toxoflavin. These results suggest that the shikimate pathway is involved in bacterial pathogenesis by B. glumae without a significant role in the production of toxoflavin, a major virulence factor of this pathogen.
Collapse
Affiliation(s)
- Hari Sharan Karki
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | | |
Collapse
|
35
|
Song S, Chen D, Ma T, Luo Y, Yang Z, Wang D, Fan X, Qin Q, Ni B, Guo X, Xian Z, Lan P, Cao X, Li M, Wang J, Wang L. Molecular mechanism of acute radiation enteritis revealed using proteomics and biological signaling network analysis in rats. Dig Dis Sci 2014; 59:2704-13. [PMID: 24927798 DOI: 10.1007/s10620-014-3224-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/21/2014] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIMS Radiation enteritis (RE) has emerged as a significant complication that can progress to severe gastrointestinal disease and the mechanisms underlying its genesis remain poorly understood. The aim of this study was to identify temporal changes in protein expression potentially associated with acute inflammation and to elucidate the mechanism underlying radiation enteritis genesis. METHODS Male Sprague-Dawley rats were irradiated in the abdomen with a single dose of 10 Gy to establish an in vivo model of acute radiation enteritis. Two-dimensional fluorescence difference gel electrophoresis, matrix-assisted laser desorption/ionization time-of-flight spectrometer (MALDI-TOF) tandem mass spectrometry, and peptide mass fingerprinting were used to determine differentially expressed proteins between normal and inflamed intestinal mucosa. Additionally, differentially expressed proteins were evaluated by KO Based Annotation System to find the biological functions associated with acute radiation enteritis. RESULTS Intensity changes of 86 spots were detected with statistical significance (ratio ≥ 1.5 or ≤ 1.5, P < 0.05). Sixty one of the 86 spots were identified by MALDI-TOF/TOF tandem mass spectrometry. These radiation-induced proteins with biological functions showed that the FAS pathway and glycolysis signaling pathways were significantly altered using the KOBAS tool. CONCLUSIONS Our results reveal an underlying mechanism of radiation-induced acute enteritis, which may help clarify the pathogenesis of RE and point to potential targets for therapeutic interventions.
Collapse
Affiliation(s)
- Shunxin Song
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, 26 Yuancunerheng Road, Guangzhou, 510655, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Leung YH, Ng AMC, Xu X, Shen Z, Gethings LA, Wong MT, Chan CMN, Guo MY, Ng YH, Djurišić AB, Lee PKH, Chan WK, Yu LH, Phillips DL, Ma APY, Leung FCC. Mechanisms of antibacterial activity of MgO: non-ROS mediated toxicity of MgO nanoparticles towards Escherichia coli. Small 2014; 10:1171-83. [PMID: 24344000 DOI: 10.1002/smll.201302434] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/28/2013] [Indexed: 05/09/2023]
Abstract
The toxicity of metal oxide nanomaterials and their antimicrobial activity is attracting increasing attention. Among these materials, MgO is particularly interesting as a low cost, environmentally-friendly material. The toxicity of MgO, similar to other metal oxide nanomaterials, is commonly attributed to the production of reactive oxygen species (ROS). We investigated the toxicity of three different MgO nanoparticle samples, and clearly demonstrated robust toxicity towards Escherichia coli bacterial cells in the absence of ROS production for two MgO nanoparticle samples. Proteomics data also clearly demonstrate the absence of oxidative stress and indicate that the primary mechanism of cell death is related to the cell membrane damage, which does not appear to be due to lipid peroxidation.
Collapse
Affiliation(s)
- Yu Hang Leung
- Department of Physics, University of Hong Kong, Pokfulam Road, Hong Kong
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Randhawa M, Sangar V, Tucker-Samaras S, Southall M. Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway. PLoS One 2014; 9:e90367. [PMID: 24603693 PMCID: PMC3946127 DOI: 10.1371/journal.pone.0090367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/31/2014] [Indexed: 11/18/2022] Open
Abstract
Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin.
Collapse
Affiliation(s)
- Manpreet Randhawa
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
- * E-mail:
| | - Vineet Sangar
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Samantha Tucker-Samaras
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
| | - Michael Southall
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
| |
Collapse
|
38
|
Ma G, Zhang L, Matsuta A, Matsutani K, Yamawaki K, Yahata M, Wahyudi A, Motohashi R, Kato M. Enzymatic formation of β-citraurin from β-cryptoxanthin and Zeaxanthin by carotenoid cleavage dioxygenase4 in the flavedo of citrus fruit. Plant Physiol 2013; 163:682-95. [PMID: 23966550 PMCID: PMC3793050 DOI: 10.1104/pp.113.223297] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/17/2013] [Indexed: 05/20/2023]
Abstract
In this study, the pathway of β-citraurin biosynthesis, carotenoid contents and the expression of genes related to carotenoid metabolism were investigated in two varieties of Satsuma mandarin (Citrus unshiu), Yamashitabeni-wase, which accumulates β-citraurin predominantly, and Miyagawa-wase, which does not accumulate β-citraurin. The results suggested that CitCCD4 (for Carotenoid Cleavage Dioxygenase4) was a key gene contributing to the biosynthesis of β-citraurin. In the flavedo of Yamashitabeni-wase, the expression of CitCCD4 increased rapidly from September, which was consistent with the accumulation of β-citraurin. In the flavedo of Miyagawa-wase, the expression of CitCCD4 remained at an extremely low level during the ripening process, which was consistent with the absence of β-citraurin. Functional analysis showed that the CitCCD4 enzyme exhibited substrate specificity. It cleaved β-cryptoxanthin and zeaxanthin at the 7,8 or 7',8' position. But other carotenoids tested in this study (lycopene, α-carotene, β-carotene, all-trans-violaxanthin, and 9-cis-violaxanthin) were not cleaved by the CitCCD4 enzyme. The cleavage of β-cryptoxanthin and zeaxanthin by CitCCD4 led to the formation of β-citraurin. Additionally, with ethylene and red light-emitting diode light treatments, the gene expression of CitCCD4 was up-regulated in the flavedo of Yamashitabeni-wase. These increases in the expression of CitCCD4 were consistent with the accumulation of β-citraurin in the two treatments. These results might provide new strategies to improve the carotenoid contents and compositions of citrus fruits.
Collapse
Affiliation(s)
| | | | - Asami Matsuta
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Kazuki Matsutani
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Kazuki Yamawaki
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Masaki Yahata
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Anung Wahyudi
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Reiko Motohashi
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| | - Masaya Kato
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422–8529, Japan
| |
Collapse
|
39
|
Davis MC, Fiehn O, Durnford DG. Metabolic acclimation to excess light intensity in Chlamydomonas reinhardtii. Plant Cell Environ 2013; 36:1391-405. [PMID: 23346954 DOI: 10.1111/pce.12071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/10/2013] [Indexed: 05/08/2023]
Abstract
There are several well-described acclimation responses to excess light in green algae but the effect on metabolism has not been thoroughly investigated. This study examines the metabolic changes during photoacclimation to high-light (HL) stress in Chlamydomonas reinhardtii using nuclear magnetic resonance and mass spectrometry. Using principal component analysis, a clear metabolic response to HL intensity was observed on global metabolite pools, with major changes in the levels of amino acids and related nitrogen metabolites. Amino acid pools increased during short-term photoacclimation, but were especially prominent in HL-acclimated cultures. Unexpectedly, we observed an increase in mitochondrial metabolism through downstream photorespiratory pathways. The expression of two genes encoding key enzymes in the photorespiratory pathway, glycolate dehydrogenase and malate synthase, were highly responsive to the HL stress. We propose that this pathway contributes to metabolite pools involved in nitrogen assimilation and may play a direct role in photoacclimation. Our results suggest that primary and secondary metabolism is highly pliable and plays a critical role in coping with the energetic imbalance during HL exposure and a necessary adjustment to support an increased growth rate that is an effective energy sink for the excess reducing power generated during HL stress.
Collapse
Affiliation(s)
- Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Oliver Fiehn
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Dion G Durnford
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada, E3B 5A3
| |
Collapse
|
40
|
Tifilova OA. [Photosensitive metabolic network in the cells of bacteria Escherichia coli: spectral selectivity and reparative functions of globin photoreceptors]. ACTA ACUST UNITED AC 2013; 53:71-5. [PMID: 23700837 DOI: 10.7868/s0869803112060148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The influence of He-Ne laser radiation (632.8), incoherent monochromatic red light (601-685 nm), as well as pulsed radiation semiconductor laser (660 nm) on the growth of the culture of wild type or uvrA strain of E. coli WP2 and on the DNA transformation of plasmid pDick (Amp, Km) in E. coli NM522 was investigated. After light signal, photoenhancement of the quantity of cells in culture retains during several generations, while the enhancement of the transformation efficiency was observed only for the kanamycin marker. This makes it possible to suppose that metabolic signaling network acts as a red light receptor. The observed spectral selectivity suggests that flavohemoglobin fatty acid peroxidase works as a photosensitive component in the reparative network. It is proposed that the enhanced effectiveness of light in the uvrA strain results from photoactivation ofglobin EcDOS phosphodiesterase as an O2 provider for AlkB demethylase.
Collapse
|
41
|
Hildebrand M, Abbriano RM, Polle JEW, Traller JC, Trentacoste EM, Smith SR, Davis AK. Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production. Curr Opin Chem Biol 2013; 17:506-14. [PMID: 23538202 DOI: 10.1016/j.cbpa.2013.02.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/18/2013] [Accepted: 02/26/2013] [Indexed: 12/18/2022]
Abstract
Microalgae are among the most diverse organisms on the planet, and as a result of symbioses and evolutionary selection, the configuration of core metabolic networks is highly varied across distinct algal classes. The differences in photosynthesis, carbon fixation and processing, carbon storage, and the compartmentation of cellular and metabolic processes are substantial and likely to transcend into the efficiency of various steps involved in biofuel molecule production. By highlighting these differences, we hope to provide a framework for comparative analyses to determine the efficiency of the different arrangements or processes. This sets the stage for optimization on the based on information derived from evolutionary selection to diverse algal classes and to synthetic systems.
Collapse
Affiliation(s)
- Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA.
| | | | | | | | | | | | | |
Collapse
|
42
|
Li Z, Sharkey TD. Metabolic profiling of the methylerythritol phosphate pathway reveals the source of post-illumination isoprene burst from leaves. Plant Cell Environ 2013; 36:429-37. [PMID: 22831282 DOI: 10.1111/j.1365-3040.2012.02584.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The methylerythritol phosphate (MEP) pathway in plants produces the prenyl precursors for all plastidic isoprenoids, including carotenoids and quinones. The MEP pathway is also responsible for synthesis of approximately 600 Tg of isoprene per year, the largest non-methane hydrocarbon flux into the atmosphere. There have been few studies of the regulation of the MEP pathway in plants under physiological conditions. In this study, we combined gas exchange techniques and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) and measured the profile of MEP pathway metabolites under different conditions. We report that in the MEP pathway, metabolites immediately preceding steps requiring reducing power were in high concentration. Inhibition of the MEP pathway by fosmidomycin caused deoxyxylulose phosphate accumulation in leaves as expected. Evidence is presented that accumulation of MEP pathway intermediates, primarily methylerythritol cyclodiphosphate, is responsible for the post-illumination isoprene burst phenomenon. Pools of intermediate metabolites stayed at approximately the same level 10 min after light was turned off, but declined eventually under prolonged darkness. In contrast, a strong inhibition of the second-to-last step of the MEP pathway caused suppression of isoprene emission in pure N(2). Our study suggests that reducing equivalents may be a key regulator of the MEP pathway and therefore isoprene emission from leaves.
Collapse
Affiliation(s)
- Ziru Li
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | |
Collapse
|
43
|
Gicquel M, Taconnat L, Renou JP, Esnault MA, Cabello-Hurtado F. Kinetic transcriptomic approach revealed metabolic pathways and genotoxic-related changes implied in the Arabidopsis response to ionising radiations. Plant Sci 2012; 195:106-19. [PMID: 22921004 DOI: 10.1016/j.plantsci.2012.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 05/22/2023]
Abstract
Plants exposed to ionising radiation (IR) have to face direct and indirect (oxidative stress) deleterious effects whose intensity depends on the dose applied and led to differential genome regulation. Transcriptomic analyses were conducted with CATMA microarray technology on Arabidopsis thaliana plantlets, 2 and 26h after exposure to the IR doses 10Gy and 40Gy. 10Gy treatment seemed to enhance antioxidative compound biosynthetic pathways whereas the 40Gy dose up-regulated ROS-scavenging enzyme genes. Transcriptomic data also highlighted a differential regulation of chloroplast constituent genes depending on the IR dose, 10Gy stimulating and 40Gy down-regulating. This probable 40Gy decrease of photosynthesis could help for the limitation of ROS production and may be coupled with programmed cell death (PCD)/senescence phenomena. Comparisons with previous transcriptomic studies on plants exposed to a 100Gy dose revealed 60 dose-dependent up-regulated genes, including notably cell cycle checkpoints to allow DNA repairing phenomena. Furthermore, the alteration of some cellular structure related gene expression corroborated a probable mitotic arrest after 40Gy. Finally, numerous heat-shock protein and chaperonin genes, known to protect proteins against stress-dependent dysfunction, were up-regulated after IR exposure.
Collapse
Affiliation(s)
- Morgane Gicquel
- Mechanisms and Origin of Biodiversity Team, UMR 6553-Ecobio, University of Rennes1, 263 Av. du Général Leclerc, Campus de Beaulieu-Bât.14A, 35042 Rennes, France
| | | | | | | | | |
Collapse
|
44
|
Nakvasina MA, Trubitsyna MS, Solov'eva EV, Artiukhov VG. [Ways of apoptosis development in human lymphocytes, induced by UV-irradiation]. Biofizika 2012; 57:631-640. [PMID: 23035529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The level of DNA damage and cytochrome c content in human lymphocytes in the dynamics of apoptosis induced by UV-light (240-390 nm) at doses of 151, 1510 and 3020 J/m2 is studied. DNA fragmentation is revealed in 20 h after UV-irradiation of lymphocytes at doses mentioned above. It is shown that DNA damages (single strand breaks) appear immediately after UV-irradiation of lymphocytes at doses of 1510 and 3020 J/m2 (comets of C1 type) and reach their maximum 6 h after cell modification (comets of C2 and C3 types). It is concluded that p53-dependent and receptor caspase pathways are involved in apoptosis development in the human lymphocytes, modified after UV-irradiation.
Collapse
|
45
|
Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA. High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. Plant J 2011; 67:869-84. [PMID: 21575090 DOI: 10.1111/j.1365-313x.2011.04640.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The time-resolved response of Arabidopsis thaliana towards changing light and/or temperature at the transcriptome and metabolome level is presented. Plants grown at 21°C with a light intensity of 150 μE m⁻² sec⁻¹ were either kept at this condition or transferred into seven different environments (4°C, darkness; 21°C, darkness; 32°C, darkness; 4°C, 85 μE m⁻² sec⁻¹; 21 °C, 75 μE m⁻² sec⁻¹; 21°C, 300 μE m⁻² sec⁻¹ ; 32°C, 150 μE m⁻² sec⁻¹). Samples were taken before (0 min) and at 22 time points after transfer resulting in (8×) 22 time points covering both a linear and a logarithmic time series totaling 177 states. Hierarchical cluster analysis shows that individual conditions (defined by temperature and light) diverge into distinct trajectories at condition-dependent times and that the metabolome follows different kinetics from the transcriptome. The metabolic responses are initially relatively faster when compared with the transcriptional responses. Gene Ontology over-representation analysis identifies a common response for all changed conditions at the transcriptome level during the early response phase (5-60 min). Metabolic networks reconstructed via metabolite-metabolite correlations reveal extensive environment-specific rewiring. Detailed analysis identifies conditional connections between amino acids and intermediates of the tricarboxylic acid cycle. Parallel analysis of transcriptional changes strongly support a model where in the absence of photosynthesis at normal/high temperatures protein degradation occurs rapidly and subsequent amino acid catabolism serves as the main cellular energy supply. These results thus demonstrate the engagement of the electron transfer flavoprotein system under short-term environmental perturbations.
Collapse
Affiliation(s)
- Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Saha R, Suthers PF, Maranas CD. Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One 2011; 6:e21784. [PMID: 21755001 PMCID: PMC3131064 DOI: 10.1371/journal.pone.0021784] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 06/09/2011] [Indexed: 11/18/2022] Open
Abstract
The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.
Collapse
Affiliation(s)
- Rajib Saha
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Patrick F. Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
47
|
Xu RY, Nan P, Yang Y, Pan H, Zhou T, Chen J. Ultraviolet irradiation induces accumulation of isoflavonoids and transcription of genes of enzymes involved in the calycosin-7-O-β-d-glucoside pathway in Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao. Physiol Plant 2011; 142:265-273. [PMID: 21438882 DOI: 10.1111/j.1399-3054.2011.01474.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Isoflavonoids are a group of phenolic secondary metabolites found almost exclusively in leguminous plants. Formononetin, calycosin and calycosin-7-O-β-d-glucoside (CG) are isoflavonoid products in the CG pathway. Accumulation of the three isoflavonoids plus daidzein and expression of six genes of enzymes involved in the CG pathway were studied in Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao with ultraviolet (UV) irradiation. Our results showed that (1) main isoflavonoids in roots, stems and leaves were CG, daidzein and calycosin, respectively; they accumulated significantly under the induction of UV irradiation during 8 days but their content declined later; (2) expression of six genes of enzymes involved in the CG pathway was inhibited slightly at early stage but the expression was increased greatly afterward; (3) chalcone synthase, chalcone reductase and chalcone isomerase were expressed to their individual maximum level within shorter hours than were cinnamate 4-hydroxylase, isoflavone synthase (IFS) and isoflavone 3'-hydroxylase and (4) more calycosin but less daidzein accumulated in leaves. IFS was highly expressed in leaves, which might lead to high accumulation of the common precursor of daidzein and 2,7-dihydroxy-4'-O-methoxy-isoflavanone, the latter of which would be converted to formononetin, calycosin and CG via a series of reactions. Little daidzein accumulated in leaves, which suggested that rather than be converted to daidzein, the 2,7,4'-trihydroxyisoflavanone was probably more easily caught by 2-hydroxyisoflavanone 4'-O-methyltransferase and hence provided more precursors for formononetin. The findings were discussed in terms of the influence of UV irradiation in the accumulation of isoflavonoids.
Collapse
Affiliation(s)
- Rong-Yan Xu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | | | | | | | | | | |
Collapse
|
48
|
Kolotilin I, Koltai H, Bar-Or C, Chen L, Nahon S, Shlomo H, Levin I, Reuveni M. Expressing yeast SAMdc gene confers broad changes in gene expression and alters fatty acid composition in tomato fruit. Physiol Plant 2011; 142:211-23. [PMID: 21338368 DOI: 10.1111/j.1399-3054.2011.01458.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tomato (Solanum lycopersicum) fruits expressing a yeast S-adenosyl methionine decarboxylase (ySAMdc) gene under control of a ripening-induced promoter show altered phytonutrient content and broad changes in gene expression. Genome-wide transcriptional alterations in pericarp tissues of the ySAMdc-expressing fruits are shown. Consistent with the ySAMdc expression pattern from the ripening-induced promoter, very minor transcriptional alterations were detected at the mature green developmental stage. At the breaker and red stages, altered levels of numerous transcripts were observed with a general tendency toward upregulation in the transgenic fruits. Ontological analysis of up- and downregulated transcript groups revealed various affected metabolic processes, mainly carbohydrate and amino acid metabolism, and protein synthesis, which appeared to be intensified in the ripening transgenic fruits. Other functional ontological categories of altered transcripts represented signal transduction, transcription regulation, RNA processing, molecular transport and stress response, as well as metabolism of lipids, glycans, xenobiotics, energy, cofactors and vitamins. In addition, transcript levels of genes encoding structural enzymes for several biosynthetic pathways showed strong correlations to levels of specific metabolites that displayed altered levels in transgenic fruits. Increased transcript levels of fatty acid biosynthesis enzymes were accompanied by a change in the fatty acid profile of transgenic fruits, most notably increasing ω-3 fatty acids at the expense of other lipids. Thus, SAMdc is a prime target in manipulating the nutritional value of tomato fruits. Combined with analyses of selected metabolites in the overripe fruits, a model of enhanced homeostasis of the pericarp tissue in the polyamine-accumulating tomatoes is proposed.
Collapse
Affiliation(s)
- Igor Kolotilin
- Vegetable Research Department, Institute of Plant Sciences, ARO Volcani Center, Bet Dagan, Israel
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Vickers CE, Possell M, Laothawornkitkul J, Ryan AC, Hewitt CN, Mullineaux PM. Isoprene synthesis in plants: lessons from a transgenic tobacco model. Plant Cell Environ 2011; 34:1043-1053. [PMID: 21388420 DOI: 10.1111/j.1365-3040.2011.02303.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Isoprene is a highly reactive gas, and is emitted in such large quantities from the biosphere that it substantially affects the oxidizing potential of the atmosphere. Relatively little is known about the control of isoprene emission at the molecular level. Using transgenic tobacco lines harbouring a poplar isoprene synthase gene, we examined control of isoprene emission. Isoprene synthase required chloroplastic localization for catalytic activity, and isoprene was produced via the methyl erythritol (MEP) pathway from recently assimilated carbon. Emission patterns in transgenic tobacco plants were remarkably similar to naturally emitting plants under a wide variety of conditions. Emissions correlated with photosynthetic rates in developing and mature leaves, and with the amount of isoprene synthase protein in mature leaves. Isoprene synthase protein levels did not change under short-term increase in heat/light, despite an increase in emissions under these conditions. A robust circadian pattern could be observed in emissions from long-day plants. The data support the idea that substrate supply and changes in enzyme kinetics (rather than changes in isoprene synthase levels or post-translational regulation of activity) are the primary controls on isoprene emission in mature transgenic tobacco leaves.
Collapse
Affiliation(s)
- Claudia E Vickers
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| | - Malcolm Possell
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| | - Jullada Laothawornkitkul
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| | - Annette C Ryan
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| | - C Nicholas Hewitt
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| | - Philip M Mullineaux
- Department of Biological Sciences, Essex University, Colchester, Essex C04 3SQLancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, England, UK
| |
Collapse
|
50
|
|