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Abstract
Alzheimer's Disease (AD) is the most frequent neurodegenerative disorder. Although proteinaceous aggregates of extracellular Amyloid-β (Aβ) and intracellular hyperphosphorylated microtubule- associated tau have long been identified as characteristic neuropathological hallmarks of AD, a disease- modifying therapy against these targets has not been successful. An emerging concept is that microglia, the innate immune cells of the brain, are major players in AD pathogenesis. Microglia are longlived tissue-resident professional phagocytes that survey and rapidly respond to changes in their microenvironment. Subpopulations of microglia cluster around Aβ plaques and adopt a transcriptomic signature specifically linked to neurodegeneration. A plethora of molecules and pathways associated with microglia function and dysfunction has been identified as important players in mediating neurodegeneration. However, whether microglia exert either beneficial or detrimental effects in AD pathology may depend on the disease stage. In this review, we summarize the current knowledge about the stage-dependent role of microglia in AD, including recent insights from genetic and gene expression profiling studies as well as novel imaging techniques focusing on microglia in human AD pathology and AD mouse models.
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Affiliation(s)
- Patrick Süß
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universitat, Erlangen- Nürnberg, Germany
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, United States
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2
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Fu J, Wei C, He J, Zhang L, Zhou J, Balaji KS, Shen S, Peng J, Sharma A, Fu J. Evaluation and characterization of HSPA5 (GRP78) expression profiles in normal individuals and cancer patients with COVID-19. Int J Biol Sci 2021; 17:897-910. [PMID: 33767597 PMCID: PMC7975696 DOI: 10.7150/ijbs.54055] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 10/03/2020] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
HSPA5 (BiP, GRP78) has been reported as a potential host-cell receptor for SARS-Cov-2, but its expression profiles on different tissues including tumors, its susceptibility to SARS-Cov-2 virus and severity of its adverse effects on malignant patients are unclear. In the current study, HSPA5 has been found to be expressed ubiquitously in normal tissues and significantly increased in 14 of 31 types of cancer tissues. In lung cancer, mRNA levels of HSPA5 were 253-fold increase than that of ACE2. Meanwhile, in both malignant tumors and matched normal samples across almost all cancer types, mRNA levels of HSPA5 were much higher than those of ACE2. Higher expression of HSPA5 significantly decreased patient overall survival (OS) in 7 types of cancers. Moreover, systematic analyses found that 7.15% of 5,068 COVID-19 cases have malignant cancer coincidental situations, and the rate of severe events of COVID-19 patients with cancers present a higher trend than that for all COVID-19 patients, showing a significant difference (33.33% vs 16.09%, p<0.01). Collectively, these data imply that the tissues with high HSPA5 expression, not low ACE2 expression, are susceptible to be invaded by SARS-CoV-2. Taken together, this study not only indicates the clinical significance of HSPA5 in COVID-19 disease and cancers, but also provides potential clues for further medical treatments and managements of COVID-19 patients.
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Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jiayue He
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Lianmei Zhang
- Department of Pathology, the Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an 223300, Jiangsu, China
| | - Ju Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | | | - Shiyi Shen
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jiangzhou Peng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510000, China
| | - Amrish Sharma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030, Texas, USA
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
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Pavelić SK, Markova-Car E, Klobučar M, Sappe L, Spaventi R. Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods. Curr Med Chem 2020; 27:1337-1349. [PMID: 31296156 DOI: 10.2174/0929867326666190711122819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates' interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.
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Affiliation(s)
- Sandra Kraljević Pavelić
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Elitza Markova-Car
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Marko Klobučar
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Lana Sappe
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia.,Novartis Oncology Region Europe Headquarter, Largo Umberto Boccioni 1, 21040 Origgio, Italia
| | - Radan Spaventi
- Triadelta Partners d.o.o., Međimurska 19/2, Zagreb, Croatia
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Akbar MW, Isbilen M, Belder N, Canli SD, Kucukkaraduman B, Turk C, Sahin O, Gure AO. A Stemness and EMT Based Gene Expression Signature Identifies Phenotypic Plasticity and is A Predictive but Not Prognostic Biomarker for Breast Cancer. J Cancer 2020; 11:949-961. [PMID: 31949498 PMCID: PMC6959010 DOI: 10.7150/jca.34649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/03/2019] [Indexed: 01/05/2023] Open
Abstract
Aims: Molecular heterogeneity of breast cancer results in variation in morphology, metastatic potential and response to therapy. We previously showed that breast cancer cell line sub-groups obtained by a clustering approach using highly variable genes overlapped almost completely with sub-groups generated by a drug cytotoxicity-profile based approach. Two distinct cell populations thus identified were CSC(cancer stem cell)-like and non-CSC-like. In this study we asked whether an mRNA based gene signature identifying these two cell types would explain variation in stemness, EMT, drug sensitivity, and prognosis in silico and in vitro. Main methods:In silico analyses were performed using publicly available cell line and patient tumor datasets. In vitro analyses of phenotypic plasticity and drug responsiveness were obtained using human breast cancer cell lines. Key findings: We find a novel gene list (CNCL) that can generate both categorical and continuous variables corresponding to the stemness/EMT (epithelial to mesenchymal transition) state of tumors. We are presenting a novel robust gene signature that unites previous observations related either to EMT or stemness in breast cancer. We show in silico, that this signature perfectly predicts behavior of tumor cells tested in vitro, and can reflect tumor plasticity. We thus demonstrate for the first time, that breast cancer subtypes are sensitive to either Lapatinib or Midostaurin. The same gene list is not capable of predicting prognosis in most cohorts, except for one that includes patients receiving neo-adjuvant taxene therapy. Significance: CNCL is a robust gene list that can identify both stemness and the EMT state of cell lines and tumors. It can be used to trace tumor cells during the course of phenotypic changes they undergo, that result in altered responses to therapeutic agents. The fact that such a list cannot be used to identify prognosis in most patient cohorts suggests that presence of factors other than stemness and EMT affect mortality.
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Affiliation(s)
- Muhammad Waqas Akbar
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Murat Isbilen
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,DNAFect Genetics Consulting R&D and Biotechnology Inc., Kocaeli, Turkey
| | - Nevin Belder
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Secil Demirkol Canli
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Molecular Pathology Application and Research Center, Hacettepe University, Ankara, Turkey
| | - Baris Kucukkaraduman
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Can Turk
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ozgur Sahin
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ali Osmay Gure
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
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Magouliotis DE, Tasiopoulou VS, Baloyiannis I, Mamaloudis I, Tzovaras G. Transcriptomic Analysis of the Aquaporin Gene Family and Associated Interactors in Rectal Cancer. Microrna 2020; 9:153-166. [PMID: 31530273 DOI: 10.2174/2211536608666190917153332] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/05/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Rectal Cancer (RC) is a common type of cancer with poor prognosis. The identification of biomarkers regarding RC diagnosis, monitoring, and prognosis is crucial. OBJECTIVES The purpose of the present study was to evaluate the differential expression of the Aquaporin (AQP) gene family network in RC, and the effect of Radiotherapy (RT) on their expression profile, to indicate novel biomarkers and prognostic factors. METHODS We used data mining techniques to construct the network of the AQP-associated genes to determine the Differentially Expressed Genes (DEGs) in RC and in irradiated as compared to nonirradiated RC patients. Furthermore, survival data of The Cancer Genome Atlas (TCGA) were analysed to assess the prognostic role of the DEGs, along with the functional enrichment of gene ontologies and miRNAs related to the DEGs in RC. RESULTS Microarray data of one PubMed GEO dataset was extracted, incorporating 22 RC and 20 normal rectal tissue samples. Eight DEGs were reported. Four DEGs were up-regulated and four downregulated in RC. Correlations were identified among the DEGs. Deming regression analysis was performed in order to demonstrate the equations describing these correlations. One gene (Aquaporin 3) was downregulated in irradiated RC samples compared with non-irradiated samples. The most significantly affected biological pathways and miRNAs were identified by functional enrichment analysis. CONCLUSION The present study demonstrates an eight-gene molecular panel that could facilitate as biomarkers regarding RC patients, which are potential targets of five miRNA families. Finally, our results highlight the effect of radiotherapy on AQPs and the associated pathways in RC.
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Affiliation(s)
- Dimitrios E Magouliotis
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, UCL, London, United Kingdom
| | | | | | - Ioannis Mamaloudis
- Department of Surgery, University of Thessaly, Biopolis, Larissa, Greece
| | - George Tzovaras
- Department of Surgery, University of Thessaly, Biopolis, Larissa, Greece
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Khan AZ, Shahid A, Cheng H, Mahboob S, Al-Ghanim KA, Bilal M, Liang F, Nawaz MZ. Omics Technologies for Microalgae-based Fuels and Chemicals: Challenges and Opportunities. Protein Pept Lett 2019; 25:99-107. [PMID: 29359650 DOI: 10.2174/0929866525666180122100722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/21/2017] [Accepted: 12/14/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Microalgae have been suggested as promising feedstocks of significant biotechnological interest due to their enormous potential for the sustainable production of industrially valuable compounds such as lipids/fatty acids, proteins, metabolites, pigments, and biofuels. However, exploitation of algal biomass for commercial purposes is still in its infancy due to the dearth of the knowledge regarding state-of-the-art sophisticated technologies. OBJECTIVES The main objective of the study was to review the explosions of innovative strategies that biological sciences have witnessed over the past several years, enabling the scientific community and research-based organizations to scrutinize entire classes of biomolecules from a cell type or whole organism, collectively titled as 'Omics, including genomics, transcriptomics, proteomics and lipidomics. METHODS An effort has been made to analyze the relative advantages and drawbacks of these technologies by reviewing and consulting the available literature. RESULTS Nevertheless, these 'Omics strategies have played a key role in the better understanding of the underlying mechanisms of specific gene products, regulatory constraints, metabolic pathways and potential genes and protein targets which might be employed in tailoring microalgae for enhanced productivity. In this critical review, an understanding of recent omics technologies, their potential applications, and limitations for microalgae-based fuel and other commodity chemicals are comprehensively discussed. CONCLUSION In the scenario of uncertain petro-based reserves, global warming and energy insecurity, the exploration of metabolic potentialities of microalgae using "Omics" are believed to be a green and environmentally-responsive approach that will further expand its industrial and environmental scope.
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Affiliation(s)
- Aqib Zafar Khan
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad-38000, Pakistan
| | - Ayesha Shahid
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad-38000, Pakistan
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fang Liang
- Wuxi Metagene Science & Technology Co., Ltd, Wuxi, China
| | - Muhammad Zohaib Nawaz
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Wuxi Metagene Science & Technology Co., Ltd, Wuxi, China.,Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan
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Danilenko M, Stones R, Rajan N. Transcriptomic profiling of human skin biopsies in the clinical trial setting: A protocol for high quality RNA extraction from skin tumours. Wellcome Open Res 2018; 3:45. [PMID: 29904728 PMCID: PMC5989147 DOI: 10.12688/wellcomeopenres.14360.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2018] [Indexed: 01/10/2023] Open
Abstract
Transcriptomic profiling of skin disease using next generation sequencing allows for detailed information on aspects of RNA biology including gene expression, non-coding regulatory elements and gene splicing. The application of RNA sequencing to human skin disease and cancer is often hampered by degraded RNA. Here we describe a protocol that allows for consistently intact RNA to be extracted from snap frozen skin biopsy samples, which has been validated in a clinical trial setting. Human skin tumour punch biopsies (n=28) ranging from 4-6mm in diameter were obtained from 14 patients with an inherited skin tumour syndrome (CYLD cutaneous syndrome) and frozen in liquid nitrogen prior to being stored at -80°C. These samples were then subject to cyrostat sectioning, allowing for histological assessment, and were homogenised using a bead-based lysis platform. RNA extraction was performed using a silica column-based system. RNA concentration was measured using fluorescent quantitation and RNA integrity assessed using microfluidic gel electrophoresis. We also processed normal skin biopsies using the same protocol (n=10). The mean RNA integrity score of the tumour and normal samples was 9.5, and the quantity of RNA obtained from the small amounts of tissue used exceeded requirements for RNA-seq library generation. We propose that the method of RNA extraction suggested here allows for transcriptomic profiling from small pieces of human tissue without the need for PCR amplification during library preparation. This protocol could be utilised in healthy and diseased skin to improve mechanistic understanding in a range of human skin diseases.
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Affiliation(s)
- Marina Danilenko
- Institute of Genetic Medicine, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 3BZ, UK
| | - Robert Stones
- Institute of Genetic Medicine, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 3BZ, UK
| | - Neil Rajan
- Institute of Genetic Medicine, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 3BZ, UK.,Department of Dermatology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
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Villar M, Mateos-Hernandez L, de la Fuente J. The Impact of Post-Genomics Approaches in Neurodegenerative Demyelinating Diseases: The Case of Guillain-Barré Syndrome. Curr Med Chem 2018. [PMID: 29542408 DOI: 10.2174/0929867325666180314121813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Why an autoimmune disease that is the main cause of the acute neuromuscular paralysis worldwide does not have a well-characterized cause or an effective treatment yet? The existence of different clinical variants for the Guillain-Barré syndrome (GBS) coupled with the fact that a high number of pathogens can cause an infection that sometimes, but not always, precedes the development of the syndrome, confers a high degree of uncertainty for both prognosis and treatment. In the post-genomic era, the development of omics technologies for the high-throughput analysis of biological molecules is allowing the characterization of biological systems in a degree of depth unimaginable before. In this context, this work summarizes the application of post-genomics technologies to the study of GBS. METHODS We performed a structured search of bibliographic databases for peer-reviewed research literature to outline the state of the art with regard the application of post-genomics technologies to the study of GBS. The quality of retrieved papers was assessed using standard tools and thirty-four were included in the review. To date, transcriptomics and proteomics have been the unique post-genomics approaches applied to GBS study. Most of these studies have been performed on cerebrospinal fluid samples and only a few studies have been conducted with other samples such as serum, Schwann cells and human peripheral nerve. RESULTS AND CONCLUSION In the post-genomics era, transcriptomics and proteomics have shown the possibilities that omics technologies can offer for a better understanding of the immunological and pathological mechanisms involved in GBS and the identification of potential biomarkers, but these results have only shown the tip of the iceberg and there is still a long way to exploit the full potential that post-genomics approaches could offer to the study of the GBS. The integration of different omics datasets through a systems biology approach could allow network-based analyses to describe the complexity and functionality of the molecular mechanisms involved in the course of disease facilitating the discovery of novel biomarkers that could be used to improve the diagnosis, predict the disease progression, improve our understanding of the pathology, and serve as therapeutic targets for GBS.
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Affiliation(s)
- Margarita Villar
- SaBio. Instituto de Investigacion en Recursos Cinegeticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Lourdes Mateos-Hernandez
- SaBio. Instituto de Investigacion en Recursos Cinegeticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio. Instituto de Investigacion en Recursos Cinegeticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, United States
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Denton AK, Maß J, Külahoglu C, Lercher MJ, Bräutigam A, Weber APM. Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. J Exp Bot 2017; 68:147-160. [PMID: 28043950 PMCID: PMC5853576 DOI: 10.1093/jxb/erw463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 08/03/2016] [Accepted: 11/18/2016] [Indexed: 05/18/2023]
Abstract
The high efficiency of C4 photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C4 tissues along a developing leaf gradient. This method treats both C4 tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set. Meta-analysis of this and the previous studies highlights the strengths and weaknesses of different C4 tissue separation techniques. While the method reported here achieves the least enrichment, it is the only one that shows neither strong 3' (degradation) bias, nor different severity of 3' bias between samples. The meta-analysis highlighted previously unappreciated observations, such as an accumulation of evidence that aspartate aminotransferase is more mesophyll specific than expected from the current NADP-ME C4 cycle model, and a shift in enrichment of protein synthesis genes from bundle sheath to mesophyll during development. The full comparative dataset is available for download, and a web visualization tool (available at http://www.plant-biochemistry.hhu.de/resources.html) facilitates comparison of the the Z. mays bundle sheath and mesophyll studies, their consistencies and their conflicts.
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Affiliation(s)
- Alisandra K Denton
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Janina Maß
- Institute of Informatics, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Canan Külahoglu
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Martin J Lercher
- Institute of Informatics, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Network Analysis and Modeling Group, IPK Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), iGRAD-Plant Program, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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De Palma G, Sallustio F, Curci C, Galleggiante V, Rutigliano M, Serino G, Ditonno P, Battaglia M, Schena FP. The Three-Gene Signature in Urinary Extracellular Vesicles from Patients with Clear Cell Renal Cell Carcinoma. J Cancer 2016; 7:1960-1967. [PMID: 27877211 PMCID: PMC5118659 DOI: 10.7150/jca.16123] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/14/2016] [Indexed: 01/14/2023] Open
Abstract
Renal cell carcinoma (RCC) accounts for more than 2% of neoplasias in humans worldwide. Renal biopsy is the gold standard among the diagnostic procedures, but it is invasive and not suitable for all patients. Therefore, new reliable and non-invasive biomarkers for RCC are required. Secretion of extracellular vesicles (EVs), containing RNA molecules that can be transferred between cells, appears to be a common feature of neoplasia. Consistently, cancer-derived EVs are increased in blood and urine. Therefore, urinary samples may be a non-invasive approach for discovering new diagnostic biomarkers. We enrolled 46 patients of whom 33 with clear cell renal cell carcinoma (ccRCC) and 22 healthy subjects (HS). Urinary EVs were isolated by differential centrifugation. Microarray analysis led to the identification of RNA molecules that were validated using RT-qPCR. We found that urinary exosomal shuttle RNA (esRNA) pattern was significantly different in ccRCC patients compared to HS and to non-clear cell RCC (non-ccRCC) and we identified three esRNAs involved in the tumor biology that may be potentially suitable as non-invasive gene signature. GSTA1, CEBPA and PCBD1 esRNA levels were decreased in urine of patients compared with HS. This pattern was specific of the ccRCC and one month after partial or radical nephrectomy the esRNA levels increased to reach the normal level. This study suggests, for the first time, the potential use of the RNA content of urinary EVs to provide a non-invasive first step to diagnose the ccRCC.
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Affiliation(s)
- Giuseppe De Palma
- C.A.R.S.O. Consortium, Valenzano, Italy;; Schena Foundation - European Research Center for Kidney Diseases, Valenzano, Italy
| | - Fabio Sallustio
- DETO, Nephrology, Dialysis and Transplantation Unit, University of Bari, Italy
| | - Claudia Curci
- C.A.R.S.O. Consortium, Valenzano, Italy;; Schena Foundation - European Research Center for Kidney Diseases, Valenzano, Italy
| | - Vanessa Galleggiante
- DETO, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Italy
| | - Monica Rutigliano
- DETO, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Italy
| | - Grazia Serino
- IRCCS "de Bellis", Laboratory of Experimental Immunopathology, Castellana Grotte, Italy
| | - Pasquale Ditonno
- DETO, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Italy
| | - Michele Battaglia
- DETO, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Italy
| | - Francesco P Schena
- C.A.R.S.O. Consortium, Valenzano, Italy;; Schena Foundation - European Research Center for Kidney Diseases, Valenzano, Italy;; DETO, Nephrology, Dialysis and Transplantation Unit, University of Bari, Italy
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Levin RA, Beltran VH, Hill R, Kjelleberg S, McDougald D, Steinberg PD, van Oppen MJH. Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances. Mol Biol Evol 2016; 33:2201-15. [PMID: 27301593 PMCID: PMC4989115 DOI: 10.1093/molbev/msw119] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Corals rely on photosynthesis by their endosymbiotic dinoflagellates (Symbiodinium spp.) to form the basis of tropical coral reefs. High sea surface temperatures driven by climate change can trigger the loss of Symbiodinium from corals (coral bleaching), leading to declines in coral health. Different putative species (genetically distinct types) as well as conspecific populations of Symbiodinium can confer differing levels of thermal tolerance to their coral host, but the genes that govern dinoflagellate thermal tolerance are unknown. Here we show physiological and transcriptional responses to heat stress by a thermo-sensitive (physiologically susceptible at 32 °C) type C1 Symbiodinium population and a thermo-tolerant (physiologically healthy at 32 °C) type C1 Symbiodinium population. After nine days at 32 °C, neither population exhibited physiological stress, but both displayed up-regulation of meiosis genes by ≥ 4-fold and enrichment of meiosis functional gene groups, which promote adaptation. After 13 days at 32 °C, the thermo-sensitive population suffered a significant decrease in photosynthetic efficiency and increase in reactive oxygen species (ROS) leakage from its cells, whereas the thermo-tolerant population showed no signs of physiological stress. Correspondingly, only the thermo-tolerant population demonstrated up-regulation of a range of ROS scavenging and molecular chaperone genes by ≥ 4-fold and enrichment of ROS scavenging and protein-folding functional gene groups. The physiological and transcriptional responses of the Symbiodinium populations to heat stress directly correlate with the bleaching susceptibilities of corals that harbored these same Symbiodinium populations. Thus, our study provides novel, foundational insights into the molecular basis of dinoflagellate thermal tolerance and coral bleaching.
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Affiliation(s)
- Rachel A Levin
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Victor H Beltran
- Australian Institute of Marine Science, Townsville MC, QLD, Australia
| | - Ross Hill
- Macquarie University, Sydney, NSW, Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Diane McDougald
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore The iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville MC, QLD, Australia School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
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12
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Walter J, Lynch F, Battchikova N, Aro EM, Gollan PJ. Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120. J Exp Bot 2016; 67:3997-4008. [PMID: 27012282 PMCID: PMC4915528 DOI: 10.1093/jxb/erw112] [Citation(s) in RCA: 13] [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: 05/23/2023]
Abstract
Calcium is integral to the perception, communication and adjustment of cellular responses to environmental changes. However, the role of Ca(2+) in fine-tuning cellular responses of wild-type cyanobacteria under favourable growth conditions has not been examined. In this study, extracellular Ca(2+) has been altered, and changes in the whole transcriptome of Anabaena sp. PCC 7120 have been evaluated under conditions replete of carbon and combined nitrogen. Ca(2+) induced differential expression of many genes driving primary cellular metabolism, with transcriptional regulation of carbon- and nitrogen-related processes responding with opposing trends. However, physiological effects of these transcriptional responses on biomass accumulation, biomass composition, and photosynthetic activity over the 24h period following Ca(2+) adjustment were found to be minor. It is well known that intracellular carbon:nitrogen balance is integral to optimal cell growth and that Ca(2+) plays an important role in the response of heterocystous cyanobacteria to combined-nitrogen deprivation. This work adds to the current knowledge by demonstrating a signalling role of Ca(2+) for making sensitive transcriptional adjustments required for optimal growth under non-limiting conditions.
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Affiliation(s)
- Julia Walter
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Fiona Lynch
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Peter J Gollan
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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13
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Pérez-Delgado CM, Moyano TC, García-Calderón M, Canales J, Gutiérrez RA, Márquez AJ, Betti M. Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism. J Exp Bot 2016; 67:3095-108. [PMID: 27117340 PMCID: PMC4867901 DOI: 10.1093/jxb/erw170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 05/08/2023]
Abstract
Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. The transcriptomic changes produced by the use of different nitrogen sources in leaves of L. japonicus plants combined with the transcriptomic changes produced in the same tissue by different photorespiratory conditions were examined. The results obtained provide novel information on the possible role of plastidic glutamine synthetase in the response to different nitrogen sources and in the C/N balance of L. japonicus plants. The use of gene co-expression networks establishes a clear relationship between photorespiration and primary nitrogen assimilation and identifies possible transcription factors connected to the genes of both routes.
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Affiliation(s)
- Carmen M Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Tomás C Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/ Profesor García González, 1, 41012-Sevilla, Spain
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Abstract
Mosses are among the earliest branching embryophytes and probably originated not later than the early Ordovician when atmospheric CO2 was higher and O2 was lower than today. The C3 biochemistry and physiology of their photosynthesis suggests, by analogy with tracheophytes, that growth of extant bryophytes in high CO2 approximating Ordovician values would increase the growth rate. This occurs for many mosses, including Physcomitrella patens in suspension culture, although recently published transcriptomic data on this species at high CO2 and present-day CO2 show down-regulation of the transcription of several genes related to photosynthesis. It would be useful if transcriptomic (and proteomic) data comparing growth conditions are linked to measurements of growth and physiology on the same, or parallel, cultures. Mosses (like later-originating embryophytes) have been subject to changes in bulk atmospheric CO2 and O2 throughout their existence, with evidence, albeit limited, for positive selection of moss Rubisco. Extant mosses are subject to a large range of CO2 and O2 concentrations in their immediate environments, especially aquatic mosses, and mosses are particularly influenced by CO2 generated by, and O2 consumed by, soil chemoorganotrophy from organic C produced by tracheophytes (if present) and bryophytes.
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Affiliation(s)
- John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK School of Plant Biology, The University of Western Australia, M084, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Timothy D Colmer
- School of Plant Biology, The University of Western Australia, M084, 35 Stirling Highway, Crawley, WA 6009, Australia
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15
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Yu J, Zhang Y, Di C, Zhang Q, Zhang K, Wang C, You Q, Yan H, Dai SY, Yuan JS, Xu W, Su Z. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. J Exp Bot 2016; 67:751-62. [PMID: 26547795 PMCID: PMC4737072 DOI: 10.1093/jxb/erv487] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [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: 05/18/2023]
Abstract
JASMONATE ZIM-domain (JAZ) proteins play important roles in plant defence and growth by regulating jasmonate signalling. Through data mining, we discovered that the JAZ7 gene was up-regulated in darkness. In the dark, the jaz7 mutant displayed more severe leaf yellowing, quicker chlorophyll degradation, and higher hydrogen peroxide accumulation compared with wild-type (WT) plants. The mutant phenotype of dark-induced leaf senescence could be rescued in the JAZ7-complemented and -overexpression lines. Moreover, the double mutants of jaz7 myc2 and jaz7 coi1 exhibited delayed leaf senescence. We further employed GeneChip analysis to study the molecular mechanism. Some key genes down-regulated in the triple mutant myc2 myc3 myc4 were up-regulated in the jaz7 mutant under darkness. The Gene Ontology terms 'leaf senescence' and 'cell death' were significantly enriched in the differentially expressed genes. Combining the genetic and transcriptomic analyses together, we proposed a model whereby darkness can induce JAZ7, which might further block MYC2 to suppress dark-induced leaf senescence. In darkness, the mutation of JAZ7 might partially liberate MYC2/MYC3/MYC4 from suppression, leading the MYC proteins to bind to the G-box/G-box-like motifs in the promoters, resulting in the up-regulation of the downstream genes related to indole-glucosinolate biosynthesis, sulphate metabolism, callose deposition, and JA-mediated signalling pathways. In summary, our genetic and transcriptomic studies established the JAZ7 protein as an important regulator in dark-induced leaf senescence.
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Affiliation(s)
- Juan Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yixiang Zhang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Chao Di
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Qunlian Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Chunchao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Susie Y Dai
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - Joshua S Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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16
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Decourcelle M, Perez-Fons L, Baulande S, Steiger S, Couvelard L, Hem S, Zhu C, Capell T, Christou P, Fraser P, Sandmann G. Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism. J Exp Bot 2015; 66:3141-50. [PMID: 25796085 PMCID: PMC4449536 DOI: 10.1093/jxb/erv120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The aim of this study was to assess whether endosperm-specific carotenoid biosynthesis influenced core metabolic processes in maize embryo and endosperm and how global seed metabolism adapted to this expanded biosynthetic capacity. Although enhancement of carotenoid biosynthesis was targeted to the endosperm of maize kernels, a concurrent up-regulation of sterol and fatty acid biosynthesis in the embryo was measured. Targeted terpenoid analysis, and non-targeted metabolomic, proteomic, and transcriptomic profiling revealed changes especially in carbohydrate metabolism in the transgenic line. In-depth analysis of the data, including changes of metabolite pools and increased enzyme and transcript concentrations, gave a first insight into the metabolic variation precipitated by the higher up-stream metabolite demand by the extended biosynthesis capacities for terpenoids and fatty acids. An integrative model is put forward to explain the metabolic regulation for the increased provision of terpenoid and fatty acid precursors, particularly glyceraldehyde 3-phosphate and pyruvate or acetyl-CoA from imported fructose and glucose. The model was supported by higher activities of fructokinase, glucose 6-phosphate isomerase, and fructose 1,6-bisphosphate aldolase indicating a higher flux through the glycolytic pathway. Although pyruvate and acetyl-CoA utilization was higher in the engineered line, pyruvate kinase activity was lower. A sufficient provision of both metabolites may be supported by a by-pass in a reaction sequence involving phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme.
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Affiliation(s)
- Mathilde Decourcelle
- Unité de Biochimie et Physiologie Moléculaire des Plantes, INRA, 34060 Montpellier, France
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 OEX, UK
| | | | - Sabine Steiger
- Biosynthesis Group, Institute of Molecular Biosciences, Goethe University Frankfurt/M, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | | | - Sonia Hem
- Unité de Biochimie et Physiologie Moléculaire des Plantes, INRA, 34060 Montpellier, France
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain Institució Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 OEX, UK
| | - Gerhard Sandmann
- Biosynthesis Group, Institute of Molecular Biosciences, Goethe University Frankfurt/M, Max von Laue Str. 9, D-60438 Frankfurt, Germany
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17
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Betti M, García-Calderón M, Pérez-Delgado CM, Credali A, Pal'ove-Balang P, Estivill G, Repčák M, Vega JM, Galván F, Márquez AJ. Reassimilation of ammonium in Lotus japonicus. J Exp Bot 2014; 65:5557-66. [PMID: 24948681 DOI: 10.1093/jxb/eru260] [Citation(s) in RCA: 14] [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] [Indexed: 05/24/2023]
Abstract
This review summarizes the most recent results obtained in the analysis of two important metabolic pathways involved in the release of internal sources of ammonium in the model legume Lotus japonicus: photorespiratory metabolism and asparagine breakdown mediated by aparaginase (NSE). The use of photorespiratory mutants deficient in plastidic glutamine synthetase (GS2) enabled us to investigate the transcriptomics and metabolomic changes associated with photorespiratory ammonium accumulation in this plant. The results obtained indicate the existence of a coordinate regulation of genes involved in photorespiratory metabolism. Other types of evidence illustrate the multiple interconnections existing among the photorespiratory pathway and other processes such as intermediate metabolism, nodule function, and secondary metabolism in this plant, all of which are substantially affected in GS2-deficient mutants because of the impairment of the photorespiratory cycle. Finally, the importance of asparagine metabolism in L. japonicus is highlighted because of the fact that asparagine constitutes the vast majority of the reduced nitrogen translocated between different organs of this plant. The different types of NSE enzymes and genes which are present in L. japonicus are described. There is a particular focus on the most abundant K(+)-dependent LjNSE1 isoform and how TILLING mutants were used to demonstrate by reverse genetics the importance of this particular isoform in plant growth and seed production.
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Affiliation(s)
- Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Carmen M Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Alfredo Credali
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Peter Pal'ove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Mánesova 23, SK-04001 Košice, Slovak Republic
| | - Guillermo Estivill
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Miroslav Repčák
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Mánesova 23, SK-04001 Košice, Slovak Republic
| | - José M Vega
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Francisco Galván
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, C/ Profesor García González, 1, 41012-Sevilla, Spain
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18
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Bräutigam A, Schliesky S, Külahoglu C, Osborne CP, Weber APM. Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. J Exp Bot 2014; 65:3579-93. [PMID: 24642845 PMCID: PMC4085959 DOI: 10.1093/jxb/eru100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
C4 photosynthesis affords higher photosynthetic carbon conversion efficiency than C3 photosynthesis and it therefore represents an attractive target for engineering efforts aiming to improve crop productivity. To this end, blueprints are required that reflect C4 metabolism as closely as possible. Such blueprints have been derived from comparative transcriptome analyses of C3 species with related C4 species belonging to the NAD-malic enzyme (NAD-ME) and NADP-ME subgroups of C4 photosynthesis. However, a comparison between C3 and the phosphoenolpyruvate carboxykinase (PEP-CK) subtype of C4 photosynthesis is still missing. An integrative analysis of all three C4 subtypes has also not been possible to date, since no comparison has been available for closely related C3 and PEP-CK C4 species. To generate the data, the guinea grass Megathyrsus maximus, which represents a PEP-CK species, was analysed in comparison with a closely related C3 sister species, Dichanthelium clandestinum, and with publicly available sets of RNA-Seq data from C4 species belonging to the NAD-ME and NADP-ME subgroups. The data indicate that the core C4 cycle of the PEP-CK grass M. maximus is quite similar to that of NAD-ME species with only a few exceptions, such as the subcellular location of transfer acid production and the degree and pattern of up-regulation of genes encoding C4 enzymes. One additional mitochondrial transporter protein was associated with the core cycle. The broad comparison identified sucrose and starch synthesis, as well as the prevention of leakage of C4 cycle intermediates to other metabolic pathways, as critical components of C4 metabolism. Estimation of intercellular transport fluxes indicated that flux between cells is increased by at least two orders of magnitude in C4 species compared with C3 species. In contrast to NAD-ME and NADP-ME species, the transcription of photosynthetic electron transfer proteins was unchanged in PEP-CK. In summary, the PEP-CK blueprint of M. maximus appears to be simpler than those of NAD-ME and NADP-ME plants.
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Affiliation(s)
- Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Simon Schliesky
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Canan Külahoglu
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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19
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Schmitz J, Heinrichs L, Scossa F, Fernie AR, Oelze ML, Dietz KJ, Rothbart M, Grimm B, Flügge UI, Häusler RE. The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities. J Exp Bot 2014; 65:1619-36. [PMID: 24523502 PMCID: PMC3967092 DOI: 10.1093/jxb/eru027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 05/18/2023]
Abstract
Retrograde signals from chloroplasts are thought to control the expression of nuclear genes associated with plastidial processes such as acclimation to varying light conditions. Arabidopsis mutants altered in the day and night path of photoassimilate export from the chloroplasts served as tools to study the involvement of carbohydrates in high light (HL) acclimation. A double mutant impaired in the triose phosphate/phosphate translocator (TPT) and ADP-glucose pyrophosphorylase (AGPase) (adg1-1/tpt-2) exhibits a HL-dependent depletion in endogenous carbohydrates combined with a severe growth and photosynthesis phenotype. The acclimation response of mutant and wild-type plants has been assessed in time series after transfer from low light (LL) to HL by analysing photosynthetic performance, carbohydrates, MgProtoIX (a chlorophyll precursor), and the ascorbate/glutathione redox system, combined with microarray-based transcriptomic and GC-MS-based metabolomic approaches. The data indicate that the accumulation of soluble carbohydrates (predominantly glucose) acts as a short-term response to HL exposure in both mutant and wild-type plants. Only if carbohydrates are depleted in the long term (e.g. after 2 d) is the acclimation response impaired, as observed in the adg1-1/tpt-2 double mutant. Furthermore, meta-analyses conducted with in-house and publicly available microarray data suggest that, in the long term, reactive oxygen species such as H₂O₂ can replace carbohydrates as signals. Moreover, a cross-talk exists between genes associated with the regulation of starch and lipid metabolism. The involvement of genes responding to phytohormones in HL acclimation appears to be less likely. Various candidate genes involved in retrograde control of nuclear gene expression emerged from the analyses of global gene expression.
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Affiliation(s)
- Jessica Schmitz
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- * Present address: Plant Molecular Physiology and Biotechnology, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Luisa Heinrichs
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
- Agriculture Research Council, Research Center for Vegetable Crops, Via Cavalleggeri 25, 84098 Pontecagnano (Salerno), Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
| | - Marie-Luise Oelze
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Maxi Rothbart
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Bernhard Grimm
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Ulf-Ingo Flügge
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Rainer E. Häusler
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- To whom correspondence should be addressed. E-mail:
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20
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Zhuang W, Gao Z, Wang L, Zhong W, Ni Z, Zhang Z. Comparative proteomic and transcriptomic approaches to address the active role of GA4 in Japanese apricot flower bud dormancy release. J Exp Bot 2013; 64:4953-66. [PMID: 24014872 PMCID: PMC3830480 DOI: 10.1093/jxb/ert284] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [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: 05/03/2023]
Abstract
Hormones are closely associated with dormancy in deciduous fruit trees, and gibberellins (GAs) are known to be particularly important. In this study, we observed that GA4 treatment led to earlier bud break in Japanese apricot. To understand better the promoting effect of GA4 on the dormancy release of Japanese apricot flower buds, proteomic and transcriptomic approaches were used to analyse the mechanisms of dormancy release following GA4 treatment, based on two-dimensional gel electrophoresis (2-DE) and digital gene expression (DGE) profiling, respectively. More than 600 highly reproducible protein spots (P<0.05) were detected and, following GA4 treatment, 38 protein spots showed more than a 2-fold difference in expression, and 32 protein spots were confidently identified according to the databases. Compared with water treatment, many proteins that were associated with energy metabolism and oxidation-reduction showed significant changes after GA4 treatment, which might promote dormancy release. We observed that genes at the mRNA level associated with energy metabolism and oxidation-reduction also played an important role in this process. Analysis of the functions of the identified proteins and genes and the related metabolic pathways would provide a comprehensive proteomic and transcriptomic view of the coordination of dormancy release after GA4 treatment in Japanese apricot flower buds.
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Affiliation(s)
- Weibing Zhuang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
| | - Zhihong Gao
- * These authors contributed equally to this paper
| | - Liangju Wang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
| | - Wenjun Zhong
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
| | - Zhen Zhang
- College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, PR China
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Abstract
Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers' needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.
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Affiliation(s)
- Sabina Leonelli
- Egenis & Department of Sociology, Philosophy and Anthropology, Byrne House, St Germans Road, Exeter EX4 4PJ, UK
- * To whom correspondence should be addressed. E-mail:
| | - Nicholas Smirnoff
- Geoffrey Pope Building, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Jonathan Moore
- Warwick Systems Biology Centre, Senate House, University of Warwick, Coventry CV4 7AL, UK
| | - Charis Cook
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
| | - Ruth Bastow
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
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22
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Henriques A, Gonzalez De Aguilar JL. Can transcriptomics cut the gordian knot of amyotrophic lateral sclerosis? Curr Genomics 2012; 12:506-15. [PMID: 22547957 PMCID: PMC3219845 DOI: 10.2174/138920211797904043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 07/27/2011] [Accepted: 09/15/2011] [Indexed: 12/31/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset degenerative disease characterized by the loss of upper and lower motor neurons, progressive muscle atrophy, paralysis and death, which occurs within 2-5 years of diagnosis. Most cases appear sporadically but some are familial, usually inherited in an autosomal dominant pattern. It is postulated that the disease results from the combination of multiple pathogenic mechanisms, which affect not only motor neurons but also non-neuronal neighboring cells. Together with the understanding of this intriguing cell biology, important challenges in the field concern the design of effective curative treatments and the discovery of molecular biomarkers for early diagnosis and accurate monitoring of disease progression. During the last decade, transcriptomics has represented a promising approach to address these questions. In this review, we revisit the major findings of the numerous studies that analyzed global gene expression in tissues and cells from biopsy or post-mortem specimens of ALS patients and related animal models. These studies corroborated the implication of previously described disease pathways, and investigated the role of new genes in the pathological process. In addition, they also identified gene expression changes that could be used as candidate biomarkers for the diagnosis and follow-up of ALS. The limitations of these transcriptomics approaches will be also discussed.
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Affiliation(s)
- Alexandre Henriques
- INSERM, U692, Laboratoire de Signalisations Moléculaires et Neurodégénérescence, Strasbourg, France
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23
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Strat YL, Ramoz N, Schumann G, Gorwood P. Molecular genetics of alcohol dependence and related endophenotypes. Curr Genomics 2011; 9:444-51. [PMID: 19506733 PMCID: PMC2691669 DOI: 10.2174/138920208786241252] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 06/11/2008] [Accepted: 06/12/2008] [Indexed: 11/22/2022] Open
Abstract
Alcohol dependence is a worldwide public health problem, and involves both environmental and genetic vulnerability factors. The heritability of alcohol dependence is rather high, ranging between 50% and 60%, although alcohol dependence is a polygenic, complex disorder. Genome-wide scans on large cohorts of multiplex families, including the collaborative study on genetics of alcoholism (COGA), emphasized the role of many chromosome regions and some candidate genes. The genes encoding the alcohol-metabolizing enzymes, or those involved in brain reward pathways, have been involved. Since dopamine is the main neurotransmitter in the reward circuit, genes involved in the dopaminergic pathway represent candidates of interest. Furthermore, gamma-amino-butyric acid (GABA) neurotransmitter mediates the acute actions of alcohol and is involved in withdrawal symptomatology. Numerous studies showed an association between variants within GABA receptors genes and the risk of alcohol dependence. In accordance with the complexity of the “alcohol dependence” phenotype, another field of research, related to the concept of endophenotypes, received more recent attention. The role of vulnerability genes in alcohol dependence is therefore re-assessed focusing on different phenotypes and endophenotypes. The latter include brain oscillations, EEG alpha and beta variants and alpha power, and amplitude of P300 amplitude elicited from a visual oddball task. Recent enhancement on global characterizations of the genome by high-throughput approach for genotyping of polymorphisms and studies of transcriptomics and proteomics in alcohol dependence is also reviewed.
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Affiliation(s)
- Yann L Strat
- INSERM U675, IFR02, Université Paris 7, 16 Rue Henri Huchard, 75018 Paris, France
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