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Sui Y, Guo X, Zhou R, Fu Z, Chai Y, Xia A, Zhao W. Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review. Mol Biotechnol 2023:10.1007/s12033-023-00775-2. [PMID: 37349610 DOI: 10.1007/s12033-023-00775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.
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Affiliation(s)
- Yaqi Sui
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaobo Guo
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Rui Zhou
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhisong Fu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yingxin Chai
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Ao Xia
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Wenhui Zhao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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2
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Fu X, Xu Y, Lu M. A proteomic study of the effect of UV-B on the regulatory mechanism of flavonoids metabolism in pea seedlings. Front Nutr 2023; 10:1184732. [PMID: 37255935 PMCID: PMC10226426 DOI: 10.3389/fnut.2023.1184732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023] Open
Abstract
This study aimed to investigate the mechanism of response of pea seedlings to UV-B stress from a proteomic perspective. In this experiment, we measured the growth of pea seedlings in two groups affected by UV-B and unaffected by UV-B and conducted proteomic analysis. The results showed that the ascorbic acid content of UV-B-irradiated pea seedlings increased by 19.0%; the relative content of flavonoids increased by 112.4%; the length of edible parts decreased by 14.2%, and the elongation of roots increased by 11.4%. Proteomics studies showed a significant increase in the levels of CHI, F3'5'H, F3H, F3'H, C4H, and CHR, which are key enzymes for flavonoid synthesis. RT-qPCR indicated that the expression of the regulatory genes of these enzymes was significantly upregulated. This study provided a basis for further studies on the flavonoid response mechanism in pea seedlings during UV stress.
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Affiliation(s)
- Xin Fu
- Food and Processing Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yinghao Xu
- College of Food, Shenyang Agricultural University, Shenyang, China
| | - Ming Lu
- Food and Processing Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, China
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3
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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4
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Nag S, Goswami B, Das Mandal S, Ray PS. Cooperation and competition by RNA-binding proteins in cancer. Semin Cancer Biol 2022; 86:286-297. [PMID: 35248729 DOI: 10.1016/j.semcancer.2022.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
Post-transcriptional regulation of gene expression plays a major role in determining the cellular proteome in health and disease. Post-transcriptional control mechanisms are disrupted in many cancers, contributing to multiple processes of tumorigenesis. RNA-binding proteins (RBPs), the main post-transcriptional regulators, often show altered expression and activity in cancer cells. Dysregulation of RBPs contributes to many cancer phenotypes, functioning in complex regulatory networks with other cellular players such as non-coding RNAs, signaling mediators and transcription factors to alter the expression of oncogenes and tumor suppressor genes. RBPs often function combinatorially, based on their binding to target sequences/structures on shared mRNA targets, to regulate the expression of cancer-related genes. This gives rise to cooperativity and competition between RBPs in mRNA binding and resultant functional outcomes in post-transcriptional processes such as mRNA splicing, stability, export and translation. Cooperation and competition is also observed in the case of interaction of RBPs and microRNAs with mRNA targets. RNA structural change is a common mechanism mediating the cooperative/competitive interplay between RBPs and between RBPs and microRNAs. RNA modifications, leading to changes in RNA structure, add a new dimension to cooperative/competitive binding of RBPs to mRNAs, further expanding the RBP regulatory landscape. Therefore, cooperative/competitive interplay between RBPs is a major determinant of the RBP interactome and post-transcriptional regulation of gene expression in cancer cells.
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Affiliation(s)
- Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
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5
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Zhao FR, Wang W, Zheng Q, Zhang YG, Chen J. The regulation of antiviral activity of interferon epsilon. Front Microbiol 2022; 13:1006481. [PMID: 36386666 PMCID: PMC9642105 DOI: 10.3389/fmicb.2022.1006481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 01/08/2023] Open
Abstract
Interferon epsilon (IFN-ε) is a type I IFN. Some biological properties has been identified in many species, such as antiproliferative, anti-tumor, and antiviral effects, of IFN-ε, which are much weaker than those of IFN-α, have also been revealed. It has been shown to play a role in mucosal immunity and bacterial infection and in the prevention of certain sexually transmitted diseases, such as human immunodeficiency virus (HIV). This paper reviews the known activity of IFN-ε, particularly in some viruses. In general, this review provides a better understanding of effective IFN-ε treatment in the future.
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Cardoso TF, Bruscadin JJ, Afonso J, Petrini J, Andrade BGN, de Oliveira PSN, Malheiros JM, Rocha MIP, Zerlotini A, Ferraz JBS, Mourão GB, Coutinho LL, Regitano LCA. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mamm Genome 2022; 33:619-628. [PMID: 35816191 DOI: 10.1007/s00335-022-09959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
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Affiliation(s)
- T F Cardoso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J J Bruscadin
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J Afonso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - B G N Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - P S N de Oliveira
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J M Malheiros
- Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - M I P Rocha
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - A Zerlotini
- Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - J B S Ferraz
- Department of Veterinary Medicine, University of São Paulo/FZEA, Pirassununga, Brazil
| | - G B Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
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7
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Vahlensieck C, Thiel CS, Pöschl D, Bradley T, Krammer S, Lauber B, Polzer J, Ullrich O. Post-Transcriptional Dynamics is Involved in Rapid Adaptation to Hypergravity in Jurkat T Cells. Front Cell Dev Biol 2022; 10:933984. [PMID: 35859900 PMCID: PMC9289288 DOI: 10.3389/fcell.2022.933984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptome of human immune cells rapidly reacts to altered gravity in a highly dynamic way. We could show in previous experiments that transcriptional patterns show profound adaption after seconds to minutes of altered gravity. To gain further insight into these transcriptional alteration and adaption dynamics, we conducted a highly standardized RNA-Seq experiment with human Jurkat T cells exposed to 9xg hypergravity for 3 and 15 min, respectively. We investigated the frequency with which individual exons were used during transcription and discovered that differential exon usage broadly appeared after 3 min and became less pronounced after 15 min. Additionally, we observed a shift in the transcript pool from coding towards non-coding transcripts. Thus, adaption of gravity-sensitive differentially expressed genes followed a dynamic transcriptional rebound effect. The general dynamics were compatible with previous studies on the transcriptional effects of short hypergravity on human immune cells and suggest that initial up-regulatory changes mostly result from increased elongation rates. The shift correlated with a general downregulation of the affected genes. All chromosome bands carried homogenous numbers of gravity-sensitive genes but showed a specific tendency towards up- or downregulation. Altered gravity affected transcriptional regulation throughout the entire genome, whereby the direction of differential expression was strongly dependent on the structural location in the genome. A correlation analysis with potential mediators of the early transcriptional response identified a link between initially upregulated genes with certain transcription factors. Based on these findings, we have been able to further develop our model of the transcriptional response to altered gravity.
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Affiliation(s)
- Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
| | - Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), Merritt Island, FL, United States
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- *Correspondence: Cora S. Thiel, ; Oliver Ullrich,
| | - Daniel Pöschl
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Sonja Krammer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
| | - Beatrice Lauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Jennifer Polzer
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Dübendorf, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), Merritt Island, FL, United States
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Space Medicine, Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
- *Correspondence: Cora S. Thiel, ; Oliver Ullrich,
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8
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Hunter KS, Miller A, Mentink-Kane M, Davies SJ. Schistosome AMPK Is Required for Larval Viability and Regulates Glycogen Metabolism in Adult Parasites. Front Microbiol 2021; 12:726465. [PMID: 34539616 PMCID: PMC8440919 DOI: 10.3389/fmicb.2021.726465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/12/2021] [Indexed: 11/25/2022] Open
Abstract
On entering the mammalian host, schistosomes transition from a freshwater environment where resources are scarce, to an environment where there is an unlimited supply of glucose, their preferred energy substrate. Adult schistosome glycolytic activity consumes almost five times the parasite's dry weight in glucose per day to meet the parasite's energy demands, and the schistosome glycolytic enzymes and mechanisms for glucose uptake that sustain this metabolic activity have previously been identified. However, little is known of the parasite processes that regulate schistosome glucose metabolism. We previously described the Schistosoma mansoni ortholog of 5' AMP-Activated Protein Kinase (AMPK), which is a central regulator of energy metabolism in eukaryotes, and characterized the developmental regulation of its expression and activity in S. mansoni. Here we sought to explore the function of AMPK in schistosomes and test whether it regulates parasite glycolysis. Adult schistosomes mounted a compensatory response to chemical inhibition of AMPK α, resulting in increased AMPK α protein abundance and activity. RNAi inhibition of AMPK α expression, however, suggests that AMPK α is not required for adult schistosome viability in vitro. Larval schistosomula, on the other hand, are sensitive to chemical AMPK α inhibition, and this correlates with inactivity of the AMPK α gene in this life cycle stage that precludes a compensatory response to AMPK inhibition. While our data indicate that AMPK is not essential in adult schistosomes, our results suggest that AMPK regulates adult worm glycogen stores, influencing both glycogen utilization and synthesis. AMPK may therefore play a role in the ability of adult schistosomes to survive in vivo stressors such as transient glucose deprivation and oxidative stress. These findings suggest that AMPK warrants further investigation as a potential drug target, especially for interventions aimed at preventing establishment of a schistosome infection.
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Affiliation(s)
- Kasandra S Hunter
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD, United States
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD, United States
| | - Stephen J Davies
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States
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Chen X, Yin J, Cao D, Xiao D, Zhou Z, Liu Y, Shou W. The Emerging Roles of the RNA Binding Protein QKI in Cardiovascular Development and Function. Front Cell Dev Biol 2021; 9:668659. [PMID: 34222237 PMCID: PMC8242579 DOI: 10.3389/fcell.2021.668659] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
RNA binding proteins (RBPs) have a broad biological and physiological function and are critical in regulating pre-mRNA posttranscriptional processing, intracellular migration, and mRNA stability. QKI, also known as Quaking, is a member of the signal transduction and activation of RNA (STAR) family, which also belongs to the heterogeneous nuclear ribonucleoprotein K- (hnRNP K-) homology domain protein family. There are three major alternatively spliced isoforms, QKI-5, QKI-6, and QKI-7, differing in carboxy-terminal domains. They share a common RNA binding property, but each isoform can regulate pre-mRNA splicing, transportation or stability differently in a unique cell type-specific manner. Previously, QKI has been known for its important role in contributing to neurological disorders. A series of recent work has further demonstrated that QKI has important roles in much broader biological systems, such as cardiovascular development, monocyte to macrophage differentiation, bone metabolism, and cancer progression. In this mini-review, we will focus on discussing the emerging roles of QKI in regulating cardiac and vascular development and function and its potential link to cardiovascular pathophysiology.
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Affiliation(s)
- Xinyun Chen
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Jianwen Yin
- Department of Foot, Ankle and Hand Surgery, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Dayan Cao
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Deyong Xiao
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Zhongjun Zhou
- Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Ying Liu
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Weinian Shou
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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Ramakrishna G, Kaur P, Singh A, Yadav SS, Sharma S, Singh NK, Gaikwad K. Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives. PLANT CELL REPORTS 2021; 40:881-898. [PMID: 33837822 DOI: 10.1007/s00299-021-02686-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Comparative transcriptome analyses accompanied by biochemical assays revealed high variability in heat stress response in Cajanus species. Among the studied species, C. scarabaeoides was the most thermotolerant followed by C. cajanifolius, C. cajan, and C. acutifolius. Pigeonpea is one of the climate-resilient grain legumes. Though the optimum temperature for cultivated pigeonpea is ~ 25-35 °C, its wild relatives grow in temperatures ranging between 18 and 45 °C. To gain insight into molecular mechanisms responsible for the heat stress tolerance in pigeonpea, we conducted time-series transcriptome analysis of one pigeonpea cultivar (Cajanus cajan) and two wild relatives, Cajanus acutifolius, and Cajanus scarabaeoides subjected to heat stress at 42 ± 2 ºC for 30 min and 3 h. A total of 9521, 12,447, and 5282 identified transcripts were differentially expressed in C. cajan, C. acutifolius, and C. scarabaeoides, respectively. In this study, we observed that a significant number of genes undergo alternative splicing in a species-specific pattern during heat stress. Gene expression profiling analysis, histochemical assay, chlorophyll content, and electrolyte leakage assay showed that C. scarabaeoides has adaptive features for heat stress tolerance. The gene set enrichment analyses of differentially expressed genes in these Cajanus species during heat stress revealed that oxidoreductase activity, transcription factor activity, oxygen-evolving complex, photosystem-II, thylakoid, phenylpropanoid biosynthetic process, secondary metabolic process, and flavonoid biosynthetic process were highly affected. The histochemical assay showed more lipid peroxidation in C. acutifolius compared to other Cajanus species inferring the presence of higher quantities of polyunsaturated fatty acids in the plasma membrane which might have led to severe damage of membrane-bound organelles like chloroplast, and high electrolyte leakage during heat stress. This study paves the way for the identification of candidate genes, which can be useful for the development of thermo-tolerant pigeonpea cultivars.
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Affiliation(s)
- G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Parampreet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anupam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Sunishtha S Yadav
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Del Giudice D, Spatola E, Valentini M, Bombelli C, Ercolani G, Di Stefano S. Time-programmable pH: decarboxylation of nitroacetic acid allows the time-controlled rising of pH to a definite value. Chem Sci 2021; 12:7460-7466. [PMID: 34163836 PMCID: PMC8171335 DOI: 10.1039/d1sc01196k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/21/2021] [Indexed: 12/24/2022] Open
Abstract
In this report it is shown that nitroacetic acid 1 (O2NCH2CO2H) can be conveniently used to control the pH of a water solution over time. Time-programmable sequences of the kind pH1(high)-pH2(low)-pH3(high) can be achieved, where both the extent of the initial pH jump (pH1(high)-pH2(low)) and the time required for the subsequent pH rising (pH2(low)-pH3(high)) can be predictably controlled by a judicious choice of the absolute and relative concentrations of the reagents (acid 1 and NaOH). Successive pH1(high)-pH2(low)-pH3(high) sequences can be obtained by subsequent additions of acid 1. As a proof of concept, the method is applied to control over time the pH-dependent host-guest interaction between alpha-cyclodextrin and p-aminobenzoic acid.
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Affiliation(s)
- Daniele Del Giudice
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Emanuele Spatola
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Matteo Valentini
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Cecilia Bombelli
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
- ISB-CNR Sede Secondaria di Roma - Meccanismi di Reazione c/o Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza" P.le A. Moro 5 I-00185 Rome Italy
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12
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Effects of pre-mixed hydraulic calcium silicate putties on osteogenic differentiation of human dental pulp stem cells in vitro. J Dent 2021; 108:103653. [PMID: 33798641 DOI: 10.1016/j.jdent.2021.103653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES An experimental tricalcium silicate and dicalcium silicate-containing endodontic putty has been designed to overcome the issue of reduced shelf life after exposure to atmospheric moisture during repeated opening of the container for clinical retrieval. The present study examined the effects of this experimental hydraulic putty on the mineralogenic characteristics of osteogenic lineage-committed human dental pulp stem cells (hDPSCs), by comparing the cellular responses with a commercially available putty (EndoSequence BC RRM Putty). METHODS The osteogenic potential of hDPSCs that had been exposed to the putties was examined using quantitative reverse-transcription polymerase chain reaction for osteogenic gene expressions and western blot for osteogenic protein expressions. Alkaline phosphatase activity assay and alizarin red S staining were performed to detect changes in production of the intracellular enzyme and extracellular matrix mineralization respectively. RESULTS Osteogenic differentiation of the hDPSCs was significantly enhanced after exposure to the pre-mixed hydraulic putties, with no significant difference between these two examined putties. CONCLUSIONS The experimental hydraulic tricalcium silicate putty enhances osteogenic differentiation of hDPSCs to the same extent as a commercially available tricalcium silicate putty. CLINICAL SIGNIFICANCE The experimental hydraulic putty appears to be an alternative to the commercial putty when used for applications involving the regeneration of bone in endodontics. Animal models are required for validating its potential in enhancing osteogenesis in vivo.
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Li J, Liu L, Zhou W, Cai L, Xu Z, Rane MJ. Roles of Krüppel-like factor 5 in kidney disease. J Cell Mol Med 2021; 25:2342-2355. [PMID: 33523554 PMCID: PMC7933973 DOI: 10.1111/jcmm.16332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Transcription factor Krüppel-like factor 5 (KLF5) is a member of the Krüppel-like factors' (KLFs) family. KLF5 regulates a number of cellular functions, such as apoptosis, proliferation and differentiation. Therefore, KLF5 can play a role in many diseases, including, cancer, cardiovascular disease and gastrointestinal disorders. An important role for KLF5 in the kidney was recently reported, such that KLF5 regulated podocyte apoptosis, renal cell proliferation, tubulointerstitial inflammation and renal fibrosis. In this review, we have summarized the available information in the literature with a brief description on how transcriptional, post-transcriptional and post-translational modifications of KLF5 modulate its function in a variety of organs including the kidney with a focus of its importance on the pathogenesis of various kidney diseases. Furthermore, we also have outlined the current and possible mechanisms of KLF5 activation in kidney diseases. These studies suggest a need for more systemic investigations, particularly for generation of animal models with renal cell-specific deletion or overexpression of KLF5 gene to examine direct contributions of KLF5 to various kidney diseases. This will promote further experimentation in the development of therapies to prevent or treat various kidney diseases.
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Affiliation(s)
- Jia Li
- Department of NephrologyThe First Hospital of Jilin UniversityChangchunChina
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
| | - Liang Liu
- Department of RadiologyChina‐Japan Union Hospital of Jilin UniversityChangchunChina
| | - Wen‐Qian Zhou
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
- The Center of Cardiovascular DiseasesThe First Hospital of Jilin UniversityChangchunChina
| | - Lu Cai
- Department of PediatricsPediatric Research InstituteUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Zhong‐Gao Xu
- Department of NephrologyThe First Hospital of Jilin UniversityChangchunChina
| | - Madhavi J. Rane
- Department of MedicineDivision of NephrologyDepartment of Biochemistry and Molecular GeneticsUniversity of LouisvilleLouisvilleKYUSA
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Chen X, Liu Y, Xu C, Ba L, Liu Z, Li X, Huang J, Simpson E, Gao H, Cao D, Sheng W, Qi H, Ji H, Sanderson M, Cai CL, Li X, Yang L, Na J, Yamamura K, Liu Y, Huang G, Shou W, Sun N. QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function. Nat Commun 2021; 12:89. [PMID: 33397958 PMCID: PMC7782589 DOI: 10.1038/s41467-020-20327-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 11/27/2020] [Indexed: 01/29/2023] Open
Abstract
The RNA-binding protein QKI belongs to the hnRNP K-homology domain protein family, a well-known regulator of pre-mRNA alternative splicing and is associated with several neurodevelopmental disorders. Qki is found highly expressed in developing and adult hearts. By employing the human embryonic stem cell (hESC) to cardiomyocyte differentiation system and generating QKI-deficient hESCs (hESCs-QKIdel) using CRISPR/Cas9 gene editing technology, we analyze the physiological role of QKI in cardiomyocyte differentiation, maturation, and contractile function. hESCs-QKIdel largely maintain normal pluripotency and normal differentiation potential for the generation of early cardiogenic progenitors, but they fail to transition into functional cardiomyocytes. In this work, by using a series of transcriptomic, cell and biochemical analyses, and the Qki-deficient mouse model, we demonstrate that QKI is indispensable to cardiac sarcomerogenesis and cardiac function through its regulation of alternative splicing in genes involved in Z-disc formation and contractile physiology, suggesting that QKI is associated with the pathogenesis of certain forms of cardiomyopathies.
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Affiliation(s)
- Xinyun Chen
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Ying Liu
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Chen Xu
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Lina Ba
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Zhuo Liu
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Xiuya Li
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jie Huang
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ed Simpson
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hongyu Gao
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Dayan Cao
- Institute of Materia Medica and Center of Translational Medicine, College of Pharmacy, Army Medical University, Chongqing, China
| | - Wei Sheng
- grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China ,grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hanping Qi
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Hongrui Ji
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Maria Sanderson
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Chen-Leng Cai
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Xiaohui Li
- Institute of Materia Medica and Center of Translational Medicine, College of Pharmacy, Army Medical University, Chongqing, China
| | - Lei Yang
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Jie Na
- grid.12527.330000 0001 0662 3178Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Kenichi Yamamura
- Institute of Resource Development and Analysis, Kumanoto University, Kumanoto, Japan
| | - Yunlong Liu
- grid.257413.60000 0001 2287 3919Department of Bioinformatics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Guoying Huang
- grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Weinian Shou
- grid.257413.60000 0001 2287 3919Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Ning Sun
- grid.8547.e0000 0001 0125 2443Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China ,grid.411333.70000 0004 0407 2968Shanghai Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
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Wu R, Chen F, Wang N, Tang D, Kang R. ACOD1 in immunometabolism and disease. Cell Mol Immunol 2020; 17:822-833. [PMID: 32601305 DOI: 10.1038/s41423-020-0489-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Immunometabolism plays a fundamental role in health and diseases and involves multiple genes and signals. Aconitate decarboxylase 1 (ACOD1; also known as IRG1) is emerging as a regulator of immunometabolism in inflammation and infection. Upregulation of ACOD1 expression occurs in activated immune cells (e.g., macrophages and monocytes) in response to pathogen infection (e.g., bacteria and viruses), pathogen-associated molecular pattern molecules (e.g., LPS), cytokines (e.g., TNF and IFNs), and damage-associated molecular patterns (e.g., monosodium urate). Mechanistically, several immune receptors (e.g., TLRs and IFNAR), adapter proteins (e.g., MYD88), ubiquitin ligases (e.g., A20), and transcription factors (e.g., NF-κB, IRFs, and STATs) form complex signal transduction networks to control ACOD1 expression in a context-dependent manner. Functionally, ACOD1 mediates itaconate production, oxidative stress, and antigen processing and plays dual roles in immunity and diseases. On the one hand, activation of the ACOD1 pathway may limit pathogen infection and promote embryo implantation. On the other hand, abnormal ACOD1 expression can lead to tumor progression, neurodegenerative disease, and immune paralysis. Further understanding of the function and regulation of ACOD1 is important for the application of ACOD1-based therapeutic strategies in disease.
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Affiliation(s)
- Runliu Wu
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Feng Chen
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nian Wang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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Dhuppar S, Mazumder A. Investigating cell cycle-dependent gene expression in the context of nuclear architecture at single-allele resolution. J Cell Sci 2020; 133:jcs246330. [PMID: 32467328 DOI: 10.1242/jcs.246330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/10/2020] [Indexed: 12/20/2022] Open
Abstract
Nuclear architecture is the organization of the genome within a cell nucleus with respect to different nuclear landmarks such as the nuclear lamina, nuclear matrix or nucleoli. Recently, nuclear architecture has emerged as a major regulator of gene expression in mammalian cells. However, studies connecting nuclear architecture with gene expression are largely population-averaged and do not report on the heterogeneity in genome organization or gene expression within a population. In this report we present a method for combining 3D DNA fluorescence in situ hybridization (FISH) with single-molecule RNA FISH (smFISH) and immunofluorescence to study nuclear architecture-dependent gene regulation on a cell-by-cell basis. We further combine our method with imaging-based cell cycle staging to correlate nuclear architecture with gene expression across the cell cycle. We present this in the context of the cyclin-A2 (CCNA2) gene, which has known cell cycle-dependent expression. We show that, across the cell cycle, the expression of a CCNA2 gene copy is stochastic and depends neither on its sub-nuclear position - which usually lies close to nuclear lamina - nor on the expression from other copies of the gene.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, Telangana, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, Telangana, India
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17
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Rodríguez A, Mundy NI, Ibáñez R, Pröhl H. Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio). BMC Genomics 2020; 21:301. [PMID: 32293261 PMCID: PMC7158012 DOI: 10.1186/s12864-020-6719-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Animal coloration is usually an adaptive attribute, under strong local selection pressures and often diversified among species or populations. The strawberry poison frog (Oophaga pumilio) shows an impressive array of color morphs across its distribution in Central America. Here we quantify gene expression and genetic variation to identify candidate genes involved in generating divergence in coloration between populations of red, green and blue O. pumilio from the Bocas del Toro archipelago in Panama. Results We generated a high quality non-redundant reference transcriptome by mapping the products of genome-guided and de novo transcriptome assemblies onto a re-scaffolded draft genome of O. pumilio. We then measured gene expression in individuals of the three color phenotypes and identified color-associated candidate genes by comparing differential expression results against a list of a priori gene sets for five different functional categories of coloration – pteridine synthesis, carotenoid synthesis, melanin synthesis, iridophore pathways (structural coloration), and chromatophore development. We found 68 candidate coloration loci with significant expression differences among the color phenotypes. Notable upregulated examples include pteridine synthesis genes spr, xdh and pts (in red and green frogs); carotenoid metabolism genes bco2 (in blue frogs), scarb1 (in red frogs), and guanine metabolism gene psat1 (in blue frogs). We detected significantly higher expression of the pteridine synthesis gene set in red and green frogs versus blue frogs. In addition to gene expression differences, we identified 370 outlier SNPs on 162 annotated genes showing signatures of diversifying selection, including eight pigmentation-associated genes. Conclusions Gene expression in the skin of the three populations of frogs with differing coloration is highly divergent. The strong signal of differential expression in pteridine genes is consistent with a major role of these genes in generating the coloration differences among the three morphs. However, the finding of differentially expressed genes across pathways and functional categories suggests that multiple mechanisms are responsible for the coloration differences, likely involving both pigmentary and structural coloration. In addition to regulatory differences, we found potential evidence of differential selection acting at the protein sequence level in several color-associated loci, which could contribute to the color polymorphism.
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Affiliation(s)
- Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, England
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092, Panamá, República de Panamá.,Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Apartado, 0816-02852, Panamá, República de Panamá
| | - Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany
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Morita A, Aoshima K, Gulay KCM, Onishi S, Shibata Y, Yasui H, Kobayashi A, Kimura T. High drug efflux pump capacity and low DNA damage response induce doxorubicin resistance in canine hemangiosarcoma cell lines. Res Vet Sci 2019; 127:1-10. [PMID: 31648115 DOI: 10.1016/j.rvsc.2019.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 09/17/2019] [Accepted: 09/22/2019] [Indexed: 01/19/2023]
Abstract
Canine hemangiosarcoma (HSA) is an aggressive malignant endothelial tumor in dogs and characterized by poor prognosis because of its high invasiveness, high metastatic potential, and poor responsiveness to anti-cancer drugs. Although doxorubicin-based chemotherapy is regularly conducted after surgical treatment, its effects on survival rates are limited. Acquisition of drug resistance is one of the causes of this problem, but the underlying mechanisms remain unclear. In the present study, we aimed to identify the drug-resistance mechanism in canine HSA by establishing doxorubicin-resistant (DR) HSA cell lines. HSA cell lines were exposed to doxorubicin at gradually increasing concentrations. When the cells were able to grow in the presence of a 16-fold higher doxorubicin concentration compared with the initial culture, they were designated DR-HSA cell lines. Characterization of these DR-HSA cell lines revealed higher drug efflux pump capacity compared with the parental cell lines. Furthermore, the DR-HSA cell lines did not show activation of the DNA damage response despite carrying high DNA damage burdens, meaning that apoptosis was not strongly induced. In conclusion, canine HSA cell lines acquired doxorubicin resistance by increasing their drug efflux pump capacity and decreasing the DNA damage response. This study provides useful findings to promote further research on the drug-resistance mechanisms in canine HSA.
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Affiliation(s)
- Atsuya Morita
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Keisuke Aoshima
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan.
| | - Kevin Christian Montecillo Gulay
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Shinichi Onishi
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Yuki Shibata
- Laboratory of Integrated Molecular Imaging, Department of Biomedical Imaging, Graduate School of Biomedical Science and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Hironobu Yasui
- Laboratory of Radiation Biology, Department of Applied Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Atsushi Kobayashi
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
| | - Takashi Kimura
- Laboratory of Comparative Pathology, Department of Clinical Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido 060-0818, Japan
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Novel sampling procedure to characterize bovine subclinical endometritis by uterine secretions and tissue. Theriogenology 2019; 141:186-196. [PMID: 31557616 DOI: 10.1016/j.theriogenology.2019.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/16/2019] [Accepted: 09/09/2019] [Indexed: 01/04/2023]
Abstract
Subclinical endometritis (SE) in cattle is defined as clinically unapparent inflammation of the endometrium. It is reported to impair fertility in affected cows and causes economic loss within the dairy industry. A gold standard for diagnosis of SE has not been set. Uterine cytology and histopathology are both applied, but low agreement between these methods has been described. The objective of the present study was to assess the capability of uterine secretions (US) as a new medium for diagnosis of SE. A novel sampling tool was applied to retrieve US as well as cytological, histological and bacteriological samples of the endometrium after a singular passage through the cervix in 108 dairy cows (43-62 days post-partum [dpp]). To assess the quality of the US samples, a proteome analysis of samples from five healthy donors was performed, demonstrating that in vivo sampling of US was feasible and generated samples suitable for diagnostic purposes. Diagnosis of SE was realized by the combination of clinical, cytological, and histopathological findings. Quantitative analysis of pro- and anti-inflammatory cytokines (interleukin (IL)1B, IL6, IL8, IL17A, IL10) in US was conducted using AlphaLISA-technology. RNAlater-fixed endometrial biopsies were used for gene expression analysis of the cytokines IL1B, IL6, IL8, IL10 and tumor necrosis factor alpha (TNFα) as well as the prostaglandin-endoperoxide synthase 2 (PTGS2) and the antimicrobial peptide S100A9 by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). Cows were assigned to groups according to their uterine health status. A large group of animals (n = 83) displayed no signs of endometritis (E.NEG). Cytological and histopathological examination revealed low agreement; hence, animals with SE were differentiated into SE(cyto) and SE(histo) groups (n = 7 and n = 13, respectively). One animal in group SE(cyto + histo) as well as four animals with signs of clinical endometritis (CE) were excluded from further analysis. SE(cyto) showed significantly higher median concentrations of IL1B, IL8 and IL17A in US as well as a significantly higher median expression of IL1B, IL8 and IL10 in endometrial biopsies compared to E.NEG. No significant differences were found for IL6 and IL10 in US and IL6, TNFα, PTGS2 and S100A9 in endometrial tissue between these groups. SE(histo) presented no differences concerning the analyzed parameters compared to E.NEG. In conclusion, a method to sample US was successfully established in dairy cows. The cytokines IL1B, IL8 and IL17A are promising candidates in diagnosing cytological endometritis by US. Further assessment of US might contribute to a better understanding of the pathological mechanisms leading to chronic endometrial inflammation and to impaired fertility in affected cows.
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Xie Y, Jiang L, Qiu J, Wang Y. A comparative evaluation of the immunotoxicity and immunomodulatory effects on macrophages exposed to aromatic trihalogenated DBPs. Immunopharmacol Immunotoxicol 2019; 41:319-326. [PMID: 31046488 DOI: 10.1080/08923973.2019.1608444] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective: 2,4,6-trichlorophenol (TCP), 2,4,6-tribromophenol (TBP), and 2,4,6-triiodophenol (TIP) are three aromatic halogenated disinfection byproducts (DBPs) identified in chlorinated saline effluents. This study aimed to evaluate and compare their immunotoxicity and immunomodulatory effects on macrophages. Materials and methods: CCK-8 assay was used to evaluate cytotoxicity of TCP, TBP, and TIP in mouse macrophage RAW264.7 cells. A light microscope and digital camera were used to record the morphological changes of RAW264.7 cells. qRT-PCR was used to measure the mRNA levels of polarization markers and secreted cytokines. Cytokine production was also detected by ELISA. Flow cytometry was performed to analyze the expression of M1 and M2 markers on macrophages. Results: TCP, TBP, and TIP had different cytotoxic effects on macrophages. The rank order of cytotoxicity was TIP > TBP > TCP. Furthermore, the three halogenated DBPs displayed different preferences for macrophage polarization. Intriguingly, 200 μM TIP remarkably induced the M2-dominant polarization of macrophages, while 200 μM TCP induced an M1-dominant polarization of macrophages. TBP has a moderate ability in inducing M1 and M2 polarization compared with TCP and TIP. Conclusions: TIP displayed higher cytotoxicity against macrophages than TBP and TCP, its brominated and chlorinated analogs. Since M1 and M2 macrophages facilitate the inflammatory and anti-inflammatory responses, respectively, the discrepancy of TCP, TBP, and TIP in inducing macrophage polarization may lead to distinct immunomodulatory and toxicological outcomes, thus giving rise to different types of diseases. This finding may provide novel insights into evaluating the toxicity of environmental pollutants on the immune system.
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Affiliation(s)
- Yanci Xie
- a Department of Pathogen Biology, Key Laboratory of Pathogen Biology of Jiangsu Province , Nanjing Medical University , Nanjing , China
| | - Liujing Jiang
- b School of the Environment, State Key Laboratory of Pollution Control and Resource Reuse , Nanjing University , Nanjing , China
| | - Jingfan Qiu
- a Department of Pathogen Biology, Key Laboratory of Pathogen Biology of Jiangsu Province , Nanjing Medical University , Nanjing , China
| | - Yong Wang
- a Department of Pathogen Biology, Key Laboratory of Pathogen Biology of Jiangsu Province , Nanjing Medical University , Nanjing , China.,c School of Public Health, Key Laboratory of Infectious Diseases , Nanjing Medical University , Nanjing , China
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Liu Y, Qian J, Sun Z, Zhangsun D, Luo S. Cervical Cancer Correlates with the Differential Expression of Nicotinic Acetylcholine Receptors and Reveals Therapeutic Targets. Mar Drugs 2019; 17:md17050256. [PMID: 31035425 PMCID: PMC6562638 DOI: 10.3390/md17050256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/02/2023] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are associated with various cancers, but the relation between nAChRs and cervical cancer remains unclear. Therefore, this study investigated the differential expression of nAChR subunits in human cervical cancer cell lines (SiHa, HeLa, and CaSki) and in normal ectocervical cell lines (Ect1/E6E7) at mRNA and protein levels. Two specific nAChR subtype blockers, αO-conotoxin GeXIVA and α-conotoxin TxID, were then selected to treat different human cervical cancer cell lines with specific nAChR subtype overexpression. The results showed that α3, α9, α10, and β4 nAChR subunits were overexpressed in SiHa cells compared with that in normal cells. α9 and α10 nAChR subunits were overexpressed in CaSki cells. α*-conotoxins that targeted either α9α10 or α3β4 nAChR were able to significantly inhibit cervical cancer cell proliferation. These findings may provide a basis for new targets for cervical cancer targeted therapy.
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Affiliation(s)
- Yiqiao Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, Hainan, China.
| | - Jiang Qian
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, Hainan, China.
| | - Zhihua Sun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, Hainan, China.
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, Hainan, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou 570228, Hainan, China.
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Angeli E, Trionfini V, Gareis NC, Matiller V, Huber E, Rey F, Salvetti NR, Ortega HH, Hein GJ. Protein and gene expression of relevant enzymes and nuclear receptor of hepatic lipid metabolism in grazing dairy cattle during the transition period. Res Vet Sci 2019; 123:223-231. [PMID: 30684909 DOI: 10.1016/j.rvsc.2019.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/15/2019] [Accepted: 01/20/2019] [Indexed: 12/15/2022]
Abstract
We aimed to study the protein and gene expression of some hepatic enzymes of lipid metabolism along with plasma biomarkers in grazing dairy cattle during the transition period. Blood and liver biopsies from a group of eight multiparous cows were sampled at -28, -14, +4, +14, +28 and +56 days relative to parturition. Peak concentrations of NEFA and beta-hydroxybutyric acid with high triacylglycerol content in the liver were recorded on day 4 postpartum. Consistent with blood biomarkers, the gene expression of carnitine palmitoyltransferase 1A (CPT1A) and acyl-CoA oxidase 1 (ACOX1) increased, whereas that of diacylglycerol O-acyltransferase 1 (DGAT1) decreased. Nevertheless, CPT1A protein expression did not change during all the period evaluated and ACOX1 protein expression increased on day 56 postpartum. In addition, the protein expression of peroxisome proliferator-activated receptor alpha (PPAR-alpha) increased on day 28 postpartum. On the other hand, DGAT1 protein expression decreased on day 14 postpartum. As expected, the expression of genes associated with fatty acid oxidation increased on the first days postpartum but, notably, protein expression was highest after transition. Since most infectious diseases and metabolic disorders in dairy cattle occur particularly on the first days postpartum, it is not so clear whether an increase in the oxidation capacity of the liver at that time could help to prevent disease and improve dairy production. The valuable results about protein expression of enzymes involved in liver lipid metabolism could help to better characterize the metabolism of dairy cattle during the transition period.
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Affiliation(s)
- E Angeli
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - V Trionfini
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - N C Gareis
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - V Matiller
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - E Huber
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - F Rey
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - N R Salvetti
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - H H Ortega
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Ciencias Veterinarias del Litoral, Universidad Nacional del Litoral (UNL), Esperanza, Santa Fe, Argentina
| | - G J Hein
- Laboratorio de Biología Celular y Molecular Aplicada, Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL)/Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Centro Universitario Gálvez, Universidad Nacional del Litoral (UNL), Gálvez, Santa Fe, Argentina.
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Xu L, Peng L, Gu T, Yu D, Yao YG. The 3′UTR of human MAVS mRNA contains multiple regulatory elements for the control of protein expression and subcellular localization. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:47-57. [DOI: 10.1016/j.bbagrm.2018.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022]
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Manna D, Lentz CS, Ehrenkaufer GM, Suresh S, Bhat A, Singh U. An NAD +-dependent novel transcription factor controls stage conversion in Entamoeba. eLife 2018; 7:e37912. [PMID: 30375973 PMCID: PMC6207428 DOI: 10.7554/elife.37912] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/17/2018] [Indexed: 12/22/2022] Open
Abstract
Developmental switching between life-cycle stages is a common feature among parasitic pathogens to facilitate disease transmission and pathogenesis. The protozoan parasite Entamoeba switches between invasive trophozoites and dormant cysts, but the encystation process remains poorly understood despite being central to amoebic biology. We identify a transcription factor, Encystation Regulatory Motif-Binding Protein (ERM-BP), that regulates encystation. Down-regulation of ERM-BP decreases encystation efficiency resulting in abnormal cysts with defective cyst walls. We demonstrate that direct binding of NAD+ to ERM-BP affects ERM-BP conformation and facilitates its binding to promoter DNA. Additionally, cellular NAD+ levels increase during encystation and exogenous NAD+ enhances encystation consistent with the role of carbon source depletion in triggering Entamoeba encystation. Furthermore, ERM-BP catalyzes conversion of nicotinamide to nicotinic acid, which might have second messenger effects on stage conversion. Our findings link the metabolic cofactors nicotinamide and NAD+ to transcriptional regulation via ERM-BP and provide the first mechanistic insights into Entamoeba encystation.
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Affiliation(s)
- Dipak Manna
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | | | - Gretchen Marie Ehrenkaufer
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Susmitha Suresh
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Amrita Bhat
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
| | - Upinder Singh
- Division of Infectious Diseases, Department of Internal MedicineStanford University School of MedicineStanfordUnited States
- Department of Microbiology and ImmunologyStanford University School of MedicineStanfordUnited States
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25
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Lin K, Zhang S, Shi Q, Zhu M, Gao L, Xia W, Geng B, Zheng Z, Xu EY. Essential requirement of mammalian Pumilio family in embryonic development. Mol Biol Cell 2018; 29:2922-2932. [PMID: 30256721 PMCID: PMC6329913 DOI: 10.1091/mbc.e18-06-0369] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mouse PUMILIO1 (PUM1) and PUMILIO2 (PUM2) belong to the PUF (Pumilio/FBF) family, a highly conserved RNA binding protein family whose homologues play critical roles in embryonic development and germ line stem cell maintenance in invertebrates. However, their roles in mammalian embryonic development and stem cell maintenance remained largely uncharacterized. Here we report an essential requirement of the Pum gene family in early embryonic development. A loss of both Pum1 and Pum2 genes led to gastrulation failure, resulting in embryo lethality at E8.5. Pum-deficient blastocysts, however, appeared morphologically normal, from which embryonic stem cells (ESCs) could be established. Both mutant ESCs and embryos exhibited reduced growth and increased expression of endoderm markers Gata6 and Lama1, making defects in growth and differentiation the likely causes of gastrulation failure. Furthermore, ESC Gata6 transcripts could be pulled down via PUM1 immunoprecipitation and mutation of conserved PUM-binding element on 3'UTR (untranslated region) of Gata6 enhanced the expression of luciferase reporter, implicating PUM-mediated posttranscriptional regulation of Gata6 expression in stem cell development and cell lineage determination. Hence, like its invertebrate homologues, mouse PUM proteins are conserved posttranscriptional regulators essential for embryonic and stem cell development.
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Affiliation(s)
- Kaibo Lin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Assisted Reproduction, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Shikun Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qinghua Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Mengyi Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Liuze Gao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Wenjuan Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Baobao Geng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zimeng Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
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Ramos A, Miow QH, Liang X, Lin QS, Putti TC, Lim YP. Phosphorylation of E-box binding USF-1 by PI3K/AKT enhances its transcriptional activation of the WBP2 oncogene in breast cancer cells. FASEB J 2018; 32:fj201801167RR. [PMID: 30183375 DOI: 10.1096/fj.201801167rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
WW domain binding protein 2 (WBP2), a transcriptional coactivator, plays a vital role in breast tumorigenesis. It positively regulates estrogen receptor, Hippo, and Wnt pathways, which subsequently enhance the transcription of downstream target genes contributing to cancer. Understanding the regulation of the expression and activity of WBP2 oncoprotein has implication in cancer therapy. We have previously reported that WBP2 is regulated at the post-translational and post-transcriptional levels. However, its regulation at the transcriptional level is not known. In this study, the minimal promoter region of WBP2 that is critical for its transcription was identified. The E-box motif in the WBP2 promoter was demonstrated to be essential for its transcription. The E-box binding protein upstream stimulatory factor 1 (USF-1) was discovered to be a key transcription factor for WBP2 by yeast one-hybrid analysis and was validated through reporter and chromatin immunoprecipitation assays and tandem mass spectrometry, which also suggested that USF-1 acts by regulating a network of genes, in addition to WBP2, associated with cell movement, proliferation, cell-cycle, and survival cellular processes. USF-1 is overexpressed in majority of the breast cancer cell lines and tissues tested, and has profound effects on cancer cell proliferation. USF-1-mediated transcription of WBP2 was demonstrated to be inducible by insulin, which led to AKT-mediated phosphorylation of USF-1 that modulated its ability to bind to the WBP2 promoter and activate its transcription. This study sheds new light onto the regulation of the WBP2 oncogene at the transcriptional level by a novel oncogenic transcription factor, USF-1. USF-1 is a potential drug target for treatment of WBP2-positive breast cancer.-Ramos, A., Miow, Q. H., Liang, X., Lin, Q. S., Putti, T. C., Lim, Y. P. Phosphorylation of E-box binding USF-1 by PI3K/AKT enhances its transcriptional activation of the WBP2 oncogene in breast cancer cells.
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Affiliation(s)
- Alisha Ramos
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qing Hao Miow
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xu Liang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qing Song Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | | | - Yoon Pin Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Cancer Institute, National University of Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
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Banchi E, Candotto Carniel F, Montagner A, Petruzzellis F, Pichler G, Giarola V, Bartels D, Pallavicini A, Tretiach M. Relation between water status and desiccation-affected genes in the lichen photobiont Trebouxia gelatinosa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:189-197. [PMID: 29894859 DOI: 10.1016/j.plaphy.2018.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
The relation between water status and expression profiles of desiccation -related genes has been studied in the desiccation tolerant (DT) aeroterrestrial green microalga Trebouxia gelatinosa, a common lichen photobiont. Algal colonies were desiccated in controlled conditions and during desiccation water content (WC) and water potential (Ψ) were measured to find the turgor loss point (Ψtlp). Quantitative real-time PCR was performed to measure the expression of ten genes related to photosynthesis, antioxidant defense, expansins, heat shock proteins (HSPs), and desiccation related proteins in algal colonies collected during desiccation when still at full turgor (WC > 6 g H2O g-1 dry weight), immediately before and after Ψtlp (-4 MPa; WC ∼ 1 g H2O g-1 dry weight) and before and after complete desiccation (WC < 0.01 g H2O g-1 dry weight), quantifying the HSP70 protein levels by immunodetection. Our analysis showed that the expression of eight out of ten genes changed immediately before and after Ψtlp. Interestingly, the expression of five out of ten genes changed also before complete desiccation, i.e. between 0.2 and 0.01 g H2O g-1 dry weight. However, the HSP70 protein levels were not affected by changes in water status. The study provides new evidences of the link between the loss of turgor and the expression of genes related to the desiccation tolerance of T. gelatinosa, suggesting the former as a signal triggering inducible mechanisms.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
| | - Fabio Candotto Carniel
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
| | - Alice Montagner
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
| | - Francesco Petruzzellis
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
| | - Gregor Pichler
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria.
| | - Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, D-53115 Bonn, Germany.
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, D-53115 Bonn, Germany.
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy.
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29
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Zhang Y, Cao S, Zhao J, Alsaihati B, Ma Q, Zhang C. MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network. QUANTITATIVE BIOLOGY 2018. [DOI: 10.1007/s40484-018-0131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Mann S, Leal Yepes F, Wakshlag J, Behling-Kelly E, McArt J. The effect of different treatments for early-lactation hyperketonemia on liver triglycerides, glycogen, and expression of key metabolic enzymes in dairy cattle. J Dairy Sci 2018; 101:1626-1637. [DOI: 10.3168/jds.2017-13360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022]
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31
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Kostich MS. A statistical framework for applying RNA profiling to chemical hazard detection. CHEMOSPHERE 2017; 188:49-59. [PMID: 28869846 PMCID: PMC6146931 DOI: 10.1016/j.chemosphere.2017.08.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/22/2017] [Accepted: 08/26/2017] [Indexed: 06/07/2023]
Abstract
Use of 'omics technologies in environmental science is expanding. However, application is mostly restricted to characterizing molecular steps leading from toxicant interaction with molecular receptors to apical endpoints in laboratory species. Use in environmental decision-making is limited, due to difficulty in elucidating mechanisms in sufficient detail to make quantitative outcome predictions in any single species or in extending predictions to aquatic communities. Here we introduce a mechanism-agnostic statistical approach, supplementing mechanistic investigation by allowing probabilistic outcome prediction even when understanding of molecular pathways is limited, and facilitating extrapolation from results in laboratory test species to predictions about aquatic communities. We use concepts familiar to environmental managers, supplemented with techniques employed for clinical interpretation of 'omics-based biomedical tests. We describe the framework in step-wise fashion, beginning with single test replicates of a single RNA variant, then extending to multi-gene RNA profiling, collections of test replicates, and integration of complementary data. In order to simplify the presentation, we focus on using RNA profiling for distinguishing presence versus absence of chemical hazards, but the principles discussed can be extended to other types of 'omics measurements, multi-class problems, and regression. We include a supplemental file demonstrating many of the concepts using the open source R statistical package.
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Affiliation(s)
- Mitchell S Kostich
- USEPA/ORD/NERL/EMMD, 26 West M. L. King Drive, Cincinnati, OH 45268, USA.
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32
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Zhang S, Yue X, Jiang F, Wang H, Liu B. Identification of an MITF gene and its polymorphisms associated with the Vibrio resistance trait in the clam Meretrix petechialis. FISH & SHELLFISH IMMUNOLOGY 2017; 68:466-473. [PMID: 28734968 DOI: 10.1016/j.fsi.2017.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 05/15/2023]
Abstract
Microphthalmia-associated transcription factor (MITF) regulates the transcription of its target genes by binding to their promoters. In this study, an MITF gene, MpMITF was identified in the clam Meretrix petechialis. The full-length cDNA of MpMITF is 3564 bp with an ORF of 1365 bp. The deduced amino acid sequence consists of a conserved functional structure of bHLH-LZ, which could bind with E-box. The mRNA and protein expression levels of MpMITF were significantly up-regulated 6 h post-Vibrio injection. The mRNA expression of MpMITF increased on day 2 and peaked on day 10 post-Vibrio immersion. Furthermore, MpMITF expression was significantly up-regulated in most resistant families of clams (P < 0.05) but did not change significantly in most susceptive families of clams after the Vibrio immersion challenge. These results suggest that, in clams, MpMITF participates in the immune response against a Vibrio infection. Genotyping in two clam groups with different resistant levels to Vibrio parahaemolyticus (i.e., 11-R and 11-S), thirteen SNPs and five haplotypes were detected in the DNA sequence of MpMITF, of which five SNPs and two haplotypes were associated with Vibrio resistance. Four SNPs (SNP2, 5, 6 and 13) and one haplotype (Hap1) were further confirmed to be associated with Vibrio resistance in M. petechialis by association analysis in different clam families. This study deepens the understanding of MITF in marine bivalves and provides potential candidate markers for resistance selection in the clam M. petechialis.
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Affiliation(s)
- Shujing Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yue
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fengjuan Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266000 Qingdao, China.
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Félix LM, Serafim C, Valentim AM, Antunes LM, Matos M, Coimbra AM. Apoptosis-related genes induced in response to ketamine during early life stages of zebrafish. Toxicol Lett 2017; 279:1-8. [DOI: 10.1016/j.toxlet.2017.07.888] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 12/01/2022]
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34
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Gan Z, Powell FL, Zambon AC, Buchholz KS, Fu Z, Ocorr K, Bodmer R, Moya EA, Stowe JC, Haddad GG, McCulloch AD. Transcriptomic analysis identifies a role of PI3K-Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo. J Physiol 2017; 595:5797-5813. [PMID: 28688178 DOI: 10.1113/jp274556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 01/13/2023] Open
Abstract
KEY POINTS Changes in gene expression that occur within hours of exposure to hypoxia in in vivo skeletal muscles remain unexplored. Two hours of hypoxia caused significant down-regulation of extracellular matrix genes followed by a shift at 6 h to altered expression of genes associated with the nuclear lumen while respiratory and blood gases were stabilized. Enrichment analysis of mRNAs classified by stability rates suggests an attenuation of post-transcriptional regulation within hours of hypoxic exposure, where PI3K-Akt signalling was suggested to have a nodal role by pathway analysis. Experimental measurements and bioinformatic analyses suggested that the dephosphorylation of Akt after 2 h of hypoxic exposure might deactivate RNA-binding protein BRF1, hence resulting in the selective degradation of mRNAs. ABSTRACT The effects of acute hypoxia have been widely studied, but there are few studies of transcriptional responses to hours of hypoxia in vivo, especially in hypoxia-tolerant tissues like skeletal muscles. We used RNA-seq to analyse gene expression in plantaris muscles while monitoring respiration, arterial blood gases, and blood glucose in mice exposed to 8% O2 for 2 or 6 h. Rapid decreases in blood gases and a slower reduction in blood glucose suggest stress, which was accompanied by widespread changes in gene expression. Early down-regulation of genes associated with the extracellular matrix was followed by a shift to genes associated with the nuclear lumen. Most of the early down-regulated genes had mRNA half-lives longer than 2 h, suggesting a role for post-transcriptional regulation. These transcriptional changes were enriched in signalling pathways in which the PI3K-Akt signalling pathway was identified as a hub. Our analyses indicated that gene targets of PI3K-Akt but not HIF were enriched in early transcriptional responses to hypoxia. Among the PI3K-Akt targets, 75% could be explained by a deactivation of adenylate-uridylate-rich element (ARE)-binding protein BRF1, a target of PI3K-Akt. Consistent decreases in the phosphorylation of Akt and BRF1 were experimentally confirmed following 2 h of hypoxia. These results suggest that the PI3K-Akt signalling pathway might play a role in responses induced by acute hypoxia in skeletal muscles, partially through the dephosphorylation of ARE-binding protein BRF1.
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Affiliation(s)
- Zhuohui Gan
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.,Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Frank L Powell
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexander C Zambon
- Department of Biopharmaceutical Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kyle S Buchholz
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhenxing Fu
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Esteban A Moya
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer C Stowe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA.,Rady Children's Hospital San Diego, 3020 Children's Way, San Diego, CA, 92123, USA
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
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Dierichs L, Kloubert V, Rink L. Cellular zinc homeostasis modulates polarization of THP-1-derived macrophages. Eur J Nutr 2017; 57:2161-2169. [PMID: 28687933 DOI: 10.1007/s00394-017-1491-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/25/2017] [Indexed: 12/12/2022]
Abstract
PURPOSE Polarization of macrophages by environmental stimuli leads to the characteristic of different phenotypes that exhibit distinct functions, ranging in a continuous spectrum from pro-inflammatory M1 up to immunoregulatory and wound-healing M2 macrophages. Diseases like cancer, allergic asthma or diabetes are associated with an M1/M2 imbalance. Owing to the importance of the essential trace element zinc for the immune system and its involvement in signal transduction as a second messenger, we investigated the impact of zinc on M1 and M2 polarization of macrophages in vitro. METHODS A polarization model with human THP-1 cells was established and validated with previously described markers using quantitative real-time PCR, Western blot and flow cytometry. Intracellular free Zn2+ was determined with FluoZin-3-AM. RESULTS Whereas pSTAT1 and HLA-DR or pSTAT6 and Dectin-1 distinguish between M1 and M2 macrophages, respectively, CD86 and CD206 failed. Depending on the used markers, both zinc supplementation in physiological dose (50 µM) and zinc deficiency promote M1 polarization of THP-1-derived macrophages. Furthermore, zinc supplementation strongly inhibits M2 polarization. CONCLUSION For the first time, we show a modulating effect of zinc for the polarization of human macrophages. The strong inhibitory effect of zinc supplementation on M2 polarization indicates a relevance regarding M2-dominated diseases like allergic asthma or cancer. All in all, zinc achieves a great potential for modulating macrophage polarization.
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Affiliation(s)
- Laura Dierichs
- Faculty of Medicine, University Hospital, Institute of Immunology, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Veronika Kloubert
- Faculty of Medicine, University Hospital, Institute of Immunology, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Lothar Rink
- Faculty of Medicine, University Hospital, Institute of Immunology, RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
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Gálvez H, Abelló G, Giraldez F. Signaling and Transcription Factors during Inner Ear Development: The Generation of Hair Cells and Otic Neurons. Front Cell Dev Biol 2017; 5:21. [PMID: 28393066 PMCID: PMC5364141 DOI: 10.3389/fcell.2017.00021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
Integration between cell signals and bHLH transcription factors plays a prominent role during the development of hair cells of the inner ear. Hair cells are the sensory receptors of the inner ear, responsible for the mechano-transduction of sound waves into electrical signals. They derive from multipotent progenitors that reside in the otic placode. Progenitor commitment is the result of cell signaling from the surrounding tissues that result in the restricted expression of SoxB1 transcription factors, Sox2 and Sox3. In turn, they induce the expression of Neurog1 and Atoh1, two bHLH factors that specify neuronal and hair cell fates, respectively. Neuronal and hair cell development, however, do not occur simultaneously. Hair cell development is prevented during neurogenesis and prosensory stages, resulting in the delay of hair cell development with respect to neuron production. Negative interactions between Neurog1 and Atoh1, and of Atoh1 with other bHLH factors driven by Notch signaling, like Hey1 and Hes5, account for this delay. In summary, the regulation of Atoh1 and hair cell development relies on interactions between cell signaling and bHLH transcription factors that dictate cell fate and timing decisions during development. Interestingly, these mechanisms operate as well during hair cell regeneration after damage and during stem cell directed differentiation, making developmental studies instrumental for improving therapies for hearing impairment.
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Affiliation(s)
- Héctor Gálvez
- Developmental Biology, CEXS, Parc de Recerca Biomèdica de Barcelona, Universitat Pompeu Fabra Barcelona, Spain
| | - Gina Abelló
- Developmental Biology, CEXS, Parc de Recerca Biomèdica de Barcelona, Universitat Pompeu Fabra Barcelona, Spain
| | - Fernando Giraldez
- Developmental Biology, CEXS, Parc de Recerca Biomèdica de Barcelona, Universitat Pompeu Fabra Barcelona, Spain
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Nie Q, Yue X, Liu B. Identification of the MmeHairy gene and expression analysis affected by two SNPs in the 3'-untranslated region in the clam Meretrix meretrix. FISH & SHELLFISH IMMUNOLOGY 2016; 51:46-52. [PMID: 26873874 DOI: 10.1016/j.fsi.2016.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 06/05/2023]
Abstract
As a bHLH transcriptional repressor, Hairy-related proteins can bind to DNA sites in target gene promoters and negatively regulate gene transcription. In the present study, the full-length cDNA of Hairy was obtained from the clam Meretrix meretrix (MmeHairy), and two SNPs in the 3'-untranslated region (UTR) of this gene, SNP1066 and 1067, were identified and characterized. Multiple sequence alignment and phylogenetic analysis revealed that MmeHairy belongs to the Hairy protein subfamily. Analysis of tissue expression patterns showed that the mRNA of MmeHairy had the highest expression level in the hepatopancreas. The expression levels of MmeHairy were up-regulated in the hepatopancreas after Vibrio challenge. Genotyping and quantitative analysis showed that the mRNA levels of MmeHairy were significantly different among individual clams with different genotypes at SNP1066 and 1067 (P < 0.05), which indicated that these two SNP loci may affect the expression of MmeHairy and could be used as candidate markers for future selection in M. meretrix breeding programs.
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Affiliation(s)
- Qing Nie
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Department of Marine Science and Technology, College of Marine and Biology Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Xin Yue
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao China.
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38
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Kim DY. Post-transcriptional regulation of gene expression in neural stem cells. Cell Biochem Funct 2016; 34:197-208. [PMID: 27001557 DOI: 10.1002/cbf.3181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 12/30/2022]
Abstract
Expression of each gene can be controlled at several steps during the flow of genetic information from DNA to protein. Tight regulation of gene expression is especially important for stem cells because of their greater ripple effects, compared with terminally differentiated cells. Dysregulation of gene expression arising in stem cells can be perpetuated within the stem cell pool via self-renewal throughout life. In addition, transcript profiles within stem cells can determine the selective advantage or disadvantage of each cell, leading to changes in cell fate, such as a tendency for proliferation, death, and differentiation. The identification of neural stem/progenitor cells (NSPCs) and greater understanding of their cellular physiology have raised the possibility of using NSPCs to replace damaged or injured neurons. However, an accurate grasp of gene expression control must take precedence in order to use NSPCs in therapies for neurological diseases. Recently, accumulating evidence has demonstrated the importance of post-transcriptional regulation in NSPC fate decisions. In this review, we will summarize and discuss the recent findings on key mRNA modulators and their vital roles in NSPC homeostasis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu, Korea
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Schmiedel D, Tai J, Yamin R, Berhani O, Bauman Y, Mandelboim O. The RNA binding protein IMP3 facilitates tumor immune escape by downregulating the stress-induced ligands ULPB2 and MICB. eLife 2016; 5. [PMID: 26982091 PMCID: PMC4805531 DOI: 10.7554/elife.13426] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 03/05/2016] [Indexed: 12/11/2022] Open
Abstract
Expression of the stress-induced ligands MICA, MICB and ULBP 1–6 are up-regulated as a cellular response to DNA damage, excessive proliferation or viral infection; thereby, they enable recognition and annihilation by immune cells that express the powerful activating receptor NKG2D. This receptor is present not exclusively, but primarily on NK cells. Knowledge about the regulatory mechanisms controlling ULBP expression is still vague. In this study, we report a direct interaction of the oncogenic RNA binding protein (RBP) IMP3 with ULBP2 mRNA, leading to ULBP2 transcript destabilization and reduced ULBP2 surface expression in several human cell lines. We also discovered that IMP3 indirectly targets MICB with a mechanism functionally distinct from that of ULBP2. Importantly, IMP3-mediated regulation of stress-ligands leads to impaired NK cell recognition of transformed cells. Our findings shed new light on the regulation of NKG2D ligands and on the mechanism of action of a powerful oncogenic RBP, IMP3. DOI:http://dx.doi.org/10.7554/eLife.13426.001 Tumor cells differ from healthy cells in many aspects. Importantly, tumor cells have the ability to divide and grow much faster than normal cells. To protect ourselves from full-grown cancers, our bodies have developed a surveillance system: when a tumor cell starts to divide without restraint, “stress-induced” proteins start to appear on its surface. These proteins help the immune system recognize abnormal or damaged cells, allowing the immune cells to eliminate the defective cells. Despite this system of protection, a tumor cell sometimes manages to avoid having stress-induced proteins placed on its surface, allowing it to remain undetected by the immune system. By studying several different types of human cancer cells, Schmiedel et al. found that a protein called IMP3 is present in cancer cells but not in healthy cells. Further investigation revealed that IMP3 prevents the production of some stress-induced proteins and stops them moving to the cell surface. Schmiedel et al. also show that the presence of the IMP3 protein in cancer cells causes nearby immune cells to become much less active. This suggests that developing drugs that block the activity of IMP3 could help the immune system to fight back and destroy cancer cells. DOI:http://dx.doi.org/10.7554/eLife.13426.002
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Affiliation(s)
- Dominik Schmiedel
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Julie Tai
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Rachel Yamin
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Orit Berhani
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yoav Bauman
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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40
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Complex patterns of differential expression in candidate master regulatory genes for social behavior in honey bees. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2071-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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41
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Wewer Albrechtsen NJ, Kuhre RE, Toräng S, Holst JJ. The intestinal distribution pattern of appetite- and glucose regulatory peptides in mice, rats and pigs. BMC Res Notes 2016; 9:60. [PMID: 26830025 PMCID: PMC4736122 DOI: 10.1186/s13104-016-1872-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/19/2016] [Indexed: 01/12/2023] Open
Abstract
Background Mice, rats, and pigs are the three most used animal models when studying gastrointestinal peptide hormones;
however their distribution from the duodenum to the distal colon has not been characterized systematically across mice, rats and pigs. We therefore performed a comparative distribution analysis of the tissue content of the major appetite- and glucose regulatory peptides: glucose-dependent insulinotropic polypeptide (GIP), glucagon-like peptide-1 (GLP-1), glucagon-like peptide-1 (GLP-2), oxyntomodulin/glicentin, neurotensin, and peptide YY (PYY) from the duodenum to distal colon in mice (n = 9), rats (n = 9) and pigs (n = 8), using validated radioimmunoassays. Results GLP-1, GLP-2 and oxyntomodulin/glicentin show similar patterns of distribution within the respective species, but for rats and pigs the highest levels were found in the distal small intestine, whereas for the mouse the highest level was found in the distal colon. In rats and pigs, neurotensin was predominantly detected in mid and lower part of the small intestine, while the mouse showed the highest levels in the distal small intestine. In contrast, the distribution of GIP was restricted to the proximal small intestine in all three species. Most surprisingly, in the pig PYY was found in large amounts in the proximal part of the small intestine whereas both rats and mice had undetectable levels until the distal small intestine. Conclusions In summary, the distribution patterns of extractable GIP, GLP-1, GLP-2, oxyntomodulin/glicentin, neurotensin are preserved across species whereas PYY distribution showed marked differences. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-1872-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolai J Wewer Albrechtsen
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 12.2, 2200, Copenhagen N, Denmark.
| | - Rune E Kuhre
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 12.2, 2200, Copenhagen N, Denmark.
| | - Signe Toräng
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 12.2, 2200, Copenhagen N, Denmark.
| | - Jens J Holst
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 12.2, 2200, Copenhagen N, Denmark.
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de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015; 381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
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43
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Nerlich A, Ruangkiattikul N, Laarmann K, Janze N, Dittrich-Breiholz O, Kracht M, Goethe R. C/EBPβ is a transcriptional key regulator of IL-36α in murine macrophages. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:966-78. [PMID: 26066982 DOI: 10.1016/j.bbagrm.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/15/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
Interleukin (IL)-36α - one of the novel members of the IL-1 family of cytokines - is a potent regulator of dendritic and T cells and plays an important role in inflammatory processes like experimental skin inflammation in mice and in mouse models for human psoriasis. Here, we demonstrate that C/EBPβ, a transcription factor required for the selective expression of inflammatory genes, is a key activator of the Il36A gene in murine macrophages. RNAi-mediated suppression of C/EBPβ expression in macrophages (C/EBPβ(low) cells) significantly impaired Il36A gene induction following challenge with LPS. Despite the presence of five predicted C/EBP binding sites, luciferase reporter assays demonstrated that C/EBPβ confers responsiveness to LPS primarily through a half-CRE•C/EBP element in the proximal Il36A promoter. Electrophoretic mobility shift assays showed that C/EBPβ but not CREB proteins interact with this critical half-CRE•C/EBP element. In addition, overexpression of C/EBPβ in C/EBPβ(low) cells enhanced the expression of Il36A whereas CREB-1 had no effect. Finally, chromatin immunoprecipitation confirmed that C/EBPβ but neither CREB-1, ATF-2 nor ATF4 is directly recruited to the proximal promoter region of the Il36A gene. Together, these findings demonstrate an essential role of C/EBPβ in the regulation of the Il36A gene via the proximal half-CRE•C/EBP element in response to inflammatory stimuli.
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Affiliation(s)
- Andreas Nerlich
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany.
| | - Nanthapon Ruangkiattikul
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Nina Janze
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | | | - Michael Kracht
- Rudolf -Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
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Mahajan NS, Dewangan V, Lomate PR, Joshi RS, Mishra M, Gupta VS, Giri AP. Structural features of diverse Pin-II proteinase inhibitor genes from Capsicum annuum. PLANTA 2015; 241:319-331. [PMID: 25269396 DOI: 10.1007/s00425-014-2177-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/15/2014] [Indexed: 06/03/2023]
Abstract
The proteinase inhibitor (PI) genes from Capsicum annuum were characterized with respect to their UTR, introns and promoter elements. The occurrence of PIs with circularly permuted domain organization was evident. Several potato inhibitor II (Pin-II) type proteinase inhibitor (PI) genes have been analyzed from Capsicum annuum (L.) with respect to their differential expression during plant defense response. However, complete gene characterization of any of these C. annuum PIs (CanPIs) has not been carried out so far. Complete gene architectures of a previously identified CanPI-7 (Beads-on-string, Type A) and a member of newly isolated Bracelet type B, CanPI-69 are reported in this study. The 5' UTR (untranslated region), 3'UTR, and intronic sequences of both the CanPI genes were obtained. The genomic sequence of CanPI-7 exhibited, exon 1 (49 base pair, bp) and exon 2 (740 bp) interrupted by a 294-bp long type I intron. We noted the occurrence of three multi-domain PIs (CanPI-69, 70, 71) with circularly permuted domain organization. CanPI-69 was found to possess exon 1 (49 bp), exon 2 (551 bp) and a 584-bp long type I intron. The upstream sequence analysis of CanPI-7 and CanPI-69 predicted various transcription factor-binding sites including TATA and CAAT boxes, hormone-responsive elements (ABRELATERD1, DOFCOREZM, ERELEE4), and a defense-responsive element (WRKY71OS). Binding of transcription factors such as zinc finger motif MADS-box and MYB to the promoter regions was confirmed using electrophoretic mobility shift assay followed by mass spectrometric identification. The 3' UTR analysis for 25 CanPI genes revealed unique/distinct 3' UTR sequence for each gene. Structures of three domain CanPIs of type A and B were predicted and further analyzed for their attributes. This investigation of CanPI gene architecture will enable the better understanding of the genetic elements present in CanPIs.
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Affiliation(s)
- Neha S Mahajan
- Division of Biochemical Sciences, Plant Molecular Biology Unit, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411 008, Maharashtra, India
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Ryan AF, Ikeda R, Masuda M. The regulation of gene expression in hair cells. Hear Res 2015; 329:33-40. [PMID: 25616095 DOI: 10.1016/j.heares.2014.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/10/2014] [Accepted: 12/29/2014] [Indexed: 01/21/2023]
Abstract
No genes have been discovered for which expression is limited only to inner ear hair cells. This is hardly surprising, since the number of mammalian genes is estimated to be 20-25,000, and each gene typically performs many tasks in various locations. Many genes are expressed in inner ear sensory cells and not in other cells of the labyrinth. However, these genes are also expressed in other locations, often in other sensory or neuronal cell types. How gene transcription is directed specifically to hair cells is unclear. Key transcription factors that act during development can specify cell phenotypes, and the hair cell is no exception. The transcription factor ATOH1 is well known for its ability to transform nonsensory cells of the developing inner ear into hair cells. And yet, ATOH1 also specifies different sensory cells at other locations, neuronal phenotypes in the brain, and epithelial cells in the gut. How it specifies hair cells in the inner ear, but alternate cell types in other locations, is not known. Studies of regulatory DNA and transcription factors are revealing mechanisms that direct gene expression to hair cells, and that determine the hair cell identity. The purpose of this review is to summarize what is known about such gene regulation in this key auditory and vestibular cell type.
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Affiliation(s)
- Allen F Ryan
- Departments of Surgery/Otolaryngology, University of California, San Diego - School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA; Departments of Neurosciences, University of California, San Diego - School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Ryoukichi Ikeda
- Departments of Surgery/Otolaryngology, University of California, San Diego - School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Masatsugu Masuda
- Departments of Surgery/Otolaryngology, University of California, San Diego - School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Correlation between Plasma Interleukin-3, the α/β Globin Ratio, and Globin mRNA Stability. Anemia 2014; 2014:640203. [PMID: 25478214 PMCID: PMC4251354 DOI: 10.1155/2014/640203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background. Globin chain synthesis (GCS) analysis is used in the diagnosis of thalassemia. However, the wide reference range limits its use as a decisive diagnostic tool. It has been shown that α and β
globin mRNA increase through stimulation of cells by interleukin-3 (IL-3). Therefore, this study investigates the relationship between plasma IL-3 and the β/α
globin ratio. Methods. Blood samples were collected from 32 healthy participants on two occasions one month apart. GCS analysis, real-time PCR, and ELISA tests were conducted to determine the β/α
globin ratio, globin mRNA expression and stability rate, and IL-3 levels. Results. On the basis of IL-3 levels, the participants were divided in two groups. One group included participants who showed a significant increase in IL-3 as indicated by a significant rise in mean values of α, β, and γ
globin mRNA, α and β
globin, RBC, and hemoglobin. The other group included participants who showed no difference in IL-3 levels with no significant variations in the above-mentioned parameters. Conclusion. The results of this study indicate that IL-3 has an equivalent positive effect on α and β
globin chain synthesis. Therefore, IL-3 levels do not explain the wide reference range of the α/β
globin ratio.
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Wu MH, Jin XK, Yu AQ, Zhu YT, Li D, Li WW, Wang Q. Caspase-mediated apoptosis in crustaceans: cloning and functional characterization of EsCaspase-3-like protein from Eriocheir. FISH & SHELLFISH IMMUNOLOGY 2014; 41:625-632. [PMID: 25462457 DOI: 10.1016/j.fsi.2014.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
The caspase-3-like gene was cloned from Eriocheir sinensis, and its properties were characterized to identify the biological implications of this caspase in apoptosis in crab. Its deduced full-length protein sequence consists of 462 amino acid residues, including the prodomain and the large and small subunits. Moreover, several residues known to be critical in the caspase-3 catalytic center and binding pocket, as well as the active site pentapeptide motif Q(220)ACRG(224), were identically present in the deduced EsCaspase-3-like protein. Subsequently, the recombinant EsCaspase-3-like (rEsCaspase-3-like) protein was expressed from Escherichia coli and obtained via affinity purification. Results of the in vitro enzymatic activity assays indicated that the rEsCaspase-3-like protein is capable of hydrolyzing the substrate Ac-DEVD-pNA, suggesting a functional role in physiology. EsCaspase-3-like gene transcripts were found to be widely distributed in all tissues as detected by quantitative RT-PCR, being especially abundant in hemocytes and comparatively rare in muscles. Furthermore, EsCaspase-3-like, at both the mRNA and protein levels, was demonstrated to participate in the apoptotic process after stimulation by different pathogen-associated molecular patterns (PAMPs) in hemocytes. In conclusion, our findings suggest that the EsCaspase-3-like protein functions as an effector caspase and contributes to immune responses against pathogens.
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Affiliation(s)
- Min-Hao Wu
- Laboratory of Immunological Defense & Reproduction Biology, School of Life Science, East China Normal University, NO 500 Dong-Chuan Road, Shanghai, China
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Tamaki Z, Asano Y, Kubo M, Ihn H, Tada Y, Sugaya M, Kadono T, Sato S. Effects of the immunosuppressant rapamycin on the expression of human α2(I) collagen and matrix metalloproteinase 1 genes in scleroderma dermal fibroblasts. J Dermatol Sci 2014; 74:251-9. [PMID: 24630239 DOI: 10.1016/j.jdermsci.2014.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 11/28/2013] [Accepted: 02/03/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND Rapamycin has been shown to exert an anti-fibrotic effect on skin fibrosis in a certain subset of patients with systemic sclerosis (SSc) and in bleomycin-treated animal models. OBJECTIVES To investigate the mechanism responsible for the anti-fibrotic effect of rapamycin especially by focusing on human α2(I) collagen (COL1A2) and matrix metalloproteinase 1 (MMP1) genes in normal and systemic sclerosis (SSc) dermal fibroblasts. METHODS The expression levels of type I procollagen and MMP1 proteins were analyzed by immunoblotting and the mRNA levels of COL1A2 and MMP1 genes were evaluated by quantitative real-time RT-PCR. The activities of COL1A2 and MMP1 promoters were determined by reporter analysis. RESULTS Rapamycin significantly decreased the levels of type I procollagen protein and COL1A2 mRNA, while significantly increasing the levels of MMP1 protein and mRNA in normal dermal fibroblasts. Similar effects of rapamycin were also observed in SSc dermal fibroblasts. Importantly, the inhibitory and stimulatory effects of rapamycin on the mRNA levels of COL1A2 and MMP1 genes, respectively, were significantly greater in SSc dermal fibroblasts than in normal dermal fibroblasts. In SSc dermal fibroblasts, rapamycin affected the expression of COL1A2 gene at the post-transcriptional level. In contrast, rapamycin altered the expression of MMP1 gene at the transcriptional level through the JNK/c-Jun signaling pathway in those cells. CONCLUSION Rapamycin has a potential to directly regulate the deposition of type I collagen in extracellular matrix through inhibiting type I collagen synthesis and promoting its degradation by MMP1, suggesting that this drug is useful for the treatment of SSc.
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Affiliation(s)
- Zenshiro Tamaki
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yoshihide Asano
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan.
| | - Masahide Kubo
- Department of Dermatology, Tokyo Kousei-Nenkin Hospital, Tokyo, Japan
| | - Hironobu Ihn
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yayoi Tada
- Department of Dermatology, Teikyo University School of Medicine, Tokyo, Japan
| | - Makoto Sugaya
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takafumi Kadono
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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49
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Abstract
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling—which measures both global mRNA levels and their translation rates—to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis- and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on several yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the underappreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of “coding” versus “regulatory” may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.
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Affiliation(s)
- Carlo G Artieri
- Department of Biology, Stanford University, Stanford, California 94305, USA
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50
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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