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Singh MK, Shin Y, Han S, Ha J, Tiwari PK, Kim SS, Kang I. Molecular Chaperonin HSP60: Current Understanding and Future Prospects. Int J Mol Sci 2024; 25:5483. [PMID: 38791521 PMCID: PMC11121636 DOI: 10.3390/ijms25105483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle's proteome integrity and homeostasis. The HSP60 family, encompassing Cpn60, plays diverse roles in cellular processes, including protein folding, cell signaling, and managing high-temperature stress. In prokaryotes, HSP60 is well understood as a GroEL/GroES complex, which forms a double-ring cavity and aids in protein folding. In eukaryotes, HSP60 is implicated in numerous biological functions, like facilitating the folding of native proteins and influencing disease and development processes. Notably, research highlights its critical involvement in sustaining oxidative stress and preserving mitochondrial integrity. HSP60 perturbation results in the loss of the mitochondria integrity and activates apoptosis. Currently, numerous clinical investigations are in progress to explore targeting HSP60 both in vivo and in vitro across various disease models. These studies aim to enhance our comprehension of disease mechanisms and potentially harness HSP60 as a therapeutic target for various conditions, including cancer, inflammatory disorders, and neurodegenerative diseases. This review delves into the diverse functions of HSP60 in regulating proteo-homeostasis, oxidative stress, ROS, apoptosis, and its implications in diseases like cancer and neurodegeneration.
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Affiliation(s)
- Manish Kumar Singh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Centre for Genomics, SOS Zoology, Jiwaji University, Gwalior 474011, India;
| | - Yoonhwa Shin
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sunhee Han
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Joohun Ha
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pramod K. Tiwari
- Centre for Genomics, SOS Zoology, Jiwaji University, Gwalior 474011, India;
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; (M.K.S.); (Y.S.); (S.H.); (J.H.)
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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Polinski JM, Castellano KR, Buckley KM, Bodnar AG. Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin. Cell Rep 2024; 43:114021. [PMID: 38564335 DOI: 10.1016/j.celrep.2024.114021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
The red sea urchin (Mesocentrotus franciscanus) is one of the Earth's longest-living animals, reported to live more than 100 years with indeterminate growth, life-long reproduction, and no increase in mortality rate with age. To understand the genetic underpinnings of longevity and negligible aging, we constructed a chromosome-level assembly of the red sea urchin genome and compared it to that of short-lived sea urchin species. Genome-wide syntenic alignments identified chromosome rearrangements that distinguish short- and long-lived species. Expanded gene families in long-lived species play a role in innate immunity, sensory nervous system, and genome stability. An integrated network of genes under positive selection in the red sea urchin was involved in genomic regulation, mRNA fidelity, protein homeostasis, and mitochondrial function. Our results implicated known longevity genes in sea urchin longevity but also revealed distinct molecular signatures that may promote long-term maintenance of tissue homeostasis, disease resistance, and negligible aging.
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Affiliation(s)
| | | | | | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Gloucester, MA 01930, USA.
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Yuan Q, Luo M, Xie Y, Song W, Wang Y, Deng D, Chen S, Guo H. Chronic trans fatty acid consumption shortens lifespan in male Drosophila melanogaster on a high-sugar and high-fat diet. Biogerontology 2024:10.1007/s10522-024-10101-1. [PMID: 38582786 DOI: 10.1007/s10522-024-10101-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/21/2024] [Indexed: 04/08/2024]
Abstract
Aging entails the progressive decline in the body's self-regulation and functionality over time. Notably, obesity and aging exhibit parallel phenotypes, with obesity further accelerating the aging process across multiple dimensions and diminishing lifespan. In this study, we explored the impact of trans fatty acid (TFA) consumption on the overall health and lifespan of male Drosophila melanogaster under an isocaloric high-sugar and high-fat diet. Our results indicate that TFA intake results in a shortened lifespan, elevated body weight, and increased triglyceride levels in flies fed a high-sugar and high-fat diet with equivalent caloric intake. Additionally, TFA exposure induces oxidative stress, locomotor deficits, and damage to the intestinal barrier in flies. Collectively, chronic TFA consumption expedites the aging process and reduces the lifespan of male Drosophila melanogaster. These results contribute supplementary evidence regarding the adverse health effects associated with TFAs.
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Affiliation(s)
- Qianhua Yuan
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Mengliu Luo
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Yutong Xie
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Wanhan Song
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Ya Wang
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Dazhang Deng
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Shuyan Chen
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Honghui Guo
- Department of Nutrition, School of Public Health, Guangdong Medical University, Dongguan, 523808, China.
- Dongguan Key Laboratory of Prevention and Treatment of Chronic Noncommunicable Diseases, School of Public Health, Guangdong Medical University, Dongguan, 523808, China.
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Kumari S, Kumari P, Sinha S, Azad GK, Yasmin S. Alleviation of arsenic-induced neurobehavioral defects with selenium in the larvae of Zaprionus indianus. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2121-2132. [PMID: 37787783 DOI: 10.1007/s00210-023-02746-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023]
Abstract
Selenium is an essential antioxidative micronutrient. This study was conducted to characterize the arsenic toxicity induced on the African fig fly, Zaprionus indianus, and its possible amelioration by selenium. We used computational tools and in vivo experiments to elucidate the mechanism of action of arsenic and selenium on Z. indianus larvae. We conducted experiments to study neurobehavioral parameters including learning and memory ability test and crawling and contraction assays. Our in silico study revealed twelve primary targets of arsenic trioxide. The gene ontology annotation of primary and secondary targets of arsenic trioxide revealed selenocysteine metabolic processes as one of the most reliable targets. To validate our in silico data, we analyzed the effect of arsenic trioxide on larvae of Z. indianus and tested the possible amelioration by sodium selenite supplementation. Our data demonstrated that the arsenic trioxide deteriorated the learning and memory ability of 2nd instar larvae of Z. indianus and such effect was reversed by sodium selenite supplementation. Furthermore, crawling and contraction assay done on 3rd instar larvae showed that there was reduction in both parameters upon arsenic trioxide exposure, which was restored with sodium selenite supplementation. Altogether, our computational and in vivo results strongly indicated that the neurobehavioral defects induced by arsenic trioxide on the larvae of Z. indianus can be successfully alleviated in the presence of sodium selenite.
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Affiliation(s)
- Shilpi Kumari
- Department of Zoology, Patna Women's College, Patna University, Patna, Bihar, India
| | - Puja Kumari
- Department of Zoology, Patna Women's College, Patna University, Patna, Bihar, India
| | - Sneha Sinha
- Department of Zoology, Patna Women's College, Patna University, Patna, Bihar, India
| | - Gajendra Kumar Azad
- Department of Zoology, Molecular Biology Laboratory, Patna University, Patna, Bihar, India
| | - Shahla Yasmin
- Department of Zoology, Patna University, Patna, Bihar, India.
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research. Sci Rep 2024; 14:7471. [PMID: 38553458 PMCID: PMC10980734 DOI: 10.1038/s41598-024-56562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Affiliation(s)
- Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India.
| | - Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait.
| | | | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Shaheed Rajguru College of Applied Science for Women, University of Delhi, New Delhi, India
- Campus of Open Learning, University of Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Adedara AO, Bressan GN, Dos Santos MM, Fachinetto R, Abolaji AO, Barbosa NV. Antioxidant responses driven by Hesperetin and Hesperidin counteract Parkinson's disease-like phenotypes in Drosophila melanogaster. Neurotoxicology 2024; 101:117-127. [PMID: 38423185 DOI: 10.1016/j.neuro.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/05/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
The study investigated the protective effects of Hesperetin (HSP) and Hesperidin (HSD) on 1 methyl, 4 phenyl, 1,2,3,6 tetrahydropyridine hydrochloride (MPTP)-induced Parkinsonism in Drosophila melanogaster (D. melanogaster). After a lifespan study to select exposure time and concentrations, flies were co-exposed to MPTP (0.4 mg/g diet), Hesperetin (0.2 and 0.4 mg/g diet), and Hesperidin (0.1 and 0.4 mg/g) for 7 days. In addition to in vivo parameters, we assayed some markers of oxidative stress and antioxidant status (lipid peroxidation, protein carbonylation, thiol content, hydrogen peroxide, and nitrate/nitrite levels, mRNA expression of Keap-1 (Kelch-like ECH associated protein 1), /Nrf2 (Nuclear factor erythroid 2 related factor 2), catalase, and glutathione-S-transferase (GST) activities), and cholinergic (acetyl cholinesterase activity (AChE) and dopaminergic signaling content and the mRNA expression of tyrosine hydroxylase (TH), monoamine oxidase (MAO-like) activity). In addition to increasing the lifespan of flies, we found that both flavonoids counteracted the adverse effects of MPTP on survival, offspring emergence, and climbing ability of flies. Both flavonoids also reduced the oxidative damage on lipids and proteins and reestablished the basal levels of pro-oxidant species and activities of antioxidant enzymes in MPTP-exposed flies. These responses were accompanied by the normalization of the mRNA expression of Keap1/Nrf2 disrupted in flies exposed to MPTP. MPTP exposure also elicited changes in mRNA expression and content of TH as well as in MAO and AChE activity, which were reversed by HST and HSD. By efficiently hindering the oxidative stress in MPTP-exposed flies, our findings support the promising role of Hesperetin and Hesperidin as adjuvant therapy to manage Parkinsonism induced by chemicals such as MPTP.
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Affiliation(s)
- Adeola Oluwatosin Adedara
- Programa de Pós-graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Avenida Roraima, 1000, Santa Maria, RS 97105-900, Brazil; Drosophila Laboratory, Drug Metabolism and Toxicology Unit, Department of Biochemistry, Faculty of Basic Medical Science, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Getúlio Nicola Bressan
- Programa de Pós-graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Avenida Roraima, 1000, Santa Maria, RS 97105-900, Brazil
| | - Matheus Mulling Dos Santos
- Programa de Pós-graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Avenida Roraima, 1000, Santa Maria, RS 97105-900, Brazil
| | - Roselei Fachinetto
- Programa de Pós-graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Avenida Roraima, 1000, Santa Maria, RS 97105-900, Brazil
| | - Amos Olalekan Abolaji
- Drosophila Laboratory, Drug Metabolism and Toxicology Unit, Department of Biochemistry, Faculty of Basic Medical Science, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
| | - Nilda Vargas Barbosa
- Programa de Pós-graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Avenida Roraima, 1000, Santa Maria, RS 97105-900, Brazil.
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Rana N, Kapil L, Singh C, Singh A. Modeling Huntington's disease: An insight on in-vitro and in-vivo models. Behav Brain Res 2024; 459:114757. [PMID: 37952684 DOI: 10.1016/j.bbr.2023.114757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Huntington's disease is a neurodegenerative illness that causes neuronal death most extensively within the basal ganglia. There is a broad class of neurologic disorders associated with the expansion of polyglutamine (polyQ) repeats in numerous proteins. Several other molecular mechanisms have also been implicated in HD pathology, including brain-derived neurotrophic factor (BDNF), mitochondrial dysfunction, and altered synaptic plasticity in central spiny neurons. HD pathogenesis and the effectiveness of therapy approaches have been better understood through the use of animal models. The pathological manifestations of the disease were reproduced by early models of glutamate analog toxicity and mitochondrial respiration inhibition. Because the treatments available for HD are quite limited, it is important to have a definite preclinical model that mimics all the aspects of the disease. It can be used to study mechanisms and validate candidate therapies. Although there hasn't been much success in translating animal research into clinical practice, each model has something special to offer in the quest for a deeper comprehension of HD's neurobehavioral foundations. This review provides insight into various in-vitro-and in-vivo models of HD which may be useful in the screening of newer therapeutics for this incapacitating disorder.
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Affiliation(s)
- Nitasha Rana
- Department of Pharmacology, ISF College of Pharmacy, Moga 142001, Affiliated to I.K Gujral Punjab Technical University, Jalandhar, Punjab, India
| | - Lakshay Kapil
- Department of Pharmacology, ISF College of Pharmacy, Moga 142001, Affiliated to I.K Gujral Punjab Technical University, Jalandhar, Punjab, India
| | - Charan Singh
- Department of Pharmaceutical Sciences, HNB Garhwal University (A Central University), Chauras Campus, Distt. Tehri Garhwal, Uttarakhand 246174, India
| | - Arti Singh
- Department of Pharmacology, ISF College of Pharmacy, Moga 142001, Affiliated to I.K Gujral Punjab Technical University, Jalandhar, Punjab, India.
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Ma S, Shi S, Xu B, Liu M, Xie L, Su Y, Li J, Liang Q, Ye S, Wang Y. Host serine protease ACOT2 assists DENV proliferation by hydrolyzing viral polyproteins. mSystems 2024; 9:e0097323. [PMID: 38112462 PMCID: PMC10804956 DOI: 10.1128/msystems.00973-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023] Open
Abstract
Dengue fever is a mosquito-borne tropical disease caused by the dengue virus (DENV). The replication of DENV relies on the processing of its genome-encoded polyprotein by both viral protease NS3 (NS3pro) and host proteases. However, the impact of host proteases on DENV proliferation is not well understood. In this study, we utilized fluorophosphonate-based probes (FPs) to investigate the up-regulation of host serine proteases during DENV infection in detail. Among the identified proteases, acyl-CoA thioesterase 2 (ACOT2), an enzyme that hydrolyzes acyl-CoA molecules to generate fatty acids and free CoA, exhibited cleavage activity against DENV polypeptide substrates. Enzymatic assays and virological experiments confirmed that ACOT2 contributes to DENV propagation during the replication stage by cleaving the viral polyprotein. Docking models provided insights into the binding pocket of viral polypeptides and the catalytic mechanism of ACOT2. Notably, this study is the first to demonstrate that ACOT2 functions as a serine protease to hydrolyze protein substrates. These findings offer novel insights into DENV infection, host response, as well as the potential development of innovative antiviral strategies.IMPORTANCEDENV, one of the major pathogens of Dengue fever, remains a significant public health concern in tropical and subtropical regions worldwide. How DENV efficiently hijacks the host and accesses its life cycle with delicate interaction remains to be elucidated. Here, we deconvoluted that the host protease ACOT2 assists the DENV replication and characterized the ACOT2 as a serine protease involved in the hydrolysis of the DENV polypeptide substrate. Our results not only further the understanding of the DENV life cycle but also provide a possibility for the usage of activity-based proteomics to reveal host-virus interactions.
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Affiliation(s)
- Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sai Shi
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Binghong Xu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Meijun Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lei Xie
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yang Su
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jiachen Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Qinqin Liang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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Thiébaut A, Altenhoff AM, Campli G, Glover N, Dessimoz C, Waterhouse RM. DrosOMA: the Drosophila Orthologous Matrix browser. F1000Res 2024; 12:936. [PMID: 38434623 PMCID: PMC10905159 DOI: 10.12688/f1000research.135250.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 03/05/2024] Open
Abstract
Background Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.
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Affiliation(s)
- Antonin Thiébaut
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Adrian M. Altenhoff
- Department of Computer Science, SIB Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Giulia Campli
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Natasha Glover
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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Alaraby M, Villacorta A, Abass D, Hernández A, Marcos R. Titanium-doped PET nanoplastics, from opaque milk bottle degradation, as a model of environmental true-to-life nanoplastics. Hazardous effects on Drosophila. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122968. [PMID: 37979650 DOI: 10.1016/j.envpol.2023.122968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023]
Abstract
Micro and nanoplastics (MNPLs) are emergent environmental pollutants, resulting from the degradation of plastic waste, requiring urgent information on their potential risks to human health. To determine such risks, reliable true-to-life materials are essential. In this work, we have used titanium-doped PET NPLs [PET(Ti)NPLs], obtained by grinding opaque milk polyethylene terephthalate (PET) bottles, as a true-to-life MNPLs model. These opaque PET bottles, with an average size of 112 nm, contain about 3% Ti in the form of titanium dioxide rod nanoparticles. TEM investigation confirmed the mixed Ti/PET nature of the obtained true-to-life NPLs, and the rod shape of the embedded TiO2NPs. In the in vivo Drosophila model neither PET(Ti)NPLs nor TiO2NPs reduced the survival rates, although their internalization was confirmed in different compartments of the larval body by using confocal and transmission electron microscopies. The presence of Ti in the PET(Ti)NPLs permitted to quantify its presence both in larvae (2.1 ± 2.2 μg/g of Ti) and in the resulting adults (3.4 ± 3.2 μg/g of Ti) after treatment with 500 μg/g food of PET(Ti)NPL, suggesting its potential use to track their fate in more complex organisms such as mammals. PET(Ti)NPLs, as well as TiO2NPs, altered the expression of genes driving different response pathways, inducing significant oxidative stress levels (up to 10 folds), and genotoxicity. This last result on the genotoxic effects is remarkable in the frame of the hot topic discussion on the risk that titanium compounds, used as food additives, may pose to humans.
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Affiliation(s)
- Mohamed Alaraby
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain; Zoology Department, Faculty of Sciences, Sohag University (82524), Sohag, Egypt
| | - Aliro Villacorta
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain; Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
| | - Doaa Abass
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain; Zoology Department, Faculty of Sciences, Sohag University (82524), Sohag, Egypt
| | - Alba Hernández
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricard Marcos
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
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11
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. Conserved Cardiovascular Network: Bioinformatics Insights into Genes and Pathways for Establishing Caenorhabditis elegans as an Animal Model for Cardiovascular Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.24.573256. [PMID: 38234826 PMCID: PMC10793405 DOI: 10.1101/2023.12.24.573256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in cardiovascular disease (CVD) research. Caenorhabditis elegans , a nematode species, has emerged as a prominent experimental organism widely utilised in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilisation for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signalling pathway, the FoxO signalling pathway, the MAPK signalling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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12
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Lv Y, Pan Y, Li J, Ding Y, Yu Z, Yan K, Shang Q. The C2H2 zinc finger transcription factor CF2-II regulates multi-insecticide resistance-related gut-predominant ABC transporters in Aphis gossypii Glover. Int J Biol Macromol 2023; 253:126765. [PMID: 37683749 DOI: 10.1016/j.ijbiomac.2023.126765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Clarifying the molecular mechanisms of cotton aphid resistance to various insecticides is crucial for the long-term safe application of insecticides in chemical control. ATP-binding cassette (ABC) transporters mediate the membrane transport of various substrates (including exogenous substances). Experiments confirmed that ABCB5, ABCF2, and MRP12 contributed to high levels of resistance to spirotetramat, cyantraniliprole, thiamethoxam or imidacloprid. Binding sites of the C2H2 zinc finger transcription factor CF2-II was predicted to be located in the promoters of ABCB5, ABCF2, and MRP12. The expression levels of ABCB5, ABCF2, and MRP12 were significantly upregulated after silencing CF2-II. The results of dual-luciferase reporter assays demonstrated a negative regulatory relationship between CF2-II and ABC transporter promoters. Furthermore, yeast one-hybrid (Y1H) and electrophoresis mobility shift assays (EMSAs) revealed that CF2-II inhibited the expression of ABC transporter genes through interaction with binding sites [ABCF2.p (-1149/-1140) or MRP12.p (-1189/-1181)]. The above results indicated that ABCB5, ABCF2, and MRP12 were negatively regulated by the transcription factor CF2-II, which will help us further understand the mechanism of transcriptional adaption of multi-insecticides resistant related ABC transporters in response to xenobiotics.
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Affiliation(s)
- Yuntong Lv
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Yiou Pan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Jianyi Li
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Yaping Ding
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Zihan Yu
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Kunpeng Yan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Qingli Shang
- College of Plant Science, Jilin University, Changchun 130062, PR China.
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13
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Hsieh TC, Chiang HC. IMD signaling in the gut and the brain modulates Amyloid-beta-induced deficits in Drosophila. Life Sci 2023; 332:122118. [PMID: 37741318 DOI: 10.1016/j.lfs.2023.122118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
AIMS Evidence indicates accumulating Aβ peptides in brain activates immune responses in neuronal and peripheral system, which may collaboratively influence pathogenesis of Alzheimer's disease (AD). We aim to investigate whether regulating intestinal innate immune signaling ameliorates Aβ-induced impairments in Drosophila melanogaster. MAIN METHODS Quantitative polymerase chain reaction (qPCR) was used to observe expression changes of innate immune responses related genes in brain and in gut under the circumstance of Aβ overexpressing in nerve system. Aversive olfactory conditioning and survival assay were used to investigate effects of modulating Attacin-A (AttA) and Dpitercin-A (DptA). Fluorometric assays of respiratory burst activity was introduced to explore whether reducing oxidative stress enables overexpressing intestinal AttA and DptA to reverse Aβ-induced deficits. KEY FINDINGS In vivo genetic analysis revealed that accumulating Aβ42 in neurons modulates innate immune signaling of the IMD pathway both in the brain and in the gut. Increased expression levels of the intestinal AttA and DptA improved learning performance and extended the lifespan of Aβ42 flies. The administration of apramycin led to alleviations of Aβ-induced behavioral changes, indicating that gram-negative bacteria are associated with the development of Aβ-induced pathologies. Further analysis showed that the neural expression of Aβ42 increased oxidative stress in the gut, which disrupted intestinal integrity and decreased learning performance. In addition, increased levels of AMPs targeting gram-negative bacteria and antioxidants reduced oxidative stress in the gut and reversed Aβ-induced behavioral damage. SIGNIFICANCE These findings suggest that innate immune responses in the gut play a pivotal role in modulating Aβ-induced pathologies.
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Affiliation(s)
- Tsung-Chi Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsueh-Cheng Chiang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan.
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14
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Wilby EL, Weil TT. Relating the Biogenesis and Function of P Bodies in Drosophila to Human Disease. Genes (Basel) 2023; 14:1675. [PMID: 37761815 PMCID: PMC10530015 DOI: 10.3390/genes14091675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Drosophila has been a premier model organism for over a century and many discoveries in flies have furthered our understanding of human disease. Flies have been successfully applied to many aspects of health-based research spanning from behavioural addiction, to dysplasia, to RNA dysregulation and protein misfolding. Recently, Drosophila tissues have been used to study biomolecular condensates and their role in multicellular systems. Identified in a wide range of plant and animal species, biomolecular condensates are dynamic, non-membrane-bound sub-compartments that have been observed and characterised in the cytoplasm and nuclei of many cell types. Condensate biology has exciting research prospects because of their diverse roles within cells, links to disease, and potential for therapeutics. In this review, we will discuss processing bodies (P bodies), a conserved biomolecular condensate, with a particular interest in how Drosophila can be applied to advance our understanding of condensate biogenesis and their role in disease.
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Affiliation(s)
| | - Timothy T. Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK;
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15
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Lovero D, Porcelli D, Giordano L, Lo Giudice C, Picardi E, Pesole G, Pignataro E, Palazzo A, Marsano RM. Structural and Comparative Analyses of Insects Suggest the Presence of an Ultra-Conserved Regulatory Element of the Genes Encoding Vacuolar-Type ATPase Subunits and Assembly Factors. BIOLOGY 2023; 12:1127. [PMID: 37627011 PMCID: PMC10452791 DOI: 10.3390/biology12081127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Gene and genome comparison represent an invaluable tool to identify evolutionarily conserved sequences with possible functional significance. In this work, we have analyzed orthologous genes encoding subunits and assembly factors of the V-ATPase complex, an important enzymatic complex of the vacuolar and lysosomal compartments of the eukaryotic cell with storage and recycling functions, respectively, as well as the main pump in the plasma membrane that energizes the epithelial transport in insects. This study involves 70 insect species belonging to eight insect orders. We highlighted the conservation of a short sequence in the genes encoding subunits of the V-ATPase complex and their assembly factors analyzed with respect to their exon-intron organization of those genes. This study offers the possibility to study ultra-conserved regulatory elements under an evolutionary perspective, with the aim of expanding our knowledge on the regulation of complex gene networks at the basis of organellar biogenesis and cellular organization.
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Affiliation(s)
- Domenica Lovero
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
- MASMEC Biomed S.p.A., Via Delle Violette 14, 70026 Modugno, Italy
| | - Damiano Porcelli
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
- METALABS S.R.L., Corso A. De Gasperi 381/1, 70125 Bari, Italy
| | - Luca Giordano
- Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Aulweg 130, 35392 Giessen, Germany;
| | - Claudio Lo Giudice
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale Delle Ricerche, Via Giovanni Amendola, 122, 70126 Bari, Italy;
| | - Ernesto Picardi
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Graziano Pesole
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Eugenia Pignataro
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Antonio Palazzo
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - René Massimiliano Marsano
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
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16
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Demir E, Kacew S. Drosophila as a Robust Model System for Assessing Autophagy: A Review. TOXICS 2023; 11:682. [PMID: 37624187 PMCID: PMC10458868 DOI: 10.3390/toxics11080682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Autophagy is the process through which a body breaks down and recycles its own cellular components, primarily inside lysosomes. It is a cellular response to starvation and stress, which plays decisive roles in various biological processes such as senescence, apoptosis, carcinoma, and immune response. Autophagy, which was first discovered as a survival mechanism during starvation in yeast, is now known to serve a wide range of functions in more advanced organisms. It plays a vital role in how cells respond to stress, starvation, and infection. While research on yeast has led to the identification of many key components of the autophagy process, more research into autophagy in more complex systems is still warranted. This review article focuses on the use of the fruit fly Drosophila melanogaster as a robust testing model in further research on autophagy. Drosophila provides an ideal environment for exploring autophagy in a living organism during its development. Additionally, Drosophila is a well-suited compact tool for genetic analysis in that it serves as an intermediate between yeast and mammals because evolution conserved the molecular machinery required for autophagy in this species. Experimental tractability of host-pathogen interactions in Drosophila also affords great convenience in modeling human diseases on analogous structures and tissues.
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Affiliation(s)
- Esref Demir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
- Medical Laboratory Techniques Program, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, 07190 Antalya, Turkey
| | - Sam Kacew
- R. Samuel McLaughllin Center for Population Health Risk Assessment, Institute of Population Health, University of Ottawa, 1 Stewart (320), Ottawa, ON K1N 6N5, Canada;
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17
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Jeanne PV, McLamb F, Feng Z, Griffin L, Gong S, Shea D, Szuch MA, Scott S, Gersberg RM, Bozinovic G. Locomotion and brain gene expression exhibit sex-specific non-monotonic dose-response to HFPO-DA during Drosophila melanogaster lifespan. Neurotoxicology 2023; 96:207-221. [PMID: 37156305 DOI: 10.1016/j.neuro.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Legacy per- and polyfluoroalkyl substances (PFAS), known for their environmental persistence and bio-accumulative properties, have been phased out in the U.S. due to public health concerns. A newer polymerization aid used in the manufacture of some fluoropolymers, hexafluoropropylene oxide-dimer acid (HFPO-DA), has lower reported bioaccumulation and toxicity, but is a potential neurotoxicant implicated in dopaminergic neurodegeneration. OBJECTIVE We investigated HFPO-DA's bio-accumulative potential and sex-specific effects on lifespan, locomotion, and brain gene expression in fruit flies. METHODS We quantified bioaccumulation of HFPO-DA in fruit flies exposed to 8.7×104µg/L of HFPO-DA in the fly media for 14 days via UHPLC-MS. Long-term effect on lifespan was determined by exposing both sexes to 8.7×102 - 8.7×105µg/L of HFPO-DA in media. Locomotion was measured following 3, 7, and 14 days of exposures at 8.7×101 - 8.7×105µg/L of HFPO-DA in media, and high-throughput 3'-end RNA-sequencing was used to quantify gene expression in fly brains across the same time points. RESULTS Bioaccumulation of HFPO-DA in fruit flies was not detected. HFPO-DA-induced effects on lifespan, locomotion, and brain gene expression, and lowest adverse effect level (LOAEL) showed sexually dimorphic patterns. Locomotion scores significantly decreased in at least one dose at all time points for females and only at 3-day exposure for males, while brain gene expression exhibited non-monotonic dose-response. Differentially expressed genes correlated to locomotion scores revealed sex-specific numbers of positively and negatively correlated genes per functional category. CONCLUSION Although HFPO-DA effects on locomotion and survival were significant at doses higher than the US EPA reference dose, the brain transcriptomic profiling reveals sex-specific changes and neurological molecular targets; gene enrichments highlight disproportionately affected categories, including immune response: female-specific co-upregulation suggests potential neuroinflammation. Consistent sex-specific exposure effects necessitate blocking for sex in experimental design during HFPO-DA risk assessment.
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Affiliation(s)
- P Vu Jeanne
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Flannery McLamb
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA
| | - Lindsey Griffin
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | - Sylvia Gong
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, Division of Extended Studies, La Jolla, CA, USA
| | | | - Mary A Szuch
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Savannah Scott
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
| | - Richard M Gersberg
- San Diego State University, Graduate School of Public Health, San Diego, CA, USA
| | - Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA; San Diego State University, Graduate School of Public Health, San Diego, CA, USA; University of California, San Diego, School of Biological Sciences, La Jolla, CA, USA.
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18
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Sun J, Lu F, Luo Y, Bie L, Xu L, Wang Y. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 2023:7146343. [PMID: 37114999 DOI: 10.1093/nar/gkad313] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https://orthovenn3.bioinfotoolkits.net.
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Affiliation(s)
- Jiahe Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Fang Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yongjiang Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Lingzi Bie
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Ling Xu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
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19
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Varte V, Munkelwitz JW, Rincon-Limas DE. Insights from Drosophila on Aβ- and tau-induced mitochondrial dysfunction: mechanisms and tools. Front Neurosci 2023; 17:1184080. [PMID: 37139514 PMCID: PMC10150963 DOI: 10.3389/fnins.2023.1184080] [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: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative dementia in older adults worldwide. Sadly, there are no disease-modifying therapies available for treatment due to the multifactorial complexity of the disease. AD is pathologically characterized by extracellular deposition of amyloid beta (Aβ) and intracellular neurofibrillary tangles composed of hyperphosphorylated tau. Increasing evidence suggest that Aβ also accumulates intracellularly, which may contribute to the pathological mitochondrial dysfunction observed in AD. According with the mitochondrial cascade hypothesis, mitochondrial dysfunction precedes clinical decline and thus targeting mitochondria may result in new therapeutic strategies. Unfortunately, the precise mechanisms connecting mitochondrial dysfunction with AD are largely unknown. In this review, we will discuss how the fruit fly Drosophila melanogaster is contributing to answer mechanistic questions in the field, from mitochondrial oxidative stress and calcium dysregulation to mitophagy and mitochondrial fusion and fission. In particular, we will highlight specific mitochondrial insults caused by Aβ and tau in transgenic flies and will also discuss a variety of genetic tools and sensors available to study mitochondrial biology in this flexible organism. Areas of opportunity and future directions will be also considered.
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Affiliation(s)
- Vanlalrinchhani Varte
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Jeremy W. Munkelwitz
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Diego E. Rincon-Limas
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
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20
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Kembro JM, Flesia AG, Nieto PS, Caliva JM, Lloyd D, Cortassa S, Aon MA. A dynamically coherent pattern of rhythms that matches between distant species across the evolutionary scale. Sci Rep 2023; 13:5326. [PMID: 37005423 PMCID: PMC10067965 DOI: 10.1038/s41598-023-32286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/25/2023] [Indexed: 04/04/2023] Open
Abstract
We address the temporal organization of circadian and ultradian rhythms, crucial for understanding biological timekeeping in behavior, physiology, metabolism, and alignment with geophysical time. Using a newly developed five-steps wavelet-based approach to analyze high-resolution time series of metabolism in yeast cultures and spontaneous movement, metabolism, and feeding behavior in mice, rats, and quails, we describe a dynamically coherent pattern of rhythms spanning over a broad range of temporal scales (hours to minutes). The dynamic pattern found shares key features among the four, evolutionary distant, species analyzed. Specifically, a branching appearance given by splitting periods from 24 h into 12 h, 8 h and below in mammalian and avian species, or from 14 h down to 0.07 h in yeast. Scale-free fluctuations with long-range correlations prevail below ~ 4 h. Synthetic time series modeling support a scenario of coexisting behavioral rhythms, with circadian and ultradian rhythms at the center of the emergent pattern observed.
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Affiliation(s)
- J M Kembro
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de los Alimentos (ICTA), Universidad Nacional de Córdoba, Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina
| | - A G Flesia
- Facultad de Matemática, Astronomía, Física y Computación, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigación y Estudios de La Matemática (CIEM, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - P S Nieto
- Facultad de Matemática, Astronomía, Física y Computación, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG, CONICET-UNC), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - J M Caliva
- Instituto de Investigaciones Biológicas y Tecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - D Lloyd
- Schools of Bioscience and Engineering, Cardiff University, Cardiff, Wales, UK
| | - S Cortassa
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD, USA
| | - M A Aon
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD, USA.
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
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21
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Han S, Xiu M, Li S, Shi Y, Wang X, Lin X, Cai H, Liu Y, He J. Exposure to cytarabine causes side effects on adult development and physiology and induces intestinal damage via apoptosis in Drosophila. Biomed Pharmacother 2023; 159:114265. [PMID: 36652735 DOI: 10.1016/j.biopha.2023.114265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Cytarabine (Ara-C) is a widely used drug in acute myeloid leukemia (AML). However, it faces serious challenges in clinical application due to serious side effects such as gastrointestinal disorders and neurologic toxicities. Until now, the mechanism of Ara-C-induced damage is not clear. Here, we used Drosophila melanogaster (fruit fly) as the in vivo model to explore the side effects and mechanism of Ara-C. Our results showed that Ara-C supplementation delayed larval development, reduced lifespan, impaired locomotor capacity, and increased susceptibility to stress response in adult flies. In addition, Ara-C led to the intestinal morphological damage and ROS accumulation in the guts. Moreover, administration of Ara-C promoted gene expressions of Toll pathway, IMD pathway, and apoptotic pathway in the guts. These findings raise the prospects of using Drosophila as in vivo model to rapidly assess chemotherapy-mediated toxicity and efficiently screen the protective drugs.
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Affiliation(s)
- Shuzhen Han
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Minghui Xiu
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; College of Public Health, Gansu University of Chinese Medicine, Lanzhou 730000, China; Key Laboratory for Transfer of Dunhuang Medicine at the Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Shuang Li
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China; Key Laboratory for Transfer of Dunhuang Medicine at the Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Yan Shi
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Xiaoqian Wang
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Xingyao Lin
- Key Laboratory for Transfer of Dunhuang Medicine at the Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Hui Cai
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China; NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China.
| | - Yongqi Liu
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; Key Laboratory for Transfer of Dunhuang Medicine at the Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou 730000, China.
| | - Jianzheng He
- Provincial-level Key Laboratory for Molecular Medicine of Major Diseases and The Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and University, Gansu University of Chinese Medicine, Lanzhou 730000, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China; Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China; NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China.
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22
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Orthologs of Human-Disease-Associated Genes in Plants Are Involved in Regulating Leaf Senescence. Life (Basel) 2023; 13:life13020559. [PMID: 36836919 PMCID: PMC9965218 DOI: 10.3390/life13020559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
As eukaryotes, plants and animals have many commonalities on the genetic level, although they differ greatly in appearance and physiological habits. The primary goal of current plant research is to improve the crop yield and quality. However, plant research has a wider aim, exploiting the evolutionary conservatism similarities between plants and animals, and applying discoveries in the field of botany to promote zoological research that will ultimately serve human health, although very few studies have addressed this aspect. Here, we analyzed 35 human-disease-related gene orthologs in plants and characterized the genes in depth. Thirty-four homologous genes were found to be present in the herbaceous annual plant Arabidopsis thaliana and the woody perennial plant Populus trichocarpa, with most of the genes having more than two exons, including the ATM gene with 78 exons. More surprisingly, 27 (79.4%) of the 34 homologous genes in Arabidopsis were found to be senescence-associated genes (SAGs), further suggesting a close relationship between human diseases and cellular senescence. Protein-protein interaction network analysis revealed that the 34 genes formed two main subnetworks, and genes in the first subnetwork interacted with 15 SAGs. In conclusion, our results show that most of the 34 homologs of human-disease-associated genes in plants are involved in the leaf senescence process, suggesting that leaf senescence may offer a means to study the pathogenesis of human diseases and to screen drugs for the treat of diseases.
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23
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Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
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Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
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24
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Silva L, Antunes A. Omics and Remote Homology Integration to Decipher Protein Functionality. Methods Mol Biol 2023; 2627:61-81. [PMID: 36959442 DOI: 10.1007/978-1-0716-2974-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
In the recent years, several "omics" technologies based on specific biomolecules (from DNA, RNA, proteins, or metabolites) have won growing importance in the scientific field. Despite each omics possess their own laboratorial protocols, they share a background of bioinformatic tools for data integration and analysis. A recent subset of bioinformatic tools, based on available templates or remote homology protocols, allow computational fast and high-accuracy prediction of protein structures. The quickly predict of actually unsolved protein structures, together with late omics findings allow a boost of scientific advances in multiple fields such as cancer, longevity, immunity, mitochondrial function, toxicology, drug design, biosensors, and recombinant protein engineering. In this chapter, we assessed methodological approaches for the integration of omics and remote homology inferences to decipher protein functionality, opening the door to the next era of biological knowledge.
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Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
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25
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Ueda K, Haskins J, Simmonds AJ. Manipulation and Visualization of Peroxisomes in Drosophila. Methods Mol Biol 2023; 2643:455-467. [PMID: 36952206 DOI: 10.1007/978-1-0716-3048-8_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Drosophila melanogaster is a proven metazoan model to investigate the fundamentals of human genetic diseases including peroxisome-related disorders. Drosophila have facile cell and animal culture but with a relatively simpler genome and organ morphology compared to vertebrates. Drosophila Schneider 2 (S2) cells have been used extensively as a platform for investigating peroxisome functions like transport along the cytoskeleton via their amenability to RNA-interference (RNAi)-based gene knockdown. Similarly, novel findings regarding tissue-specific roles for peroxisomes have come from studies in developing flies. Individual organs can be targeted for RNAi or gene mutations affecting a limited group of cells in the context of the entire animal. Here, we provide basic protocols on how to visualize peroxisomes and manipulate expression of the Peroxin or other peroxisome genes in S2 cells and developing Drosophila organs.
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Affiliation(s)
- Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Julie Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew James Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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26
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Wong A, Bi C, Chi W, Hu N, Gehring C. Amino acid motifs for the identification of novel protein interactants. Comput Struct Biotechnol J 2022; 21:326-334. [PMID: 36582434 PMCID: PMC9791077 DOI: 10.1016/j.csbj.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy,Corresponding author.
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27
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Nitta Y, Sugie A. Studies of neurodegenerative diseases using Drosophila and the development of novel approaches for their analysis. Fly (Austin) 2022; 16:275-298. [PMID: 35765969 PMCID: PMC9336468 DOI: 10.1080/19336934.2022.2087484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The use of Drosophila in neurodegenerative disease research has contributed to the identification of modifier genes for the pathology. The basis for neurodegenerative disease occurrence in Drosophila is the conservation of genes across species and the ability to perform rapid genetic analysis using a compact brain. Genetic findings previously discovered in Drosophila can reveal molecular pathologies involved in human neurological diseases in later years. Disease models using Drosophila began to be generated during the development of genetic engineering. In recent years, results of reverse translational research using Drosophila have been reported. In this review, we discuss research on neurodegenerative diseases; moreover, we introduce various methods for quantifying neurodegeneration in Drosophila.
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Affiliation(s)
- Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, Japan,CONTACT Atsushi Sugie Brain Research Institute, Niigata University, Niigata, Japan
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28
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Bonini NM. A perspective on Drosophila genetics and its insight into human neurodegenerative disease. Front Mol Biosci 2022; 9:1060796. [PMID: 36518845 PMCID: PMC9743296 DOI: 10.3389/fmolb.2022.1060796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 09/07/2023] Open
Abstract
Drosophila has been long appreciated as a classic genetic system for its ability to define gene function in vivo. Within the last several decades, the fly has also emerged as a premiere system for modeling and defining mechanisms of human disease by expressing dominant human disease genes and analyzing the effects. Here I discuss key aspects of this latter approach that first intrigued me to focus my laboratory research on this idea. Differences between the loss-of-function vs. the gain-of-function approach are raised-and the insight of these approaches for appreciating mechanisms that contribute to human neurodegenerative disease. The application of modifier genetics, which is a prominent goal of models of human disease, has implications for how specific genes or pathways intersect with the dominant disease-associated mechanisms. Models of human disease will continue to reveal unanticipated insight into fundamental cellular processes-insight that might be harder to glean from classical genetic methodologies vs modifier genetics of disease.
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Affiliation(s)
- Nancy M. Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
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29
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Posadas-García YS, Espinosa-Soto C. Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. BMC Bioinformatics 2022; 23:509. [DOI: 10.1186/s12859-022-05067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
Background
Research on gene duplication is abundant and comes from a wide range of approaches, from high-throughput analyses and experimental evolution to bioinformatics and theoretical models. Notwithstanding, a consensus is still lacking regarding evolutionary mechanisms involved in evolution through gene duplication as well as the conditions that affect them. We argue that a better understanding of evolution through gene duplication requires considering explicitly that genes do not act in isolation. It demands studying how the perturbation that gene duplication implies percolates through the web of gene interactions. Due to evolution’s contingent nature, the paths that lead to the final fate of duplicates must depend strongly on the early stages of gene duplication, before gene copies have accumulated distinctive changes.
Methods
Here we use a widely-known model of gene regulatory networks to study how gene duplication affects network behavior in early stages. Such networks comprise sets of genes that cross-regulate. They organize gene activity creating the gene expression patterns that give cells their phenotypic properties. We focus on how duplication affects two evolutionarily relevant properties of gene regulatory networks: mitigation of the effect of new mutations and access to new phenotypic variants through mutation.
Results
Among other observations, we find that those networks that are better at maintaining the original phenotype after duplication are usually also better at buffering the effect of single interaction mutations and that duplication tends to enhance further this ability. Moreover, the effect of mutations after duplication depends on both the kind of mutation and genes involved in it. We also found that those phenotypes that had easier access through mutation before duplication had higher chances of remaining accessible through new mutations after duplication.
Conclusion
Our results support that gene duplication often mitigates the impact of new mutations and that this effect is not merely due to changes in the number of genes. The work that we put forward helps to identify conditions under which gene duplication may enhance evolvability and robustness to mutations.
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30
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Pratomo AR, Salim E, Hori A, Kuraishi T. Drosophila as an Animal Model for Testing Plant-Based Immunomodulators. Int J Mol Sci 2022; 23:ijms232314801. [PMID: 36499123 PMCID: PMC9735809 DOI: 10.3390/ijms232314801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
Allopathic medicines play a key role in the prevention and treatment of diseases. However, long-term consumption of these medicines may cause serious undesirable effects that harm human health. Plant-based medicines have emerged as alternatives to allopathic medicines because of their rare side effects. They contain several compounds that have the potential to improve health and treat diseases in humans, including their function as immunomodulators to treat immune-related diseases. Thus, the discovery of potent and safe immunomodulators from plants is gaining considerable research interest. Recently, Drosophila has gained prominence as a model organism in evaluating the efficacy of plant and plant-derived substances. Drosophila melanogaster "fruit fly" is a well-known, high-throughput model organism that has been used to study different biological aspects of development and diseases for more than 110 years. Most developmental and cell signaling pathways and 75% of human disease-related genes are conserved between humans and Drosophila. Using Drosophila, one can easily examine the pharmacological effects of plants/plant-derived components by employing a variety of tests in flies, such as survival, anti-inflammatory, antioxidant, and cell death tests. This review focused on D. melanogaster's potential for identifying immunomodulatory features associated with plants/plant-derived components.
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Affiliation(s)
- Andre Rizky Pratomo
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Emil Salim
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia
- Correspondence: (E.S.); (T.K.)
| | - Aki Hori
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takayuki Kuraishi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
- JST-FOREST, Japan Science and Technology Agency, Tokyo 102-0081, Japan
- Correspondence: (E.S.); (T.K.)
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31
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Insect Models in Nutrition Research. Biomolecules 2022; 12:biom12111668. [DOI: 10.3390/biom12111668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Insects are the most diverse organisms on earth, accounting for ~80% of all animals. They are valuable as model organisms, particularly in the context of genetics, development, behavior, neurobiology and evolutionary biology. Compared to other laboratory animals, insects are advantageous because they are inexpensive to house and breed in large numbers, making them suitable for high-throughput testing. They also have a short life cycle, facilitating the analysis of generational effects, and they fulfil the 3R principle (replacement, reduction and refinement). Many insect genomes have now been sequenced, highlighting their genetic and physiological similarities with humans. These factors also make insects favorable as whole-animal high-throughput models in nutritional research. In this review, we discuss the impact of insect models in nutritional science, focusing on studies investigating the role of nutrition in metabolic diseases and aging/longevity. We also consider food toxicology and the use of insects to study the gut microbiome. The benefits of insects as models to study the relationship between nutrition and biological markers of fitness and longevity can be exploited to improve human health.
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32
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Lakhotia SC. Delayed discovery of Hsp60 and subsequent characterization of moonlighting functions of multiple Hsp60 genes in Drosophila: a personal historical perspective. J Genet 2022. [DOI: 10.1007/s12041-022-01389-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Ogienko AA, Omelina ES, Bylino OV, Batin MA, Georgiev PG, Pindyurin AV. Drosophila as a Model Organism to Study Basic Mechanisms of Longevity. Int J Mol Sci 2022; 23:ijms231911244. [PMID: 36232546 PMCID: PMC9569508 DOI: 10.3390/ijms231911244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The spatio-temporal regulation of gene expression determines the fate and function of various cells and tissues and, as a consequence, the correct development and functioning of complex organisms. Certain mechanisms of gene activity regulation provide adequate cell responses to changes in environmental factors. Aside from gene expression disorders that lead to various pathologies, alterations of expression of particular genes were shown to significantly decrease or increase the lifespan in a wide range of organisms from yeast to human. Drosophila fruit fly is an ideal model system to explore mechanisms of longevity and aging due to low cost, easy handling and maintenance, large number of progeny per adult, short life cycle and lifespan, relatively low number of paralogous genes, high evolutionary conservation of epigenetic mechanisms and signalling pathways, and availability of a wide range of tools to modulate gene expression in vivo. Here, we focus on the organization of the evolutionarily conserved signaling pathways whose components significantly influence the aging process and on the interconnections of these pathways with gene expression regulation.
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Affiliation(s)
- Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Laboratory of Biotechnology, Novosibirsk State Agrarian University, 630039 Novosibirsk, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Alexey V. Pindyurin
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-90-42
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Qiu X, Campos Y, van de Vlekkert D, Gomero E, Tanwar A, Kalathur R, Weesner JA, Bongiovanni A, Demmers J, d'Azzo A. Distinct functions of dimeric and monomeric scaffold protein Alix in regulating F-actin assembly and loading of exosomal cargo. J Biol Chem 2022; 298:102425. [PMID: 36030822 PMCID: PMC9531180 DOI: 10.1016/j.jbc.2022.102425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Alix is a ubiquitously expressed scaffold protein that participates in numerous cellular processes related to the remodeling/repair of membranes and the actin cytoskeleton. Alix exists in monomeric and dimeric/multimeric configurations, but how dimer formation occurs and what role the dimer has in Alix-mediated processes are still largely elusive. Here, we reveal a mechanism for Alix homodimerization mediated by disulfide bonds under physiological conditions, and demonstrate that the Alix dimer is enriched in exosomes and F-actin cytoskeleton subcellular fractions. Proteomic analysis of exosomes derived from Alix-/- primary cells underlined the indispensable role of Alix in loading syntenin into exosomes, thereby regulating the cellular levels of this protein. Using a set of deletion mutants, we define the function of Alix Bro1 domain, which is solely required for its exosomal localization, and that of the V domain, which is needed for recruiting syntenin into exosomes. We reveal an essential role for Cys814 within the disordered proline rich domain (PRD) for Alix dimerization. By mutating this residue, we show that Alix remains exclusively monomeric and, in this configuration, is effective in loading syntenin into exosomes. In contrast, loss of dimerization affects the ability of Alix to associate with F-actin, thereby compromising Alix-mediated cytoskeleton remodeling. We propose that dimeric and monomeric forms of Alix selectively execute two of the protein's main functions: exosomal cargo loading and cytoskeleton remodeling.
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Affiliation(s)
- Xiaohui Qiu
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA
| | - Yvan Campos
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA
| | - Diantha van de Vlekkert
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA
| | - Elida Gomero
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA
| | - Ajay Tanwar
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jason A Weesner
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA; Department of Anatomy and Neurobiology, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Antonella Bongiovanni
- Institute of Biomedical Research and Innovation (IRIB), National Research Council (CNR) of Italy, Palermo, Italy
| | - Jeroen Demmers
- Proteomics Center, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Alessandra d'Azzo
- Department of Genetics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis Tennessee 38105, USA.
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Miao Y, Chen R, Wang X, Zhang J, Tang W, Zhang Z, Liu Y, Xu Q. Drosophila melanogaster diabetes models and its usage in the research of anti-diabetes management with traditional Chinese medicines. Front Med (Lausanne) 2022; 9:953490. [PMID: 36035393 PMCID: PMC9403128 DOI: 10.3389/fmed.2022.953490] [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: 05/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The prevalence of diabetes mellitus (DM) is increasing rapidly worldwide, but the underlying molecular mechanisms of disease development have not been elucidated, and the current popular anti-diabetic approaches still have non-negligible limitations. In the last decades, several different DM models were established on the classic model animal, the fruit fly (Drosophila melanogaster), which provided a convenient way to study the mechanisms underlying diabetes and to discover and evaluate new anti-diabetic compounds. In this article, we introduce the Drosophila Diabetes model from three aspects, including signal pathways, established methods, and pharmacodynamic evaluations. As a highlight, the progress in the treatments and experimental studies of diabetes with Traditional Chinese Medicine (TCM) based on the Drosophila Diabetes model is reviewed. We believe that the values of TCMs are underrated in DM management, and the Drosophila Diabetes models can provide a much more efficient tool to explore its values of it.
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Affiliation(s)
- Yaodong Miao
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Yaodong Miao,
| | - Rui Chen
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaolu Wang
- Jimo District Qingdao Hospital of Traditional Chinese Medicine, Qingdao, China
| | - Jie Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Weina Tang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zeyu Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Yaoyuan Liu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Qiang Xu
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Qiang Xu,
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Abstract
In Darwin's and Mendel's times, researchers investigated a wealth of organisms, chosen to solve particular problems for which they seemed especially well suited. Later, a focus on a few organisms, which are accessible to systematic genetic investigations, resulted in larger repertoires of methods and applications in these few species. Genetic animal model organisms with large research communities are the nematode Caenorhabditis elegans, the fly Drosophila melanogaster, the zebrafish Danio rerio, and the mouse Mus musculus. Due to their specific strengths, these model organisms have their strongest impacts in rather different areas of biology. C. elegans is unbeatable in the analysis of cell-to-cell contacts by saturation mutagenesis, as worms can be grown very fast in very high numbers. In Drosophila, a rich pattern is generated in the embryo as well as in adults that is used to unravel the underlying mechanisms of morphogenesis. The transparent larvae of zebrafish are uniquely suited to study organ development in a vertebrate, and the superb versatility of reverse genetics in the mouse made it the model organism to study human physiology and diseases. The combination of these models allows the in-depth genetic analysis of many fundamental biological processes using a plethora of different methods, finally providing many specific approaches to combat human diseases. The plant model Arabidopsis thaliana provides an understanding of many aspects of plant biology that might ultimately be useful for breeding crops.
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Hegde R, Hegde S, Gataraddi S, Kulkarni SS, Gai PB. Novel and PCR ready rapid DNA isolation from Drosophila. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1162-1173. [PMID: 35875860 DOI: 10.1080/15257770.2022.2104313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Isolation of genomic DNA is an initial step in molecular biology techniques. The quality of isolated DNA depends on procedures and chemicals, as well as source and types of the sample used. Several existing procedures are expensive and time consuming. In this study, we isolated high quality genomic DNA with an inexpensive and least time consuming procedure using Drosophila melanogaster flies, larvae, and pupae. METHODS Drosophila melanogaster samples were collected from pre-cultured bottles, and genomic DNA was extracted using a proposed novel and PCR-ready method from three different pools of flies [PF1, PF2, and PF3], similarly from larvae and pupae [PL1, PL2, PL3, PP1, PP2, and PP3, respectively]. Isolated genomic DNA was subjected to PCR amplification with different dilutions using the COI gene and further amplicons were used for RAPD and DNA sequencing. RESULTS The high quality of isolated genomic DNA was confirmed by 0.8% agarose gel electrophoresis and the purity and quantity of the DNA isolated from single fly, larva and pupa was similar to the purity and quantity of the DNA isolated using the NucleoSpinR Tissue kit method. Isolated genomic DNA was successfully amplified when the template was diluted in the ratio of 1:10. Further successful RAPD amplification and sequencing analysis of the COI gene confirms the efficiency of the downstream application of the proposed novel method. CONCLUSION The present Novel and PCR ready rapid DNA isolation method will be potentially beneficial, and it can be successfully used for quick isolation of high molecular weight DNA from Drosophila flies larvae and pupae for DNA barcoding, identification of new species, genotyping, RAPD analysis, etc. Moreover, it can also be easily scaled up for bulk preparations.
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Affiliation(s)
- Rajat Hegde
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
| | - Smita Hegde
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
| | | | | | - Pramod B Gai
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
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Shin GJE, Abaci HE, Smith MC. Cellular Pathogenesis of Chemotherapy-Induced Peripheral Neuropathy: Insights From Drosophila and Human-Engineered Skin Models. FRONTIERS IN PAIN RESEARCH 2022; 3:912977. [PMID: 35875478 PMCID: PMC9304629 DOI: 10.3389/fpain.2022.912977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a highly prevalent and complex condition arising from chemotherapy cancer treatments. Currently, there are no treatment or prevention options in the clinic. CIPN accompanies pain-related sensory functions starting from the hands and feet. Studies focusing on neurons in vitro and in vivo models significantly advanced our understanding of CIPN pathological mechanisms. However, given the direct toxicity shown in both neurons and non-neuronal cells, effective in vivo or in vitro models that allow the investigation of neurons in their local environment are required. No single model can provide a complete solution for the required investigation, therefore, utilizing a multi-model approach would allow complementary advantages of different models and robustly validate findings before further translation. This review aims first to summarize approaches and insights from CIPN in vivo models utilizing small model organisms. We will focus on Drosophila melanogaster CIPN models that are genetically amenable and accessible to study neuronal interactions with the local environment in vivo. Second, we will discuss how these findings could be tested in physiologically relevant vertebrate models. We will focus on in vitro approaches using human cells and summarize the current understanding of engineering approaches that may allow the investigation of pathological changes in neurons and the skin environment.
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Affiliation(s)
- Grace Ji-eun Shin
- Zuckerman Mind Brain and Behavior Institute, Jerome L. Greene Science Center, Columbia University, New York, NY, United States
- *Correspondence: Grace Ji-eun Shin
| | - Hasan Erbil Abaci
- Department of Dermatology, Columbia University Medical Center, Saint Nicholas Avenue, New York, NY, United States
| | - Madison Christine Smith
- Zuckerman Mind Brain and Behavior Institute, Jerome L. Greene Science Center, Columbia University, New York, NY, United States
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Mingione VR, Foda Z, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations. J Mol Biol 2022; 434:167628. [PMID: 35595169 DOI: 10.1016/j.jmb.2022.167628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by revisiting our previously published ligand binding simulations using the first identified viral proto-oncogene, Src kinase, as a model system. The binding paths for kinase inhibitor PP1 uncovered three metastable intermediate states before binding the high-affinity ATP-binding pocket, revealing two previously known allosteric sites and one novel site. Herein, we validate the novel site using a combination of virtual screening and experimental assays to identify a v-type allosteric small-molecule inhibitor that targets this novel site with specificity for Src over closely related kinases. This study provides a proof-of-concept for employing unbiased ligand binding simulations to identify cryptic allosteric binding sites and is widely applicable to other protein-ligand systems.
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Affiliation(s)
- Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachariah Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hannah Philipose
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yibing Shan
- Antidote Health Foundation for Cure of Cancer, Cambridge, MA 02139, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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Crow M, Suresh H, Lee J, Gillis J. Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Res 2022; 50:4302-4314. [PMID: 35451481 PMCID: PMC9071420 DOI: 10.1093/nar/gkac276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.
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Affiliation(s)
- Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - John Lee
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
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41
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Chakrabarty R, Yousuf S, Singh MP. Contributive Role of Hyperglycemia and Hypoglycemia Towards the Development of Alzheimer's Disease. Mol Neurobiol 2022; 59:4274-4291. [PMID: 35503159 DOI: 10.1007/s12035-022-02846-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is one of the causes of dementia that results from several infections/biological conditions leading to either cell disruption or loss of neuronal communication. Studies have documented the accumulation of two proteins, beta-amyloid (Aβ), which accumulates on the exteriors of neurons, and tau (Tau), which assembles at the interiors of brain cells and is chiefly liable for the progression of the disease. Several molecular and cellular pathways account for the accumulation of amyloid-β and the formation of neurofibrillary tangles, which are phosphorylated variants of Tau protein. Moreover, research has revealed a potential connection between AD and diabetes. It has also been demonstrated that both hypoglycemia and hyperglycemia have a significant role in the development of AD. In addition, SUMO (small ubiquitin-like modifier protein) plays a crucial role in the pathogenesis of AD. SUMOylation is the process by which modification of amyloid precursor protein (APP) and Tau takes place. Furthermore, Drosophila melanogaster has proven to be an efficient model organism in studies to establish the relationship between AD and variations in blood glucose levels. In addition, the review successfully identifies the common pathway that links the effects of fluctuations in glucose levels on AD pathogenesis and advancements.
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Affiliation(s)
- Riya Chakrabarty
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India
| | - Sumaira Yousuf
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India
| | - Mahendra P Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Ludhiana National Highway, Phagwara, Punjab, 144411, India.
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Recurrent circadian circuitry regulates central brain activity to maintain sleep. Neuron 2022; 110:2139-2154.e5. [PMID: 35525241 DOI: 10.1016/j.neuron.2022.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 12/19/2022]
Abstract
Animal brains have discrete circadian neurons, but little is known about how they are coordinated to influence and maintain sleep. Here, through a systematic optogenetic screening, we identified a subtype of uncharacterized circadian DN3 neurons that is strongly sleep promoting in Drosophila. These anterior-projecting DN3s (APDN3s) receive signals from DN1 circadian neurons and then output to newly identified noncircadian "claw" neurons (CLs). CLs have a daily Ca2+ cycle, which peaks at night and correlates with DN1 and DN3 Ca2+ cycles. The CLs feedback onto a subset of DN1s to form a positive recurrent loop that maintains sleep. Using trans-synaptic photoactivatable green fluorescent protein (PA-GFP) tracing and functional in vivo imaging, we demonstrated that the CLs drive sleep by interacting with and releasing acetylcholine onto the mushroom body γ lobe. Taken together, the data identify a novel self-reinforcing loop within the circadian network and a new sleep-promoting neuropile that are both essential for maintaining normal sleep.
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Abstract
Fatty acid–and retinol-binding proteins (FARs) belong to a unique family of excreted/secreted proteins (ESPs) found exclusively in nematodes. Much of our understanding of these proteins, however, is limited to their in vitro binding characteristics toward various fatty acids and retinol and has provided little insight into their in vivo functions or mechanisms. Recent research, however, has shown that FARs elicit an immunomodulatory role in plant and animal model systems, likely by sequestering lipids involved in immune signaling. This alludes to the intricate relationship between parasitic nematode effectors and their hosts.
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Rahul, Siddique YH. Drosophila: A Model to Study the Pathogenesis of Parkinson's Disease. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 21:259-277. [PMID: 35040399 DOI: 10.2174/1871527320666210809120621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/15/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022]
Abstract
Human Central Nervous System (CNS) is the complex part of the human body, which regulates multiple cellular and molecular events taking place simultaneously. Parkinsons Disease (PD) is the second most common neurodegenerative disease after Alzheimer's disease (AD). The pathological hallmarks of PD are loss of dopaminergic neurons in the substantianigra (SN) pars compacta (SNpc) and accumulation of misfolded α-synuclein, in intra-cytoplasmic inclusions called Lewy bodies (LBs). So far, there is no cure for PD, due to the complexities of molecular mechanisms and events taking place during the pathogenesis of PD. Drosophila melanogaster is an appropriate model organism to unravel the pathogenicity not only behind PD but also other NDs. In this context as numerous biological functions are preserved between Drosophila and humans. Apart from sharing 75% of human disease-causing genes homolog in Drosophila, behavioral responses like memory-based tests, negative geotaxis, courtship and mating are also well studied. The genetic, as well as environmental factors, can be studied in Drosophila to understand the geneenvironment interactions behind the disease condition. Through genetic manipulation, mutant flies can be generated harboring human orthologs, which can prove to be an excellent model to understand the effect of the mutant protein on the pathogenicity of NDs.
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Affiliation(s)
- Rahul
- Drosophila Transgenic Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh,India
| | - Yasir Hasan Siddique
- Drosophila Transgenic Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh,India
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Cohen-Paes ADN, de Carvalho DC, Pastana LF, Dobbin EAF, Moreira FC, de Souza TP, Fernandes MR, Leal DFDVB, de Sá RBA, de Alcântara AL, Guerreiro JF, Ribeiro-dos-Santos Â, dos Santos SEB, de Assumpção PP, dos Santos NPC. Characterization of PCLO Gene in Amazonian Native American Populations. Genes (Basel) 2022; 13:genes13030499. [PMID: 35328053 PMCID: PMC8950494 DOI: 10.3390/genes13030499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic variations in PCLO have been associated with different pathologies in global literature, but there are no data regarding this gene in Native American populations. The Amazonian Native American populations have lower genetic diversity and are more different from other continental groups. We investigated 18 genetic variants in the PCLO gene in Amazonian indigenous and compared our results with the ones found in global populations, which were publicly available in the 1000 Genomes Project, gnmAD and ABraOM databases. The results demonstrated that the variants of the PCLO, especially rs17156844, rs550369696, rs61741659 and rs2877, have a significantly higher frequency in Amerindian populations in comparison with other continental populations. These data outline the singular genetic profile of the Native American population from the Brazilian Amazon region.
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Affiliation(s)
- Amanda de Nazaré Cohen-Paes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Darlen Cardoso de Carvalho
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Lucas Favacho Pastana
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Elizabeth Ayres Fragoso Dobbin
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Fabiano Cordeiro Moreira
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
- Correspondence: ; Tel.: +55-91-99123-4727
| | - Diana Feio da Veiga Borges Leal
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Roberta Borges Andrade de Sá
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Angélica Leite de Alcântara
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Ândrea Ribeiro-dos-Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
| | - Paulo Pimentel de Assumpção
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
| | - Ney Pereira Carneiro dos Santos
- Núcleo de Pesquisa em Oncologia, Federal University of Pará, Belém 66073-000, Brazil; (A.d.N.C.-P.); (D.C.d.C.); (L.F.P.); (E.A.F.D.); (F.C.M.); (D.F.d.V.B.L.); (R.B.A.d.S.); (A.L.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.); (P.P.d.A.); (N.P.C.d.S.)
- Laboratório de Genética Humana e Médica, Federal University of Pará, Belém 66073-000, Brazil; (T.P.d.S.); (J.F.G.)
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The great small organisms of developmental genetics: Caenorhabditis elegans and Drosophila melanogaster. Dev Biol 2022; 485:93-122. [PMID: 35247454 PMCID: PMC9092520 DOI: 10.1016/j.ydbio.2022.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/30/2022]
Abstract
Experimental embryologists working at the turn of the 19th century suggested fundamental mechanisms of development, such as localized cytoplasmic determinants and tissue induction. However, the molecular basis underlying these processes proved intractable for a long time, despite concerted efforts in many developmental systems to isolate factors with a biological role. That road block was overcome by combining developmental biology with genetics. This powerful approach used unbiased genome-wide screens to isolate mutants with developmental defects and to thereby identify genes encoding key determinants and regulatory pathways that govern development. Two small invertebrates were the pioneers: the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Their modes of development differ in many ways, but the two together led the way to unraveling the molecular mechanisms of many fundamental developmental processes. The discovery of the grand homologies between key players in development throughout the animal kingdom underscored the usefulness of studying these small invertebrate models for animal development and even human disease. We describe developmental genetics in Drosophila and C. elegans up to the rise of genomics at the beginning of the 21st Century. Finally, we discuss themes that emerge from the histories of such distinct organisms and prospects of this approach for the future.
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Abstract
Six years ago, DMM launched a subject collection called ‘Drosophila as a Disease Model’. This collection features Review-type articles and original research that highlight the power of Drosophila research in many aspects of human disease modeling. In the ensuing years, Drosophila research has further expanded to capitalize on genome editing, development of resources, and further interest in studying rare disease mechanisms. In the current issue of DMM, we again highlight the versatility, breadth, and scope of Drosophila research in human disease modeling and translational medicine. While many researchers have embraced the power of the fly, many more could still be encouraged to appreciate the strengths of Drosophila and how such research can integrate across species in a multi-pronged approach. Only when we truly acknowledge that all models contribute to our understanding of human biology, can we take advantage of the scope of current research endeavors. Summary: This Editorial encourages us to embrace the power of the fly in studying human disease and highlights how Drosophila studies can be integrated with research in other species to further our understanding of human biology.
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Affiliation(s)
- Esther M Verheyen
- Department of Molecular Biology and Biochemistry, Centre for Cell Biology, Development and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, CanadaV5A 1S6
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48
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Ecovoiu AA, Ratiu AC, Micheu MM, Chifiriuc MC. Inter-Species Rescue of Mutant Phenotype—The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. Int J Mol Sci 2022; 23:ijms23052613. [PMID: 35269756 PMCID: PMC8909942 DOI: 10.3390/ijms23052613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
Drosophila melanogaster (the fruit fly) is arguably a superstar of genetics, an astonishing versatile experimental model which fueled no less than six Nobel prizes in medicine. Nowadays, an evolving research endeavor is to simulate and investigate human genetic diseases in the powerful D. melanogaster platform. Such a translational experimental strategy is expected to allow scientists not only to understand the molecular mechanisms of the respective disorders but also to alleviate or even cure them. In this regard, functional gene orthology should be initially confirmed in vivo by transferring human or vertebrate orthologous transgenes in specific mutant backgrounds of D. melanogaster. If such a transgene rescues, at least partially, the mutant phenotype, then it qualifies as a strong candidate for modeling the respective genetic disorder in the fruit fly. Herein, we review various examples of inter-species rescue of relevant mutant phenotypes of the fruit fly and discuss how these results recommend several human genes as candidates to study and validate genetic variants associated with human diseases. We also consider that a wider implementation of this evolutionist exploratory approach as a standard for the medicine of genetic disorders would allow this particular field of human health to advance at a faster pace.
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Affiliation(s)
- Alexandru Al. Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
| | - Attila Cristian Ratiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
- Correspondence: ; Tel.: +40-722250366
| | - Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, 014461 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest and Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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Maitra U, Stephen C, Ciesla LM. Drug discovery from natural products - Old problems and novel solutions for the treatment of neurodegenerative diseases. J Pharm Biomed Anal 2022; 210:114553. [PMID: 34968995 PMCID: PMC8792363 DOI: 10.1016/j.jpba.2021.114553] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/19/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022]
Abstract
The use of natural products has been shown to be a fruitful approach in the discovery of novel pharmaceuticals. In fact, many currently approved drugs originated from compounds that were first identified in nature. Chemical diversity of natural compounds cannot be matched by man-made libraries of chemically synthesized molecules. Many natural compounds interact with and modulate regulatory protein targets and can be considered evolutionarily-optimized drug-like molecules. Despite this, many pharmaceutical companies have reduced or eliminated their natural product discovery programs in the last two decades. Screening natural products for pharmacologically active compounds is a challenging task that requires high resource commitment. Novel approaches at the early stage of the drug discovery pipeline are needed to allow for rapid screening and identification of the most promising molecules. Here, we review the possible evolutionary roots for drug-like characteristics of numerous natural compounds. Since many of these compounds target evolutionarily conserved cellular signaling pathways, we propose novel, early-stage drug discovery approaches to identify drug candidates that can be used for the potential prevention and treatment of neurodegenerative diseases. Invertebrate in vivo animal models of neurodegenerative diseases and innovative tools used within these models are proposed here as a screening funnel to identify new drug candidates and to shuttle these hits into further stages of the drug discovery pipeline.
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Affiliation(s)
- Urmila Maitra
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Cayman Stephen
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Lukasz M Ciesla
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA.
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50
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Aspatwar A, Tolvanen MEE, Barker H, Syrjänen L, Valanne S, Purmonen S, Waheed A, Sly WS, Parkkila S. Carbonic Anhydrases in Metazoan Model Organisms: Molecules, Mechanisms, and Physiology. Physiol Rev 2022; 102:1327-1383. [PMID: 35166161 DOI: 10.1152/physrev.00018.2021] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During the past three decades, mice, zebrafish, fruit flies, and Caenorhabditis elegans have been the primary model organisms used for the study of various biological phenomena. These models have also been adopted and developed to investigate the physiological roles of carbonic anhydrases (CAs) and carbonic anhydrase-related proteins (CARPs). These proteins belong to eight CA families and are identified by Greek letters: α, β, γ, δ, ζ, η, θ, and ι. Studies using model organisms have focused on two CA families, α-CAs and β-CAs, which are expressed in both prokaryotic and eukaryotic organisms with species-specific distribution patterns and unique functions. This review covers the biological roles of CAs and CARPs in light of investigations performed in model organisms. Functional studies demonstrate that CAs are not only linked to the regulation of pH homeostasis, the classical role of CAs but also contribute to a plethora of previously undescribed functions.
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Affiliation(s)
- Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Harlan Barker
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd and TAYS Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Leo Syrjänen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Otorhinolaryngology, Tampere University Hospital, Tampere, Finland
| | - Susanna Valanne
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Purmonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Abdul Waheed
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research Center, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - William S Sly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research Center, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Ltd and TAYS Cancer Centre, Tampere University Hospital, Tampere, Finland
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