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Li C, Liang S, Huang Q, Zhou Z, Ding Z, Long N, Wi K, Li L, Jiang X, Fan Y, Xu Y. Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307804. [PMID: 38837887 PMCID: PMC11304329 DOI: 10.1002/advs.202307804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Indexed: 06/07/2024]
Abstract
RNA splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with DNA- and other RNA-processing machineries in the nucleus. However, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. Here, through affinity purification using Drosophila lysates, an interaction is identified between the minor spliceosomal 65K/RNPC3 and ANKRD11, a cofactor of histone deacetylase 3 (HDAC3). Using a CRISPR/Cas9 system, Deletion strains are constructed and found that both Dm65KΔ/Δ and Dmankrd11Δ/Δ mutants have reduced histone deacetylation at Lys9 of histone H3 (H3K9) and Lys5 of histone H4 (H4K5) in their heads, exhibiting various neural-related defects. The 65K-ANKRD11 interaction is also conserved in human cells, and the HsANKRD11 middle-uncharacterized domain mediates Hs65K association with HDAC3. Cleavage under targets and tagmentation (CUT&Tag) assays revealed that HsANKRD11 is a bridging factor, which facilitates the synergistic common chromatin-binding of HDAC3 and Hs65K. Knockdown (KD) of HsANKRD11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby H3K9. Ultimately, this study demonstrates that expression changes of many genes caused by HsANKRD11-KD are due to the decreased common chromatin-binding of HDAC3 and Hs65K and subsequently reduced deacetylation of H3K9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.
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Affiliation(s)
- Chen‐Hui Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Shao‐Bo Liang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Qi‐Wei Huang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhen‐Zhen Zhou
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhan Ding
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
- Key Laboratory of Insect Developmental and Evolutionary BiologyCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200032China
| | - Ni Long
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Kwang‐Chon Wi
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Liang Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Xi‐Ping Jiang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yu‐Jie Fan
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yong‐Zhen Xu
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
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2
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Aleman TS, Uyhazi KE, Serrano LW, Vasireddy V, Bowman SJ, Ammar MJ, Pearson DJ, Maguire AM, Bennett J. RDH12 Mutations Cause a Severe Retinal Degeneration With Relatively Spared Rod Function. Invest Ophthalmol Vis Sci 2019; 59:5225-5236. [PMID: 30372751 DOI: 10.1167/iovs.18-24708] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To describe the retinal phenotype of pediatric patients with mutations in the retinol dehydrogenase 12 (RDH12) gene. Methods Twenty-one patients from 14 families (ages 2-17 years) with RDH12-associated inherited retinal degeneration (RDH12-IRD) underwent a complete ophthalmic exam and imaging with spectral domain optical coherence tomography (SD-OCT) and near infrared and short-wavelength fundus autofluorescence. Visual field extent was measured with Goldmann kinetic perimetry, visual thresholds with dark-adapted static perimetry or with dark-adapted chromatic full-field stimulus testing (FST) and transient pupillometry. Results Visual acuity ranged from 20/40 to light perception. There was parafoveal depigmentation or atrophic maculopathies accompanied by midperipheral intraretinal pigment migration. SD-OCT revealed foveal thinning in all patients and detectable but thinned outer nuclear layer (ONL) at greater eccentricities from the fovea. Photoreceptor outer segment (POS) signals were only detectable in small pockets within the central retina. Measurable kinetic visual fields were limited to small (<5-10°) central islands of vision. Electroretinograms were reported as undetectable or severely reduced in amplitude. FST sensitivities to a 467 nm stimulus were rod-mediated and reduced on average by ∼2.5 log units. A thinned central ONL colocalized with severely reduced to nondetectable cone-mediated sensitivities. Pupillometry confirmed the psychophysically measured abnormalities. Conclusions RDH12-IRD causes an early-onset, retina-wide disease with particularly severe central retinal abnormalities associated with relatively less severe rod photoreceptor dysfunction, a pattern consistent with an early-onset cone-rod dystrophy. Severely abnormal POS but detectable ONL in the pericentral and peripapillary retina suggest these regions may become targets for gene therapy.
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Affiliation(s)
- Tomas S Aleman
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States.,Department of Ophthalmology, Center for Advanced Ocular and Retinal Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Katherine E Uyhazi
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States
| | - Leona W Serrano
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States
| | - Vidyullatha Vasireddy
- Department of Ophthalmology, Center for Advanced Ocular and Retinal Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Scott J Bowman
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States
| | - Michael J Ammar
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States
| | - Denise J Pearson
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States
| | - Albert M Maguire
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States.,Department of Ophthalmology, Center for Advanced Ocular and Retinal Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Jean Bennett
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Philadelphia, Pennsylvania, United States.,Department of Ophthalmology, Center for Advanced Ocular and Retinal Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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3
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Gauthier M, Aras P, Paquin J, Boily M. Chronic exposure to imidacloprid or thiamethoxam neonicotinoid causes oxidative damages and alters carotenoid-retinoid levels in caged honey bees (Apis mellifera). Sci Rep 2018; 8:16274. [PMID: 30390008 PMCID: PMC6214897 DOI: 10.1038/s41598-018-34625-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
Over the last decade, the persistent dwindling of the populations of honey bees has become a growing concern. While this phenomenon is partly attributed to neonicotinoids (NEOCs), chronic exposures to these insecticides at environmentally-relevant concentrations are needed to fully estimate their implications. In this study, honey bees were orally exposed for 10 days to low field-realistic concentrations of NEOCs known for their effects on the cholinergic system (imidacloprid – IMI or thiamethoxam – THM). Selected biomarkers were measured such as acetylcholinesterase (AChE) activity, lipid peroxidation (LPO), α-tocopherol as well as several forms of vitamin A (retinoids) and carotenoids. Bees exposed to IMI showed lower levels of two carotenoids (α-carotene and α-cryptoxanthin) and α-tocopherol. The THM exposure increased the oxidized vitamin A metabolites in bees conjointly with the LPO. These results could be the consequence of a pro-oxidant effect of NEOCs and were observed at levels where no effects were recorded for AChE activity. This study reveals that exposure to low levels of NEOCs alters the carotenoid-retinoid system in honey bees. This would merit further investigation as these compounds are important in various aspects of bees’ health. Overall, this study contributes to the development of biomonitoring tools for the health of bees and other pollinators.
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Affiliation(s)
- Maxime Gauthier
- Département des Sciences Biologiques, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, Québec, H3C 3P8, Canada
| | - Philippe Aras
- Département des Sciences Biologiques, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, Québec, H3C 3P8, Canada
| | - Joanne Paquin
- Département de Chimie, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Québec, H3C 3P8, Canada
| | - Monique Boily
- Département des Sciences Biologiques, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal, Québec, H3C 3P8, Canada.
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Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Sci Rep 2018; 8:5518. [PMID: 29615780 PMCID: PMC5882950 DOI: 10.1038/s41598-018-23749-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/17/2023] Open
Abstract
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
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Affiliation(s)
- Simon Blanchoud
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Lisa Zondag
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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5
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Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C. Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate. Mol Biol Evol 2016; 33:2401-16. [PMID: 27406791 DOI: 10.1093/molbev/msw118] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The bloom of genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metabolic gene network (RA-MGN) in the chordate Oikopleura dioica as a case study, we combine approaches of comparative genomics, phylogenetics, biochemistry, and developmental biology to investigate the mutational robustness associated to biased patterns of gene loss. We demonstrate the absence of alternative pathways for RA-synthesis in O. dioica, which suggests that gene losses of RA-MGN were not compensated by mutational robustness, but occurred in a scenario of regressive evolution. In addition, the lack of drastic phenotypic changes associated to the loss of RA-signaling provides an example of the inverse paradox of Evo-Devo. This work illustrates how the identification of patterns of gene coelimination-in our case five losses (Rdh10, Rdh16, Bco1, Aldh1a, and Cyp26)-is a useful strategy to recognize gene network modules associated to distinct functions. Our work also illustrates how the identification of survival genes helps to recognize neofunctionalization events and ancestral functions. Thus, the survival and extensive duplication of Cco and RdhE2 in O. dioica correlated with the acquisition of complex compartmentalization of expression domains in the digestive system and a process of enzymatic neofunctionalization of the Cco, while the surviving Aldh8 could be related to its ancestral housekeeping role against toxic aldehydes.
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Affiliation(s)
- Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Nuria P Torres-Aguila
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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6
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Diniz MS, Salgado R, Pereira VJ, Carvalho G, Oehmen A, Reis MAM, Noronha JP. Ecotoxicity of ketoprofen, diclofenac, atenolol and their photolysis byproducts in zebrafish (Danio rerio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 505:282-289. [PMID: 25461029 DOI: 10.1016/j.scitotenv.2014.09.103] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 06/04/2023]
Abstract
The occurrence of pharmaceutical compounds in wastewater treatment plants and surface waters has been detected worldwide, constituting a potential risk for aquatic ecosystems. Adult zebrafish, of both sexes, were exposed to three common pharmaceutical compounds (atenolol, ketoprofen and diclofenac) and their UV photolysis by-products over seven days. The results show that diclofenac was removed to concentrations<LOD after 5 min of UV irradiation. The oxidative stress response of zebrafish to pharmaceuticals and their photolysis by-products was evaluated through oxidative stress enzymes (glutathione-S-transferase, catalase, superoxide dismutase) and lipid peroxidation. Results suggest that the photolysis by-products of diclofenac were more toxic than those from the other compounds tested, showing an increase in GST and CAT levels, which are also supported by higher MDA levels. Overall, the toxicity of waters containing atenolol and ketoprofen was reduced after the parent compounds were transformed by photolysis, whereas the toxicity increased significantly from the by-products generated through diclofenac photolysis. Therefore, diclofenac photolysis would possibly necessitate higher irradiation time to ensure that the associated by-products are completely degraded to harmless form(s).
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Affiliation(s)
- M S Diniz
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - R Salgado
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; ESTS-IPS, Escola Superior de Tecnologia de Setúbal do Instituto Politécnico de Setúbal, Rua Vale de Chaves, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal.
| | - V J Pereira
- Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República (EAN), 2784-505 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica (ITQB)-Universidade Nova de Lisboa (UNL), Estação Agronómica Nacional, Av. da República, 2780-157 Oeiras, Portugal.
| | - G Carvalho
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Av. da República (EAN), 2784-505 Oeiras, Portugal.
| | - A Oehmen
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - M A M Reis
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - J P Noronha
- REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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7
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André A, Ruivo R, Gesto M, Castro LFC, Santos MM. Retinoid metabolism in invertebrates: when evolution meets endocrine disruption. Gen Comp Endocrinol 2014; 208:134-45. [PMID: 25132059 DOI: 10.1016/j.ygcen.2014.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/20/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023]
Abstract
Recent genomic and biochemical evidence in invertebrate species pushes back the origin of the retinoid metabolic and signaling modules to the last common ancestor of all bilaterians. However, the evolution of retinoid pathways are far from fully understood. In the majority of non-chordate invertebrate lineages, the ongoing functional characterization of retinoid-related genes (metabolism and signaling pathways), as well as the characterization of the endogenous retinoid content (precursors and active retinoids), is still incomplete. Despite limited, the available data supports the presence of biologically active retinoid pathways in invertebrates. Yet, the mechanisms controlling the spatial and temporal distribution of retinoids as well as their physiological significance share similarities and differences with vertebrates. For instance, retinol storage in the form of retinyl esters, a key feature for the maintenance of retinoid homeostatic balance in vertebrates, was only recently demonstrated in some mollusk species, suggesting that such ability is older than previously anticipated. In contrast, the enzymatic repertoire involved in this process is probably unlike that of vertebrates. The suggested ancestry of active retinoid pathways implies that many more metazoan species might be potential targets for endocrine disrupting chemicals. Here, we review the current knowledge about the occurrence and functionality of retinoid metabolic and signaling pathways in invertebrate lineages, paying special attention to the evolutionary origin of retinoid storage mechanisms. Additionally, we summarize existing information on the endocrine disruption of invertebrate retinoid modules by environmental chemicals. Research priorities in the field are highlighted.
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Affiliation(s)
- A André
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - R Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - M Gesto
- Laboratorio de Fisioloxía Animal, Facultade de Bioloxía, Universidade de Vigo, 36310 Vigo, Spain.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - M M Santos
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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8
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Moskalev A, Shaposhnikov M, Snezhkina A, Kogan V, Plyusnina E, Peregudova D, Melnikova N, Uroshlev L, Mylnikov S, Dmitriev A, Plusnin S, Fedichev P, Kudryavtseva A. Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation. PLoS One 2014; 9:e86051. [PMID: 24475070 PMCID: PMC3901678 DOI: 10.1371/journal.pone.0086051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/04/2013] [Indexed: 12/28/2022] Open
Abstract
General and specific effects of molecular genetic responses to adverse environmental factors are not well understood. This study examines genome-wide gene expression profiles of Drosophila melanogaster in response to ionizing radiation, formaldehyde, toluene, and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We performed RNA-seq analysis on 25,415 transcripts to measure the change in gene expression in males and females separately. An analysis of the genes unique to each treatment yielded a list of genes as a gene expression signature. In the case of radiation exposure, both sexes exhibited a reproducible increase in their expression of the transcription factors sugarbabe and tramtrack. The influence of dioxin up-regulated metabolic genes, such as anachronism, CG16727, and several genes with unknown function. Toluene activated a gene involved in the response to the toxins, Cyp12d1-p; the transcription factor Fer3's gene; the metabolic genes CG2065, CG30427, and CG34447; and the genes Spn28Da and Spn3, which are responsible for reproduction and immunity. All significantly differentially expressed genes, including those shared among the stressors, can be divided into gene groups using Gene Ontology Biological Process identifiers. These gene groups are related to defense response, biological regulation, the cell cycle, metabolic process, and circadian rhythms. KEGG molecular pathway analysis revealed alteration of the Notch signaling pathway, TGF-beta signaling pathway, proteasome, basal transcription factors, nucleotide excision repair, Jak-STAT signaling pathway, circadian rhythm, Hippo signaling pathway, mTOR signaling pathway, ribosome, mismatch repair, RNA polymerase, mRNA surveillance pathway, Hedgehog signaling pathway, and DNA replication genes. Females and, to a lesser extent, males actively metabolize xenobiotics by the action of cytochrome P450 when under the influence of dioxin and toluene. Finally, in this work we obtained gene expression signatures pollutants (dioxin, toluene), low dose of gamma-irradiation and common molecular pathways for different kind of stressors.
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Affiliation(s)
- Alexey Moskalev
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shaposhnikov
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Anastasia Snezhkina
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Valeria Kogan
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Quantum Pharmaceuticals, Moscow, Russia
| | - Ekaterina Plyusnina
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Darya Peregudova
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
| | - Nataliya Melnikova
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Leonid Uroshlev
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Moscow, Russia
| | - Sergey Mylnikov
- Department of Genetics, St. Petersburg State University, St. Petersburg, Russia
| | - Alexey Dmitriev
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Sergey Plusnin
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Peter Fedichev
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Quantum Pharmaceuticals, Moscow, Russia
| | - Anna Kudryavtseva
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
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9
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Chávez-Galarza J, Henriques D, Johnston JS, Azevedo JC, Patton JC, Muñoz I, De la Rúa P, Pinto MA. Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms. Mol Ecol 2013; 22:5890-907. [PMID: 24118235 DOI: 10.1111/mec.12537] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 12/30/2022]
Abstract
Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST -based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST -based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes.
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Affiliation(s)
- Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal
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10
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Kedishvili NY. Enzymology of retinoic acid biosynthesis and degradation. J Lipid Res 2013; 54:1744-60. [PMID: 23630397 PMCID: PMC3679379 DOI: 10.1194/jlr.r037028] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/17/2013] [Indexed: 12/18/2022] Open
Abstract
All-trans-retinoic acid is a biologically active derivative of vitamin A that regulates numerous physiological processes. The concentration of retinoic acid in the cells is tightly regulated, but the exact mechanisms responsible for this regulation are not completely understood, largely because the enzymes involved in the biosynthesis of retinoic acid have not been fully defined. Recent studies using in vitro and in vivo models suggest that several members of the short-chain dehydrogenase/reductase superfamily of proteins are essential for retinoic acid biosynthesis and the maintenance of retinoic acid homeostasis. However, the exact roles of some of these recently identified enzymes are yet to be characterized. The properties of the known contributors to retinoid metabolism have now been better defined and allow for more detailed understanding of their interactions with retinoid-binding proteins and other retinoid enzymes. At the same time, further studies are needed to clarify the interactions between the cytoplasmic and membrane-bound proteins involved in the processing of hydrophobic retinoid metabolites. This review summarizes current knowledge about the roles of various biosynthetic and catabolic enzymes in the regulation of retinoic acid homeostasis and outlines the remaining questions in the field.
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Affiliation(s)
- Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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11
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Mayoral JG, Leonard KT, Nouzova M, Noriega FG, Defelipe LA, Turjanski AG. Functional analysis of a mosquito short-chain dehydrogenase cluster. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2013; 82:96-115. [PMID: 23238893 PMCID: PMC3697000 DOI: 10.1002/arch.21078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The short-chain dehydrogenases (SDR) constitute one of the oldest and largest families of enzymes with over 46,000 members in sequence databases. About 25% of all known dehydrogenases belong to the SDR family. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, hormone, and xenobiotic metabolism as well as in redox sensor mechanisms. This family is present in archaea, bacteria, and eukaryota, emphasizing their versatility and fundamental importance for metabolic processes. We identified a cluster of eight SDRs in the mosquito Aedes aegypti (AaSDRs). Members of the cluster differ in tissue specificity and developmental expression. Heterologous expression produced recombinant proteins that had diverse substrate specificities, but distinct from the conventional insect alcohol (ethanol) dehydrogenases. They are all NADP⁺-dependent and they have S-enantioselectivity and preference for secondary alcohols with 8-15 carbons. Homology modeling was used to build the structure of AaSDR1 and two additional cluster members. The computational study helped explain the selectivity toward the (10S)-isomers as well as the reduced activity of AaSDR4 and AaSDR9 for longer isoprenoid substrates. Similar clusters of SDRs are present in other species of insects, suggesting similar selection mechanisms causing duplication and diversification of this family of enzymes.
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Affiliation(s)
- Jaime G Mayoral
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
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12
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Albalat R. Evolution of the genetic machinery of the visual cycle: a novelty of the vertebrate eye? Mol Biol Evol 2011; 29:1461-9. [PMID: 22319134 DOI: 10.1093/molbev/msr313] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The discovery in invertebrates of ciliary photoreceptor cells and ciliary (c)-opsins established that at least two of the three elements that characterize the vertebrate photoreceptor system were already present before vertebrate evolution. However, the origin of the third element, a series of biochemical reactions known as the "retinoid cycle," remained uncertain. To understand the evolution of the retinoid cycle, I have searched for the genetic machinery of the cycle in invertebrate genomes, with special emphasis on the cephalochordate amphioxus. Amphioxus is closely related to vertebrates, has a fairly prototypical genome, and possesses ciliary photoreceptor cells and c-opsins. Phylogenetic and structural analyses of the amphioxus sequences related with the vertebrate machinery do not support a function of amphioxus proteins in chromophore regeneration but suggest that the genetic machinery of the retinoid cycle arose in vertebrates due to duplications of ancestral nonvisual genes. These results favor the hypothesis that the retinoid cycle machinery was a functional innovation of the primitive vertebrate eye.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.
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