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A metagenomic approach to unveil the association between fecal gut microbiota and short-chain fatty acids in diarrhea caused by diarrheagenic Escherichia coli in children. 用元基因组学方法揭示儿童腹泻性大肠埃希氏菌引起的腹泻中粪便肠道微生物群与短链脂肪酸之间的关系。
IF 4.1 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-04-30 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.04.820
Pablo Gallardo, Mariana Izquierdo, Tomeu Viver, Esteban Bustos-Caparros, Dana Piras, Roberto M Vidal, Hermie M J Harmsen, Mauricio J Farfan

Diarrheagenic Escherichia coli (DEC) is the main cause of diarrhea in children under five years old. The virulence of DEC is tightly regulated by environmental signals influenced by the gut microbiota and its metabolites. Short-chain fatty acids (SCFAs) are the main metabolic product of anaerobic fermentation in the gut, but their role in DEC diarrhea has not yet been established. In this study, we determine the levels of acetate, propionate, and butyrate in stool samples from children with diarrhea caused by DEC, and we identify bacteria from the fecal gut microbiota associated with the production of SCFAs. The microbiota and SCFAs levels in stool samples obtained from 40 children with diarrhea and 43 healthy children were determined by 16S rRNA gene sequencing and HPLC, respectively. Additionally, shotgun metagenomics was used to identify metagenome-assembled genomes (MAGs) in a subgroup of samples. The results showed significantly higher levels of all SCFAs tested in diarrheal samples than in healthy controls. The abundance of Streptococcus sp., Limosilactobacillus, Blautia, Escherichia, Bacteroides, Megamonas, and Roseburia was higher in the DEC group than in healthy individuals. Functional analysis of bacteria and their main metabolic pathways made it possible to identify species MAGs that could be responsible for the detected SCFAs levels in DEC-positive diarrhea. In conclusion, based on our results and published data, we suggest that SCFAs may be important in the crosstalk between the microbiota and DEC pathogens in the gut.

致腹泻大肠杆菌(DEC)是导致五岁以下儿童腹泻的主要原因。DEC 的致病力受到肠道微生物群及其代谢产物影响的环境信号的严格调控。短链脂肪酸(SCFA)是肠道厌氧发酵的主要代谢产物,但其在 DEC 腹泻中的作用尚未确定。在本研究中,我们测定了由 DEC 引起的腹泻患儿粪便样本中乙酸盐、丙酸盐和丁酸盐的含量,并从粪便肠道微生物群中找出了与 SCFAs 的产生有关的细菌。通过 16S rRNA 基因测序和高效液相色谱法,分别测定了 40 名腹泻患儿和 43 名健康儿童粪便样本中的微生物群和 SCFAs 含量。此外,研究人员还利用霰弹枪元基因组学鉴定了一部分样本中的元基因组组装基因组(MAGs)。结果显示,腹泻样本中所有受测 SCFAs 的含量均明显高于健康对照组。在 DEC 组中,链球菌、Limosilactobacillus、Blautia、Escherichia、Bacteroides、Megamonas 和 Roseburia 的含量高于健康人。通过对细菌及其主要代谢途径进行功能分析,可以确定在 DEC 阳性腹泻中检测到的 SCFAs 水平可能是由 MAGs 物种引起的。总之,根据我们的研究结果和已发表的数据,我们认为 SCFAs 可能在肠道微生物群和 DEC 病原体之间的相互影响中起着重要作用。
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引用次数: 0
The effect of multiple sclerosis therapy on gut microbiota dysbiosis: a longitudinal prospective study. 多发性硬化症治疗对肠道微生物群失调的影响:一项纵向前瞻性研究。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-04-04 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.03.819
Andreea-Cristina Paraschiv, Vitalie Vacaras, Cristina Nistor, Cristiana Vacaras, Stefan Strilciuc, Dafin F Muresanu

Gut microbiota has complex immune functions, related to different pathologies, including multiple sclerosis (MS).This study evaluated the influence of treatments on gut microbiota in people with MS (PwMS). The research comprised 60 participants, including 39 PwMS and 21 healthy controls (HC). Among the PwMS, 20 were prescribed a disease-modifying therapy (DMT), either interferon beta1a or teriflunomide, while 19 received a combination of classical DMT and an immunoglobulin Y (IgY) supplement. For each participant, two sets of gut samples were collected: one at the study's outset and another after two months. Alpha and beta diversity analyses revealed no significant differences between groups. In comparison to the HC, the MS group exhibited an increase in Prevotella stercorea and a decrease in Faecalibacterium prausnitzii. Following treatment, individuals with MS showed enrichment in Lachnospiraceae and Streptococcus. The second sample, compared to the first one, demonstrated an increase in Bifidobacterium angulatum and a decrease in Oscillospira for individuals with MS. Gut microbiota diversity in PwMS is not significantly different to HC.However, specific taxonomic changes indicate the presence of a dysbiosis state. The use of DMTs and immunoglobulin Y supplements may contribute to alterations in microbial composition, potentially leading to the restoration of a healthier microbiome.

肠道微生物群具有复杂的免疫功能,与包括多发性硬化症(MS)在内的不同病症有关。本研究评估了治疗对多发性硬化症患者(PwMS)肠道微生物群的影响。这项研究共有 60 名参与者,包括 39 名多发性硬化症患者和 21 名健康对照组(HC)。在多发性硬化症患者中,有20人接受了疾病改变疗法(DMT),即干扰素β1a或特立氟胺,19人接受了传统DMT和免疫球蛋白Y(IgY)补充剂的组合治疗。研究人员为每位参与者采集了两组肠道样本:一组在研究开始时采集,另一组在两个月后采集。阿尔法和贝塔多样性分析表明,组间无明显差异。与 HC 相比,MS 组的 Stercorea Prevotella 增加,Faecalibacterium prausnitzii 减少。治疗后,多发性硬化症患者的粪链球菌和链球菌富集。与第一份样本相比,第二份样本显示,多发性硬化症患者的双歧杆菌(Bifidobacterium angulatum)增加,而摇蚊杆菌(Oscillospira)减少。多发性硬化症患者的肠道微生物群多样性与多发性硬化症患者并无明显差异。然而,特定分类学变化表明存在菌群失调状态。使用DMTs和免疫球蛋白Y补充剂可能会导致微生物组成的改变,从而有可能恢复更健康的微生物群。
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引用次数: 0
The cAMP-PKA signalling crosstalks with CWI and HOG-MAPK pathways in yeast cell response to osmotic and thermal stress. 在酵母细胞对渗透压和热应力的反应中,cAMP-PKA 信号与 CWI 和 HOG-MAPK 通路相互交叉。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-03-15 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.03.818
Fiorella Galello, Mariana Bermúdez-Moretti, María Clara Ortolá Martínez, Silvia Rossi, Paula Portela

The yeast Saccharomyces cerevisiae is widely used in food and non-food industries. During industrial fermentation yeast strains are exposed to fluctuations in oxygen concentration, osmotic pressure, pH, ethanol concentration, nutrient availability and temperature. Fermentation performance depends on the ability of the yeast strains to adapt to these changes. Suboptimal conditions trigger responses to the external stimuli to allow homeostasis to be maintained. Stress-specific signalling pathways are activated to coordinate changes in transcription, translation, protein function, and metabolic fluxes while a transient arrest of growth and cell cycle progression occur. cAMP-PKA, HOG-MAPK and CWI signalling pathways are turned on during stress response. Comprehension of the mechanisms involved in the responses and in the adaptation to these stresses during fermentation is key to improving this industrial process. The scope of this review is to outline the advancement of knowledge about the cAMP-PKA signalling and the crosstalk of this pathway with the CWI and HOG-MAPK cascades in response to the environmental challenges heat and hyperosmotic stress.

酵母菌广泛应用于食品和非食品行业。在工业发酵过程中,酵母菌株会受到氧气浓度、渗透压、pH 值、乙醇浓度、养分供应和温度波动的影响。发酵性能取决于酵母菌株适应这些变化的能力。次优条件会触发对外部刺激的反应,以维持平衡。在应激反应过程中,cAMP-PKA、HOG-MAPK 和 CWI 信号通路被开启。了解发酵过程中这些应激反应和适应所涉及的机制是改进这一工业过程的关键。本综述的范围是概述有关 cAMP-PKA 信号通路以及该通路与 CWI 和 HOG-MAPK 级联在应对环境挑战热和高渗透压时的相互作用的知识进展。
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引用次数: 0
Comparison of microbial communities and the profile of sulfate-reducing bacteria in patients with ulcerative colitis and their association with bowel diseases: a pilot study. 溃疡性结肠炎患者体内微生物群落和硫酸盐还原菌概况的比较及其与肠道疾病的关联:一项试点研究。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-03-14 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.03.817
Ivan Kushkevych, Kristýna Martínková, Lenka Mráková, Francesco Giudici, Simone Baldi, David Novak, Márió Gajdács, Monika Vítězová, Dani Dordevic, Amedeo Amedei, Simon K-M R Rittmann

Considerable evidence has accumulated regarding the molecular relationship between gut microbiota (GM) composition and the onset (clinical presentation and prognosis of ulcerative colitis (UC)). In addition, it is well documented that short-chain fatty acid (SCFA)-producing bacteria may play a fundamental role in maintaining an anti-inflammatory intestinal homeostasis, but sulfate- and sulfite reducing bacteria may be responsible for the production of toxic metabolites, such as hydrogen sulfide and acetate. Hence, the present study aimed to assess the GM composition - focusing on sulfate-reducing bacteria (SRB) - in patients with severe, severe-active and moderate UC. Each one of the six enrolled patients provided two stool samples in the following way: one sample was cultivated in a modified SRB-medium before 16S rRNA sequencing and the other was not cultivated. Comparative phylogenetic analysis was conducted on each sample. Percentage of detected gut microbial genera showed considerable variation based on the patients' disease severity and cultivation in the SRB medium. In detail, samples without cultivation from patients with moderate UC showed a high abundance of the genera Bacteroides, Bifidobacterium and Ruminococcus, but after SRB cultivation, the dominant genera were Bacteroides, Klebsiella and Bilophila. On the other hand, before SRB cultivation, the main represented genera in patients with severe UC were Escherichia-Shigella, Proteus, Methanothermobacter and Methanobacterium. However, after incubation in the SRB medium Bacteroides, Proteus, Alistipes and Lachnoclostridium were predominant. Information regarding GM compositional changes in UC patients may aid the development of novel therapeutic strategies (e.g., probiotic preparations containing specific bacterial strains) to counteract the mechanisms of virulence of harmful bacteria and the subsequent inflammatory response that is closely related to the pathogenesis of inflammatory bowel diseases.

关于肠道微生物群(GM)组成与溃疡性结肠炎(UC)发病(临床表现和预后)之间的分子关系,已经积累了大量证据。此外,有大量文献表明,产生短链脂肪酸(SCFA)的细菌可能在维持抗炎性肠道平衡中发挥着重要作用,但硫酸盐和亚硫酸盐还原菌可能是产生硫化氢和乙酸盐等有毒代谢物的罪魁祸首。因此,本研究旨在评估重度、重度活动性和中度 UC 患者的转基因组成,重点是硫酸盐还原菌(SRB)。六名入组患者每人提供了两份粪便样本,具体做法如下:一份样本在 16S rRNA 测序前在改良的 SRB 培养基中培养,另一份样本不培养。每个样本都进行了系统发生比较分析。检测到的肠道微生物属的百分比因患者的疾病严重程度和在 SRB 培养基中的培养情况而有很大差异。具体而言,中度 UC 患者未经培养的样本显示出大量的乳杆菌属、双歧杆菌属和反刍球菌属,但经 SRB 培养后,主要的菌属为乳杆菌属、克雷伯氏菌属和双嗜血杆菌属。另一方面,在 SRB 培养前,重症 UC 患者的主要菌属是志贺氏菌、变形杆菌、甲烷杆菌和甲烷杆菌。然而,在 SRB 培养基中培养后,主要是乳酸杆菌、变形杆菌、嗜水杆菌和漆膜杆菌。有关 UC 患者转基因成分变化的信息可能有助于开发新的治疗策略(如含有特定菌株的益生菌制剂),以对抗有害细菌的毒力机制和随后的炎症反应,而炎症反应与炎症性肠病的发病机制密切相关。
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引用次数: 0
Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination. 酵母的复制衰老涉及与 mRNA 处理/输出和蛋白质泛素化相关的动态内含子保留模式。
IF 4.1 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-02-23 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.02.816
Jesús Gómez-Montalvo, Alvaro de Obeso Fernández Del Valle, Luis Fernando De la Cruz Gutiérrez, Jose Mario Gonzalez-Meljem, Christian Quintus Scheckhuber

Saccharomyces cerevisiae (baker's yeast) has yielded relevant insights into some of the basic mechanisms of organismal aging. Among these are genomic instability, oxidative stress, caloric restriction and mitochondrial dysfunction. Several genes are known to have an impact on the aging process, with corresponding mutants exhibiting short- or long-lived phenotypes. Research dedicated to unraveling the underlying cellular mechanisms can support the identification of conserved mechanisms of aging in other species. One of the hitherto less studied fields in yeast aging is how the organism regulates its gene expression at the transcriptional level. To our knowledge, we present the first investigation into alternative splicing, particularly intron retention, during replicative aging of S. cerevisiae. This was achieved by utilizing the IRFinder algorithm on a previously published RNA-seq data set by Janssens et al. (2015). In the present work, 44 differentially retained introns in 43 genes were identified during replicative aging. We found that genes with altered intron retention do not display significant changes in overall transcript levels. It was possible to functionally assign distinct groups of these genes to the cellular processes of mRNA processing and export (e.g., YRA1) in early and middle-aged yeast, and protein ubiquitination (e.g., UBC5) in older cells. In summary, our work uncovers a previously unexplored layer of the transcriptional program of yeast aging and, more generally, expands the knowledge on the occurrence of alternative splicing in baker's yeast.

面包酵母(Saccharomyces cerevisiae)对机体衰老的一些基本机制产生了相关的认识。其中包括基因组不稳定性、氧化应激、热量限制和线粒体功能障碍。已知有几个基因对衰老过程有影响,相应的突变体表现出寿命短或寿命长的表型。致力于揭示潜在细胞机制的研究可以帮助确定其他物种的衰老保守机制。迄今为止,酵母衰老研究较少的领域之一是生物体如何在转录水平调节其基因表达。据我们所知,我们首次研究了酵母菌复制衰老过程中的替代剪接,尤其是内含子的保留。这是通过在 Janssens 等人(2015 年)之前发表的 RNA-seq 数据集上使用 IRFinder 算法实现的。在本研究中,我们在 43 个基因中发现了 44 个在复制衰老过程中不同程度保留的内含子。我们发现,内含子保留发生变化的基因在总体转录水平上并没有显示出显著的变化。我们可以从功能上将这些基因的不同组分配给早期和中期酵母的 mRNA 处理和输出(如 YRA1)以及老年细胞的蛋白质泛素化(如 UBC5)等细胞过程。总之,我们的研究揭示了酵母衰老转录程序中一个以前未曾探索过的层次,并从更广泛的意义上扩展了人们对面包酵母中发生的替代剪接的认识。
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引用次数: 0
Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics. 用高效薄层色谱法 (HPTLC) 定量酵母脂质组学并与基于质谱的枪式脂质组学进行比较。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-02-21 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.02.815
Thorsten Meyer, Oskar Knittelfelder, Martin Smolnig, Patrick Rockenfeller

Lipidomic analysis in diverse biological settings has become a frequent tool to increase our understanding of the processes of life. Cellular lipids play important roles not only as being the main components of cellular membranes, but also in the regulation of cell homeostasis as lipid signaling molecules. Yeast has been harnessed for biomedical research based on its good conservation of genetics and fundamental cell organisation principles and molecular pathways. Further application in so-called humanised yeast models have been developed which take advantage of yeast as providing the basics of a living cell with full control over heterologous expression. Here we present evidence that high-performance thin-layer chromatography (HPTLC) represents an effective alternative to replace cost intensive mass spectrometry-based lipidomic analyses. We provide statistical comparison of identical samples by both methods, which support the use of HPTLC for quantitative analysis of the main yeast lipid classes.

在各种生物环境中进行脂质组学分析已成为一种常用工具,可加深我们对生命过程的了解。细胞脂质不仅是细胞膜的主要成分,而且作为脂质信号分子在调节细胞稳态方面发挥着重要作用。酵母具有良好的遗传学和基本细胞组织原理和分子途径,因此已被用于生物医学研究。利用酵母提供的活细胞基础知识和对异源表达的完全控制,人们开发了所谓的人源化酵母模型,并将其进一步应用于生物医学研究。在此,我们提出证据表明,高效薄层色谱法(HPTLC)是取代基于质谱的脂质体分析的有效替代方法。我们用两种方法对相同样品进行了统计比较,结果支持使用 HPTLC 对主要的酵母脂质类别进行定量分析。
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引用次数: 0
A cobalt concentration sensitive Btu-like system facilitates cobalamin uptake in Anabaena sp. PCC 7120. 钴浓度敏感的 Btu-like 系统促进了 Anabaena sp.
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-02-20 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.02.814
Julia Graf, Leonard Fresenborg, Hans-Michael Seitz, Rafael Pernil, Enrico Schleiff

Metal homeostasis is central to all forms of life, as metals are essential micronutrients with toxic effects at elevated levels. Macromolecular machines facilitate metal uptake into the cells and their intracellular level is regulated by multiple means, which can involve RNA elements and proteinaceous components. While the general principles and components for uptake and cellular content regulation of, e.g., cobalt have been identified for proteobacteria, the corresponding mechanism in other Gram-negative bacteria such as cyanobacteria remain to be established. Based on their photosynthetic activity, cyanobacteria are known to exhibit a special metal demand in comparison to other bacteria. Here, the regulation by cobalt and cobalamin as well as their uptake is described for Anabaena sp. PCC 7120, a model filamentous heterocyst-forming cyanobacterium. Anabaena contains at least three cobalamin riboswitches in its genome, for one of which the functionality is confirmed here. Moreover, two outer membrane-localized cobalamin TonB-dependent transporters, namely BtuB1 and BtuB2, were identified. BtuB2 is important for fast uptake of cobalamin under conditions with low external cobalt, whereas BtuB1 appears to function in cobalamin uptake under conditions of sufficient cobalt supply. While the general function is comparable, the specific function of the two genes differs and mutants thereof show distinct phenotypes. The uptake of cobalamin depends further on the TonB and a BtuFCD machinery, as mutants of tonB3 and btuD show reduced cobalamin uptake rates. Thus, our results provide novel information on the uptake of cobalamin and the regulation of the cellular cobalt content in cyanobacteria.

金属平衡是所有生命形式的核心,因为金属是人体必需的微量营养素,含量过高会产生毒性作用。大分子机器有助于金属被吸收到细胞中,而细胞内的金属含量则通过多种方式进行调节,其中可能涉及核糖核酸(RNA)元素和蛋白质成分。虽然蛋白细菌吸收钴等金属并调节其细胞含量的一般原理和成分已经确定,但蓝藻等其他革兰氏阴性细菌的相应机制仍有待确定。与其他细菌相比,蓝藻因其光合作用活性而对金属有特殊需求。在此,我们将介绍钴和钴胺素对蓝藻的调节作用以及蓝藻对钴和钴胺素的吸收。Anabaena 的基因组中至少含有三个钴胺素核糖开关,其中一个的功能在本文中得到了证实。此外,还发现了两个外膜定位的钴胺素 TonB 依赖性转运体,即 BtuB1 和 BtuB2。BtuB2 在外部钴含量低的条件下对钴胺素的快速吸收非常重要,而 BtuB1 似乎在钴供应充足的条件下对钴胺素的吸收起作用。虽然总体功能相似,但这两个基因的具体功能不同,其突变体表现出不同的表型。钴胺素的摄取进一步依赖于 TonB 和 BtuFCD 机制,因为 tonB3 和 btuD 的突变体显示出较低的钴胺素摄取率。因此,我们的研究结果为蓝藻中钴胺素的吸收和细胞钴含量的调节提供了新的信息。
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引用次数: 0
Predictable regulation of survival by intratumoral microbe-immune crosstalk in patients with lung adenocarcinoma. 肺腺癌患者瘤内微生物-免疫串扰对生存的可预测性调节
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-02-19 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.02.813
Shuo Shi, Yuwen Chu, Haiyan Liu, Lan Yu, Dejun Sun, Jialiang Yang, Geng Tian, Lei Ji, Cong Zhang, Xinxin Lu

Intratumoral microbiota can regulate the tumor immune microenvironment (TIME) and mediate tumor prognosis by promoting inflammatory response or inhibiting anti-tumor effects. Recent studies have elucidated the potential role of local tumor microbiota in the development and progression of lung adenocarcinoma (LUAD). However, whether intratumoral microbes are involved in the TIME that mediates the prognosis of LUAD remains unknown. Here, we obtained the matched tumor microbiome and host transcriptome and survival data of 478 patients with LUAD in The Cancer Genome Atlas (TCGA). Machine learning models based on immune cell marker genes can predict 1- to 5-year survival with relative accuracy. Patients were stratified into high- and low-survival-risk groups based on immune cell marker genes, with significant differences in intratumoral microbial communities. Specifically, patients in the high-risk group had significantly higher alpha diversity (p < 0.05) and were characterized by an enrichment of lung cancer-related genera such as Streptococcus. However, network analysis highlighted a more active pattern of dominant bacteria and immune cell crosstalk in TIME in the low-risk group compared to the high-risk group. Our study demonstrated that intratumoral microbiota-immune crosstalk was strongly associated with prognosis in LUAD patients, which would provide new targets for the development of precise therapeutic strategies.

瘤内微生物群可调节肿瘤免疫微环境(TIME),并通过促进炎症反应或抑制抗肿瘤作用来介导肿瘤预后。最近的研究阐明了局部肿瘤微生物群在肺腺癌(LUAD)发生和发展中的潜在作用。然而,瘤内微生物是否参与了介导 LUAD 预后的 TIME 仍是未知数。在此,我们从癌症基因组图谱(TCGA)中获得了478名LUAD患者的匹配肿瘤微生物组和宿主转录组及生存数据。基于免疫细胞标记基因的机器学习模型可以相对准确地预测1至5年的生存率。根据免疫细胞标记基因将患者分为高生存风险组和低生存风险组,肿瘤内微生物群落存在显著差异。具体来说,高风险组患者的α多样性明显更高(p < 0.05),其特点是富含链球菌等肺癌相关菌属。然而,网络分析显示,与高风险组相比,低风险组 TIME 中的优势菌和免疫细胞串扰模式更为活跃。我们的研究表明,瘤内微生物与免疫细胞间的串扰与肺癌患者的预后密切相关,这将为制定精确的治疗策略提供新的靶点。
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引用次数: 0
Two TonB-dependent outer membrane transporters involved in heme uptake in Anabaena sp. PCC 7120. Anabaena sp. PCC 7120 中参与血红素吸收的两个依赖于 TonB 的外膜转运体。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-09 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.01.812
Julia Graf, Martin Schöpperle, Rafael Pernil, Enrico Schleiff

Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium Anabaena sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by alr2153 (hutA1) and alr3242 (hutA2) are assigned as outer membrane heme transporters. Indeed, Anabaena sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll a synthesis and in an increase of the chlorophyll a content. Moreover, iron starvation induced the expression of hutA1, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in hutA2 induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that Anabaena sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.

由于铁等微量营养元素的供应量较低,所有生物界都在不断进化吸收系统。在革兰氏阴性细菌中,外膜、质粒周围和质粒膜定位蛋白促进了铁螯合剂的吸收,TonB 蛋白则为其提供能量。不同摄取系统的特异性可能取决于内源产生的铁螯合剂或环境中铁螯合剂复合物的生物利用率。因此,模式蓝藻 Anabaena sp. PCC 7120 产生的裂殖素的摄取系统是存在的,而生物信息学分析表明还存在其他系统,可能用于摄取异苷酸。同样,alr2153(hutA1)和 alr3242(hutA2)编码的蛋白质被认为是外膜血红素转运体。事实上,Anabaena sp.添加血红素会诱导参与血红素降解和叶绿素 a 合成的基因,并增加叶绿素 a 的含量。此外,铁饥饿会诱导 hutA1 的表达,而添加血红素则会抑制其表达。值得注意的是,添加高浓度血红素而不是铁饥饿会诱导 hutA2 的表达。这两个基因的质粒插入突变体通过添加血红素从铁饥饿中恢复的能力都有所下降,这表明血红素吸收依赖于功能性 HutA1 和 HutA2 蛋白。通过生物信息学方法生成的结构模型进一步证实了其在血红素吸收中的作用。因此,我们提供的证据表明,Anabaena sp.
{"title":"Two TonB-dependent outer membrane transporters involved in heme uptake in <i>Anabaena</i> sp. PCC 7120.","authors":"Julia Graf, Martin Schöpperle, Rafael Pernil, Enrico Schleiff","doi":"10.15698/mic2024.01.812","DOIUrl":"10.15698/mic2024.01.812","url":null,"abstract":"<p><p>Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium <i>Anabaena</i> sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by <i>alr2153</i> (<i>hutA1</i>) and <i>alr3242</i> (<i>hutA2</i>) are assigned as outer membrane heme transporters. Indeed, <i>Anabaena</i> sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll <i>a</i> synthesis and in an increase of the chlorophyll <i>a</i> content. Moreover, iron starvation induced the expression of <i>hutA1</i>, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in <i>hutA2</i> induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that <i>Anabaena</i> sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"11 ","pages":"16-28"},"PeriodicalIF":4.6,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10792254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139485630","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}
引用次数: 0
The last two transmembrane helices in the APC-type FurE transporter act as an intramolecular chaperone essential for concentrative ER-exit. APC型FurE转运体的最后两个跨膜螺旋起到了分子内伴侣的作用,这对浓缩的ER排出至关重要。
IF 4.6 3区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-05 eCollection Date: 2024-01-01 DOI: 10.15698/mic2024.01.811
Yiannis Pyrris, Georgia F Papadaki, Emmanuel Mikros, George Diallinas

FurE is a H+ symporter specific for the cellular uptake of uric acid, allantoin, uracil, and toxic nucleobase analogues in the fungus Aspergillus nidulans. Being member of the NCS1 protein family, FurE is structurally related to the APC-superfamily of transporters. APC-type transporters are characterised by a 5+5 inverted repeat fold made of ten transmembrane segments (TMS1-10) and function through the rocking-bundle mechanism. Most APC-type transporters possess two extra C-terminal TMS segments (TMS11-12), the function of which remains elusive. Here we present a systematic mutational analysis of TMS11-12 of FurE and show that two specific aromatic residues in TMS12, Trp473 and Tyr484, are essential for ER-exit and trafficking to the plasma membrane (PM). Molecular modeling shows that Trp473 and Tyr484 might be essential through dynamic interactions with residues in TMS2 (Leu91), TMS3 (Phe111), TMS10 (Val404, Asp406) and other aromatic residues in TMS12. Genetic analysis confirms the essential role of Phe111, Asp406 and TMS12 aromatic residues in FurE ER-exit. We further show that co-expression of FurE-Y484F or FurE-W473A with wild-type FurE leads to a dominant negative phenotype, compatible with the concept that FurE molecules oligomerize or partition in specific microdomains to achieve concentrative ER-exit and traffic to the PM. Importantly, truncated FurE versions lacking TMS11-12 are unable to reproduce a negative effect on the trafficking of co-expressed wild-type FurE. Overall, we show that TMS11-12 acts as an intramolecular chaperone for proper FurE folding, which seems to provide a structural code for FurE partitioning in ER-exit sites.

FurE 是真菌黑曲霉(Aspergillus nidulans)中的一种 H+ 交感器,专门用于细胞吸收尿酸、尿囊素、尿嘧啶和有毒的核碱基类似物。作为 NCS1 蛋白家族的成员,FurE 在结构上与 APC 超家族转运体有关。APC 型转运体的特征是由十个跨膜片段(TMS1-10)组成的 5+5 反向重复折叠,并通过摇动捆绑机制发挥作用。大多数 APC 型转运体都有两个额外的 C 端 TMS 区段(TMS11-12),但其功能仍不明确。在这里,我们对 FurE 的 TMS11-12 进行了系统突变分析,结果表明,TMS12 中的两个特定芳香残基 Trp473 和 Tyr484 对于 ER 出体和向质膜(PM)的转运至关重要。分子建模显示,Trp473 和 Tyr484 可能通过与 TMS2(Leu91)、TMS3(Phe111)、TMS10(Val404、Asp406)中的残基以及 TMS12 中的其他芳香残基的动态相互作用而发挥重要作用。遗传分析证实了 Phe111、Asp406 和 TMS12 芳香残基在 FurE ER 退出中的重要作用。我们进一步发现,FurE-Y484F或FurE-W473A与野生型FurE共表达会导致显性阴性表型,这与FurE分子在特定微域中寡聚或分化以实现集中的ER排出和向PM运输的概念是一致的。重要的是,缺乏 TMS11-12 的截短型 FurE 无法再现对共表达野生型 FurE 运输的负面影响。总之,我们的研究表明,TMS11-12可作为分子内伴侣促进FurE的正常折叠,这似乎为FurE在ER-出口位点的分区提供了结构密码。
{"title":"The last two transmembrane helices in the APC-type FurE transporter act as an intramolecular chaperone essential for concentrative ER-exit.","authors":"Yiannis Pyrris, Georgia F Papadaki, Emmanuel Mikros, George Diallinas","doi":"10.15698/mic2024.01.811","DOIUrl":"10.15698/mic2024.01.811","url":null,"abstract":"<p><p>FurE is a H<sup>+</sup> symporter specific for the cellular uptake of uric acid, allantoin, uracil, and toxic nucleobase analogues in the fungus <i>Aspergillus</i> nidulans. Being member of the NCS1 protein family, FurE is structurally related to the APC-superfamily of transporters. APC-type transporters are characterised by a 5+5 inverted repeat fold made of ten transmembrane segments (TMS1-10) and function through the rocking-bundle mechanism. Most APC-type transporters possess two extra C-terminal TMS segments (TMS11-12), the function of which remains elusive. Here we present a systematic mutational analysis of TMS11-12 of FurE and show that two specific aromatic residues in TMS12, Trp473 and Tyr484, are essential for ER-exit and trafficking to the plasma membrane (PM). Molecular modeling shows that Trp473 and Tyr484 might be essential through dynamic interactions with residues in TMS2 (Leu91), TMS3 (Phe111), TMS10 (Val404, Asp406) and other aromatic residues in TMS12. Genetic analysis confirms the essential role of Phe111, Asp406 and TMS12 aromatic residues in FurE ER-exit. We further show that co-expression of FurE-Y484F or FurE-W473A with wild-type FurE leads to a dominant negative phenotype, compatible with the concept that FurE molecules oligomerize or partition in specific microdomains to achieve concentrative ER-exit and traffic to the PM. Importantly, truncated FurE versions lacking TMS11-12 are unable to reproduce a negative effect on the trafficking of co-expressed wild-type FurE. Overall, we show that TMS11-12 acts as an intramolecular chaperone for proper FurE folding, which seems to provide a structural code for FurE partitioning in ER-exit sites.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"11 ","pages":"1-15"},"PeriodicalIF":4.6,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10788122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472710","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}
引用次数: 0
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Microbial Cell
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