Open BiologyPub Date : 2025-05-01Epub Date: 2025-05-21DOI: 10.1098/rsob.240331
Rachel James
{"title":"Relationship troubles at the mitochondrial level and what it might mean for human disease.","authors":"Rachel James","doi":"10.1098/rsob.240331","DOIUrl":"10.1098/rsob.240331","url":null,"abstract":"<p><p>Understanding and treating disease depend upon our knowledge of how the body works. The biomedical approach to disease describes health purely in terms of biological factors, with a focus on the genome as the molecular basis for cellular function and dysfunction in disease. However, the eukaryotic cell has evolved as a partnership between prokaryotic cells with mitochondria being crucial to this relationship. Aside from their role as bioenergetic and biosynthetic hubs, mitochondria are also involved in cell signalling and cell fate pathways, playing a multifaceted role in cell function and health. Crucially, mitochondria are implicated in most diseases. Perhaps then, visualizing biomedical function on the backdrop of endosymbiosis may provide another viewpoint for explaining and treating disease.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240331"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-23DOI: 10.1098/rsob.240221
Ronie Haro, Renny Lee, Claudio H Slamovits
{"title":"Unveiling the functional nature of retrogenes in dinoflagellates.","authors":"Ronie Haro, Renny Lee, Claudio H Slamovits","doi":"10.1098/rsob.240221","DOIUrl":"https://doi.org/10.1098/rsob.240221","url":null,"abstract":"<p><p>Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retrogenes with DNA-encoded remnants of the dinoflagellate-specific splice-leader motif at their 5' end. We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy. We obtained a high-confidence set of hypothetical functional retrogenes widespread through the dinoflagellate lineage. Through annotations and gene ontology enrichment analysis, we found that the functional diversity of retrogenes reflects the most prevalent and active processes during stress periods, particularly those involving post-translational modifications and cell signalling pathways. Additionally, the significant presence of retrogenes linked to specific biological processes involved in symbiosis and toxin production underscores the role of retrogenes in adaptation. The expression profile and codon composition similar to protein-coding genes confirm the operational status of retrogenes and strengthen the idea that retrogenes recapitulate parental gene expression and function. This study provides new evidence supporting widespread gene retroposition across dinoflagellates and highlights the functional link of retrogenes with the core activity of the cell.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240221"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12014239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A zinc finger protein shapes the temperature adaptability of a cosmopolitan pest.","authors":"Xin Miao, Fang Cao, Xiao-Fei Yu, Tian-Pu Li, Hai-Yin Su, Jiao Guo, Gui-Lei Hu, Bing-Wei Chen, Min-Sheng You, Yuan-Yuan Liu, Gao-Ke Lei, Shijun You","doi":"10.1098/rsob.240346","DOIUrl":"10.1098/rsob.240346","url":null,"abstract":"<p><p>Global climate change is characterized by increased extreme temperatures affecting insects at all trophic levels. Zinc finger proteins (ZFPs) are key regulators of gene expression and cell differentiation in eukaryotes, essential for stress resistance in both animals and plants. Using CRISPR/Cas9 for gene deletion, this study predicted and examined the structure of ZFP320 in the diamondback moth (<i>Plutella xylostella</i>) and investigated its function in temperature stress response through a comprehensive age-stage, two-sex life table analysis. We found <i>ZFP320</i> encodes a 387 amino acid protein (43 kDa) with no transmembrane domains, featuring a ZnF-C2H2 domain. Quantitative fluorescence analysis showed that ZFP320 expression increased under high temperatures. ZFP320 knockout altered antioxidant gene expression, resulting in higher levels of superoxide dismutase and catalase in mutant strains compared with wild-type strain. Life table analysis revealed that the mutant strains had shorter fecundity and oviposition periods under both normal and high temperatures. Additionally, mutant strains exhibited lower parameters (<i>r</i>, <i>λ</i>, <i>R<sub>0</sub></i>), as well as reduced survival rates and critical thermal maxima. Notably, <i>PxZFP320</i> plays a crucial role in temperature adaptation, paving the way for future investigations on the significance of ZFPs in <i>P. xylostella</i>'s temperature tolerance.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240346"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-02DOI: 10.1098/rsob.240361
Athina Paterou, Julia Sáez Conde, Jiří Týč, Jack Daniel Sunter, Sue Vaughan, Keith Gull, Samuel Dean
{"title":"A comprehensive toolkit for protein localization and functional analysis in trypanosomatids.","authors":"Athina Paterou, Julia Sáez Conde, Jiří Týč, Jack Daniel Sunter, Sue Vaughan, Keith Gull, Samuel Dean","doi":"10.1098/rsob.240361","DOIUrl":"10.1098/rsob.240361","url":null,"abstract":"<p><p>African trypanosomes are medically important parasites that cause sleeping sickness in humans and nagana in animals. In addition to their pathogenic role, they have emerged as valuable model organisms for studying fundamental biological processes. Protein tagging is a powerful tool for investigating protein localization and function. In a previous study, we developed two plasmids for rapid and reproducible polymerase chain reaction-based protein tagging in trypanosomes, which enabled the subcellular mapping of 89% of the trypanosome proteome. However, the limited selection of fluorescent protein tags and selectable markers restricted the flexibility of this approach. Here, we present an extended set of >100 plasmids that incorporate universal primer annealing sequences, enabling protein tagging with a range of fluorescent, biochemical and epitope tags, using five different selection markers. We evaluated the suitability of various fluorescent proteins for live and fixed cell imaging, fluorescent movies, and we demonstrate the use of tagging plasmids encoding tandem epitope tags to support expansion microscopy approaches. We show that this series of plasmids is functional in other trypanosomatid parasites, significantly increasing its value. Finally, we developed a new plasmid for tagging glycosylphosphatidylinositol-anchored proteins. We anticipate that this will be an important toolset for investigating trypanosomatid protein localization and function.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240361"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Notch and LIM-homeodomain protein Arrowhead regulate each other in a feedback mechanism to play a role in wing and neuronal development in <i>Drosophila</i>.","authors":"Jyoti Singh, Dipti Verma, Bappi Sarkar, Maimuna Sali Paul, Mousumi Mutsuddi, Ashim Mukherjee","doi":"10.1098/rsob.240247","DOIUrl":"https://doi.org/10.1098/rsob.240247","url":null,"abstract":"<p><p>The Notch pathway is an evolutionarily conserved signalling system that operates to influence an astonishing array of cell fate decisions in different developmental contexts. To identify novel effectors of Notch signalling, we analysed the whole transcriptome of <i>Drosophila</i> wing and eye imaginal discs in which an activated form of Notch was overexpressed. A LIM-homeodomain protein, Arrowhead (Awh), was identified as a novel candidate that plays a crucial role in Notch-mediated developmental events. <i>Awh</i> alleles show strong genetic interaction with Notch pathway components. Awh loss-of-function upregulates Notch targets Cut and Wingless. Awh gain-of-function downregulates Notch targets by reducing the expression of the ligand Delta. Consequently, the expression of the Wingless effector molecule Armadillo and its downstream targets, Senseless and Vestigial, also gets downregulated. Awh overexpression leads to ectopic expression of <i>engrailed</i>, a segment polarity gene in the anterior region of wing disc, leading to patterning defects. Additionally, Notch gain-of-function-mediated neuronal defects get significantly rescued with Awh overexpression. Activated Notch inhibits Awh activity, suggesting a regulatory loop between Awh and Notch. Additionally, the defects caused by Awh gain-of-function were remarkably rescued by Chip, a LIM interaction domain containing transcriptional co-factor. The present study highlights the novel feedback regulation between Awh and Notch.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240247"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-16DOI: 10.1098/rsob.240342
Rory L Cooper, Ebrahim Jahanbakhsh, Gabriel N Santos Durán, Michel C Milinkovitch
{"title":"Exacerbated sonic hedgehog signalling promotes a transition from chemical pre-patterning of chicken reticulate scales to mechanical skin folding.","authors":"Rory L Cooper, Ebrahim Jahanbakhsh, Gabriel N Santos Durán, Michel C Milinkovitch","doi":"10.1098/rsob.240342","DOIUrl":"https://doi.org/10.1098/rsob.240342","url":null,"abstract":"<p><p>Many examples of self-organized embryonic patterning can be attributed to chemically mediated systems comprising interacting morphogens. However, mechanical patterning also contributes to the emergence of biological forms. For example, various studies have demonstrated that diverse patterns arise from elastic instabilities associated with the constrained growth of soft materials, which generate wrinkles, creases and folds. Here, we show that between days 12 and 13 of <i>in ovo</i> development, transient experimentally increased activity of the sonic hedgehog pathway in the chicken embryo, through a single intravenous injection of smoothened agonist (SAG), abolishes the Turing-like chemical patterning of reticulate scales on the ventral footpad and promotes a transition to mechanical labyrinthine skin folding. Using <i>in situ</i> hybridization, nanoindentation and labelling of proliferating cells, we confirm that skin surface folding is associated with the loss of signalling placode pre-patterning as well as increased epidermal growth and stiffness. Using additional <i>in ovo</i> hydrocortisone treatments, we also demonstrate that experimentally induced hyper-keratinization of the skin mechanically restricts SAG-induced folding. Finally, we verify our experimental findings with mechanical growth simulations built from volumetric light sheet fluorescence microscopy data. Overall, we reveal that pharmacological perturbation of the underlying gene regulatory network can abolish chemical skin appendage patterning and replace it with self-organized mechanical folding.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240342"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-02DOI: 10.1098/rsob.240358
Alexa Di Pede, Bokang Ko, Abdelrahman AlOkda, Aura A Tamez González, Shusen Zhu, Jeremy M Van Raamsdonk
{"title":"Mild activation of the mitochondrial unfolded protein response increases lifespan without increasing resistance to stress.","authors":"Alexa Di Pede, Bokang Ko, Abdelrahman AlOkda, Aura A Tamez González, Shusen Zhu, Jeremy M Van Raamsdonk","doi":"10.1098/rsob.240358","DOIUrl":"10.1098/rsob.240358","url":null,"abstract":"<p><p>The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway that responds to mitochondrial insults by altering gene expression to recover mitochondrial homeostasis. The mitoUPR is mediated by the stress-activated transcription factor ATFS-1 (activating transcription factor associated with stress 1). Constitutive activation of ATFS-1 increases resistance to exogenous stressors but paradoxically decreases lifespan. In this work, we determined the optimal levels of expression of activated ATFS-1 with respect to lifespan and resistance to stress by treating constitutively active <i>atfs-1(et17</i>) worms with different concentrations of RNA interference (RNAi) bacteria targeting <i>atfs-1</i>. We observed the maximum lifespan of <i>atfs-1(et17</i>) worms at full-strength <i>atfs-1</i> RNAi, which was significantly longer than wild-type lifespan. Under the conditions of maximum lifespan, <i>atfs-1(et17</i>) worms did not show enhanced resistance to stress, suggesting a trade-off between stress resistance and longevity. The maximum resistance to stress in <i>atfs-1(et17</i>) worms occurred on empty vector. Under these conditions, <i>atfs-1(et17</i>) worms are short-lived. This indicates that constitutive activation of ATFS-1 can increase lifespan or enhance resistance to stress but not both, at the same time. Overall, these results demonstrate that constitutively active ATFS-1 can extend lifespan when expressed at low levels and that this lifespan extension is not dependent on the ability of ATFS-1 to enhance resistance to stress.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240358"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-09DOI: 10.1098/rsob.240402
Jin Zhang, Zicheng Tan, Qishu Qin, Hongzhe Peng, Wenjie Shi, Haiyan Yu, Bo Dong
{"title":"Integrated multi-omics identify key signalling pathways for notochord lumenogenesis in ascidian <i>Ciona savignyi</i>.","authors":"Jin Zhang, Zicheng Tan, Qishu Qin, Hongzhe Peng, Wenjie Shi, Haiyan Yu, Bo Dong","doi":"10.1098/rsob.240402","DOIUrl":"10.1098/rsob.240402","url":null,"abstract":"<p><p>Lumen formation and inflation are crucial for tubular organ morphogenesis and function. However, the key signalling pathways for lumenogenesis regulation were not well identified. Here, we performed tissue-specific transcriptomic sequencing for the isolated <i>Ciona</i> notochord tissue, in which 10 551 genes in total were identified. To investigate crucial signalling pathways in regulating lumenogenesis, KEGG was performed and the results showed that the Rap1 signalling pathway, vascular endothelial growth factor signalling pathway, mitogen activated protein kinase (MAPK) signalling pathway (plant) and Ras signalling pathway might play important roles in lumenogenesis. Moreover, correlation analysis with proteomic data and comparison analysis of single-cell transcriptomic data were further utilized to identify the potential critical roles of the Rap1 signalling pathway and Ras signalling pathway in lumenogenesis. To verify their functions in lumenogenesis, the Ras/calcium-Rap1-MAPK signalling axis was blocked, and the results showed that the notochord lumenogenesis failed. Meanwhile, we identified that CDC42 was a potential downstream target factor of the Ras-Rap1-MAPK signalling axis, playing crucial functions in notochord lumenogenesis. Overall, we systematically revealed the key regulatory signalling pathways for notochord lumen formation and verified a lumenogenesis-related signalling axis, providing a foundational data resource for exploring the mechanisms of lumenogenesis.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240402"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Open BiologyPub Date : 2025-04-01Epub Date: 2025-04-30DOI: 10.1098/rsob.240262
Laurent Duchatelet, Gabriela A Galeazzo, Constance Coubris, Laure Bridoux, René Rezsohazy, Marcelo R S Melo, Milan Marek, Danilo T Amaral, Sam Dupont, Anderson Garbuglio de Oliveira, Jérôme Delroisse
{"title":"Insights into the bioluminescence systems of three sea pens (Cnidaria: Anthozoa): from de novo transcriptome analyses to biochemical assays.","authors":"Laurent Duchatelet, Gabriela A Galeazzo, Constance Coubris, Laure Bridoux, René Rezsohazy, Marcelo R S Melo, Milan Marek, Danilo T Amaral, Sam Dupont, Anderson Garbuglio de Oliveira, Jérôme Delroisse","doi":"10.1098/rsob.240262","DOIUrl":"https://doi.org/10.1098/rsob.240262","url":null,"abstract":"<p><p>Bioluminescence is the production of visible light by living organisms. It occurs through the oxidation of luciferin substrates catalysed by luciferase enzymes. Auxiliary proteins, such as fluorescent proteins and luciferin-binding proteins, can modify the light emitted wavelength or stabilize reactive luciferin molecules, respectively. Additionally, calcium ions are crucial for the luminescence across various species. Despite the large phylogenetic distribution of bioluminescent organisms, only a few systems have been comprehensively studied. Notably, cnidarian species of the <i>Renilla</i> genus utilize a coelenterazine-dependent luciferase, a calcium-dependent coelenterazine-binding protein and a green fluorescent protein. We investigated the bioluminescence of three sea pen species: <i>Pennatula phosphorea</i>, <i>Anthoptilum murrayi</i> and <i>Funiculina quadrangularis</i> (Pennatuloidea, Anthozoa). Their light-emission spectra reveal peaks at 510, 513 and 485 nm, respectively. A coelenterazine-based reaction was demonstrated in all three species. Using transcriptome analyses, we identified transcripts coding for luciferases, green fluorescent proteins and coelenterazine-binding proteins for <i>P. phosphorea</i> and <i>A. murrayi</i>. Immunodetection confirmed the expression of luciferase in <i>P. phosphorea</i> and <i>F. quadrangularis</i>. We also expressed recombinant luciferase of <i>A. murrayi</i>, confirming its activity. We highlighted the role of calcium ions in bioluminescence, possibly associated with the mechanism of substrate release at the level of coelenterazine-binding proteins. The study proposes a model for anthozoan bioluminescence, offering new avenues for future ecological and functional research on these luminous organisms.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240262"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}