Pub Date : 2024-07-02DOI: 10.1186/s12915-024-01943-9
Huirong Xie, Katrina Linning-Duffy, Elena Y Demireva, Huishi Toh, Bana Abolibdeh, Jiaming Shi, Bo Zhou, Shigeki Iwase, Lily Yan
Background: Diurnal and nocturnal mammals have evolved distinct pathways to optimize survival for their chronotype-specific lifestyles. Conventional rodent models, being nocturnal, may not sufficiently recapitulate the biology of diurnal humans in health and disease. Although diurnal rodents are potentially advantageous for translational research, until recently, they have not been genetically tractable. The present study aims to address this major limitation by developing experimental procedures necessary for genome editing in a well-established diurnal rodent model, the Nile grass rat (Arvicanthis niloticus).
Results: A superovulation protocol was established, which yielded nearly 30 eggs per female grass rat. Fertilized eggs were cultured in a modified rat 1-cell embryo culture medium (mR1ECM), in which grass rat embryos developed from the 1-cell stage into blastocysts. A CRISPR-based approach was then used for gene editing in vivo and in vitro, targeting Retinoic acid-induced 1 (Rai1), the causal gene for Smith-Magenis Syndrome, a neurodevelopmental disorder. The CRISPR reagents were delivered in vivo by electroporation using an improved Genome-editing via Oviductal Nucleic Acids Delivery (i-GONAD) method. The in vivo approach produced several edited founder grass rats with Rai1 null mutations, which showed stable transmission of the targeted allele to the next generation. CRISPR reagents were also microinjected into 2-cell embryos in vitro. Large deletion of the Rai1 gene was confirmed in 70% of the embryos injected, demonstrating high-efficiency genome editing in vitro.
Conclusion: We have established a set of methods that enabled the first successful CRISPR-based genome editing in Nile grass rats. The methods developed will guide future genome editing of this and other diurnal rodent species, which will promote greater utility of these models in basic and translational research.
{"title":"CRISPR-based genome editing of a diurnal rodent, Nile grass rat (Arvicanthis niloticus).","authors":"Huirong Xie, Katrina Linning-Duffy, Elena Y Demireva, Huishi Toh, Bana Abolibdeh, Jiaming Shi, Bo Zhou, Shigeki Iwase, Lily Yan","doi":"10.1186/s12915-024-01943-9","DOIUrl":"10.1186/s12915-024-01943-9","url":null,"abstract":"<p><strong>Background: </strong>Diurnal and nocturnal mammals have evolved distinct pathways to optimize survival for their chronotype-specific lifestyles. Conventional rodent models, being nocturnal, may not sufficiently recapitulate the biology of diurnal humans in health and disease. Although diurnal rodents are potentially advantageous for translational research, until recently, they have not been genetically tractable. The present study aims to address this major limitation by developing experimental procedures necessary for genome editing in a well-established diurnal rodent model, the Nile grass rat (Arvicanthis niloticus).</p><p><strong>Results: </strong>A superovulation protocol was established, which yielded nearly 30 eggs per female grass rat. Fertilized eggs were cultured in a modified rat 1-cell embryo culture medium (mR1ECM), in which grass rat embryos developed from the 1-cell stage into blastocysts. A CRISPR-based approach was then used for gene editing in vivo and in vitro, targeting Retinoic acid-induced 1 (Rai1), the causal gene for Smith-Magenis Syndrome, a neurodevelopmental disorder. The CRISPR reagents were delivered in vivo by electroporation using an improved Genome-editing via Oviductal Nucleic Acids Delivery (i-GONAD) method. The in vivo approach produced several edited founder grass rats with Rai1 null mutations, which showed stable transmission of the targeted allele to the next generation. CRISPR reagents were also microinjected into 2-cell embryos in vitro. Large deletion of the Rai1 gene was confirmed in 70% of the embryos injected, demonstrating high-efficiency genome editing in vitro.</p><p><strong>Conclusion: </strong>We have established a set of methods that enabled the first successful CRISPR-based genome editing in Nile grass rats. The methods developed will guide future genome editing of this and other diurnal rodent species, which will promote greater utility of these models in basic and translational research.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11218167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change.
Results: Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO2 from organic matter and boost the bioavailability of mineral nitrogen.
Conclusions: Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.
{"title":"Genomics-based identification of a cold adapted clade in Deinococcus.","authors":"Liang Shen, Jiayu Hu, Luyao Zhang, Zirui Wu, Liangzhong Chen, Namita Paudel Adhikari, Mukan Ji, Shaoxing Chen, Fang Peng, Yongqin Liu","doi":"10.1186/s12915-024-01944-8","DOIUrl":"10.1186/s12915-024-01944-8","url":null,"abstract":"<p><strong>Background: </strong>Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change.</p><p><strong>Results: </strong>Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO<sub>2</sub> from organic matter and boost the bioavailability of mineral nitrogen.</p><p><strong>Conclusions: </strong>Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11218099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Metabolic associated fatty liver disease (MAFLD), a prevalent liver disorder affecting one-third of the global population, encompasses a spectrum ranging from fatty liver to severe hepatic steatosis. Both genetic and lifestyle factors, particularly diet and nutrition, contribute to its etiology. Folate deficiency, a frequently encountered type of malnutrition, has been associated with the pathogenesis of MAFLD and shown to impact lipid deposition. However, the underlying mechanisms of this relationship remain incompletely understood. We investigated the impact of disturbed folate-mediated one-carbon metabolism (OCM) on hepatic lipid metabolism both in vitro using human hepatoma cells and in vivo using transgenic fluorescent zebrafish displaying extent-, stage-, and duration-controllable folate deficiency upon induction.
Results: Disturbed folate-mediated one-carbon metabolism, either by inducing folate deficiency or adding anti-folate drug, compromises autophagy and causes lipid accumulation in liver cells. Disturbed folate status down-regulates cathepsin L, a key enzyme involved in autophagy, through inhibiting mTOR signaling. Interfered mitochondrial biology, including mitochondria relocation and increased fusion-fission dynamics, also occurs in folate-deficient hepatocytes. Folate supplementation effectively mitigated the impaired autophagy and lipid accumulation caused by the inhibition of cathepsin L activity, even when the inhibition was not directly related to folate deficiency.
Conclusions: Disruption of folate-mediated OCM diminishes cathepsin L expression and impedes autophagy via mTOR signaling, leading to lipid accumulation within hepatocytes. These findings underscore the crucial role of folate in modulating autophagic processes and regulating lipid metabolism in the liver.
{"title":"Disturbed intracellular folate homeostasis impairs autophagic flux and increases hepatocytic lipid accumulation.","authors":"Wan-Yu Chi, Gang-Hui Lee, Ming-Jer Tang, Bing-Hung Chen, Wei-Ling Lin, Tzu-Fun Fu","doi":"10.1186/s12915-024-01946-6","DOIUrl":"10.1186/s12915-024-01946-6","url":null,"abstract":"<p><strong>Background: </strong>Metabolic associated fatty liver disease (MAFLD), a prevalent liver disorder affecting one-third of the global population, encompasses a spectrum ranging from fatty liver to severe hepatic steatosis. Both genetic and lifestyle factors, particularly diet and nutrition, contribute to its etiology. Folate deficiency, a frequently encountered type of malnutrition, has been associated with the pathogenesis of MAFLD and shown to impact lipid deposition. However, the underlying mechanisms of this relationship remain incompletely understood. We investigated the impact of disturbed folate-mediated one-carbon metabolism (OCM) on hepatic lipid metabolism both in vitro using human hepatoma cells and in vivo using transgenic fluorescent zebrafish displaying extent-, stage-, and duration-controllable folate deficiency upon induction.</p><p><strong>Results: </strong>Disturbed folate-mediated one-carbon metabolism, either by inducing folate deficiency or adding anti-folate drug, compromises autophagy and causes lipid accumulation in liver cells. Disturbed folate status down-regulates cathepsin L, a key enzyme involved in autophagy, through inhibiting mTOR signaling. Interfered mitochondrial biology, including mitochondria relocation and increased fusion-fission dynamics, also occurs in folate-deficient hepatocytes. Folate supplementation effectively mitigated the impaired autophagy and lipid accumulation caused by the inhibition of cathepsin L activity, even when the inhibition was not directly related to folate deficiency.</p><p><strong>Conclusions: </strong>Disruption of folate-mediated OCM diminishes cathepsin L expression and impedes autophagy via mTOR signaling, leading to lipid accumulation within hepatocytes. These findings underscore the crucial role of folate in modulating autophagic processes and regulating lipid metabolism in the liver.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse.
Results: We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes.
Conclusions: Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.
背景:确定性造血过程中的内皮到造血转变(EHT)过程在脊椎动物中高度保守。在斑马鱼EHT过程中已检测到转座元件(TEs)的阶段特异性表达,并可能通过激活炎症信号促进造血干细胞(HSC)的形成。然而,人们对转座元件如何促进人类和小鼠的EHT过程知之甚少:结果:我们重建了人和小鼠的单细胞EHT轨迹,并解析了TEs在EHT过程中的动态表达模式。大多数TE沿着保守的EHT轨迹呈现瞬时共调模式,与表观遗传沉默系统的时间松弛相吻合。TE产物可被多种模式识别受体感知,从而触发炎症信号,促进造血干细胞的出现。有趣的是,我们观察到缺氧相关信号在 TE 表达较高的细胞中富集。此外,我们还构建了可访问TE的造血顺式调控网络,并确定了可能促进特定EHT标记基因表达的潜在TE衍生增强子:我们的研究为我们提供了一个系统的视角,让我们了解 TEs 是如何通过转录和顺式调控网络被动态控制以促进造血命运的决定,并对新生造血干细胞的免疫力进行预训练的。
{"title":"Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition.","authors":"Cong Feng, Ruxiu Tie, Saige Xin, Yuhao Chen, Sida Li, Yifan Chen, Xiaotian Hu, Yincong Zhou, Yongjing Liu, Yueming Hu, Yanshi Hu, Hang Pan, Zexu Wu, Haoyu Chao, Shilong Zhang, Qingyang Ni, Jinyan Huang, Wenda Luo, He Huang, Ming Chen","doi":"10.1186/s12915-024-01939-5","DOIUrl":"https://doi.org/10.1186/s12915-024-01939-5","url":null,"abstract":"<p><strong>Background: </strong>The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse.</p><p><strong>Results: </strong>We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes.</p><p><strong>Conclusions: </strong>Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-26DOI: 10.1186/s12915-024-01935-9
Heiner Kuhl, Peter T Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A Larson, John H Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, Yann Guiguen
Background: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems.
Results: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary.
Conclusions: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
背景:鲈科包括许多对水产养殖和渔业具有重要意义的鱼类物种。基于鲈鱼、石首鲈和桑德鲈的三个新染色体组以及其他鲈科鱼类的参考基因组,我们对它们的性别决定系统进行了进化和比较基因组分析:结果:我们探讨了重复的抗苗勒氏激素受体2型基因(amhr2bY)的命运,该基因之前被认为是P. flavescens的主性别决定(MSD)基因。在P. schrenkii和Sander lucioperca中发现了系统发育相关且结构相似的amhr2重复基因(amhr2b),有可能将这一重复事件追溯到19-27 Mya左右的最后共同祖先。在P. fluviatilis和S. vitreus中,这个amhr2b重复序列很可能已经丢失,而在S. lucioperca中,这个重复序列则被扩增。对 P. schrenkii 中 amhr2b 基因座的分析表明,该重复位点也可能具有雄性特异性,就像在 P. flavescens 中一样。在 P. fluviatilis 中,利用种群基因组学方法确定了 18 号染色体上一个相对较小(100 kb)的非重复性决定区(SDR)的特征。该SDR具有许多雄性特异性单核苷酸变异(SNV),但没有大的重复/插入事件,这表明P. fluviatilis具有雄性异配性别决定系统(XX/XXY),由等位基因多样化产生。该性别决定系统包含六个注释基因,其中三个(c18h1orf198、hsdl1、tbc1d32)在睾丸中的表达量高于卵巢:总之,我们的研究结果为长尾目动物性染色体的高度动态更替提供了一个新的实例,并为鲈形目动物提供了新的基因组资源,包括所有三个已知鲈形目物种的性别基因分型工具。
{"title":"Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae.","authors":"Heiner Kuhl, Peter T Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A Larson, John H Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, Yann Guiguen","doi":"10.1186/s12915-024-01935-9","DOIUrl":"10.1186/s12915-024-01935-9","url":null,"abstract":"<p><strong>Background: </strong>The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems.</p><p><strong>Results: </strong>We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary.</p><p><strong>Conclusions: </strong>Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-26DOI: 10.1186/s12915-024-01940-y
Constanza Ahumada-Marchant, Carlos Ancatén-Gonzalez, Henny Haensgen, Bastian Brauer, Nicolas Merino-Veliz, Rita Droste, Felipe Arancibia, H Robert Horvitz, Martha Constantine-Paton, Gloria Arriagada, Andrés E Chávez, Fernando J Bustos
Background: The VPS50 protein functions in synaptic and dense core vesicle acidification, and perturbations of VPS50 function produce behavioral changes in Caenorhabditis elegans. Patients with mutations in VPS50 show severe developmental delay and intellectual disability, characteristics that have been associated with autism spectrum disorders (ASDs). The mechanisms that link VPS50 mutations to ASD are unknown.
Results: To examine the role of VPS50 in mammalian brain function and behavior, we used the CRISPR/Cas9 system to generate knockouts of VPS50 in both cultured murine cortical neurons and living mice. In cultured neurons, KO of VPS50 did not affect the number of synaptic vesicles but did cause mislocalization of the V-ATPase V1 domain pump and impaired synaptic activity, likely as a consequence of defects in vesicle acidification and vesicle content. In mice, mosaic KO of VPS50 in the hippocampus altered synaptic transmission and plasticity and generated robust cognitive impairments.
Conclusions: We propose that VPS50 functions as an accessory protein to aid the recruitment of the V-ATPase V1 domain to synaptic vesicles and in that way plays a crucial role in controlling synaptic vesicle acidification. Understanding the mechanisms controlling behaviors and synaptic function in ASD-associated mutations is pivotal for the development of targeted interventions, which may open new avenues for therapeutic strategies aimed at ASD and related conditions.
背景:VPS50蛋白在突触和致密核心囊泡酸化过程中发挥作用,VPS50功能紊乱会导致秀丽隐杆线虫的行为发生变化。VPS50突变患者表现出严重的发育迟缓和智力障碍,这些特征与自闭症谱系障碍(ASD)有关。VPS50突变与自闭症谱系障碍的关联机制尚不清楚:为了研究VPS50在哺乳动物大脑功能和行为中的作用,我们使用CRISPR/Cas9系统在培养的小鼠皮质神经元和活体小鼠中产生了VPS50基因敲除。在培养的神经元中,敲除 VPS50 不会影响突触小泡的数量,但会导致 V-ATPase V1 结构域泵的错误定位和突触活动受损,这可能是小泡酸化和小泡含量缺陷的结果。在小鼠的海马中,镶嵌式 KO VPS50 会改变突触传递和可塑性,并产生严重的认知障碍:我们认为,VPS50是一种辅助蛋白,可帮助V-ATP酶V1结构域招募到突触囊泡,从而在控制突触囊泡酸化方面发挥关键作用。了解控制ASD相关突变的行为和突触功能的机制对于开发有针对性的干预措施至关重要,这可能为针对ASD和相关疾病的治疗策略开辟新的途径。
{"title":"Deletion of VPS50 protein in mouse brain impairs synaptic function and behavior.","authors":"Constanza Ahumada-Marchant, Carlos Ancatén-Gonzalez, Henny Haensgen, Bastian Brauer, Nicolas Merino-Veliz, Rita Droste, Felipe Arancibia, H Robert Horvitz, Martha Constantine-Paton, Gloria Arriagada, Andrés E Chávez, Fernando J Bustos","doi":"10.1186/s12915-024-01940-y","DOIUrl":"10.1186/s12915-024-01940-y","url":null,"abstract":"<p><strong>Background: </strong>The VPS50 protein functions in synaptic and dense core vesicle acidification, and perturbations of VPS50 function produce behavioral changes in Caenorhabditis elegans. Patients with mutations in VPS50 show severe developmental delay and intellectual disability, characteristics that have been associated with autism spectrum disorders (ASDs). The mechanisms that link VPS50 mutations to ASD are unknown.</p><p><strong>Results: </strong>To examine the role of VPS50 in mammalian brain function and behavior, we used the CRISPR/Cas9 system to generate knockouts of VPS50 in both cultured murine cortical neurons and living mice. In cultured neurons, KO of VPS50 did not affect the number of synaptic vesicles but did cause mislocalization of the V-ATPase V1 domain pump and impaired synaptic activity, likely as a consequence of defects in vesicle acidification and vesicle content. In mice, mosaic KO of VPS50 in the hippocampus altered synaptic transmission and plasticity and generated robust cognitive impairments.</p><p><strong>Conclusions: </strong>We propose that VPS50 functions as an accessory protein to aid the recruitment of the V-ATPase V1 domain to synaptic vesicles and in that way plays a crucial role in controlling synaptic vesicle acidification. Understanding the mechanisms controlling behaviors and synaptic function in ASD-associated mutations is pivotal for the development of targeted interventions, which may open new avenues for therapeutic strategies aimed at ASD and related conditions.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-25DOI: 10.1186/s12915-024-01924-y
Chung-Shien Wu, Rui-Jiang Wang, Shu-Miaw Chaw
Background: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.
Results: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.
Conclusions: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.
背景:横向基因转移(HGT)事件在裸子植物中鲜有报道。Gnetum 是一种裸子植物属,由 25-35 个物种组成,与西非、南美和东南亚热带雨林中的被子植物共生。迄今为止,在亚洲网纹草的有丝分裂基因组中,仅有一个获得被子植物线粒体内含子的记录。我们希望更全面地了解此类事件的频率和片段长度分布以及该属的进化历史:结果:我们对五个亚洲网纹草物种的有丝分裂基因组进行了测序和组装。这些基因组在大小和外来 DNA 含量方面差异显著。我们发现了15个线粒体来源的外来基因和5个质体来源的外来基因(MTPT)。我们的系统发育分析强烈表明,这些外来基因是从不同的裸子植物中转移过来的--主要来自茜草科 Coptosapelta 属和 Malpighiales 的 10 个属。这表明亚洲石竹经历了多个独立的 HGT 事件。序列进化模式强烈表明,线粒体之间以 DNA 为媒介的转移是导致这些 HGT 事件的主要机制。亚洲的大多数蛇床子属植物都是藤本植物,经常与同域的被子植物缠绕在一起。因此,我们认为,石竹科植物和被子植物茎的紧密结合为通过摩擦和伤口进行种间细胞间接触提供了机会,从而导致 HGT:我们的研究揭示了多种HGT事件导致大量被子植物线粒体DNA整合到亚洲石竹的有丝分裂基因组中。蛇麻属植物及其邻近的被子植物经常相互缠绕,这可能是这两个在系统发育上相距遥远的种系之间频繁发生HGT的原因。
{"title":"Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.","authors":"Chung-Shien Wu, Rui-Jiang Wang, Shu-Miaw Chaw","doi":"10.1186/s12915-024-01924-y","DOIUrl":"10.1186/s12915-024-01924-y","url":null,"abstract":"<p><strong>Background: </strong>Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.</p><p><strong>Results: </strong>We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.</p><p><strong>Conclusions: </strong>Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-24DOI: 10.1186/s12915-024-01936-8
H Charles J Godfray, Joseph Poore, Hannah Ritchie
The vast majority of the food we eat comes from land-based agriculture, but recent technological advances in agriculture and food technology offer the prospect of producing food using substantially less or even virtually no land. For example, indoor vertical farming can achieve very high yields of certain crops with a very small area footprint, and some foods can be synthesized from inorganic precursors in industrial facilities. Animal-based foods require substantial land per unit of protein or per calorie and switching to alternatives could reduce demand for some types of agricultural land. Plant-based meat substitutes and those produced through fermentation are widely available and becoming more sophisticated while in the future cellular agricultural may become technically and economical viable at scale. We review the state of play of these potentially disruptive technologies and explore how they may interact with other factors, both endogenous and exogenous to the food system, to affect future demand for land.
{"title":"Opportunities to produce food from substantially less land.","authors":"H Charles J Godfray, Joseph Poore, Hannah Ritchie","doi":"10.1186/s12915-024-01936-8","DOIUrl":"10.1186/s12915-024-01936-8","url":null,"abstract":"<p><p>The vast majority of the food we eat comes from land-based agriculture, but recent technological advances in agriculture and food technology offer the prospect of producing food using substantially less or even virtually no land. For example, indoor vertical farming can achieve very high yields of certain crops with a very small area footprint, and some foods can be synthesized from inorganic precursors in industrial facilities. Animal-based foods require substantial land per unit of protein or per calorie and switching to alternatives could reduce demand for some types of agricultural land. Plant-based meat substitutes and those produced through fermentation are widely available and becoming more sophisticated while in the future cellular agricultural may become technically and economical viable at scale. We review the state of play of these potentially disruptive technologies and explore how they may interact with other factors, both endogenous and exogenous to the food system, to affect future demand for land.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-24DOI: 10.1186/s12915-024-01942-w
Jiyoung Jang, Hyun Jung Park, Wonyoung Seong, Jiyoon Kim, Chungho Kim
Background: The intermediate filament protein vimentin is widely recognized as a molecular marker of epithelial-to-mesenchymal transition. Although vimentin expression is strongly associated with cancer metastatic potential, the exact role of vimentin in cancer metastasis and the underlying mechanism of its pro-metastatic functions remain unclear.
Results: This study revealed that vimentin can enhance integrin β1 surface expression and induce integrin-dependent clustering of cells, shielding them against anoikis cell death. The increased integrin β1 surface expression in suspended cells was caused by vimentin-mediated protection of the internal integrin β1 pool against lysosomal degradation. Additionally, cell detachment was found to induce vimentin Ser38 phosphorylation, allowing the translocation of internal integrin β1 to the plasma membrane. Furthermore, the use of an inhibitor of p21-activated kinase PAK1, one of the kinases responsible for vimentin Ser38 phosphorylation, significantly reduced cancer metastasis in animal models.
Conclusions: These findings suggest that vimentin can act as an integrin buffer, storing internalized integrin β1 and releasing it when needed. Overall, this study provides insights regarding the strong correlation between vimentin expression and cancer metastasis and a basis for blocking metastasis using this novel therapeutic mechanism.
{"title":"Vimentin-mediated buffering of internal integrin β1 pool increases survival of cells from anoikis.","authors":"Jiyoung Jang, Hyun Jung Park, Wonyoung Seong, Jiyoon Kim, Chungho Kim","doi":"10.1186/s12915-024-01942-w","DOIUrl":"10.1186/s12915-024-01942-w","url":null,"abstract":"<p><strong>Background: </strong>The intermediate filament protein vimentin is widely recognized as a molecular marker of epithelial-to-mesenchymal transition. Although vimentin expression is strongly associated with cancer metastatic potential, the exact role of vimentin in cancer metastasis and the underlying mechanism of its pro-metastatic functions remain unclear.</p><p><strong>Results: </strong>This study revealed that vimentin can enhance integrin β1 surface expression and induce integrin-dependent clustering of cells, shielding them against anoikis cell death. The increased integrin β1 surface expression in suspended cells was caused by vimentin-mediated protection of the internal integrin β1 pool against lysosomal degradation. Additionally, cell detachment was found to induce vimentin Ser38 phosphorylation, allowing the translocation of internal integrin β1 to the plasma membrane. Furthermore, the use of an inhibitor of p21-activated kinase PAK1, one of the kinases responsible for vimentin Ser38 phosphorylation, significantly reduced cancer metastasis in animal models.</p><p><strong>Conclusions: </strong>These findings suggest that vimentin can act as an integrin buffer, storing internalized integrin β1 and releasing it when needed. Overall, this study provides insights regarding the strong correlation between vimentin expression and cancer metastasis and a basis for blocking metastasis using this novel therapeutic mechanism.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-20DOI: 10.1186/s12915-024-01934-w
Yukang Liang, Rebecca B Dikow, Xu Su, Jun Wen, Zhumei Ren
Background: Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids.
Results: We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels.
Conclusions: Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
{"title":"Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships.","authors":"Yukang Liang, Rebecca B Dikow, Xu Su, Jun Wen, Zhumei Ren","doi":"10.1186/s12915-024-01934-w","DOIUrl":"10.1186/s12915-024-01934-w","url":null,"abstract":"<p><strong>Background: </strong>Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids.</p><p><strong>Results: </strong>We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels.</p><p><strong>Conclusions: </strong>Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11188193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}