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A somatic view of the genomic impact of mitochondrial endosymbiosis. 从体细胞角度看线粒体共生对基因组的影响。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-23 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002756
Rose M Doss, Martin W Breuss

The endosymbiosis of mitochondrial ancestors resulted in the transfer of genetic material on an evolutionary scale for eukaryotic species. A new study in PLOS Biology expands this to the genome of somatic cells within individuals and highlights its correlation with aging and disease.

线粒体祖先的内共生导致真核生物物种在进化过程中遗传物质的转移。发表在《公共科学图书馆生物学》(PLOS Biology)上的一项新研究将这一现象扩展到了个体内的体细胞基因组,并强调了它与衰老和疾病的相关性。
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引用次数: 0
Metabolic specialization drives reduced pathogenicity in Pseudomonas aeruginosa isolates from cystic fibrosis patients. 代谢特化促使从囊性纤维化患者中分离出的铜绿假单胞菌致病性降低。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-23 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002781
Bjarke Haldrup Pedersen, Filipa Bica Simões, Ivan Pogrebnyakov, Martin Welch, Helle Krogh Johansen, Søren Molin, Ruggero La Rosa

Metabolism provides the foundation for all cellular functions. During persistent infections, in adapted pathogenic bacteria metabolism functions radically differently compared with more naïve strains. Whether this is simply a necessary accommodation to the persistence phenotype or if metabolism plays a direct role in achieving persistence in the host is still unclear. Here, we characterize a convergent shift in metabolic function(s) linked with the persistence phenotype during Pseudomonas aeruginosa colonization in the airways of people with cystic fibrosis. We show that clinically relevant mutations in the key metabolic enzyme, pyruvate dehydrogenase, lead to a host-specialized metabolism together with a lower virulence and immune response recruitment. These changes in infection phenotype are mediated by impaired type III secretion system activity and by secretion of the antioxidant metabolite, pyruvate, respectively. Our results show how metabolic adaptations directly impinge on persistence and pathogenicity in this organism.

新陈代谢是所有细胞功能的基础。在持续感染过程中,适应病原菌的新陈代谢功能与较幼稚的菌株截然不同。这究竟是对持久性表型的必要适应,还是新陈代谢在实现宿主持久性感染中发挥了直接作用,目前尚不清楚。在这里,我们描述了铜绿假单胞菌在囊性纤维化患者气道中定植期间与持久性表型相关的代谢功能的趋同性转变。我们的研究表明,关键代谢酶丙酮酸脱氢酶的临床相关突变会导致宿主特化代谢,同时降低毒力和免疫反应招募。感染表型的这些变化分别是由 III 型分泌系统活性受损和抗氧化代谢产物丙酮酸的分泌介导的。我们的研究结果表明,新陈代谢的适应性如何直接影响到这种生物的持久性和致病性。
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引用次数: 0
The ion channel Anoctamin 10/TMEM16K coordinates organ morphogenesis across scales in the urochordate notochord. 离子通道Anoctamin 10/TMEM16K可协调泌尿脊索动物脊索上不同尺度的器官形态发生。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-22 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002762
Zonglai Liang, Daniel Christiaan Dondorp, Marios Chatzigeorgiou

During embryonic development, tissues and organs are gradually shaped into their functional morphologies through a series of spatiotemporally tightly orchestrated cell behaviors. A highly conserved organ shape across metazoans is the epithelial tube. Tube morphogenesis is a complex multistep process of carefully choreographed cell behaviors such as convergent extension, cell elongation, and lumen formation. The identity of the signaling molecules that coordinate these intricate morphogenetic steps remains elusive. The notochord is an essential tubular organ present in the embryonic midline region of all members of the chordate phylum. Here, using genome editing, pharmacology and quantitative imaging in the early chordate Ciona intestinalis we show that Ano10/Tmem16k, a member of the evolutionarily ancient family of transmembrane proteins called Anoctamin/TMEM16 is essential for convergent extension, lumen expansion, and connection during notochord morphogenesis. We find that Ano10/Tmem16k works in concert with the plasma membrane (PM) localized Na+/Ca2+ exchanger (NCX) and the endoplasmic reticulum (ER) residing SERCA, RyR, and IP3R proteins to establish developmental stage specific Ca2+ signaling molecular modules that regulate notochord morphogenesis and Ca2+ dynamics. In addition, we find that the highly conserved Ca2+ sensors calmodulin (CaM) and Ca2+/calmodulin-dependent protein kinase (CaMK) show an Ano10/Tmem16k-dependent subcellular localization. Their pharmacological inhibition leads to convergent extension, tubulogenesis defects, and deranged Ca2+ dynamics, suggesting that Ano10/Tmem16k is involved in both the "encoding" and "decoding" of developmental Ca2+ signals. Furthermore, Ano10/Tmem16k mediates cytoskeletal reorganization during notochord morphogenesis, likely by altering the localization of 2 important cytoskeletal regulators, the small GTPase Ras homolog family member A (RhoA) and the actin binding protein Cofilin. Finally, we use electrophysiological recordings and a scramblase assay in tissue culture to demonstrate that Ano10/Tmem16k likely acts as an ion channel but not as a phospholipid scramblase. Our results establish Ano10/Tmem16k as a novel player in the prevertebrate molecular toolkit that controls organ morphogenesis across scales.

在胚胎发育过程中,组织和器官通过一系列时空紧密配合的细胞行为逐渐形成其功能形态。上皮管是后生动物高度保守的器官形态。管的形态发生是一个复杂的多步骤过程,包括精心编排的细胞行为,如会聚延伸、细胞伸长和管腔形成。协调这些错综复杂的形态发生步骤的信号分子的身份仍然难以确定。脊索是一种重要的管状器官,存在于脊索动物门所有成员的胚胎中线区域。在这里,我们利用基因组编辑、药理学和定量成像技术对早期脊索动物脊索动物肠(Ciona intestinalis)进行了研究,结果表明 Ano10/Tmem16k(一种进化古老的跨膜蛋白家族成员,被称为 Anoctamin/TMEM16 )对于脊索形态发生过程中的会聚延伸、管腔扩张和连接至关重要。我们发现 Ano10/Tmem16k 与质膜(PM)定位的 Na+/Ca2+ 交换器(NCX)和内质网(ER)驻留的 SERCA、RyR 和 IP3R 蛋白协同作用,建立了发育阶段特异性 Ca2+ 信号分子模块,从而调控脊索形态发生和 Ca2+ 动态。此外,我们发现高度保守的钙离子传感器钙调蛋白(CaM)和钙离子/钙调蛋白依赖性蛋白激酶(CaMK)显示出依赖于 Ano10/Tmem16k 的亚细胞定位。对它们的药理抑制会导致会聚延伸、肾小管生成缺陷和 Ca2+ 动态失常,这表明 Ano10/Tmem16k 参与了发育 Ca2+ 信号的 "编码 "和 "解码"。此外,在脊索形态发生过程中,Ano10/Tmem16k 可能通过改变两种重要的细胞骨架调节因子--小 GTPase Ras 同源家族成员 A(RhoA)和肌动蛋白结合蛋白 Cofilin 的定位,介导细胞骨架重组。最后,我们利用组织培养中的电生理记录和扰乱酶试验证明,Ano10/Tmem16k 很可能充当离子通道,而不是磷脂扰乱酶。我们的研究结果确立了 Ano10/Tmem16k 在前脊椎动物分子工具包中的新角色地位,该工具包控制着不同尺度的器官形态发生。
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引用次数: 0
Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. 体细胞核线粒体 DNA 插入在人脑中十分普遍,并随着时间的推移在成纤维细胞中积累。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-22 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002723
Weichen Zhou, Kalpita R Karan, Wenjin Gu, Hans-Ulrich Klein, Gabriel Sturm, Philip L De Jager, David A Bennett, Michio Hirano, Martin Picard, Ryan E Mills

The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.

在非人类物种中,线粒体DNA转移到真核生物的核基因组(Numts)与寿命有关,最近的研究表明,在极少数情况下,线粒体DNA会从人类一代转移到下一代。在这里,我们从两个方面研究了人类的Numtogenesis动态。首先,我们对来自不同个体的1 187份死后大脑和血液样本中的Numts进行了量化。与循环免疫细胞(n = 389)相比,死后脑组织(n = 798)含有更多的Numts,这与它们潜在的体细胞积累相一致。在大脑样本中,我们观察到与小脑样本相比,体细胞Numt插入在背外侧前额叶皮层(DLPFC)中富集了5.5倍,这表明大脑Numts是在发育过程中或整个生命周期中自发产生的。此外,大脑Numts数量的增加与较早死亡有关。与寿命较长的人相比,在较年轻时死亡的无认知障碍(NCI)个体的大脑中,每10年多出约2个Numts。其次,我们采用重复测量全基因组测序设计,在人类成纤维细胞模型中测试了Numts的动态转移,该模型再现了衰老的若干分子特征。这些纵向实验显示,每隔约 13 天就会逐渐积累 1 个 Numt。Numt发生与大规模基因组不稳定性无关,也不太可能由细胞克隆驱动。包括慢性糖皮质激素信号转导或损害线粒体氧化磷酸化(OxPhos)在内的靶向药理学干扰仅适度增加了Numt发生的速度,而表现出mtDNA不稳定性的患者来源SURF1突变细胞积累Numt的速度是健康供体的4.7倍。综上所述,我们的数据记录了人类细胞中自发的Numt发生,并证明了大脑皮层体细胞Numts与人类寿命之间的联系。这些发现为有丝分裂-核水平基因在人类有丝分裂后组织间的转移提供了可能性,这种转移产生与功能相关的人类Numts的时间尺度比以前假设的要短。
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引用次数: 0
An empirical appraisal of eLife's assessment vocabulary. 对 eLife 评估词汇的实证评估。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-22 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002645
Tom E Hardwicke, Sarah R Schiavone, Beth Clarke, Simine Vazire

Research articles published by the journal eLife are accompanied by short evaluation statements that use phrases from a prescribed vocabulary to evaluate research on 2 dimensions: importance and strength of support. Intuitively, the prescribed phrases appear to be highly synonymous (e.g., important/valuable, compelling/convincing) and the vocabulary's ordinal structure may not be obvious to readers. We conducted an online repeated-measures experiment to gauge whether the phrases were interpreted as intended. We also tested an alternative vocabulary with (in our view) a less ambiguous structure. A total of 301 participants with a doctoral or graduate degree used a 0% to 100% scale to rate the importance and strength of support of hypothetical studies described using phrases from both vocabularies. For the eLife vocabulary, most participants' implied ranking did not match the intended ranking on both the importance (n = 59, 20% matched, 95% confidence interval [15% to 24%]) and strength of support dimensions (n = 45, 15% matched [11% to 20%]). By contrast, for the alternative vocabulary, most participants' implied ranking did match the intended ranking on both the importance (n = 188, 62% matched [57% to 68%]) and strength of support dimensions (n = 201, 67% matched [62% to 72%]). eLife's vocabulary tended to produce less consistent between-person interpretations, though the alternative vocabulary still elicited some overlapping interpretations away from the middle of the scale. We speculate that explicit presentation of a vocabulary's intended ordinal structure could improve interpretation. Overall, these findings suggest that more structured and less ambiguous language can improve communication of research evaluations.

eLife》杂志发表的研究文章都附有简短的评价语句,这些评价语句使用规定词汇中的短语从两个维度对研究进行评价:重要性和支持力度。从直观上看,规定的短语似乎是高度同义的(例如,重要/有价值、令人信服/有说服力),而词汇的顺序结构对读者来说可能并不明显。我们进行了一次在线重复测量实验,以衡量这些短语是否被按照预期进行了解释。我们还测试了另一个(我们认为)结构不那么模糊的词汇。共有 301 位拥有博士学位或研究生学位的参与者使用 0% 到 100% 的评分标准,对使用这两个词汇表中的短语描述的假设研究的重要性和支持力度进行评分。对于 eLife 词汇表,大多数参与者的隐含排名在重要性(n = 59,20% 匹配,95% 置信区间[15%-24%])和支持强度(n = 45,15% 匹配[11%-20%])两个维度上都与预期排名不符。相比之下,对于替代词汇,大多数参与者的隐含排序在重要性(n = 188,62% 匹配[57%-68%])和支持强度(n = 201,67% 匹配[62%-72%])两个维度上都与预期排序一致。eLife 的词汇倾向于产生不太一致的人与人之间的解释,尽管替代词汇仍然引起了一些远离量表中间的重叠解释。我们推测,明确呈现词汇的预期序数结构可以改善解释。总之,这些研究结果表明,使用结构性更强、含糊度更低的语言可以改善研究评价的交流。
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引用次数: 0
Cryo-EM structures of the human band 3 transporter indicate a transport mechanism involving the coupled movement of chloride and bicarbonate ions. 人类带3转运体的低温电子显微镜结构表明,其转运机制涉及氯离子和碳酸氢根离子的耦合移动。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-21 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002719
Chih-Chia Su, Zhemin Zhang, Meinan Lyu, Meng Cui, Edward W Yu

The band 3 transporter is a critical integral membrane protein of the red blood cell (RBC), as it is responsible for catalyzing the exchange of bicarbonate and chloride anions across the plasma membrane. To elucidate the structural mechanism of the band 3 transporter, detergent solubilized human ghost membrane reconstituted in nanodiscs was applied to a cryo-EM holey carbon grid to define its composition. With this approach, we identified and determined structural information of the human band 3 transporter. Here, we present 5 different cryo-EM structures of the transmembrane domain of dimeric band 3, either alone or bound with chloride or bicarbonate. Interestingly, we observed that human band 3 can form both symmetric and asymmetric dimers with a different combination of outward-facing (OF) and inward-facing (IF) states. These structures also allow us to obtain the first model of a human band 3 molecule at the IF conformation. Based on the structural data of these dimers, we propose a model of ion transport that is in favor of the elevator-type mechanism.

带3转运体是红细胞(RBC)的一种重要的整体膜蛋白,它负责催化碳酸氢盐和氯离子在质膜上的交换。为了阐明带3转运体的结构机制,我们将去垢溶解的人鬼膜重组在纳米盘中,并将其应用于低温电子显微镜孔状碳网格,以确定其组成。通过这种方法,我们识别并确定了人类带3转运体的结构信息。在这里,我们展示了二聚体 band 3 跨膜结构域的 5 种不同的低温电子显微镜结构,有的单独存在,有的与氯化物或碳酸氢盐结合。有趣的是,我们观察到人类 band 3 可以形成对称和不对称的二聚体,并具有不同的外向(OF)和内向(IF)状态组合。通过这些结构,我们还首次获得了人类 band 3 分子的 IF 构象模型。根据这些二聚体的结构数据,我们提出了一个有利于电梯型机制的离子传输模型。
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引用次数: 0
Slow-wave sleep drives sleep-dependent renormalization of synaptic AMPA receptor levels in the hypothalamus. 慢波睡眠驱动下丘脑中依赖睡眠的突触 AMPA 受体水平重新正常化。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-20 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002768
Jianfeng Liu, Niels Niethard, Yu Lun, Stoyan Dimitrov, Ingrid Ehrlich, Jan Born, Manfred Hallschmid

According to the synaptic homeostasis hypothesis (SHY), sleep serves to renormalize synaptic connections that have been potentiated during the prior wake phase due to ongoing encoding of information. SHY focuses on glutamatergic synaptic strength and has been supported by numerous studies examining synaptic structure and function in neocortical and hippocampal networks. However, it is unknown whether synaptic down-regulation during sleep occurs in the hypothalamus, i.e., a pivotal center of homeostatic regulation of bodily functions including sleep itself. We show that sleep, in parallel with the synaptic down-regulation in neocortical networks, down-regulates the levels of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) in the hypothalamus of rats. Most robust decreases after sleep were observed at both sites for AMPARs containing the GluA1 subunit. Comparing the effects of selective rapid eye movement (REM) sleep and total sleep deprivation, we moreover provide experimental evidence that slow-wave sleep (SWS) is the driving force of the down-regulation of AMPARs in hypothalamus and neocortex, with no additional contributions of REM sleep or the circadian rhythm. SWS-dependent synaptic down-regulation was not linked to EEG slow-wave activity. However, spindle density during SWS predicted relatively increased GluA1 subunit levels in hypothalamic synapses, which is consistent with the role of spindles in the consolidation of memory. Our findings identify SWS as the main driver of the renormalization of synaptic strength during sleep and suggest that SWS-dependent synaptic renormalization is also implicated in homeostatic control processes in the hypothalamus.

根据 "突触稳态假说"(SHY),睡眠可以使之前清醒阶段因持续编码信息而增强的突触连接恢复正常。该假说主要针对谷氨酸能突触强度,并得到了大量研究的支持,这些研究考察了新皮层和海马网络中的突触结构和功能。然而,下丘脑是包括睡眠本身在内的身体机能平衡调节的关键中心,它在睡眠过程中是否会出现突触下调,目前还不得而知。我们的研究表明,睡眠与新皮层网络中的突触下调同步,下调了大鼠下丘脑中的α-氨基-3-羟基-5-甲基-4-异恶唑丙酸受体(AMPARs)的水平。在这两个部位观察到,含有 GluA1 亚基的 AMPARs 在睡眠后会出现最明显的减少。通过比较选择性快速眼动(REM)睡眠和完全剥夺睡眠的影响,我们还提供了实验证据,证明慢波睡眠(SWS)是下丘脑和新皮质中 AMPARs 下调的驱动力,而 REM 睡眠或昼夜节律没有额外的贡献。依赖于SWS的突触下调与脑电图慢波活动无关。然而,SWS 期间的纺锤体密度预示着下丘脑突触中 GluA1 亚基水平的相对增加,这与纺锤体在巩固记忆中的作用是一致的。我们的研究结果表明,SWS 是睡眠期间突触强度重新正常化的主要驱动因素,并表明依赖于 SWS 的突触重新正常化也与下丘脑的稳态控制过程有关。
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引用次数: 0
Adenosine diphosphate released from stressed cells triggers mitochondrial transfer to achieve tissue homeostasis. 受压细胞释放的二磷酸腺苷会触发线粒体转移,以实现组织平衡。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-20 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002753
Hao Li, Hongping Yu, Delin Liu, Peng Liao, Chuan Gao, Jian Zhou, Jialun Mei, Yao Zong, Peng Ding, Meng Yao, Bingqi Wang, Yafei Lu, Yigang Huang, Youshui Gao, Changqing Zhang, Minghao Zheng, Junjie Gao

Cell-to-cell mitochondrial transfer has recently been shown to play a role in maintaining physiological functions of cell. We previously illustrated that mitochondrial transfer within osteocyte dendritic network regulates bone tissue homeostasis. However, the mechanism of triggering this process has not been explored. Here, we showed that stressed osteocytes in mice release adenosine diphosphate (ADP), resulting in triggering mitochondrial transfer from healthy osteocytes to restore the oxygen consumption rate (OCR) and to alleviate reactive oxygen species accumulation. Furthermore, we identified that P2Y2 and P2Y6 transduced the ADP signal to regulate osteocyte mitochondrial transfer. We showed that mitochondrial metabolism is impaired in aged osteocytes, and there were more extracellular nucleotides release into the matrix in aged cortical bone due to compromised membrane integrity. Conditioned medium from aged osteocytes triggered mitochondrial transfer between osteocytes to enhance the energy metabolism. Together, using osteocyte as an example, this study showed new insights into how extracellular ADP triggers healthy cells to rescue energy metabolism crisis in stressed cells via mitochondrial transfer in tissue homeostasis.

细胞间线粒体转移最近被证明在维持细胞生理功能方面发挥作用。我们以前曾指出,线粒体在骨细胞树突网络内的转移调节着骨组织的平衡。然而,引发这一过程的机制尚未探明。在这里,我们发现小鼠受压骨细胞会释放二磷酸腺苷(ADP),从而引发健康骨细胞的线粒体转移,以恢复耗氧率(OCR)并缓解活性氧积累。此外,我们还发现 P2Y2 和 P2Y6 可转导 ADP 信号以调节骨细胞线粒体转移。我们发现老化骨细胞的线粒体代谢受损,由于膜完整性受损,老化皮质骨中有更多的胞外核苷酸释放到基质中。来自老化骨细胞的条件培养基可触发骨细胞间的线粒体转移,从而增强能量代谢。总之,这项研究以骨细胞为例,揭示了细胞外ADP如何通过线粒体转移在组织稳态中触发健康细胞挽救受压细胞的能量代谢危机。
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引用次数: 0
Distinct melanocyte subpopulations defined by stochastic expression of proliferation or maturation programs enable a rapid and sustainable pigmentation response. 通过随机表达增殖或成熟程序来定义不同的黑色素细胞亚群,可实现快速、可持续的色素沉着反应。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-20 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002776
Ayush Aggarwal, Ayesha Nasreen, Babita Sharma, Sarthak Sahoo, Keerthic Aswin, Mohammed Faruq, Rajesh Pandey, Mohit K Jolly, Abhyudai Singh, Rajesh S Gokhale, Vivek T Natarajan

The ultraviolet (UV) radiation triggers a pigmentation response in human skin, wherein, melanocytes rapidly activate divergent maturation and proliferation programs. Using single-cell sequencing, we demonstrate that these 2 programs are segregated in distinct subpopulations in melanocytes of human and zebrafish skin. The coexistence of these 2 cell states in cultured melanocytes suggests possible cell autonomy. Luria-Delbrück fluctuation test reveals that the initial establishment of these states is stochastic. Tracking of pigmenting cells ascertains that the stochastically acquired state is faithfully propagated in the progeny. A systemic approach combining single-cell multi-omics (RNA+ATAC) coupled to enhancer mapping with H3K27 acetylation successfully identified state-specific transcriptional networks. This comprehensive analysis led to the construction of a gene regulatory network (GRN) that under the influence of noise, establishes a bistable system of pigmentation and proliferation at the population level. This GRN recapitulates melanocyte behaviour in response to external cues that reinforce either of the states. Our work highlights that inherent stochasticity within melanocytes establishes dedicated states, and the mature state is sustained by selective enhancers mark through histone acetylation. While the initial cue triggers a proliferation response, the continued signal activates and maintains the pigmenting subpopulation via epigenetic imprinting. Thereby our study provides the basis of coexistence of distinct populations which ensures effective pigmentation response while preserving the self-renewal capacity.

紫外线(UV)辐射会引发人类皮肤的色素沉着反应,其中黑色素细胞会迅速激活不同的成熟和增殖程序。通过单细胞测序,我们证明这两种程序在人类和斑马鱼皮肤的黑色素细胞中以不同的亚群分离。这两种细胞状态在培养的黑色素细胞中共存,表明细胞可能具有自主性。Luria-Delbrück波动测试表明,这些状态的初始建立是随机的。对色素沉着细胞的追踪证实,随机获得的状态会在后代中忠实地传播。将单细胞多组学(RNA+ATAC)与增强子图谱和 H3K27 乙酰化相结合的系统方法成功地确定了特定状态的转录网络。通过这种综合分析,我们构建了一个基因调控网络(GRN),在噪声的影响下,该网络在群体水平上建立了一个色素沉着和增殖的双稳态系统。这个基因调控网络再现了黑色素细胞在外界刺激下的行为,这些刺激会强化其中任何一种状态。我们的研究突出表明,黑色素细胞内固有的随机性建立了专用状态,而成熟状态则通过组蛋白乙酰化标记的选择性增强子来维持。最初的提示触发了增殖反应,而持续的信号则通过表观遗传印记激活并维持色素沉着亚群。因此,我们的研究为不同种群的共存提供了基础,从而确保了有效的色素沉着反应,同时保留了自我更新能力。
{"title":"Distinct melanocyte subpopulations defined by stochastic expression of proliferation or maturation programs enable a rapid and sustainable pigmentation response.","authors":"Ayush Aggarwal, Ayesha Nasreen, Babita Sharma, Sarthak Sahoo, Keerthic Aswin, Mohammed Faruq, Rajesh Pandey, Mohit K Jolly, Abhyudai Singh, Rajesh S Gokhale, Vivek T Natarajan","doi":"10.1371/journal.pbio.3002776","DOIUrl":"10.1371/journal.pbio.3002776","url":null,"abstract":"<p><p>The ultraviolet (UV) radiation triggers a pigmentation response in human skin, wherein, melanocytes rapidly activate divergent maturation and proliferation programs. Using single-cell sequencing, we demonstrate that these 2 programs are segregated in distinct subpopulations in melanocytes of human and zebrafish skin. The coexistence of these 2 cell states in cultured melanocytes suggests possible cell autonomy. Luria-Delbrück fluctuation test reveals that the initial establishment of these states is stochastic. Tracking of pigmenting cells ascertains that the stochastically acquired state is faithfully propagated in the progeny. A systemic approach combining single-cell multi-omics (RNA+ATAC) coupled to enhancer mapping with H3K27 acetylation successfully identified state-specific transcriptional networks. This comprehensive analysis led to the construction of a gene regulatory network (GRN) that under the influence of noise, establishes a bistable system of pigmentation and proliferation at the population level. This GRN recapitulates melanocyte behaviour in response to external cues that reinforce either of the states. Our work highlights that inherent stochasticity within melanocytes establishes dedicated states, and the mature state is sustained by selective enhancers mark through histone acetylation. While the initial cue triggers a proliferation response, the continued signal activates and maintains the pigmenting subpopulation via epigenetic imprinting. Thereby our study provides the basis of coexistence of distinct populations which ensures effective pigmentation response while preserving the self-renewal capacity.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009776","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}
引用次数: 0
AlphaFold2-guided engineering of split-GFP technology enables labeling of endogenous tubulins across species while preserving function. AlphaFold2- 指导的工程化分裂-GFP 技术可在保留功能的同时标记不同物种的内源性微管蛋白。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-08-19 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002615
Kaiming Xu, Zhiyuan Li, Linfan Mao, Zhengyang Guo, Zhe Chen, Yongping Chai, Chao Xie, Xuerui Yang, Jie Na, Wei Li, Guangshuo Ou

Dynamic properties are essential for microtubule (MT) physiology. Current techniques for in vivo imaging of MTs present intrinsic limitations in elucidating the isotype-specific nuances of tubulins, which contribute to their versatile functions. Harnessing the power of the AlphaFold2 pipeline, we engineered a strategy for the minimally invasive fluorescence labeling of endogenous tubulin isotypes or those harboring missense mutations. We demonstrated that a specifically designed 16-amino acid linker, coupled with sfGFP11 from the split-sfGFP system and integration into the H1-S2 loop of tubulin, facilitated tubulin labeling without compromising MT dynamics, embryonic development, or ciliogenesis in Caenorhabditis elegans. Extending this technique to human cells and murine oocytes, we visualized MTs with the minimal background fluorescence and a pathogenic tubulin isoform with fidelity. The utility of our approach across biological contexts and species set an additional paradigm for studying tubulin dynamics and functional specificity, with implications for understanding tubulin-related diseases known as tubulinopathies.

动态特性对微管(MT)生理学至关重要。目前的 MT 体内成像技术在阐明微管蛋白同种型特异性的细微差别方面存在固有的局限性,而这些细微差别促成了微管蛋白的多种功能。利用 AlphaFold2 管道的强大功能,我们设计了一种对内源性管蛋白异型或携带错义突变的管蛋白异型进行微创荧光标记的策略。我们证明,专门设计的 16 氨基酸连接体与来自 split-sfGFP 系统的 sfGFP11 相结合,并整合到微管蛋白的 H1-S2 环中,可促进微管蛋白标记,而不会影响 MT 的动态、胚胎发育或 elegans 中纤毛的生成。将这一技术推广到人类细胞和小鼠卵母细胞后,我们用最小的背景荧光和致病性微管蛋白异构体对MT进行了可靠的可视化。我们的方法在不同生物环境和物种中的应用为研究微管蛋白动态和功能特异性提供了新的范例,对了解微管蛋白相关疾病(即微管蛋白病)具有重要意义。
{"title":"AlphaFold2-guided engineering of split-GFP technology enables labeling of endogenous tubulins across species while preserving function.","authors":"Kaiming Xu, Zhiyuan Li, Linfan Mao, Zhengyang Guo, Zhe Chen, Yongping Chai, Chao Xie, Xuerui Yang, Jie Na, Wei Li, Guangshuo Ou","doi":"10.1371/journal.pbio.3002615","DOIUrl":"10.1371/journal.pbio.3002615","url":null,"abstract":"<p><p>Dynamic properties are essential for microtubule (MT) physiology. Current techniques for in vivo imaging of MTs present intrinsic limitations in elucidating the isotype-specific nuances of tubulins, which contribute to their versatile functions. Harnessing the power of the AlphaFold2 pipeline, we engineered a strategy for the minimally invasive fluorescence labeling of endogenous tubulin isotypes or those harboring missense mutations. We demonstrated that a specifically designed 16-amino acid linker, coupled with sfGFP11 from the split-sfGFP system and integration into the H1-S2 loop of tubulin, facilitated tubulin labeling without compromising MT dynamics, embryonic development, or ciliogenesis in Caenorhabditis elegans. Extending this technique to human cells and murine oocytes, we visualized MTs with the minimal background fluorescence and a pathogenic tubulin isoform with fidelity. The utility of our approach across biological contexts and species set an additional paradigm for studying tubulin dynamics and functional specificity, with implications for understanding tubulin-related diseases known as tubulinopathies.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11361732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005613","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}
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PLoS Biology
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