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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Rai LS, Chauvel M, Permal E, d'Enfert C, Bachellier-Bassi S. Transcript profiling reveals the role of PDB1, a subunit of the pyruvate dehydrogenase complex, in Candida albicans biofilm formation. Res Microbiol 2023; 174:104014. [PMID: 36535619 DOI: 10.1016/j.resmic.2022.104014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Candida albicans, the most prevalent fungal pathogen in the human microbiota can form biofilms on implanted medical devices. These biofilms are tolerant to conventional antifungal drugs and the host immune system as compared to the free-floating planktonic cells. Several in vitro models of biofilm formation have been used to determine the C. albicans biofilm-forming process, regulatory networks, and their properties. Here, we performed a genome-wide transcript profiling with C. albicans cells grown in YPD medium both in planktonic and biofilm condition. Transcript profiling of YPD-grown biofilms was further compared with published Spider medium-grown biofilm transcriptome data. This comparative analysis highlighted the differentially expressed genes and the pathways altered during biofilm formation. In addition, we demonstrated that overexpression of the PDB1 gene encoding a subunit of the pyruvate dehydrogenase resulted in defective biofilm formation. Altogether, this comparative analysis of transcript profiles from two different studies provides a robust reading on biofilm-altered genes and pathways during C. albicans biofilm development.
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Corton JC, Lee JS, Liu J, Ren H, Vallanat B, DeVito M. Determinants of gene expression in the human liver: Impact of aging and sex on xenobiotic metabolism. Exp Gerontol 2022; 169:111976. [PMID: 36244585 PMCID: PMC10586520 DOI: 10.1016/j.exger.2022.111976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/15/2022]
Abstract
There is a need to characterize the potential susceptibility of older adults to toxicity from environmental chemical exposures. Liver xenobiotic metabolizing enzymes (XMEs) play important roles in detoxifying and eliminating xenobiotics. We examined global gene expression in the livers of young (21-45 years) and old (69+ years) men and women. Differentially expressed genes (DEG) were identified using two-way ANOVA (p ≤ 0.05). We identified 1437 and 1670 DEGs between young and old groups in men and women, respectively. Only a minor number of the total number of genes overlapped (146 genes). Aging increased or decreased pathways involved in inflammation and intermediary metabolism, respectively. Aging led to numerous changes in the expression of XME genes or genes known to control their expression (~90 genes). Out of 10 cytochrome P450s activities examined, there were increased activities of CYP1A2 and CYP2C9 enzymes in the old groups. We also identified sex-dependent genes that were more numerous in the young group (1065) than in the old group (202) and included changes in XMEs. These studies indicate that the livers from aging humans when compared to younger adults exhibit changes in XMEs that may lead to differences in the metabolism of xenobiotics.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Janice S Lee
- Center for Public Health and Environmental Assessment, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Hongzu Ren
- Center for Public Health and Environmental Assessment, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Beena Vallanat
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
| | - Michael DeVito
- Center for Computational Toxicology and Exposure, US EPA, Research Triangle Park, NC 27711, United States of America.
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Bhat A, Yadav J, Thakur K, Aggarwal N, Chhokar A, Tripathi T, Singh T, Jadli M, Veerapandian V, Bharti AC. Transcriptome analysis of cervical cancer exosomes and detection of HPVE6*I transcripts in exosomal RNA. BMC Cancer 2022; 22:164. [PMID: 35148692 PMCID: PMC8840784 DOI: 10.1186/s12885-022-09262-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/06/2021] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Background Exosomes play a key role in cell-to-cell communication and are integral component of the tumor microenvironment. Recent observations suggest transfer of RNA through tumor-derived exosomes that can potentially translate into regulatory proteins in the recipient cells. Role of cervical cancer-derived exosomes and their transcript cargo is poorly understood. Materials and methods The total RNA of exosomes from HPV-positive (SiHa and HeLa) and HPV-negative (C33a) cervical cancer cell lines were extracted and the transcripts were estimated using Illumina HiSeq X. Further, validation of HPV transcripts were performed using RT-PCR. Results 3099 transcripts were found to be differentially-exported in HPV-positive vs. HPV-negative exosomes (p value <0.05). Analysis of top 10 GO terms and KEGG pathways showed enrichment of transcripts belonging to axon guidance and tumor innervation in HPV-positive exosomes. Among top 20 overexpressed transcripts, EVC2, LUZP1 and ANKS1B were the most notable due to their involvement in Hh signaling, cellular migration and invasion, respectively. Further, low levels of HPV-specific reads were detected. RT-PCR validation revealed presence of E6*I splice variant of HPV18 in exosomal RNA of HeLa cells. The E6*I transcripts were consistently retained in exosomes obtained from HeLa cells undergoing 5-FU and cisplatin-induced oxidative stress. Conclusion Our data suggests the enrichment of poly-A RNA transcripts in the exosomal cargo of cervical cancer cells, which includes pro-tumorigenic cellular RNA and viral transcripts such as HPV E6, which may have clinical utility as potential exosomal biomarkers of cervical cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09262-4.
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Affiliation(s)
- Anjali Bhat
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Joni Yadav
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Kulbhushan Thakur
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Nikita Aggarwal
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Arun Chhokar
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Tanya Tripathi
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Tejveer Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | - Mohit Jadli
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India
| | | | - Alok Chandra Bharti
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi (North Campus), Delhi, 110007, India.
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Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. 3 Biotech 2022; 12:48. [PMID: 35127303 PMCID: PMC8787009 DOI: 10.1007/s13205-022-03113-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/08/2022] [Indexed: 02/05/2023] Open
Abstract
Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03113-6.
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Affiliation(s)
- C. Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - R. Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - P. Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - A. Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
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Baltan S, Jawaid SS, Chomyk AM, Kidd GJ, Chen J, Battapady HD, Chan R, Dutta R, Trapp BD. Neuronal hibernation following hippocampal demyelination. Acta Neuropathol Commun 2021; 9:34. [PMID: 33648591 PMCID: PMC7923530 DOI: 10.1186/s40478-021-01130-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Cognitive dysfunction occurs in greater than 50% of individuals with multiple sclerosis (MS). Hippocampal demyelination is a prominent feature of postmortem MS brains and hippocampal atrophy correlates with cognitive decline in MS patients. Cellular and molecular mechanisms responsible for neuronal dysfunction in demyelinated hippocampi are not fully understood. Here we investigate a mouse model of hippocampal demyelination where twelve weeks of treatment with the oligodendrocyte toxin, cuprizone, demyelinates over 90% of the hippocampus and causes decreased memory/learning. Long-term potentiation (LTP) of hippocampal CA1 pyramidal neurons is considered to be a major cellular readout of learning and memory in the mammalian brain. In acute slices, we establish that hippocampal demyelination abolishes LTP and excitatory post-synaptic potentials of CA1 neurons, while pre-synaptic function of Schaeffer collateral fibers is preserved. Demyelination also reduced Ca2+-mediated firing of hippocampal neurons in vivo. Using three-dimensional electron microscopy, we investigated the number, shape (mushroom, stubby, thin), and post-synaptic densities (PSDs) of dendritic spines that facilitate LTP. Hippocampal demyelination did not alter the number of dendritic spines. Surprisingly, dendritic spines appeared to be more mature in demyelinated hippocampi, with a significant increase in mushroom-shaped spines, more perforated PSDs, and more astrocyte participation in the tripartite synapse. RNA sequencing experiments identified 400 altered transcripts in demyelinated hippocampi. Gene transcripts that regulate myelination, synaptic signaling, astrocyte function, and innate immunity were altered in demyelinated hippocampi. Hippocampal remyelination rescued synaptic transmission, LTP, and the majority of gene transcript changes. We establish that CA1 neurons projecting demyelinated axons silence their dendritic spines and hibernate in a state that may protect the demyelinated axon and facilitates functional recovery following remyelination.
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Lewis RW, Hill T, Corton JC. A set of six Gene expression biomarkers and their thresholds identify rat liver tumorigens in short-term assays. Toxicology 2020; 443:152547. [PMID: 32755643 PMCID: PMC10439517 DOI: 10.1016/j.tox.2020.152547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/01/2023]
Abstract
Traditional methods for cancer risk assessment are retrospective, resource-intensive, and not feasible for the vast majority of environmental chemicals. In earlier studies, we used a set of six biomarkers to accurately identify liver tumorigens in transcript profiles derived from chemically-treated rats using either a Toxicological Priority Index (ToxPi) approach or using derived biomarker thresholds for cancer. The biomarkers consisting of 7-113 genes are used to predict the most common liver cancer molecular initiating events: genotoxicity, cytotoxicity and activation of the xenobiotic receptors AhR, CAR, ER, and PPARα. In the present study, we apply and evaluate the performance of these methods for cancer prediction in an independent rat liver study of 44 chemicals (6 h-7d exposures) examined by Affymetrix arrays. In the first approach, ToxPi ranking of biomarker scores consistently gave the highest scores to tumorigenic chemical-dose pairs; balanced accuracies for identification of liver tumorigenic chemicals were up to 89 %. The second approach used tumorigenic thresholds derived in the present study or from our earlier study that were set at the maximum value for chemical-dose exposures without detectable liver tumor outcomes. Using these thresholds, balanced accuracies were up to 90 %. Both approaches identified all tumorigenic chemicals. Almost all of the tumorigenic chemicals activated more than one MIE. We also compared biomarker responses between two types of profiling platforms (Affymetrix full-genome array, TempO-Seq 1500+ array containing ∼2600 genes) and found that the lack of the full set of biomarker genes on the 1500+ array resulted in decreased ability to identify chemicals that activate the MIEs. Overall, these results demonstrate that predictive approaches based on the 6 biomarkers could be used in short-term assays to identify chemicals and their doses that induce liver tumors, the most common endpoint in rodent bioassays.
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Affiliation(s)
- Robert W Lewis
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States.
| | - Thomas Hill
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States; Oak Ridge Institute for Science and Education (ORISE) fellow Office of Research and Development, U.S. Environmental Protection Agency (EPA), Research Triangle Park, NC, United States.
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States.
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Liu H, Qu W, Zhu K, Cheng ZMM. The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection. BMC Genomics 2020; 21:635. [PMID: 32928117 PMCID: PMC7490889 DOI: 10.1186/s12864-020-07053-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 03/05/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.
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Affiliation(s)
- Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaikai Zhu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. .,Department of Plant Sciences, University of Tennessee, Knoxville, 37996, USA.
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Penning BW, Shiga TM, Klimek JF, SanMiguel PJ, Shreve J, Thimmapuram J, Sykes RW, Davis MF, McCann MC, Carpita NC. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. BMC Genomics 2019; 20:785. [PMID: 31664907 PMCID: PMC6819468 DOI: 10.1186/s12864-019-6117-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. Results High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Conclusions Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.
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Affiliation(s)
- Bryan W Penning
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,, Present Address: USDA-ARS, Wheat Quality Research Unit, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Tânia M Shiga
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil
| | - John F Klimek
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Philip J SanMiguel
- Genomics Core Facility, Purdue University, 170 South University Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA.,, Present Address: Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jyothi Thimmapuram
- Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil.,Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA
| | - Robert W Sykes
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,, Present Address: Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, Los Alamos, NM, 87545, USA
| | - Mark F Davis
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, West Lafayette, USA
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, West Lafayette, USA.
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Rodrigues AS, De Vega JJ, Miguel CM. Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos. BMC Plant Biol 2018; 18:379. [PMID: 30594130 PMCID: PMC6310951 DOI: 10.1186/s12870-018-1564-2] [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: 05/06/2018] [Accepted: 11/22/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND There are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis. RESULTS Total RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons. CONCLUSIONS Our results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.
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Affiliation(s)
- Andreia S. Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - José J. De Vega
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Célia M. Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisbon, Portugal
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Pholo M, Coetzee B, Maree HJ, Young PR, Lloyd JR, Kossmann J, Hills PN. Cell division and turgor mediate enhanced plant growth in Arabidopsis plants treated with the bacterial signalling molecule lumichrome. Planta 2018; 248:477-488. [PMID: 29777364 DOI: 10.1007/s00425-018-2916-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
Transcriptomic analysis indicates that the bacterial signalling molecule lumichrome enhances plant growth through a combination of enhanced cell division and cell enlargement, and possibly enhances photosynthesis. Lumichrome (7,8 dimethylalloxazine), a novel multitrophic signal molecule produced by Sinorhizobium meliloti bacteria, has previously been shown to elicit growth promotion in different plant species (Phillips et al. in Proc Natl Acad Sci USA 96:12275-12280, https://doi.org/10.1073/pnas.96.22.12275 , 1999). However, the molecular mechanisms that underlie this plant growth promotion remain obscure. Global transcript profiling using RNA-seq suggests that lumichrome enhances growth by inducing genes impacting on turgor driven growth and mitotic cell cycle that ensures the integration of cell division and expansion of developing leaves. The abundance of XTH9 and XPA4 transcripts was attributed to improved mediation of cell-wall loosening to allow turgor-driven cell enlargement. Mitotic CYCD3.3, CYCA1.1, SP1L3, RSW7 and PDF1 transcripts were increased in lumichrome-treated Arabidopsis thaliana plants, suggesting enhanced growth was underpinned by increased cell differentiation and expansion with a consequential increase in biomass. Synergistic ethylene-auxin cross-talk was also observed through reciprocal over-expression of ACO1 and SAUR54, in which ethylene activates the auxin signalling pathway and regulates Arabidopsis growth by both stimulating auxin biosynthesis and modulating the auxin transport machinery to the leaves. Decreased transcription of jasmonate biosynthesis and responsive-related transcripts (LOX2; LOX3; LOX6; JAL34; JR1) might contribute towards suppression of the negative effects of methyl jasmonate (MeJa) such as chlorophyll loss and decreases in RuBisCO and photosynthesis. This work contributes towards a deeper understanding of how lumichrome enhances plant growth and development.
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Affiliation(s)
- Motlalepula Pholo
- Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - Beatrix Coetzee
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij, Institute for Deciduous Fruit, Vines and Wine, Private Bag X5026, Stellenbosch, 7599, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij, Institute for Deciduous Fruit, Vines and Wine, Private Bag X5026, Stellenbosch, 7599, South Africa
| | - Philip R Young
- Institute for Wine Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - James R Lloyd
- Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - Jens Kossmann
- Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - Paul N Hills
- Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
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12
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Liu YJ, Wang GL, Ma J, Xu ZS, Wang F, Xiong AS. Transcript profiling of sucrose synthase genes involved in sucrose metabolism among four carrot (Daucus carota L.) cultivars reveals distinct patterns. BMC Plant Biol 2018; 18:8. [PMID: 29304728 PMCID: PMC5756371 DOI: 10.1186/s12870-017-1221-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 08/16/2017] [Accepted: 12/21/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Carrot which contains lots of nutrients has a large demand around the world. The soluble sugar content in fleshy root of carrot directly influences its taste and quality. Sucrose, as an important member of soluble sugar, is the main product of photosynthesis in higher plants and it plays pivotal roles in physiological processes including energy supply, signal transduction, transcriptional regulation, starch and cellulose synthesis, and stress tolerance. Sucrose synthase is a key enzyme involved in sucrose metabolism and is closely related to sucrose content. However, the molecular mechanism involved in sucrose metabolism in carrot has lagged behind. RESULTS Here, carrot roots of five developmental stages from four carrot cultivars were collected, and the contents of soluble sugar and sucrose in different stages and cultivars were surveyed. Three DcSus genes (DcSus1, DcSus2, and DcSus3), with lengths of 2427 bp, 2454 bp and 2628 bp, respectively, were identified and cloned in carrot. Phylogenetic analysis from the deduced amino acid sequences suggested that three DcSus were clustered into three distinct groups (SUSI, II and III). Results of enzymatic profiles demonstrated that the DcSus activities showed decrease trends during taproot development. Correlation analysis indicated that the DcSus activity showed negative correlation with soluble sugar content and strong negative correlation with sucrose concentration. Quantitative real-time PCR analysis showed that the expression profiles of the DcSus genes are significantly different in carrot tissues (root, leaf blade, and petiole), and the expression levels of the DcSus genes in the leaf blade were much higher than that in the root and petiole. The expression profiles of DcSus genes showed strong negative correlation with both sucrose content and soluble sugar content. CONCLUSIONS During carrot root development, the soluble sugar content and sucrose content showed increasing trends, while DcSus activities had persisting declinations, which may be due to the decreasing expression levels of genes encoding sucrose synthase. Our data demonstrate that synthesis of sucrose in carrot tissue is closely related with DcSus genes. The results from our study would not only provide effective insights of sucrose metabolism in carrot, but also are beneficial for biologists to improve carrot quality.
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Affiliation(s)
- Yan-Jun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Jing Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 China
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Schmidt R, Boudichevskaia A, Cao HX, He S, Meyer RC, Reif JC. Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays. Plant Cell Rep 2017; 36:1871-1881. [PMID: 28856445 DOI: 10.1007/s00299-017-2200-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Polymorphic probes identified via a sequence-based approach are suitable to infer the genotypes of recombinant inbred lines from hybridisation intensities of GeneChip ® transcript profiling experiments. The sequences of the probes of the ATH1 GeneChip® exactly match transcript sequences of the Arabidopsis thaliana reference genome Col-0, whereas nucleotide differences and/or insertions/deletions may be observed for transcripts of other A. thaliana accessions. Individual probes of the GeneChip® that show sequence polymorphisms between different A. thaliana accessions may serve as single-feature polymorphism (SFP) markers, provided that the sequence changes cause differences in hybridisation intensity for the accessions of interest. A sequence-based approach identified features on the high-density oligonucleotide array that showed sequence polymorphisms between A. thaliana accessions Col-0 and C24. Hybridisation intensities of polymorphic probes were extracted from genome-wide transcript profiles of Col-0/C24 and C24/Col-0 recombinant inbred lines and assessed after standardisation via sliding window analyses to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and the resulting data were integrated with information, which had been established previously with single nucleotide polymorphism and insertion/deletion markers, to enrich the linkage map of the Col-0/C24 and C24/Col-0 recombinant inbred populations. Congruence between the molecular marker map and the sequence maps of the A. thaliana Col-0 chromosomes proved the reliability of the genotype information which was deduced from the transcript profiles of the Col-0/C24 and C24/Col-0 recombinant inbred lines.
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Affiliation(s)
- Renate Schmidt
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany.
| | - Anastassia Boudichevskaia
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Hieu Xuan Cao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Sang He
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
| | - Jochen Christoph Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Seeland, Germany
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Boudichevskaia A, Cao HX, Schmidt R. Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach. Plant Cell Rep 2017; 36:1323-1332. [PMID: 28534065 DOI: 10.1007/s00299-017-2157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/17/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
Excluding polymorphic probes from GeneChip ® transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24. GeneChip® arrays represent a powerful tool for transcript profiling experiments. The ATH1 GeneChip® has been designed based on the sequence of the Arabidopsis thaliana reference genome Col-0, hence the features on the array exactly match the sequences of Col-0 transcripts. In contrast, transcripts of other A. thaliana accessions or related species may show nucleotide differences and/or insertions/deletions when compared to the corresponding Col-0 transcripts, therefore, comparisons of transcript abundance involving different A. thaliana accessions or related species may be compromised for a certain number of transcripts. To tackle this limitation, a sequence-based strategy was developed. Only features on the array that were identical in sequence for the specimen to be compared were considered for transcript profiling. The impact of the proposed strategy was evaluated for transcript profiles that were established for developing seeds of A. thaliana accessions Col-0 and C24.
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Affiliation(s)
- Anastassia Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Hieu Xuan Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany
| | - Renate Schmidt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany.
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Rosen MB, Das KP, Rooney J, Abbott B, Lau C, Corton JC. PPARα-independent transcriptional targets of perfluoroalkyl acids revealed by transcript profiling. Toxicology 2017; 387:95-107. [PMID: 28558994 DOI: 10.1016/j.tox.2017.05.013] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 01/09/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are ubiquitous and persistent environmental contaminants. Compounds such as perfluoroocanoic acid (PFOA), perfluorooctane sulfonate (PFOS), perfluorononanoic acid (PFNA), and perfluorohexane sulfonate (PFHxS) are readily found in the tissues of humans and wildlife. While PFOA and PFOS have been the subject of numerous studies since they were first described over a decade ago, less is known about the biological activity of PFHxS and PFNA. Most PFAAs are activators of peroxisome proliferator-activated receptor α (PPARα), although the biological effects of these compounds are likely mediated by other factors in addition to PPARα. To evaluate the effects of PFHxS and PFNA, male wild-type and Pparα-null mice were dosed by oral gavage with PFHxS (3 or 10mg/kg/day), PFNA (1 or 3mg/kg/day), or vehicle for 7days, and liver gene expression was evaluated by full-genome microarrays. Gene expression patterns were then compared to historical in-house data for PFOA and PFOS in addition to the experimental hypolipidemic agent, WY-14,643. While WY-14,643 altered most genes in a PPARα-dependent manner, approximately 11-24% of regulated genes in PFAA-treated mice were independent of PPARα. The possibility that PFAAs regulate gene expression through other molecular pathways was evaluated. Using data available through a microarray database, PFAA gene expression profiles were found to exhibit significant similarity to profiles from mouse tissues exposed to agonists of the constitutive activated receptor (CAR), estrogen receptor α (ERα), and PPARγ. Human PPARγ and ERα were activated by all four PFAAs in trans-activation assays from the ToxCast screening program. Predictive gene expression biomarkers showed that PFAAs activate CAR in both genotypes and cause feminization of the liver transcriptome through suppression of signal transducer and activator of transcription 5B (STAT5B). These results indicate that, in addition to activating PPARα as a primary target, PFAAs also have the potential to activate CAR, PPARγ, and ERα as well as suppress STAT5B.
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16
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Agarrwal R, Padmakumari AP, Bentur JS, Nair S. Metabolic and transcriptomic changes induced in host during hypersensitive response mediated resistance in rice against the Asian rice gall midge. Rice (N Y) 2016; 9:5. [PMID: 26892000 PMCID: PMC4759115 DOI: 10.1186/s12284-016-0077-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND An incompatible interaction between rice (Oryza sativa) and the Asian rice gall midge (AGM, Orseolia oryzae Wood-Mason), that is usually manifested through a hypersensitive response (HR), represents an intricate relationship between the resistant host and its avirulent pest. We investigated changes in the transcriptome and metabolome of the host (indica rice variety: RP2068-18-3-5, RP), showing HR when attacked by an avirulent gall midge biotype (GMB1), to deduce molecular and biochemical bases of such a complex interaction. Till now, such an integrated analysis of host transcriptome and metabolome has not been reported for any rice-insect interaction. RESULTS Transcript and metabolic profiling data revealed more than 7000 differentially expressed genes and 80 differentially accumulated metabolites, respectively, in the resistant host. Microarray data revealed deregulation of carbon (C) and nitrogen (N) metabolism causing a C/N shift; up-regulation of tetrapyrrole synthesis and down-regulation of chlorophyll synthesis and photosynthesis. Integrated results revealed that genes involved in lipid peroxidation (LPO) were up-regulated and a marker metabolite for LPO (azelaic acid) accumulated during HR. This coincided with a greater accumulation of GABA (neurotransmitter and an insect antifeedant) at the feeding site. Validation of microarray results by semi-quantitative RT-PCR revealed temporal variation in gene expression profiles. CONCLUSIONS The study revealed extensive reprogramming of the transcriptome and metabolome of RP upon GMB1 infestation leading to an HR that was induced by the generation and release of reactive oxygen species i.e. singlet oxygen and resulted in LPO-mediated cell death. RP thus used HR as a means to limit nutrient supply to the feeding maggots and simultaneously accumulated GABA, strategies that could have led to maggot mortality. The integrated results of transcript and metabolic profiling, for the first time, provided insights into an HR+ type of resistance in rice against gall midge.
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Affiliation(s)
- Ruchi Agarrwal
- />International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Ayyagari Phani Padmakumari
- />Indian Institute of Rice Research (formerly Directorate of Rice Research), Rajendranagar, Hyderabad, 500030 India
| | - Jagadish S. Bentur
- />Indian Institute of Rice Research (formerly Directorate of Rice Research), Rajendranagar, Hyderabad, 500030 India
- />Present address: AgriBiotech Foundation, Rajendranagar, Hyderabad, 500030 India
| | - Suresh Nair
- />International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
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17
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Vicente R, Pérez P, Martínez-Carrasco R, Feil R, Lunn JE, Watanabe M, Arrivault S, Stitt M, Hoefgen R, Morcuende R. Metabolic and Transcriptional Analysis of Durum Wheat Responses to Elevated CO2 at Low and High Nitrate Supply. Plant Cell Physiol 2016; 57:2133-2146. [PMID: 27440546 DOI: 10.1093/pcp/pcw131] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/14/2016] [Indexed: 05/03/2023]
Abstract
Elevated [CO2] (eCO2) can lead to photosynthetic acclimation and this is often intensified by low nitrogen (N). Despite intensive studies of plant responses to eCO2, the regulation mechanism of primary metabolism at the whole-plant level in interaction with [Formula: see text] supply remains unclear. We examined the metabolic and transcriptional responses triggered by eCO2 in association with physiological-biochemical traits in flag leaves and roots of durum wheat grown hydroponically in ambient and elevated [CO2] with low (LN) and high (HN) [Formula: see text] supply. Multivariate analysis revealed a strong interaction between eCO2 and [Formula: see text] supply. Photosynthetic acclimation induced by eCO2 in LN plants was accompanied by an increase in biomass and carbohydrates, and decreases of leaf organic N per unit area, organic acids, inorganic ions, Calvin-Benson cycle intermediates, Rubisco, nitrate reductase activity, amino acids and transcripts for N metabolism, particularly in leaves, whereas [Formula: see text] uptake was unaffected. In HN plants, eCO2 did not decrease photosynthetic capacity or leaf organic N per unit area, but induced transcripts for N metabolism, especially in roots. In conclusion, the photosynthetic acclimation in LN plants was associated with an inhibition of leaf [Formula: see text] assimilation, whereas up-regulation of N metabolism in roots could have mitigated the acclimatory effect of eCO2 in HN plants.
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Affiliation(s)
- Rubén Vicente
- Abiotic Stress Department, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Pilar Pérez
- Abiotic Stress Department, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Rafael Martínez-Carrasco
- Abiotic Stress Department, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Regina Feil
- Metabolic Networks Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - John E Lunn
- Metabolic Networks Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Amino Acid and Sulfur Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stephanie Arrivault
- Metabolic Networks Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Metabolic Networks Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Amino Acid and Sulfur Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Rosa Morcuende
- Abiotic Stress Department, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Cordel de Merinas 40-52, 37008 Salamanca, Spain
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Chawla LS, Toma I, Davison D, Vaziri K, Lee J, Lucas R, Seneff MG, Nyhan A, McCaffrey TA. Acute appendicitis: transcript profiling of blood identifies promising biomarkers and potential underlying processes. BMC Med Genomics 2016; 9:40. [PMID: 27417541 PMCID: PMC4946184 DOI: 10.1186/s12920-016-0200-y] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/09/2016] [Indexed: 12/31/2022] Open
Abstract
Background The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Circulating blood cells may carry informative changes in their RNA expression profile that would signal internal infection or inflammation of the appendix. Methods Genome-wide expression profiling was applied to whole blood RNA of acute appendicitis patients versus patients with other abdominal disorders, in order to identify biomarkers of appendicitis. From a large cohort of emergency patients, a discovery set of patients with surgically confirmed appendicitis, or abdominal pain from other causes, was identified. RNA from whole blood was profiled by microarrays, and RNA levels were filtered by a combined fold-change (>2) and p value (<0.05). A separate set of patients, including patients with respiratory infections, was used to validate a partial least squares discriminant (PLSD) prediction model. Results Transcript profiling identified 37 differentially expressed genes (DEG) in appendicitis versus abdominal pain patients. The DEG list contained 3 major ontologies: infection-related, inflammation-related, and ribosomal processing. Appendicitis patients had lower level of neutrophil defensin mRNA (DEFA1,3), but higher levels of alkaline phosphatase (ALPL) and interleukin-8 receptor-ß (CXCR2/IL8RB), which was confirmed in a larger cohort of 60 patients using droplet digital PCR (ddPCR). Conclusions Patients with acute appendicitis have detectable changes in the mRNA expression levels of factors related to neutrophil innate defense systems. The low defensin mRNA levels suggest that appendicitis patient’s immune cells are not directly activated by pathogens, but are primed by diffusible factors in the microenvironment of the infection. The detected biomarkers are consistent with prior evidence that biofilm-forming bacteria in the appendix may be an important factor in appendicitis. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0200-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lakhmir S Chawla
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA.,The Department of Medicine, Veterans Affairs Medical Center, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Ian Toma
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Danielle Davison
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Khashayar Vaziri
- Department of Surgery, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Juliet Lee
- Department of Anesthesiology and Critical Care Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA.,Department of Surgery, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Raymond Lucas
- Department of Emergency Medicine, The George Washington University Medical School and GW Medical Faculty Associates, Washington, DC, USA
| | - Michael G Seneff
- Department of Emergency Medicine, The George Washington University Medical School and GW Medical Faculty Associates, Washington, DC, USA
| | - Aoibhinn Nyhan
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA
| | - Timothy A McCaffrey
- Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA. .,Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, 2300 I Street, NW Ross 443, Washington, DC, 20037, USA.
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Fasoli M, Dell'Anna R, Dal Santo S, Balestrini R, Sanson A, Pezzotti M, Monti F, Zenoni S. Pectins, Hemicelluloses and Celluloses Show Specific Dynamics in the Internal and External Surfaces of Grape Berry Skin During Ripening. Plant Cell Physiol 2016; 57:1332-49. [PMID: 27095736 DOI: 10.1093/pcp/pcw080] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 08/14/2015] [Accepted: 04/12/2016] [Indexed: 05/06/2023]
Abstract
Grapevine berry skin is a complex structure that contributes to the final size and shape of the fruit and affects its quality traits. The organization of cell wall polysaccharides in situ and their modification during ripening are largely uncharacterized. The polymer structure of Corvina berry skin, its evolution during ripening and related modifying genes were determined by combing mid-infrared micro-spectroscopy and multivariate statistical analysis with transcript profiling and immunohistochemistry. Spectra were acquired in situ using a surface-sensitive technique on internal and external sides of the skin without previous sample pre-treatment, allowing comparison of the related cell wall polymer dynamics. The external surface featured cuticle-related bands; the internal surface showed more adsorbed water. Application of surface-specific normalization revealed the major molecular changes related to hemicelluloses and pectins in the internal surface and to cellulose and pectins in the external surface and that they occur between mid-ripening and full ripening in both sides of the skin. Transcript profiling of cell wall-modifying genes indicated a general suppression of cell wall metabolism during ripening. Genes related to pectin metabolism-a β-galactosidase, a pectin(methyl)esterase and a pectate lyase-and a xyloglucan endotransglucosylase/hydrolase, involved in hemicellulose modification, showed enhanced expression. In agreement with Fourier transform infrared spectroscopy, patterns due to pectin methyl esterification provided new insights into the relationship between pectin modifications and the associated transcript profile during skin ripening. This study proposes an original description of polymer dynamics in grape berries during ripening, highlighting differences between the internal and external sides of the skin.
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Affiliation(s)
- Marianna Fasoli
- Department of Biotechnology, University of Verona, 37134 Verona, Italy These authors contributed equally to this work
| | - Rossana Dell'Anna
- Micro Nano Facility, Fondazione Bruno Kessler, 38123 Trento, Italy These authors contributed equally to this work
| | - Silvia Dal Santo
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Andrea Sanson
- Department of Computer Science, University of Verona, 37134 Verona, Italy Present address: Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Francesca Monti
- Department of Computer Science, University of Verona, 37134 Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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Widdup EE, Chatfield-Reed K, Henry D, Chua G, Samuel MA, Muench DG. Identification of detoxification pathways in plants that are regulated in response to treatment with organic compounds isolated from oil sands process-affected water. Chemosphere 2015; 139:47-53. [PMID: 26052061 DOI: 10.1016/j.chemosphere.2015.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 03/02/2015] [Revised: 05/16/2015] [Accepted: 05/18/2015] [Indexed: 06/04/2023]
Abstract
Bitumen mining in the Athabasca oil sands region of northern Alberta results in the accumulation of large volumes of oil sands process-affected water (OSPW). The acid-extractable organic (AEO) fraction of OSPW contains a variety of compounds, including naphthenic acids, aromatics, and sulfur- and nitrogen-containing compounds that are toxic to aquatic and terrestrial organisms. We have studied the effect of AEO treatment on the transcriptome of root and shoot tissues in seedlings of the model plant, Arabidopsis thaliana. Several genes encoding enzymes involved in the xenobiotic detoxification pathway were upregulated, including cytochrome P450s (CYPs), UDP-dependent glycosyltransferases (UGTs), glutathione-S-transferases (GSTs), and membrane transporters. In addition, gene products involved in oxidative stress, β-oxidation, and glucosinolate degradation were also upregulated, indicating other potential mechanisms of the adaptive response to AEO exposure. These results provide insight into the pathways that plants use to detoxify the organic acid component of OSPW. Moreover, this study advances our understanding of genes that could be exploited to potentially develop phytoremediation and biosensing strategies for AEO contaminants resulting from oil sands mining.
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Affiliation(s)
- Ellen E Widdup
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Darren Henry
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
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Oshida K, Vasani N, Thomas RS, Applegate D, Gonzalez FJ, Aleksunes LM, Klaassen CD, Corton JC. Screening a mouse liver gene expression compendium identifies modulators of the aryl hydrocarbon receptor (AhR). Toxicology 2015; 336:99-112. [PMID: 26215100 DOI: 10.1016/j.tox.2015.07.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), dioxin-like compounds (DLC) as well as some drugs and endogenous tryptophan metabolites. Short-term activation of AhR can lead to hepatocellular steatosis, and chronic activation can lead to liver cancer in mice and rats. Analytical approaches were developed to identify biosets in a genomic database in which AhR activity was altered. A set of 63 genes was identified (the AhR gene expression biomarker) that was dependent on AhR for regulation after exposure to TCDD or benzo[a]pyrene and includes the known AhR targets Cyp1a1 and Cyp1b1. A fold-change rank-based test (Running Fisher's test; p-value ≤ 10(-4)) was used to evaluate the similarity between the AhR biomarker and a test set of 37 and 41 biosets positive or negative, respectively for AhR activation. The test resulted in a balanced accuracy of 95%. The rank-based test was used to identify factors that activate or suppress AhR in an annotated mouse liver/mouse primary hepatocyte gene expression database of ∼ 1850 comparisons. In addition to the expected activation of AhR by TCDD and DLC, AhR was activated by AP20189 and phenformin. AhR was suppressed by phenobarbital and 1,4-Bis[2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) in a constitutive activated receptor (CAR)-dependent manner and pregnenolone-16α-carbonitrile in a pregnane X receptor (PXR)-dependent manner. Inactivation of individual genes in nullizygous models led to AhR activation (Pxr, Ghrhr, Taf10) or suppression (Ahr, Ilst6st, Hnf1a). This study describes a novel screening strategy for identifying factors in mouse liver that perturb AhR in a gene expression compendium.
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Rasmussen S, Parsons AJ, Xue H, Liu Q, Jones CS, Ryan GD, Newman JA. Transcript profiling of fructan biosynthetic pathway genes reveals association of a specific fructosyltransferase isoform with the high sugar trait in Lolium perenne. J Plant Physiol 2014; 171:475-85. [PMID: 24655383 DOI: 10.1016/j.jplph.2013.12.008] [Citation(s) in RCA: 5] [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: 10/17/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 05/18/2023]
Abstract
Lolium perenne cultivars with elevated levels of fructans in leaf blades (high sugar-content grasses) have been developed to improve animal nutrition and reduce adverse environmental impacts of pastoral agricultural systems. Expression of the high sugar trait can vary substantially depending on genotype×environment (G×E) interactions. We grew three potential high sugar-content and a control cultivar in three temperature regimes and quantified water soluble carbohydrates (WSCs) and the expression of all functionally characterised L. perenne fructan pathway genes in leaf tissues. We also analysed the distribution, expression and sequence variation of two specific isoforms of Lp6G-FFT (fructan: fructan 6G-fructosyltransferase). Our study confirmed a significant G×E interaction affecting the accumulation of fructans in the high sugar-content cultivar AberDart, which accumulated higher levels of high DP (degree of polymerisation) fructans in blades compared to the control cultivar only when grown at 20°C (day)/10°C (night) temperatures. The cultivar Expo on the other hand accumulated significantly higher levels of high DP fructans in blades independent of temperature. Fructan levels in pseudostems were higher than in blades, and they increased markedly with decreasing temperature, but there was no consistent effect of cultivar in this tissue. The expression of the high sugar trait was generally positively correlated with transcript levels of fructosyltransferases. Presence and expression of only one of the two known 6G-FFT isoforms was positively correlated with high fructan biosynthesis, while the second isoform was associated with low fructan concentrations and positively correlated with fructan exohydrolase gene expression. The presence of distinct 6G-FFT sequence variants appears to be associated with the capacity of high sugar-content grasses to accumulate higher fructan levels particularly at warmer temperatures. These findings might be exploited for the selection and breeding of 'warm-effective' high sugar-content grasses to overcome some of the limitations of current high sugar-content ryegrass cultivars.
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Affiliation(s)
- Susanne Rasmussen
- AgResearch Grasslands Research Centre, P.B. 11008, Palmerston North, New Zealand.
| | - Anthony J Parsons
- Institute of Agriculture and Environment, Massey University, P.B. 11222, Palmerston North, New Zealand
| | - Hong Xue
- AgResearch Grasslands Research Centre, P.B. 11008, Palmerston North, New Zealand
| | - Qianhe Liu
- AgResearch Grasslands Research Centre, P.B. 11008, Palmerston North, New Zealand
| | - Christopher S Jones
- AgResearch Grasslands Research Centre, P.B. 11008, Palmerston North, New Zealand
| | - Geraldine D Ryan
- School of Environmental Sciences, University of Guelph, Ontario, Canada N1G 2W1
| | - Jonathan A Newman
- School of Environmental Sciences, University of Guelph, Ontario, Canada N1G 2W1
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Max D, Brandsch C, Schumann S, Kühne H, Frommhagen M, Schutkowski A, Hirche F, Staege MS, Stangl GI. Maternal vitamin D deficiency causes smaller muscle fibers and altered transcript levels of genes involved in protein degradation, myogenesis, and cytoskeleton organization in the newborn rat. Mol Nutr Food Res 2013; 58:343-52. [PMID: 23963738 DOI: 10.1002/mnfr.201300360] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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: 05/17/2013] [Revised: 06/24/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022]
Abstract
SCOPE Epidemiologic data reveal associations between low serum concentrations of 25-hydroxyvitamin D (25(OH)D) and higher risk of falls and muscle weakness. Fetal stage is critical for the development of skeletal muscle, but little information is available on the impact of maternal vitamin D deficiency on muscles of offspring. METHODS AND RESULTS To investigate the morphology and transcriptome of gastrocnemius muscle in newborns in response to maternal vitamin D deficiency, 14 female rats were fed either a vitamin D₃ deficient (0 IU/kg) or a vitamin D₃ adequate diet (1000 IU/kg) 8 weeks prior to conception, during pregnancy, and lactation. Analysis of cholecalciferol, 25(OH)D₃ and 1,25-dihydroxyvitamin D₃ show that dams fed the vitamin D deficient diet and their newborns suffered from a relevant vitamin D deficiency. Muscle cells of vitamin D deficient newborns were smaller than those of vitamin D adequate newborns (p < 0.05). Muscle transcriptome of the newborns revealed 426 probe sets as differentially expressed (259 upregulated, 167 downregulated) in response to vitamin D deficiency (fold change ≥1.5, p < 0.05). The effected genes are involved in protein catabolism, cell differentiation and proliferation, muscle cell development, and cytoskeleton organization. CONCLUSION Maternal vitamin D deficiency has a major impact on morphology and gene expression profile of skeletal muscle in newborns.
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Affiliation(s)
- Daniela Max
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
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