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Enogieru AB, Iyoha EN. Role of Nitric Oxide, TNF-α and Caspase-3 in Lead Acetate-Exposed Rats Pretreated with Aqueous Rosmarinus officinalis Leaf Extract. Biol Trace Elem Res 2024; 202:4021-4031. [PMID: 38012512 DOI: 10.1007/s12011-023-03974-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
Lead (Pb) toxicity is a worldwide significant public health challenge causing several neurological disorders. Reports indicate that plants rich in antioxidants, such as Rosmarinus officinalis (RO), can counteract Pb accumulation and its toxicity in the brain. Due to a dearth of literature evidence demonstrating the protective activity of RO against Pb toxicity, this study investigated such activity in Wistar rats. Thirty-six Wistar rats were allocated into six groups (n=6), namely I (control), II (lead acetate [Pb]; 100 mg/kg b.w.), III (100 mg/kg of RO and 100 mg/kg of Pb), IV (200 mg/kg of RO and 100 mg/kg of Pb), V (100 mg/kg b.w. of RO) and VI (200 mg/kg b.w. of RO). After 28 days, neurobehavioural, antioxidant, lipid peroxidation, apoptotic and inflammatory activities as well as the histology of the cerebellum were evaluated. Body weight, locomotion and exploration as well as antioxidant enzymes were significantly (p < 0.05) decreased in Pb-exposed rats when compared to control. Conversely, lipid peroxidation, nitric oxide, tumour necrosis factor-alpha and caspase-3 activities were significantly (p < 0.05) upregulated in the Pb-exposed rats when compared to control. These parameters were, however, significantly (p<0.05) attenuated in the RO-pretreated rats when compared to Pb-exposed rats. Cerebellar histology of the Pb-exposed rats showed severe degeneration of the Purkinje cells whereas the RO-pretreated rats showed better cerebellar architecture. These findings demonstrate that the neuroprotective activity of RO is facilitated via its effective antioxidant, anti-inflammatory and anti-apoptotic effects.
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Affiliation(s)
- Adaze Bijou Enogieru
- Department of Anatomy, School of Basic Medical Sciences, University of Benin, Benin City, Edo State, Nigeria.
| | - Etinosa Nathan Iyoha
- Department of Anatomy, School of Basic Medical Sciences, University of Benin, Benin City, Edo State, Nigeria
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Vikram A, Patel SK, Singh A, Pathania D, Ray RS, Upadhyay AK, Dwivedi A. Natural autophagy activators: A promising strategy for combating photoaging. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155508. [PMID: 38901286 DOI: 10.1016/j.phymed.2024.155508] [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: 10/27/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Photodamage to the skin stands out as one of the most widespread epidermal challenges globally. Prolonged exposure to sunlight containing ultraviolet radiation (UVR) instigates stress, thereby compromising the skin's functionality and culminating in photoaging. Recent investigations have shed light on the importance of autophagy in shielding the skin from photodamage. Despite the acknowledgment of numerous phytochemicals possessing photoprotective attributes, their potential to induce autophagy remains relatively unexplored. PURPOSE Diminished autophagy activity in photoaged skin underscores the potential benefits of restoring autophagy through natural compounds to enhance photoprotection. Consequently, this study aims to highlight the role of natural compounds in safeguarding against photodamage and to assess their potential to induce autophagy via an in-silico approach. METHODS A thorough search of the literature was done using several databases, including PUBMED, Science Direct, and Google Scholar, to gather relevant studies. Several keywords such as Phytochemical, Photoprotection, mTOR, Ultraviolet Radiation, Reactive oxygen species, Photoaging, and Autophagy were utilized to ensure thorough exploration. To assess the autophagy potential of phytochemicals through virtual screening, computational methodologies such as molecular docking were employed, utilizing tools like AutoDock Vina. Receptor preparation for docking was facilitated using MGLTools. RESULTS The initiation of structural and functional deterioration in the skin due to ultraviolet radiation (UVR) or sunlight-induced reactive oxygen species/reactive nitrogen species (ROS/RNS) involves the modulation of various pathways. Natural compounds like phenolics, flavonoids, flavones, and anthocyanins, among others, possess chromophores capable of absorbing light, thereby offering photoprotection by modulating these pathways. In our molecular docking study, these phytochemicals have shown binding affinity with mTOR, a negative regulator of autophagy, indicating their potential as autophagy modulators. CONCLUSION This integrated review underscores the photoprotective characteristics of natural compounds, while the in-silico analysis reveals their potential to modulate autophagy, which could significantly contribute to their anti-photoaging properties. The findings of this study hold promise for the advancement of cosmeceuticals and therapeutics containing natural compounds aimed at addressing photoaging and various skin-related diseases. By leveraging their dual benefits of photoprotection and autophagy modulation, these natural compounds offer a multifaceted approach to combatting skin aging and related conditions.
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Affiliation(s)
- Apeksha Vikram
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Sunil Kumar Patel
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Arshwinder Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala-147004 Punjab, India
| | - Diksha Pathania
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Ratan Singh Ray
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Atul Kumar Upadhyay
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala-147004 Punjab, India.
| | - Ashish Dwivedi
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India.
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103
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Surati U, Niranjan SK, Pundir RK, Koul Y, Vohra V, Gandham RK, Kumar A. Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo. Physiol Genomics 2024; 56:609-620. [PMID: 38949516 DOI: 10.1152/physiolgenomics.00028.2024] [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: 03/06/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.
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Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - Ymberzal Koul
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Ma T, Ma L, Wei R, Xu L, Ma Y, Chen Z, Dang J, Ma S, Li S. Physiology, Biochemistry, and Transcriptomics Jointly Reveal the Phytotoxicity Mechanism of Acetochlor on Pisum sativum L. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:2005-2019. [PMID: 38988284 DOI: 10.1002/etc.5936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/10/2024] [Accepted: 05/23/2024] [Indexed: 07/12/2024]
Abstract
Acetochlor, as a commonly used pre-emergent herbicide, can be toxic to crops and affect production if used improperly. However, the toxic mechanism of acetochlor on plants is not fully understood. The present study used a combination of transcriptomic analysis and physiological measurements to investigate the effects of short-term (15-day) exposure to different concentrations of acetochlor (1, 10, 20 mg/kg) on the morphology, physiology, and transcriptional levels of pea seedlings, aiming to elucidate the toxic response and resistance mechanisms in pea seedlings under herbicide stress. The results showed that the toxicity of acetochlor to pea seedlings was dose-dependent, manifested as dwarfing and stem base browning with increasing concentrations, especially at 10 mg/kg and above. Analysis of the antioxidant system showed that from the 1 mg/kg treatment, malondialdehyde, superoxide dismutase, peroxidase, and glutathione peroxidase in peas increased with increasing concentrations of acetochlor, indicating oxidative damage. Analysis of the glutathione (GSH) metabolism system showed that under 10 mg/kg treatment, the GSH content of pea plants significantly increased, and GSH transferase activity and gene expression were significantly induced, indicating a detoxification response in plants. Transcriptomic analysis showed that after acetochlor treatment, differentially expressed genes in peas were significantly enriched in the phenylpropane metabolic pathway, and the levels of key metabolites (flavonoids and lignin) were increased. In addition, we found that acetochlor-induced dwarfing of pea seedlings may be related to gibberellin signal transduction. Environ Toxicol Chem 2024;43:2005-2019. © 2024 SETAC.
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Affiliation(s)
- Tingfeng Ma
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Lei Ma
- Agronomy College, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Ruonan Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Ling Xu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Yantong Ma
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Zhen Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Junhong Dang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Shaoying Ma
- Laboratory and Practice Base Management Center, Gansu Agricultural University, Lanzhou, People's Republic of China
| | - Sheng Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, People's Republic of China
- Agronomy College, Gansu Agricultural University, Lanzhou, People's Republic of China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, People's Republic of China
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105
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Marquez-Molins J, Cheng J, Corell-Sierra J, Juarez-Gonzalez VT, Villalba-Bermell P, Annacondia ML, Gomez G, Martinez G. Hop stunt viroid infection induces heterochromatin reorganization. THE NEW PHYTOLOGIST 2024; 243:2351-2367. [PMID: 39030826 DOI: 10.1111/nph.19986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
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Affiliation(s)
- Joan Marquez-Molins
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Jinping Cheng
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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106
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Dilissen S, Silva PL, Smolentseva A, Kache T, Thoelen R, Hendrix J. Characterisation of biocondensate microfluidic flow using array-detector FCS. Biochim Biophys Acta Gen Subj 2024; 1868:130673. [PMID: 39029539 DOI: 10.1016/j.bbagen.2024.130673] [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: 03/30/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Biomolecular condensation via liquid-liquid phase separation (LLPS) is crucial for orchestrating cellular activities temporospatially. Although the rheological heterogeneity of biocondensates and the structural dynamics of their constituents carry critical functional information, methods to quantitatively study biocondensates are lacking. Single-molecule fluorescence research can offer insights into biocondensation mechanisms. Unfortunately, as dense condensates tend to sink inside their dilute aqueous surroundings, studying their properties via methods relying on Brownian diffusion may fail. METHODS We take a first step towards single-molecule research on condensates of Tau protein under flow in a microfluidic channel of an in-house developed microfluidic chip. Fluorescence correlation spectroscopy (FCS), a well-known technique to collect molecular characteristics within a sample, was employed with a newly commercialised technology, where FCS is performed on an array detector (AD-FCS), providing detailed diffusion and flow information. RESULTS The AD-FCS technology allowed characterising our microfluidic chip, revealing 3D flow profiles. Subsequently, AD-FCS allowed mapping the flow of Tau condensates while measuring their burst durations through the stationary laser. Lastly, AD-FCS allowed obtaining flow velocity and burst duration data, the latter of which was used to estimate the condensate size distribution within LLPS samples. CONCLUSION Studying biocondensates under flow through AD-FCS is promising for single-molecule experiments. In addition, AD-FCS shows its ability to estimate the size distribution in condensate samples in a convenient manner, prompting a new way of investigating biocondensate phase diagrams. GENERAL SIGNIFICANCE We show that AD-FCS is a valuable tool for advancing research on understanding and characterising LLPS properties of biocondensates.
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Affiliation(s)
- Stijn Dilissen
- UHasselt, Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), B3590 Diepenbeek, Belgium; UHasselt, Biomedical Device Engineering group, Institute for Materials Research (IMO-IMOMEC), Wetenschapspark 1, B3590 Diepenbeek, Belgium
| | - Pedro L Silva
- UHasselt, Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), B3590 Diepenbeek, Belgium
| | - Anastasia Smolentseva
- UHasselt, Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), B3590 Diepenbeek, Belgium
| | - Tom Kache
- UHasselt, Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), B3590 Diepenbeek, Belgium
| | - Ronald Thoelen
- UHasselt, Biomedical Device Engineering group, Institute for Materials Research (IMO-IMOMEC), Wetenschapspark 1, B3590 Diepenbeek, Belgium; IMOMEC Division, IMEC vzw, Wetenschapspark 1, B3590 Diepenbeek, Belgium
| | - Jelle Hendrix
- UHasselt, Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), B3590 Diepenbeek, Belgium.
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107
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Su D, Shu P, Hu N, Chen Y, Wu Y, Deng H, Du X, Zhang X, Wang R, Li H, Zeng Y, Li D, Xie Y, Li M, Hong Y, Liu K, Liu M. Dynamic m6A mRNA methylation reveals the involvement of AcALKBH10 in ripening-related quality regulation in kiwifruit. THE NEW PHYTOLOGIST 2024; 243:2265-2278. [PMID: 39056285 DOI: 10.1111/nph.20008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Kiwifruit ripening is a complex and highly coordinated process that occurs in conjunction with the formation of fruit edible quality. The significance of epigenetic changes, particularly the impact of N6-methyladenosine (m6A) RNA modification on fruit ripening and quality formation, has been largely overlooked. We monitored m6A levels and gene expression changes in kiwifruit at four different stages using LC-MS/MS, MeRIP, RNA-seq, and validated the function of AcALKBH10 through heterologous transgenic expression in tomato. Notable m6A modifications occurred predominantly at the stop codons and the 3' UTRs and exhibited a gradual reduction in m6A levels during the fruit ripening process. Moreover, these m6A modifications in the aforementioned sites demonstrated a discernible inverse relationship with the levels of mRNA abundance throughout the ripening process, suggesting a repression effect of m6A modification in the modulation of kiwifruit ripening. We further demonstrated that AcALKBH10 rather than AcECT9 predominantly regulates m6A levels in ripening-related genes, thereby exerting the regulatory control over the ripening process and the accumulation of soluble sugars and organic acids, ultimately influencing fruit ripening and quality formation. In conclusion, our findings illuminate the epi-regulatory mechanism involving m6A in kiwifruit ripening, offering a fresh perspective for cultivating high-quality kiwifruit with enhanced nutritional attributes.
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Affiliation(s)
- Dan Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Peng Shu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- Clinical Medical Research Center, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yuan Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yi Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xiaofei Du
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xumeng Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Ruochen Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Huajia Li
- Institute of Agro-Products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yunliu Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dawei Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan, 430074, Hubei, China
| | - Yue Xie
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Mingzhang Li
- China-New Zealand the Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Academy of Natural Resource Sciences, Chengdu, 610041, China
| | - Yiguo Hong
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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108
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Gao Y, Kwan J, Orofino J, Burrone G, Mitra S, Fan TY, English J, Hekman R, Emili A, Lyons SM, Cardamone MD, Perissi V. Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation. Pharmacol Res 2024; 207:107336. [PMID: 39094987 DOI: 10.1016/j.phrs.2024.107336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
G-Protein Pathway Suppressor 2 (GPS2) is an inhibitor of non-proteolytic K63 ubiquitination mediated by the E2 ubiquitin-conjugating enzyme Ubc13. Previous studies have associated GPS2-mediated restriction of ubiquitination with the regulation of insulin signaling, inflammatory responses and mitochondria-nuclear communication across different tissues and cell types. However, a detailed understanding of the targets of GPS2/Ubc13 activity is lacking. Here, we have dissected the GPS2-regulated K63 ubiquitome in mouse embryonic fibroblasts and human breast cancer cells, unexpectedly finding an enrichment for proteins involved in RNA binding and translation on the outer mitochondrial membrane. Validation of selected targets of GPS2-mediated regulation, including the RNA-binding protein PABPC1 and translation factors RPS1, RACK1 and eIF3M, revealed a mitochondrial-specific strategy for regulating the translation of nuclear-encoded mitochondrial proteins via non-proteolytic ubiquitination. Removal of GPS2-mediated inhibition, either via genetic deletion or stress-induced nuclear translocation, promotes the import-coupled translation of selected mRNAs leading to the increased expression of an adaptive antioxidant program. In light of GPS2 role in nuclear-mitochondria communication, these findings reveal an exquisite regulatory network for modulating mitochondrial gene expression through spatially coordinated transcription and translation.
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Affiliation(s)
- Yuan Gao
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Julian Kwan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Joseph Orofino
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Giulia Burrone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Department of Computer Science, University of Torino, Torino, Italy; Department of Clinical and Biological Science, University of Torino, Torino, Italy; Graduate Program in Complex Systems for Quantitative Biomedicine, University of Torino, Torino, Italy
| | - Sahana Mitra
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ting-Yu Fan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Justin English
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Graduate Program in Pharmacology and Experimental Therapeutics, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ryan Hekman
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Andrew Emili
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States; Biology Department, Boston University, Boston, MA 02115, United States
| | - Shawn M Lyons
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Maria Dafne Cardamone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Valentina Perissi
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States.
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109
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. Repair of genomic interstrand crosslinks. DNA Repair (Amst) 2024; 141:103739. [PMID: 39106540 DOI: 10.1016/j.dnarep.2024.103739] [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: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
Genomic interstrand crosslinks (ICLs) are formed by reactive species generated during normal cellular metabolism, produced by the microbiome, and employed in cancer chemotherapy. While there are multiple options for replication dependent and independent ICL repair, the crucial step for each is unhooking one DNA strand from the other. Much of our insight into mechanisms of unhooking comes from powerful model systems based on plasmids with defined ICLs introduced into cells or cell free extracts. Here we describe the properties of exogenous and endogenous ICL forming compounds and provide an historical perspective on early work on ICL repair. We discuss the modes of unhooking elucidated in the model systems, the concordance or lack thereof in drug resistant tumors, and the evolving view of DNA adducts, including ICLs, formed by metabolic aldehydes.
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Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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110
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Al-Rawi DH, Lettera E, Li J, DiBona M, Bakhoum SF. Targeting chromosomal instability in patients with cancer. Nat Rev Clin Oncol 2024; 21:645-659. [PMID: 38992122 DOI: 10.1038/s41571-024-00923-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2024] [Indexed: 07/13/2024]
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and a driver of metastatic dissemination, therapeutic resistance, and immune evasion. CIN is present in 60-80% of human cancers and poses a formidable therapeutic challenge as evidenced by the lack of clinically approved drugs that directly target CIN. This limitation in part reflects a lack of well-defined druggable targets as well as a dearth of tractable biomarkers enabling direct assessment and quantification of CIN in patients with cancer. Over the past decade, however, our understanding of the cellular mechanisms and consequences of CIN has greatly expanded, revealing novel therapeutic strategies for the treatment of chromosomally unstable tumours as well as new methods of assessing the dynamic nature of chromosome segregation errors that define CIN. In this Review, we describe advances that have shaped our understanding of CIN from a translational perspective, highlighting both challenges and opportunities in the development of therapeutic interventions for patients with chromosomally unstable cancers.
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Affiliation(s)
- Duaa H Al-Rawi
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emanuele Lettera
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jun Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melody DiBona
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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111
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Jian P, Liu J, Li L, Song Q, Zhang D, Zhang S, Chai C, Zhao H, Zhao G, Zhu H, Qiao J. AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44. J Dairy Sci 2024; 107:6576-6591. [PMID: 38762103 DOI: 10.3168/jds.2024-24754] [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: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 05/20/2024]
Abstract
Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) greater than that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multidrug resistance, and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR assays. Additionally, AcrR1 could repress the transcription of the nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.
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Affiliation(s)
- Pingqiu Jian
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Jiaheng Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China.
| | - Li Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Di Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Shenyi Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Chaofan Chai
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Hui Zhao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
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112
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Kazimierczyk M, Fedoruk-Wyszomirska A, Gurda-Woźna D, Wyszko E, Swiatkowska A, Wrzesinski J. The expression profiles of piRNAs and their interacting Piwi proteins in cellular model of renal development: Focus on Piwil1 in mitosis. Eur J Cell Biol 2024; 103:151444. [PMID: 39024988 DOI: 10.1016/j.ejcb.2024.151444] [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: 02/02/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Piwi proteins and Piwi interacting RNAs, piRNAs, presented in germline cells play a role in transposon silencing during germline development. In contrast, the role of somatic Piwi proteins and piRNAs still remains obscure. Here, we characterize the expression pattern and distribution of piRNAs in human renal cells in terms of their potential role in kidney development. Further, we show that all PIWI genes are expressed at the RNA level, however, only PIWIL1 gene is detected at the protein level by western blotting in healthy and cancerous renal cells. So far, the expression of human Piwil1 protein has only been shown in testes and cancer cells, but not in healthy somatic cell lines. Since we observe only Piwil1 protein, the regulation of other PIWI genes is probably more intricated, and depends on environmental conditions. Next, we demonstrate that downregulation of Piwil1 protein results in a decrease in the rate of cell proliferation, while no change in the level of apoptotic cells is observed. Confocal microscopy analysis reveals that Piwil1 protein is located in both cellular compartments, cytoplasm and nucleus in renal cells. Interestingly, in nucleus region Piwil1 is observed close to the spindle during all phases of mitosis in all tested cell lines. It strongly indicates that Piwil1 protein plays an essential role in proliferation of somatic cells. Moreover, involvement of Piwil1 in cell division could, at least partly, explain invasion and metastasis of many types of cancer cells with upregulation of PIWIL1 gene expression. It also makes Piwil1 protein as a potential target in the anticancer therapy.
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Affiliation(s)
- Marek Kazimierczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | | | - Dorota Gurda-Woźna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Agata Swiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
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113
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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024; 25:683-700. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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114
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Manoharan MM, Montes GC, Acquarone M, Swan KF, Pridjian GC, Nogueira Alencar AK, Bayer CL. Metabolic theory of preeclampsia: implications for maternal cardiovascular health. Am J Physiol Heart Circ Physiol 2024; 327:H582-H597. [PMID: 38968164 DOI: 10.1152/ajpheart.00170.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Preeclampsia (PE) is a multisystemic disorder of pregnancy that not only causes perinatal mortality and morbidity but also has a long-term toll on the maternal and fetal cardiovascular system. Women diagnosed with PE are at greater risk for the subsequent development of hypertension, ischemic heart disease, cardiomyopathy, cerebral edema, seizures, and end-stage renal disease. Although PE is considered heterogeneous, inefficient extravillous trophoblast (EVT) migration leading to deficient spiral artery remodeling and increased uteroplacental vascular resistance is the likely initiation of the disease. The principal pathophysiology is placental hypoxia, causing subsequent oxidative stress, leading to mitochondrial dysfunction, mitophagy, and immunological imbalance. The damage imposed on the placenta in turn results in the "stress response" categorized by the dysfunctional release of vasoactive components including oxidative stressors, proinflammatory factors, and cytokines into the maternal circulation. These bioactive factors have deleterious effects on systemic endothelial cells and coagulation leading to generalized vascular dysfunction and hypercoagulability. A better understanding of these metabolic factors may lead to novel therapeutic approaches to prevent and treat this multisystemic disorder. In this review, we connect the hypoxic-oxidative stress and inflammation involved in the pathophysiology of PE to the resulting persistent cardiovascular complications in patients with preeclampsia.
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Affiliation(s)
- Mistina M Manoharan
- Department of Biomedical Engineering, Tulane University, New Orleans, Louisiana, United States
| | - Guilherme C Montes
- Department of Pharmacology and Psychobiology, Roberto Alcântara Gomes Institute Biology (IBRAG), Rio de Janeiro State University (UERJ), Rio de Janeiro, Brazil
| | - Mariana Acquarone
- Department of Neurology, Tulane University, New Orleans, Louisiana, United States
| | - Kenneth F Swan
- Department of Obstetrics and Gynecology, Tulane University, New Orleans, Louisiana, United States
| | - Gabriella C Pridjian
- Department of Obstetrics and Gynecology, Tulane University, New Orleans, Louisiana, United States
| | | | - Carolyn L Bayer
- Department of Biomedical Engineering, Tulane University, New Orleans, Louisiana, United States
- Department of Obstetrics and Gynecology, Tulane University, New Orleans, Louisiana, United States
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115
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Ozen S, Aksentijevich I. The past 25 years in paediatric rheumatology: insights from monogenic diseases. Nat Rev Rheumatol 2024; 20:585-593. [PMID: 39112602 DOI: 10.1038/s41584-024-01145-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2024] [Indexed: 08/29/2024]
Abstract
The past 25 years have seen major novel developments in the field of paediatric rheumatology. The concept of autoinflammation was introduced to this field, and medicine more broadly, with studies of familial Mediterranean fever, the most common autoinflammatory disease globally. New data on the positive evolutionary selection of familial Mediterranean fever-associated genetic variants might be pertinent to mild gain-of-function variants reported in other disease-associated genes. Genetic studies have unveiled the complexity of human heritability to inflammation and flourishing data from rare monogenic disorders have contributed to a better understanding of general disease mechanisms in paediatric rheumatic conditions. Beyond genomics, the application of other 'omics' technologies, including transcriptomics, proteomics and metabolomics, has generated an enormous dataset that can be applied to the development of new therapies and in the practice of precision medicine. Novel biomarkers for monitoring disease activity and progression have also emerged. A surge in the development of targeted biologic therapies has led to durable remission and improved prognosis for many diseases that in the past caused major complications. Last but not least, the COVID-19 pandemic has affected paediatric rheumatology practice and has sparked new investigations into the link between viral infections and unregulated inflammatory responses in children.
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Affiliation(s)
- Seza Ozen
- Department of Paediatric Rheumatology, Hacettepe University, Ankara, Turkey.
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116
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Li H, Gao S, Shi S, Zhao X, Ye H, Luo Y. Rational construction of genome-minimized Streptomyces host for the expression of secondary metabolite gene clusters. Synth Syst Biotechnol 2024; 9:600-608. [PMID: 38774831 PMCID: PMC11106782 DOI: 10.1016/j.synbio.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Streptomyces offer a wealth of naturally occurring compounds with diverse structures, many of which possess significant pharmaceutical values. However, new product exploration and increased yield of specific compounds in Streptomyces have been technically challenging due to their slow growth rate, complex culture conditions and intricate genetic backgrounds. In this study, we screened dozens of Streptomyces strains inhabiting in a plant rhizosphere for fast-growing candidates, and further employed CRISPR/Cas-based engineering techniques for stepwise refinement of a particular strain, Streptomyces sp. A-14 that harbors a 7.47 Mb genome. After strategic removal of nonessential genomic regions and most gene clusters, we reduced its genome size to 6.13 Mb, while preserving its growth rate to the greatest extent. We further demonstrated that cleaner metabolic background of this engineered strain was well suited for the expression and characterization of heterologous gene clusters, including the biosynthetic pathways of actinorhodin and polycyclic tetramate macrolactams. Moreover, this streamlined genome is anticipated to facilitate directing the metabolic flux towards the production of desired compounds and increasing their yields.
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Affiliation(s)
- Hui Li
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Sheng Gao
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Sanyuan Shi
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaomin Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Haoyu Ye
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunzi Luo
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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117
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Zhao R, Wu WA, Huang YH, Li XK, Han JQ, Jiao W, Su YN, Zhao H, Zhou Y, Cao WQ, Zhang X, Wei W, Zhang WK, Song QX, He XJ, Ma B, Chen SY, Tao JJ, Yin CC, Zhang JS. An RRM domain protein SOE suppresses transgene silencing in rice. THE NEW PHYTOLOGIST 2024; 243:1724-1741. [PMID: 38509454 DOI: 10.1111/nph.19686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.
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Affiliation(s)
- Rui Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Ai Wu
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi-Hua Huang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin-Kai Li
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Qi Han
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - He Zhao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wu-Qiang Cao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xun Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wei
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Xin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Biao Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shou-Yi Chen
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Jun Tao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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118
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Liu C, Han X, Zhang S, Huang M, Guo B, Zhao Z, Yang S, Jin J, Pu W, Yu H. The role of NCAPH in cancer treatment. Cell Signal 2024; 121:111262. [PMID: 38901722 DOI: 10.1016/j.cellsig.2024.111262] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Many solid tumors frequently overexpress Non-SMC Condensin I Complex Subunit H (NCAPH), and new studies suggest that NCAPH may be a target gene for clinical cancer therapy. Numerous investigations have shown that a variety of transcription factors, including as MYBL2, FOXP3, GATA3, and OTC1, can stimulate the transcription of NCAPH. Additionally, NCAPH stimulates many oncogenic signaling pathways, such as β-Catenin/PD-L1, PI3K/AKT/SGK3, MEK/ERK, AURKB/AKT/mTOR, PI3K/PDK1/AKT, and Chk1/Chk2. Tumor immune microenvironment modification and tumor growth, apoptosis, metastasis, stemness, and treatment resistance all depend on these signals. NCAPH has the ability to form complexes with other proteins that are involved in glycolysis, DNA damage repair, and chromatin remodeling. This review indicates that NCAPH expression in most malignant tumors is associated with poor prognosis and low recurrence-free survival.
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Affiliation(s)
- Caiyan Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiao Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Siqi Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Manru Huang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bin Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zixuan Zhao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shenshen Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jun Jin
- International Education College, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Weiling Pu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Haiyang Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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119
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Lyu F, Yang D, Rao L, Liao X. Alanine and glutamate catabolism collaborate to ensure the success of Bacillus subtilis sporulation. Microbiol Res 2024; 286:127828. [PMID: 38991478 DOI: 10.1016/j.micres.2024.127828] [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: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Sporulation as a typical bacterial differentiation process has been studied for decades. However, two crucial aspects of sporulation, (i) the energy sources supporting the process, and (ii) the maintenance of spore dormancy throughout sporulation, are scarcely explored. Here, we reported the crucial role of RocG-mediated glutamate catabolism in regulating mother cell lysis, a critical step for sporulation completion of Bacillus subtilis, likely by providing energy metabolite ATP. Notably, rocG overexpression resulted in an excessive ATP accumulation in sporulating cells, leading to adverse effects on future spore properties, e.g. increased germination efficiency, reduced DPA content, and lowered heat resistance. Additionally, we revealed that Ald-mediated alanine metabolism was highly related to the inhibition of premature germination and the maintenance of spore dormancy during sporulation, which might be achieved by decreasing the typical germinant L-alanine concentration in sporulating environment. Our data inferred that sporulation of B. subtilis was a highly orchestrated biological process requiring a delicate balance in diverse metabolic pathways, hence ensuring both the completion of sporulation and production of high-quality spores.
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Affiliation(s)
- Fengzhi Lyu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
| | - Dong Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China.
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China; Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, Beijing, China
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120
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Golob A, Kravanja P, Concato M, Leskovar T, Zupanič Pajnič I. Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains. Forensic Sci Int 2024; 362:112184. [PMID: 39098141 DOI: 10.1016/j.forsciint.2024.112184] [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: 06/22/2024] [Revised: 07/24/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations.
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Affiliation(s)
- Aja Golob
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia
| | - Pia Kravanja
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia
| | - Monica Concato
- Department of Medicine, Surgery, and Health, University of Trieste, Trieste 34137, Italy
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana 1000, Slovenia.
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Dasgupta A, Nandi S, Gupta S, Roy S, Das C. To Ub or not to Ub: The epic dilemma of histones that regulate gene expression and epigenetic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195033. [PMID: 38750882 DOI: 10.1016/j.bbagrm.2024.195033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
A dynamic array of histone post-translational modifications (PTMs) regulate diverse cellular processes in the eukaryotic chromatin. Among them, histone ubiquitination is particularly complex as it alters nucleosome surface area fostering intricate cross-talk with other chromatin modifications. Ubiquitin signaling profoundly impacts DNA replication, repair, and transcription. Histones can undergo varied extent of ubiquitination such as mono, multi-mono, and polyubiquitination, which brings about distinct cellular fates. Mechanistic studies of the ubiquitin landscape in chromatin have unveiled a fascinating tapestry of events that orchestrate gene regulation. In this review, we summarize the key contributors involved in mediating different histone ubiquitination and deubiquitination events, and discuss their mechanism which impacts cell transcriptional identity and DNA damage response. We also focus on the proteins bearing epigenetic reader modules critical in discerning site-specific histone ubiquitination, pivotal for establishing complex epigenetic crosstalk. Moreover, we highlight the role of histone ubiquitination in different human diseases including neurodevelopmental disorders and cancer. Overall the review elucidates the intricate orchestration of histone ubiquitination impacting diverse cellular functions and disease pathogenesis, and provides insights into the current challenges of targeting them for therapeutic interventions.
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Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sayan Gupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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122
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Mouland AJ, Chau BA, Uversky VN. Methodological approaches to studying phase separation and HIV-1 replication: Current and future perspectives. Methods 2024; 229:147-155. [PMID: 39002735 DOI: 10.1016/j.ymeth.2024.07.002] [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: 12/25/2023] [Revised: 06/26/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024] Open
Abstract
This article reviews tried-and-tested methodologies that have been employed in the first studies on phase separating properties of structural, RNA-binding and catalytic proteins of HIV-1. These are described here to stimulate interest for any who may want to initiate similar studies on virus-mediated liquid-liquid phase separation. Such studies serve to better understand the life cycle and pathogenesis of viruses and open the door to new therapeutics.
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Affiliation(s)
- Andrew J Mouland
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
| | - Bao-An Chau
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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123
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Fernando GCP, Khansari AR, Tort L. Response to chronic crowding stress in shy and bold behavioral groups of male and female zebrafish. Am J Physiol Regul Integr Comp Physiol 2024; 327:R275-R290. [PMID: 38842516 DOI: 10.1152/ajpregu.00041.2024] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
In recent years, there has been a burgeoning interest in exploring the nuances of animal stress physiology, particularly in relation to parameters such as sex and behavioral phenotype-dependent variations, which is crucial for understanding phenotypic variation and its role in evolutionary selection. However, a significant dearth remains in how chronic stressors affect organismal stress physiology concerning the aforesaid parameters. This void is even wider pertaining to the response of peripheral tissues, such as the skin, the organ with the highest surface contact area with the environment. Hence, we behaviorally grouped the zebrafishes based on their boldness and the body condition, whole body cortisol response, along with examining the transcriptional response, global DNA methylome, and oxidative DNA damage in the skin upon chronic crowding. Upon baseline conditions, clear distinction between bold and shy phenotypes was found, particularly in males. The boldness index score distribution exhibited greater uniformity in males than in females. Regarding the body condition response to chronic crowding, shy males showed a significant relative decline compared with their bold counterparts, while this trend did not hold true for females. qPCR data revealed distinctive expression patterns in key genes that play critical roles in cellular processes such as stress-mediated gene regulation, immune response, oxidative stress protection, and maintenance of genomic integrity through epigenetic modifications across behavioral phenotypes and sexes under both with and without chronic crowding stress. Global DNA methylation levels significantly declined only in chronically crowded shy males, and sex/behavioral phenotype-dependent trends in oxidative DNA damage were identified.NEW & NOTEWORTHY This paper analyzes the response of zebrafish to crowding stress through a new approach focused on the peripheral response dynamics of the skin, the main mucosal tissue, and involving sex and behavioral phenotype influences. Shy males showed significant distress as observed by body condition, physiological and transcriptional response, and global DNA methylation. Nuances in stress response across behavioral phenotypes and sex indicate a genetic and behavioral specificity and further inherent epigenetic regulatory dimension.
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Affiliation(s)
- Gallage Chanuka P Fernando
- Department of Cell Biology Physiology and Immunology, Autonomous University of Barcelona, Bellaterra, Spain
| | - Ali R Khansari
- Department of Cell Biology Physiology and Immunology, Autonomous University of Barcelona, Bellaterra, Spain
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lluis Tort
- Department of Cell Biology Physiology and Immunology, Autonomous University of Barcelona, Bellaterra, Spain
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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125
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Fu H, Zhong J, Zhao J, Huo L, Wang C, Ma D, Pan W, Sun L, Ren Z, Fan T, Wang Z, Wang W, Lei X, Yu G, Li J, Zhu Y, Geelen D, Liu B. Ultraviolet attenuates centromere-mediated meiotic genome stability and alters gametophytic ploidy consistency in flowering plants. THE NEW PHYTOLOGIST 2024; 243:2214-2234. [PMID: 39039772 DOI: 10.1111/nph.19978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/29/2024] [Indexed: 07/24/2024]
Abstract
Ultraviolet (UV) radiation influences development and genome stability in organisms; however, its impact on meiosis, a special cell division essential for the delivery of genetic information across generations in eukaryotes, has not yet been elucidated. In this study, by performing cytogenetic studies, we reported that UV radiation does not damage meiotic chromosome integrity but attenuates centromere-mediated chromosome stability and induces unreduced gametes in Arabidopsis thaliana. We showed that functional centromere-specific histone 3 (CENH3) is required for obligate crossover formation and plays a role in the protection of sister chromatid cohesion under UV stress. Moreover, we found that UV specifically alters the orientation and organization of spindles and phragmoplasts at meiosis II, resulting in meiotic restitution and unreduced gametes. We determined that UV-induced meiotic restitution does not rely on the UV Resistance Locus8-mediated UV perception and the Tapetal Development and Function1- and Aborted Microspores-dependent tapetum development, but possibly occurs via altered JASON function and downregulated Parallel Spindle1. This study provides evidence that UV radiation influences meiotic genome stability and gametophytic ploidy consistency in flowering plants.
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Affiliation(s)
- Huiqi Fu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Jiaqi Zhong
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Jiayi Zhao
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Li Huo
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Chong Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Dexuan Ma
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenjing Pan
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Limin Sun
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Ziming Ren
- Department of Landscape Architecture, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tianyi Fan
- Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Ze Wang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wenyi Wang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Xiaoning Lei
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guanghui Yu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Jing Li
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yan Zhu
- Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Danny Geelen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Bing Liu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
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126
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Li B, Ni S, Liu Y, Lin J, Wang X. The histone-like nucleoid-structuring protein encoded by the plasmid pMBL6842 regulates both plasmid stability and host physiology of Pseudoalteromonas rubra SCSIO 6842. Microbiol Res 2024; 286:127817. [PMID: 38941922 DOI: 10.1016/j.micres.2024.127817] [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: 02/28/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Plasmids orchestrate bacterial adaptation across diverse environments and facilitate lateral gene transfer within bacterial communities. Their presence can perturb host metabolism, creating a competitive advantage for plasmid-free cells. Plasmid stability hinges on efficient replication and partition mechanisms. While plasmids commonly encode histone-like nucleoid-structuring (H-NS) family proteins, the precise influence of plasmid-encoded H-NS proteins on stability remains elusive. In this study, we examined the conjugative plasmid pMBL6842, harboring the hns gene, and observed its positive regulation of parAB transcription, critical for plasmid segregation. Deletion of hns led to rapid plasmid loss, which was remedied by hns complementation. Further investigations unveiled adverse effects of hns overexpression on the bacterial host. Transcriptome analysis revealed hns's role in regulating numerous bacterial genes, impacting both host growth and swimming motility in the presence of the hns gene. Therefore, our study unveils the multifaceted roles of H-NS in both plasmid stability and host physiology, underscoring its biological significance and paving the way for future inquiries into the involvement of H-NS in horizontal gene transfer events.
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Affiliation(s)
- Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yabo Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianzhong Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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127
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Park SY, Koh WG, Lee HJ. Enhanced hepatotoxicity assessment through encapsulated HepG2 spheroids in gelatin hydrogel matrices: Bridging the gap from 2D to 3D culture. Eur J Pharm Biopharm 2024; 202:114417. [PMID: 39013493 DOI: 10.1016/j.ejpb.2024.114417] [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: 04/30/2024] [Revised: 07/07/2024] [Accepted: 07/13/2024] [Indexed: 07/18/2024]
Abstract
Conventional 2D drug screening often fails to accurately predict clinical outcomes. We present an innovative approach to improve hepatotoxicity assessment by encapsulating HepG2 spheroids in gelatin hydrogel matrices with different mechanical properties. Encapsulated spheroids exhibit sustained liver-specific functionality, enhanced expression of drug-metabolizing enzymes, and increased drug sensitivity compared to 2D cultures. The platform detects critical variations in drug response, with significant differences in IC50 values between 2D and spheroid cultures ranging from 1.3-fold to > 13-fold, particularly for acetaminophen. Furthermore, drug-metabolizing enzyme expression varies across hydrogel concentrations, suggesting a role for matrix mechanical properties in modulating hepatocyte function. This novel spheroid-hydrogel platform offers a transformative approach to hepatotoxicity assessment, providing increased sensitivity, improved prediction, and a more physiologically relevant environment. The use of such advanced in vitro models can accelerate drug development, reduce animal testing, and contribute to improved patient safety and clinical outcomes.
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Affiliation(s)
- Se Yeon Park
- School of Chemical, Biological and Battery Engineering, Gachon University, 1342 Seongnam-daero, Seongnam-si, Gyeonggi-do 13120, Republic of Korea
| | - Won-Gun Koh
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Hyun Jong Lee
- School of Chemical, Biological and Battery Engineering, Gachon University, 1342 Seongnam-daero, Seongnam-si, Gyeonggi-do 13120, Republic of Korea.
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128
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El-Deek HEDM, El-Naggar MS, Morsy AMM, Sedik MF, Osman HA, Ahmed AM. P4HA2 involved in SLUG-associated EMT predicts poor prognosis of patients with KRAS-positive colorectal cancer. Med Mol Morphol 2024; 57:167-176. [PMID: 38522060 PMCID: PMC11343967 DOI: 10.1007/s00795-024-00385-0] [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: 12/17/2023] [Accepted: 02/18/2024] [Indexed: 03/25/2024]
Abstract
This study aimed to examine the immunohistochemical expression of epithelial-mesenchymal transition biomarkers: P4HA2 and SLUG in colorectal carcinoma (CRC) specimens, then to assess their relation to clinicopathological features including KRAS mutations and patients' survival, and finally to study the correlation between them in CRC. The result of this study showed that SLUG and P4HA2 were significantly higher in association with adverse prognostic factors: presence of lympho-vascular invasion, perineural invasion, higher tumor budding, tumor stage, presence of lymph node metastasis, and presence of distant metastasis. CRC specimens with KRAS mutation were associated with significant higher SLUG and P4HA2 expression. High expression of both SLUG and P4HA2 was significantly unfavorable prognostic indicator as regards overall survival (OS) and disease-free survival (DFS). In KRAS mutated cases, high P4HA2 expression was the only significant poor prognostic indicator as regarding DFS. In conclusions, our data highlight that both SLUG and P4HA2 expression may serve as potentially important poor prognostic biomarkers in CRC and targeting these molecules may be providing a novel therapeutic strategy. In KRAS mutation group, high P4HA2 expression is the only independent prognostic factor for tumor recurrence, so it can be suggested to be a novel target for therapy.
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Affiliation(s)
| | - Maha Salah El-Naggar
- Department of Clinical Oncology, Faculty of Medicine, Assiut University Hospital, Assiut, Egypt
| | | | - Mayada Fawzy Sedik
- Department of Medical Oncology and Hematological Malignancies, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Heba Ahmed Osman
- Department of Tropical Medicine and Gastroenterology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Asmaa M Ahmed
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
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129
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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130
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Dries E, Meyers Y, Liesner D, Gonzaga FM, Becker JFM, Zakka EE, Beeckman T, Coelho SM, De Clerck O, Bogaert KA. Cell wall-mediated maternal control of apical-basal patterning of the kelp Undaria pinnatifida. THE NEW PHYTOLOGIST 2024; 243:1887-1898. [PMID: 38984686 DOI: 10.1111/nph.19953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024]
Abstract
The role of maternal tissue in embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical-basal patterning in the kelp embryo. Focussing on Undaria pinnatifida, we studied the effects of detachment from the maternal tissue using microsurgery, staining of cell wall modifications, morphometric measurements, flow cytometry, genotyping and a modified kelp fertilisation protocol synchronising kelp embryogenesis. Detached embryos are rounder and often show aberrant morphologies. When a part of the oogonial cell wall remains attached to the zygote, the apical-basal patterning is rescued. Furthermore, the absence of contact with maternal tissue increases parthenogenesis, highlighting the critical role of maternal signals in the initial stages of development. These results show a key role for the connection to the maternal oogonial cell wall in apical-basal patterning in kelps. This observation is reminiscent of another brown alga, Fucus, where the cell wall directs the cell fate. Our findings suggest a conserved mechanism across phylogenetically distant oogamous lineages, where localised secretion of sulphated F2 fucans mediates the establishment of the apical-basal polarity. In this model, the maternal oogonial cell wall mediates basal cell fate determination by providing an extrinsic patterning cue to the future kelp embryo.
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Affiliation(s)
- Eloise Dries
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
- Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Yannick Meyers
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Daniel Liesner
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Floriele M Gonzaga
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Jakob F M Becker
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Eliane E Zakka
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Tom Beeckman
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Kenny A Bogaert
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
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131
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Shen R, Yao Q, Tan X, Ren W, Zhong D, Zhang X, Li X, Dong C, Cao X, Tian Y, Zhu JK, Lu Y. In-locus gene silencing in plants using genome editing. THE NEW PHYTOLOGIST 2024; 243:2501-2511. [PMID: 38798233 DOI: 10.1111/nph.19856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/29/2024]
Abstract
Gene silencing is crucial in crop breeding for desired trait development. RNA interference (RNAi) has been used widely but is limited by ectopic expression of transgenes and genetic instability. Introducing an upstream start codon (uATG) into the 5'untranslated region (5'UTR) of a target gene may 'silence' the target gene by inhibiting protein translation from the primary start codon (pATG). Here, we report an efficient gene silencing method by introducing a tailor-designed uATG-containing element (ATGE) into the 5'UTR of genes in plants, occupying the original start site to act as a new pATG. Using base editing to introduce new uATGs failed to silence two of the tested three rice genes, indicating complex regulatory mechanisms. Precisely inserting an ATGE adjacent to pATG achieved significant target protein downregulation. Through extensive optimization, we demonstrated this strategy substantially and consistently downregulated target protein expression. By designing a bidirectional multifunctional ATGE4, we enabled tunable knockdown from 19% to 89% and observed expected phenotypes. Introducing ATGE into Waxy, which regulates starch synthesis, generated grains with lower amylose, revealing the value for crop breeding. Together, we have developed a programmable and robust method to knock down gene expression in plants, with potential for biological mechanism exploration and crop enhancement.
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Affiliation(s)
- Rundong Shen
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qi Yao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xinhang Tan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Wendan Ren
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dating Zhong
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xuening Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinbo Li
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Chao Dong
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yifu Tian
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Jian-Kang Zhu
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuming Lu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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132
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Vera-Vives AM, Novel P, Zheng K, Tan SL, Schwarzländer M, Alboresi A, Morosinotto T. Mitochondrial respiration is essential for photosynthesis-dependent ATP supply of the plant cytosol. THE NEW PHYTOLOGIST 2024; 243:2175-2186. [PMID: 39073122 DOI: 10.1111/nph.19989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/29/2024] [Indexed: 07/30/2024]
Abstract
Plants rely on solar energy to synthesize ATP and NADPH for photosynthetic carbon fixation and all cellular need. Mitochondrial respiration is essential in plants, but this may be due to heterotrophic bottlenecks during plant development or because it is also necessary in photosynthetically active cells. In this study, we examined in vivo changes of cytosolic ATP concentration in response to light, employing a biosensing strategy in the moss Physcomitrium patens and revealing increased cytosolic ATP concentration caused by photosynthetic activity. Plants depleted of respiratory Complex I showed decreased cytosolic ATP accumulation, highlighting a critical role of mitochondrial respiration in light-dependent ATP supply of the cytosol. Consistently, targeting mitochondrial ATP production directly, through the construction of mutants deficient in mitochondrial ATPase (complex V), led to drastic growth reduction, despite only minor alterations in photosynthetic electron transport activity. Since P. patens is photoautotrophic throughout its development, we conclude that heterotrophic bottlenecks cannot account for the indispensable role of mitochondrial respiration in plants. Instead, our results support that mitochondrial respiration is essential for ATP provision to the cytosol in photosynthesizing cells. Mitochondrial respiration provides metabolic integration, ensuring supply of cytosolic ATP essential for supporting plant growth and development.
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Affiliation(s)
- Antoni M Vera-Vives
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Piero Novel
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Ke Zheng
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, Münster, D-48143, Germany
| | - Shun-Ling Tan
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, Münster, D-48143, Germany
| | - Alessandro Alboresi
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy
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133
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Li X, Yang C, Wu H, Chen H, Gao X, Zhou S, Zhang TC, Ma W. DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism. DNA Repair (Amst) 2024; 141:103730. [PMID: 39018963 DOI: 10.1016/j.dnarep.2024.103730] [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: 10/02/2023] [Revised: 06/21/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
While that ROS causes DNA damage is well documented, there has been limited investigation into whether DNA damages and their repair processes can conversely induce oxidative stress. By generating a site-specific DNA double strand break (DSB) via I-SceI endonuclease expression in S. cerevisiae without damaging other cellular components, this study demonstrated that DNA repair does trigger oxidative stress. Deleting genes participating in the initiation of the resection step of homologous recombination (HR), like the MRX complex, resulted in stimulation of ROS. In contrast, deleting genes acting downstream of HR resection suppressed ROS levels. Additionally, blocking non-homologous end joining (NHEJ) also suppressed ROS. Further analysis identified Rad53 as a key player that relays DNA damage signals to alter redox metabolism in an HR-specific manner. These results suggest both HR and NHEJ can drive metabolism changes and oxidative stress, with NHEJ playing a more prominent role in ROS stimulation. Further analysis revealed a correlation between DSB-induced ROS increase and enhanced activity of NADPH oxidase Yno1 and various antioxidant enzymes. Deleting the antioxidant gene SOD1 induced synthetic lethality in HR-deficient mutants like mre11Δ and rad51Δ upon DSB induction. These findings uncover a significant interplay between DNA repair mechanisms and cellular metabolism, providing insights into understanding the side effects of genotoxic therapies and potentially aiding development of more effective cancer treatment strategies.
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Affiliation(s)
- Xinyu Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Caini Yang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hengyu Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hongran Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xing Gao
- Qilu Institute of Technology, Shandong, China
| | - Sa Zhou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.
| | - Tong-Cun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China; Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Wenjian Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China; Qilu Institute of Technology, Shandong, China.
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134
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Danylovych HV, Danylovych YV, Pavliuk MR, Kosterin SO. Products of oxidative and non-oxidative metabolism of L-arginine as potential regulators of Ca 2+ transport in mitochondria of uterine smooth muscle. Biochim Biophys Acta Gen Subj 2024; 1868:130652. [PMID: 38857773 DOI: 10.1016/j.bbagen.2024.130652] [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: 03/14/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Mitochondria play a crucial role in maintaining Ca2+ homeostasis in cells. Due to the critical regulatory role of the products of oxidative and non-oxidative metabolism of L-arginine, it is essential to clarify their effect on Ca2+ transport in smooth muscle mitochondria. Experiments were performed on the uterine myocytes of rats and isolated mitochondria. The possibility of NO synthesis by mitochondria was demonstrated by confocal microscopy and spectrofluorimetry methods using the NO-sensitive fluorescent probe DAF-FM and Mitotracker Orange CM-H2TMRos. It was shown that 50 μM L-arginine stimulates the energy-dependent accumulation of Ca2+ in mitochondria using the fluorescent probe Fluo-4 AM. A similar effect occurred when using nitric oxide donors 100 μM SNP, SNAP, and sodium nitrite (SN) directly. The stimulating effect was eliminated in the presence of the NO scavenger C-PTIO. Nitric oxide reduces the electrical potential in mitochondria without causing them to swell. The stimulatory effect of spermine on the accumulation of Ca2+ by mitochondria is attributed to the enhancement of NO synthesis, which was demonstrated with the use of C-PTIO, NO-synthase inhibitors (100 μM NA and L-NAME), as well as by direct monitoring of NO synthesis fluorescent probe DAF-FM. A conclusion was drawn about the potential regulatory effect of the product of the oxidative metabolism of L-arginine - NO on the transport of Ca2+ in the mitochondria of the myometrium, as well as the corresponding effect of the product of non-oxidative metabolism -spermine by increasing the synthesis of NO in these subcellular structures.
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Affiliation(s)
- Hanna V Danylovych
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine.
| | - Yuriy V Danylovych
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Maksym R Pavliuk
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Sergiy O Kosterin
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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135
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Takayama J, Makino S, Funayama T, Ueki M, Narita A, Murakami K, Orui M, Ishikuro M, Obara T, Kuriyama S, Yamamoto M, Tamiya G. A fine-scale genetic map of the Japanese population. Clin Genet 2024; 106:284-292. [PMID: 38719617 DOI: 10.1111/cge.14536] [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: 10/03/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 08/13/2024]
Abstract
Genetic maps are fundamental resources for linkage and association studies. A fine-scale genetic map can be constructed by inferring historical recombination events from the genome-wide structure of linkage disequilibrium-a non-random association of alleles among loci-by using population-scale sequencing data. We constructed a fine-scale genetic map and identified recombination hotspots from 10 092 551 bi-allelic high-quality autosomal markers segregating among 150 unrelated Japanese individuals whose genotypes were determined by high-coverage (30×) whole-genome sequencing, and the genotype quality was carefully controlled by using their parents' and offspring's genotypes. The pedigree information was also utilized for haplotype phasing. The resulting genome-wide recombination rate profiles were concordant with those of the worldwide population on a broad scale, and the resolution was much improved. We identified 9487 recombination hotspots and confirmed the enrichment of previously known motifs in the hotspots. Moreover, we demonstrated that the Japanese genetic map improved the haplotype phasing and genotype imputation accuracy for the Japanese population. The construction of a population-specific genetic map will help make genetics research more accurate.
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Affiliation(s)
- Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoshi Makino
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
| | - Takamitsu Funayama
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Masao Ueki
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Akira Narita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
| | - Keiko Murakami
- Department of Preventive Medicine and Epidemiology, ToMMo, Tohoku University, Sendai, Japan
| | - Masatsugu Orui
- Department of Preventive Medicine and Epidemiology, ToMMo, Tohoku University, Sendai, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, Sendai, Japan
| | - Mami Ishikuro
- Department of Preventive Medicine and Epidemiology, ToMMo, Tohoku University, Sendai, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, Sendai, Japan
| | - Taku Obara
- Department of Preventive Medicine and Epidemiology, ToMMo, Tohoku University, Sendai, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, ToMMo, Tohoku University, Sendai, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization (ToMMo) Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
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136
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Ramirez-Otero MA, Costanzo V. "Bridging the DNA divide": Understanding the interplay between replication- gaps and homologous recombination proteins RAD51 and BRCA1/2. DNA Repair (Amst) 2024; 141:103738. [PMID: 39084178 DOI: 10.1016/j.dnarep.2024.103738] [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: 03/31/2024] [Revised: 06/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
A key but often neglected component of genomic instability is the emergence of single-stranded DNA (ssDNA) gaps during DNA replication in the absence of functional homologous recombination (HR) proteins, such as RAD51 and BRCA1/2. Research in prokaryotes has shed light on the dual role of RAD51's bacterial ortholog, RecA, in HR and the protection of replication forks, emphasizing its essential role in preventing the formation of ssDNA gaps, which is vital for cellular viability. This phenomenon was corroborated in eukaryotic cells deficient in HR, where the formation of ssDNA gaps within newly synthesized DNA and their subsequent processing by the MRE11 nuclease were observed. Without functional HR proteins, cells employ alternative ssDNA gap-filling mechanisms to ensure survival, though this compensatory response can compromise genomic stability. A notable example is the involvement of the translesion synthesis (TLS) polymerase POLζ, along with the repair protein POLθ, in the suppression of replicative ssDNA gaps. Persistent ssDNA gaps may result in replication fork collapse, chromosomal anomalies, and cell death, which contribute to cancer progression and resistance to therapy. Elucidating the processes that avert ssDNA gaps and safeguard replication forks is critical for enhancing cancer treatment approaches by exploiting the vulnerabilities of cancer cells in these pathways.
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Affiliation(s)
| | - Vincenzo Costanzo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
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137
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Kesmezacar FF, Tunçman D, Nayci AE, Günay O, Yeyin N, Üzüm G, Demir M, Akkuş B, Elshami W, Almisned G, Tekin HO. In-depth exploration of the radiation exposure to staff performing endoscopic retrograde cholangiopancreatography procedures (ERCP) through RANDO phantom and TLDs. Jpn J Radiol 2024; 42:1058-1066. [PMID: 38720059 DOI: 10.1007/s11604-024-01586-4] [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: 02/12/2024] [Accepted: 04/30/2024] [Indexed: 08/31/2024]
Abstract
This study provides a comprehensive evaluation of the occupational radiation exposure faced by healthcare professionals during Endoscopic Retrograde Cholangiopancreatography (ERCP) procedures. Utilizing an anthropomorphic RANDO phantom equipped with Thermoluminescent Dosimeters (TLDs), we replicated ERCP scenarios to measure radiation doses received by medical staff. The study meticulously assessed radiation exposure in various corresponding body regions typically occupied by medical staff during ERCP, with a focus on eyes, thyroid, hands, and reproductive corresponding organ regions. The findings revealed significant variations in radiation doses across different body parts, highlighting areas of higher exposure and underscoring the need for improved protective measures and procedural adjustments. The effective radiation doses were calculated using standard protocols, considering the varying levels of protection offered by lead aprons and thyroid shields. The results demonstrate the substantial radiation exposure experienced by healthcare staff, particularly in regions not adequately shielded. This study emphasizes the necessity for enhanced radiation safety protocols in clinical settings, advocating for advanced protective equipment, training in radiation safety, and the exploration of alternative imaging modalities. The findings have crucial implications for both patient and staff safety, ensuring the continued efficacy and safety of ERCP and similar interventional procedures. This research contributes significantly to the field of occupational health and safety in interventional radiology, providing vital data for the development of safer medical practices.
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Affiliation(s)
- Fahrettin Fatih Kesmezacar
- Vocational School of Health Services, Medical Imaging Techniques Program, Istanbul University - Cerrahpaşa, Istanbul, Turkey
| | - Duygu Tunçman
- Science Faculty, Physics Department, Istanbul University, Istanbul, Turkey
- Vocational School of Health Services, Radiotherapy Program, Istanbul University - Cerrahpaşa, Istanbul, Turkey
| | - Ali Emre Nayci
- General Surgery Department, Istanbul Training and Research Hospital, Istanbul, Turkey
| | - Osman Günay
- Electrical and Electronics Faculty, Biomedical Engineering, Yıldız Technical University, Istanbul, Turkey
| | - Nami Yeyin
- Medical Faculty, Nuclear Medicine Department, Istanbul University - Cerrahpaşa, Istanbul, Turkey
| | - Güngör Üzüm
- General Surgery Department, Istanbul Training and Research Hospital, Istanbul, Turkey
| | - Mustafa Demir
- Medical Faculty, Nuclear Medicine Department, Istanbul University - Cerrahpaşa, Istanbul, Turkey
| | - Baki Akkuş
- Science Faculty, Physics Department, Istanbul University, Istanbul, Turkey
| | - Wiam Elshami
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Ghada Almisned
- Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - H O Tekin
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates.
- Faculty of Engineering and Natural Sciences, Computer Engineering Department, Istinye University, Istanbul, 34396, Turkey.
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138
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Zhao Y, Wang T, Wan S, Tong Y, Wei Y, Li P, Hu N, Liu Y, Chen H, Pan X, Zhang B, Peng R, Hu S. Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.). Gene 2024; 921:148499. [PMID: 38718970 DOI: 10.1016/j.gene.2024.148499] [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: 02/12/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.
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Affiliation(s)
- Yongqing Zhao
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Sumei Wan
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Yan Tong
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Hongqi Chen
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, United States.
| | - Renhai Peng
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
| | - Shoulin Hu
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
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139
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Maas EJ, DeBortoli E, Nathan V, Freeman NP, Mothershaw A, Smit DJ, Betz-Stablein B, Aoude LG, Stark MS, Sturm RA, Soyer HP, McInerney-Leo AM. POT1 and multiple primary melanomas: the dermatological phenotype. J Med Genet 2024; 61:891-894. [PMID: 38724174 DOI: 10.1136/jmg-2023-109637] [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: 09/14/2023] [Accepted: 04/21/2024] [Indexed: 08/31/2024]
Abstract
POT1 is the second most frequently reported gene (after CDKN2A) in familial melanoma. Pathogenic variants are associated with earlier onset and/or multiple primary melanomas (MPMs). To date, POT1 phenotypical reports have been largely restricted to associated malignancies, and description of the dermatological landscape has been limited. We identified 10 variants in n=18 of 384 (4.7%) unrelated individuals (n=13 MPMs; n=5 single primary melanomas) of European ancestry. Five variants were rare (minor allele frequency <0.001) or novel (two loss-of-function (LOF), one splice acceptor and two missense) and were predicted to be functionally significant, in five unrelated probands with MPMs (≥3 melanomas). We performed three-dimensional total body photography on both individuals with confirmed pathogenic LOF variants to characterise the dermatological phenotype. Total body naevus counts (≥2 mm diameter) were significantly higher (p=7.72×10-12) in carriers compared with a control population. Majority of naevi were on the probands' back and lower limb regions, where only mild to moderate ultraviolet (UV) damage was observed. Conversely, the head/neck region, where both probands exhibited severe UV damage, had comparably fewer naevi. We hypothesise that carriage of functionally significant POT1 variants is associated with increased naevus counts generally, and naevi >5 mm in diameter specifically and the location of these are independent of UV damage.
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Affiliation(s)
- Ellie J Maas
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Emily DeBortoli
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Vaishnavi Nathan
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Ned P Freeman
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Adam Mothershaw
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Darren J Smit
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Brigid Betz-Stablein
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, Surgical Oncology Group, Brisbane, Queensland, Australia
| | - Mitchell S Stark
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Richard A Sturm
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - H Peter Soyer
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Aideen M McInerney-Leo
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
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140
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Pradhan S, Campanile M, Sharma S, Oliva R, Patra S. Mechanistic Insights into the c-MYC G-Quadruplex and Berberine Binding inside an Aqueous Two-Phase System Mimicking Biomolecular Condensates. J Phys Chem Lett 2024; 15:8706-8714. [PMID: 39159468 DOI: 10.1021/acs.jpclett.4c01806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
We investigated the binding between the c-MYC G-quadruplex (GQ) and berberine chloride (BCl) in an aqueous two-phase system (ATPS) with 12.3 wt % polyethylene glycol and 5.6 wt % dextran, mimicking the highly crowded intracellular biomolecular condensates formed via liquid-liquid phase separation. We found that in the ATPS, complex formation is significantly altered, leading to an increase in affinity and a change in the stoichiometry of the complex with respect to neat buffer conditions. Thermodynamic studies reveal that binding becomes more thermodynamically favorable in the ATPS due to entropic effects, as the strong excluded volume effect inside ATPS droplets reduces the entropic penalty associated with binding. Finally, the binding affinity of BCl for the c-MYC GQ is higher than those for other DNA structures, indicating potential specific interactions. Overall, these findings will be helpful in the design of potential drugs targeting the c-MYC GQ structures in cancer-related biocondensates.
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Affiliation(s)
- Susmita Pradhan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Marco Campanile
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 26, 80126 Naples, Italy
| | - Shubhangi Sharma
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 26, 80126 Naples, Italy
| | - Satyajit Patra
- Department of Chemistry, Birla Institute of Technology and Science-Pilani, Pilani Campus, Pilani 333031, Rajasthan, India
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141
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Chen X, Hu X, Li G, Grover CE, You J, Wang R, Liu Z, Qi Z, Luo X, Peng Y, Zhu M, Zhang Y, Lu S, Zhang YM, Lin Z, Wendel JF, Zhang X, Wang M. Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401549. [PMID: 39196795 DOI: 10.1002/advs.202401549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/23/2024] [Indexed: 08/30/2024]
Abstract
Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3-79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi-locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non-introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression-mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber.
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Affiliation(s)
- Xinyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guo Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruipeng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yabin Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengmeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sifan Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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142
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Lv Y, Li J, Wang Z, Liu Y, Jiang Y, Li Y, Lv Z, Huang X, Peng X, Cao Y, Yang H. Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4822-4836. [PMID: 38717070 DOI: 10.1093/jxb/erae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/07/2024] [Indexed: 08/29/2024]
Abstract
A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.
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Affiliation(s)
- Yanfang Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jian Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Zheng Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yili Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhaopeng Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ying Cao
- College of Life Sciences, RNA Center, Capital Normal University, Beijing 100048, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- RNA Institute, Wuhan University, Wuhan 430072, China
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143
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G Koch
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- Chemical Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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144
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Hu H, Yan HL, Nguyen THD. Structural biology of shelterin and telomeric chromatin: the pieces and an unfinished puzzle. Biochem Soc Trans 2024; 52:1551-1564. [PMID: 39109533 DOI: 10.1042/bst20230300] [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: 06/14/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024]
Abstract
The six-subunit shelterin complex binds to mammalian telomeres and protects them from triggering multiple DNA damage response pathways. The loss of this protective function by shelterin can have detrimental effects on cells. In this review, we first discuss structural studies of shelterin, detailing the contributions of each subunit and inter-subunit interactions in protecting chromosome ends. We then examine the influence of telomeric chromatin dynamics on the function of shelterin at telomeres. These studies provide valuable insights and underscore the challenges that future research must tackle to attain high-resolution structures of shelterin.
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Affiliation(s)
- Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, U.K
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145
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Wolf YI, Schurov IV, Makarova KS, Katsnelson MI, Koonin EV. Long range segmentation of prokaryotic genomes by gene age and functionality. Nucleic Acids Res 2024:gkae745. [PMID: 39193895 DOI: 10.1093/nar/gkae745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/19/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
Bacterial and archaeal genomes encompass numerous operons that typically consist of two to five genes. On larger scales, however, gene order is poorly conserved through the evolution of prokaryotes. Nevertheless, non-random localization of different classes of genes on prokaryotic chromosomes could reflect important functional and evolutionary constraints. We explored the patterns of genomic localization of evolutionarily conserved (ancient) and variable (young) genes across the diversity of bacteria and archaea. Nearly all bacterial and archaeal chromosomes were found to encompass large segments of 100-300 kb that were significantly enriched in either ancient or young genes. Similar clustering of genes with lethal knockout phenotype (essential genes) was observed as well. Mathematical modeling of genome evolution suggests that this long-range gene clustering in prokaryotic chromosomes reflects perpetual genome rearrangement driven by a combination of selective and neutral processes rather than evolutionary conservation.
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ilya V Schurov
- Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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146
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McLamb F, Feng Z, Vu JP, Griffin L, Vasquez MF, Bozinovic G. Lagging Brain Gene Expression Patterns of Drosophila melanogaster Young Adult Males Confound Comparisons Between Sexes. Mol Neurobiol 2024:10.1007/s12035-024-04427-7. [PMID: 39196495 DOI: 10.1007/s12035-024-04427-7] [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: 03/28/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024]
Abstract
Many species, including fruit flies (Drosophila melanogaster), are sexually dimorphic. Phenotypic variation in morphology, physiology, and behavior can affect development, reproduction, health, and aging. Therefore, designating sex as a variable and sex-blocking should be considered when designing experiments. The brain regulates phenotypes throughout the lifespan by balancing survival and reproduction, and sex-specific development at each life stage is likely. Changes in morphology and physiology are governed by differential gene expression, a quantifiable molecular marker for age- and sex-specific variations. We assessed the fruit fly brain transcriptome at three adult ages for gene expression signatures of sex, age, and sex-by-age: 6698 genes were differentially expressed between sexes, with the most divergence at 3 days. Between ages, 31.1% of 6084 differentially expressed genes (1890 genes) share similar expression patterns from 3 to 7 days in females, and from 7 to 14 days in males. Most of these genes (90.5%, 1712) were upregulated and enriched for chemical stimulus detection and/or cilium regulation. Our data highlight an important delay in male brain gene regulation compared to females. Because significant delays in expression could confound comparisons between sexes, studies of sexual dimorphism at phenotypically comparable life stages rather than chronological age should be more biologically relevant.
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Affiliation(s)
- Flannery McLamb
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, USA
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA
| | - Jeanne P Vu
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA
- Graduate School of Public Health, San Diego State University, San Diego, CA, USA
| | - Lindsey Griffin
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, USA
| | - Miguel F Vasquez
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Goran Bozinovic
- Boz Life Science Research and Teaching Institute, La Jolla, CA, USA.
- Graduate School of Public Health, San Diego State University, San Diego, CA, USA.
- Center for Life in Extreme Environments, Portland State University, Portland, OR, USA.
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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147
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Singh M, Raseley K, Perez AM, MacKenzie D, Kosiyatrakul ST, Desai S, Batista N, Guru N, Loomba KK, Abid HZ, Wang Y, Udo-Bellner L, Stout RF, Schildkraut CL, Xiao M, Zhang D. Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model. Nucleic Acids Res 2024:gkae747. [PMID: 39193906 DOI: 10.1093/nar/gkae747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/04/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during tumorigenesis and tumor evolution. However, the detailed mechanism for the individual steps of the BFB cycle warrants further investigation. Here, we demonstrate that a nuclease-dead Cas9 (dCas9) coupled with a telomere-specific single-guide RNA (sgTelo) can be used to model the BFB cycle. First, we show that targeting dCas9 to telomeres using sgTelo impedes DNA replication at telomeres and induces a pronounced increase of replication stress and DNA damage. Using Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM), we investigate the genome-wide features of telomeres in the dCas9/sgTelo cells and observe a dramatic increase of chromosome end fusions, including fusion/ITS+ and fusion/ITS-. Consistently, we also observe an increase in the formation of dicentric chromosomes, anaphase bridges, and intercellular telomeric chromosome bridges (ITCBs). Utilizing the dCas9/sgTelo system, we uncover many interesting molecular and structural features of the ITCB and demonstrate that multiple DNA repair pathways are implicated in the formation of ITCBs. Our studies shed new light on the molecular mechanisms of the BFB cycle, which will advance our understanding of tumorigenesis, tumor evolution, and drug resistance.
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Affiliation(s)
- Manrose Singh
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
| | - Alexis M Perez
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Danny MacKenzie
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | | | - Sanket Desai
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Noelle Batista
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Navjot Guru
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Katherine K Loomba
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Heba Z Abid
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
| | - Lars Udo-Bellner
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Randy F Stout
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Center for Cancer Research, New York Institute of Technology, Old Westbury, NY 11568, USA
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148
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Dehaene N, Boussardon C, Andrey P, Charif D, Brandt D, Gilouppe Taillefer C, Nietzel T, Ricou A, Simon M, Tran J, Vezon D, Camilleri C, Arimura SI, Schwarzländer M, Budar F. The mitochondrial orf117Sha gene desynchronizes pollen development and causes pollen abortion in Arabidopsis Sha cytoplasmic male sterility. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4851-4872. [PMID: 38733289 DOI: 10.1093/jxb/erae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024]
Abstract
Cytoplasmic male sterility (CMS) is of major agronomical relevance in hybrid breeding. In gametophytic CMS, abortion of pollen is determined by the grain genotype, while in sporophytic CMS, it is determined by the mother plant genotype. While several CMS mechanisms have been dissected at the molecular level, gametophytic CMS has not been straightforwardly accessible. We used the gametophytic Sha-CMS in Arabidopsis to characterize the cause and process of pollen abortion by implementing in vivo biosensing in single pollen and mitoTALEN mutagenesis. We obtained conclusive evidence that orf117Sha is the CMS-causing gene, despite distinct characteristics from other CMS genes. We measured the in vivo cytosolic ATP content in single pollen, followed pollen development, and analyzed pollen mitochondrial volume in two genotypes that differed only by the presence of the orf117Sha locus. Our results showed that the Sha-CMS is not triggered by ATP deficiency. Instead, we observed desynchronization of a pollen developmental program. Pollen death occurred independently in pollen grains at diverse stages and was preceded by mitochondrial swelling. We conclude that pollen death is grain-autonomous in Sha-CMS and propose that mitochondrial permeability transition, which was previously described as a hallmark of developmental and environmental-triggered cell death programs, precedes pollen death in Sha-CMS.
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Affiliation(s)
- Noémie Dehaene
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Clément Boussardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Delphine Charif
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Dennis Brandt
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Clémence Gilouppe Taillefer
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Thomas Nietzel
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Anthony Ricou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Matthieu Simon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Joseph Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Daniel Vezon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Christine Camilleri
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Françoise Budar
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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149
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BenDavid E, Yang C, Zhou Y, Pfaller CK, Samuel CE, Ma D. Host WD repeat-containing protein 5 inhibits protein kinase R-mediated integrated stress response during measles virus infection. J Virol 2024:e0102024. [PMID: 39194235 DOI: 10.1128/jvi.01020-24] [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: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Some negative-sense RNA viruses, including measles virus (MeV), share the characteristic that during their infection cycle, cytoplasmic inclusion bodies (IBs) are formed where components of the viral replication machinery are concentrated. As a foci of viral replication, how IBs act to enhance the efficiency of infection by affecting virus-host interactions remains an important topic of investigation. We previously established that upon MeV infection, the epigenetic host protein, WD repeat-containing protein 5 (WDR5), translocates to cytoplasmic viral IBs and facilitates MeV replication. We now show that WDR5 is recruited to IBs by forming a complex with IB-associated MeV phosphoprotein via a conserved binding motif located on the surface of WDR5. Furthermore, we provide evidence that WDR5 promotes viral replication by suppressing a major innate immune response pathway, the double-stranded RNA-mediated activation of protein kinase R and integrated stress response. IMPORTANCE MeV is a pathogen that remains a global concern, with an estimated 9 million measles cases and 128,000 measles deaths in 2022 according to the World Health Organization. A large population of the world still has inadequate access to the effective vaccine against the exceptionally transmissible MeV. Measles disease is characterized by a high morbidity in children and in immunocompromised individuals. An important area of research for negative-sense RNA viruses, including MeV, is the characterization of the complex interactome between virus and host occurring at cytoplasmic IBs where viral replication occurs. Despite the progress made in understanding IB structures, little is known regarding the virus-host interactions within IBs and the role of these interactions in promoting viral replication and antagonizing host innate immunity. Herein we provide evidence suggesting a model by which MeV IBs utilize the host protein WDR5 to suppress the protein kinase R-integrated stress response pathway.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Chuyuan Yang
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Yuqin Zhou
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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150
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Gao Y, Stein M, Oshana L, Zhao W, Matsubara S, Stich B. Exploring natural genetic variation in photosynthesis-related traits of barley in the field. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4904-4925. [PMID: 38700102 DOI: 10.1093/jxb/erae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/01/2024] [Indexed: 05/05/2024]
Abstract
Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbred lines across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variation in photosystem II quantum yield observed among the inbred lines in the field largely reflected the variation in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variation under field conditions. Heritability (H2) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open photosystem II center. Two parameters, the maximum photosystem II efficiency in the light-adapted state (H2=0.58) and the total non-photochemical quenching (H2=0.53), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbred lines. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.
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Affiliation(s)
- Yanrong Gao
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- IBG-2: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Merle Stein
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Lilian Oshana
- IBG-2: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Wenxia Zhao
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- Xinjiang Seed Industry Development Center of China, Urumqi, China
| | - Shizue Matsubara
- IBG-2: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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