Pub Date : 2024-03-15eCollection Date: 2024-01-01DOI: 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.
{"title":"The cAMP-PKA signalling crosstalks with CWI and HOG-MAPK pathways in yeast cell response to osmotic and thermal stress.","authors":"Fiorella Galello, Mariana Bermúdez-Moretti, María Clara Ortolá Martínez, Silvia Rossi, Paula Portela","doi":"10.15698/mic2024.03.818","DOIUrl":"10.15698/mic2024.03.818","url":null,"abstract":"<p><p>The yeast <i>Saccharomyces cerevisiae</i> 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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140143760","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}
Pub Date : 2024-03-14eCollection Date: 2024-01-01DOI: 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.
{"title":"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.","authors":"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","doi":"10.15698/mic2024.03.817","DOIUrl":"10.15698/mic2024.03.817","url":null,"abstract":"<p><p>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 <i>Bacteroides</i>, <i>Bifidobacterium</i> and <i>Ruminococcus,</i> but after SRB cultivation, the dominant genera were <i>Bacteroides</i>, <i>Klebsiella</i> and <i>Bilophila</i>. On the other hand, before SRB cultivation, the main represented genera in patients with severe UC were <i>Escherichia-Shigella</i>, <i>Proteus</i>, <i>Methanothermobacter</i> and <i>Methanobacterium</i>. However, after incubation in the SRB medium <i>Bacteroides, Proteus, Alistipes</i> and <i>Lachnoclostridium</i> 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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140131865","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}
Pub Date : 2024-02-23eCollection Date: 2024-01-01DOI: 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.
{"title":"Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination.","authors":"Jesús Gómez-Montalvo, Alvaro de Obeso Fernández Del Valle, Luis Fernando De la Cruz Gutiérrez, Jose Mario Gonzalez-Meljem, Christian Quintus Scheckhuber","doi":"10.15698/mic2024.02.816","DOIUrl":"10.15698/mic2024.02.816","url":null,"abstract":"<p><p><i>Saccharomyces cerevisiae</i> (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 <i>S. cerevisiae</i>. This was achieved by utilizing the IRFinder algorithm on a previously published RNA-seq data set by Janssens <i>et al.</i> (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., <i>YRA1</i>) in early and middle-aged yeast, and protein ubiquitination (e.g., <i>UBC5</i>) 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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10897858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139983301","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}
Pub Date : 2024-02-21eCollection Date: 2024-01-01DOI: 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.
{"title":"Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics.","authors":"Thorsten Meyer, Oskar Knittelfelder, Martin Smolnig, Patrick Rockenfeller","doi":"10.15698/mic2024.02.815","DOIUrl":"10.15698/mic2024.02.815","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10879857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139931852","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}
Pub Date : 2024-02-20eCollection Date: 2024-01-01DOI: 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.
{"title":"A cobalt concentration sensitive Btu-like system facilitates cobalamin uptake in <i>Anabaena</i> sp. PCC 7120.","authors":"Julia Graf, Leonard Fresenborg, Hans-Michael Seitz, Rafael Pernil, Enrico Schleiff","doi":"10.15698/mic2024.02.814","DOIUrl":"10.15698/mic2024.02.814","url":null,"abstract":"<p><p>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 <i>Anabaena</i> sp. PCC 7120, a model filamentous heterocyst-forming cyanobacterium. <i>Anabaena</i> 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 <i>tonB3 and btuD</i> 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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10878165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912948","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}
Pub Date : 2024-02-19eCollection Date: 2024-01-01DOI: 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。
{"title":"Predictable regulation of survival by intratumoral microbe-immune crosstalk in patients with lung adenocarcinoma.","authors":"Shuo Shi, Yuwen Chu, Haiyan Liu, Lan Yu, Dejun Sun, Jialiang Yang, Geng Tian, Lei Ji, Cong Zhang, Xinxin Lu","doi":"10.15698/mic2024.02.813","DOIUrl":"10.15698/mic2024.02.813","url":null,"abstract":"<p><p>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 <i>Streptococcus</i>. 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.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139905969","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}
Pub Date : 2024-01-09eCollection Date: 2024-01-01DOI: 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.
{"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":null,"pages":null},"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}
Pub Date : 2024-01-05eCollection Date: 2024-01-01DOI: 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.
{"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":null,"pages":null},"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}
Pub Date : 2023-11-23eCollection Date: 2023-12-04DOI: 10.15698/mic2023.12.810
Elisabetta de Alteriis, Guido Incerti, Fabrizio Cartenì, Maria Luisa Chiusano, Chiara Colantuono, Emanuela Palomba, Pasquale Termolino, Francesco Monticolo, Alfonso Esposito, Giuliano Bonanomi, Rosanna Capparelli, Marco Iannaccone, Alessandro Foscari, Carmine Landi, Palma Parascandola, Massimo Sanchez, Valentina Tirelli, Bruna de Falco, Virginia Lanzotti, Stefano Mazzoleni
Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.
细胞外 DNA(exDNA)可由活细胞主动释放,并被认为具有不同的功能。此外,据报道,同源的 exDNA 对多种生物具有物种特异性抑制作用。在这里,我们通过不同的实验证据(包括 1H-NMR 代谢组指纹图谱)证明,酿酒酵母喂养批次培养的生长率下降是由培养基中 exDNA 的积累决定的。这种分泌的 exDNA 测序代表了整个基因组的一部分,与已报道的酵母细胞内的染色体外环状 DNA(eccDNA)极为相似。回收的 DNA 分子大多为单链,与细胞生长过程中的酵母新陈代谢特别相关。流式细胞分析表明,观察到的 exDNA 生长抑制与细胞周期 S 期的停滞相对应。这些史无前例的发现为活体细胞产生的外脱氧核糖核酸的功能作用打开了一个新局面。
{"title":"Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation.","authors":"Elisabetta de Alteriis, Guido Incerti, Fabrizio Cartenì, Maria Luisa Chiusano, Chiara Colantuono, Emanuela Palomba, Pasquale Termolino, Francesco Monticolo, Alfonso Esposito, Giuliano Bonanomi, Rosanna Capparelli, Marco Iannaccone, Alessandro Foscari, Carmine Landi, Palma Parascandola, Massimo Sanchez, Valentina Tirelli, Bruna de Falco, Virginia Lanzotti, Stefano Mazzoleni","doi":"10.15698/mic2023.12.810","DOIUrl":"10.15698/mic2023.12.810","url":null,"abstract":"<p><p>Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including <sup>1</sup>H-NMR metabolomic fingerprint, that the growth rate decline in <i>Saccharomyces cerevisiae</i> fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138487934","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}
Pub Date : 2023-11-14eCollection Date: 2023-12-04DOI: 10.15698/mic2023.12.809
Miguel Antunes, Deepika Kale, Hana Sychrová, Isabel Sá-Correia
Acetic acid-induced stress is a common challenge in natural environments and industrial bioprocesses, significantly affecting the growth and metabolic performance of Saccharomyces cerevisiae. The adaptive response and tolerance to this stress involves the activation of a complex network of molecular pathways. This study aims to delve deeper into these mechanisms in S. cerevisiae, particularly focusing on the role of the Hrk1 kinase. Hrk1 is a key determinant of acetic acid tolerance, belonging to the NPR/Hal family, whose members are implicated in the modulation of the activity of plasma membrane transporters that orchestrate nutrient uptake and ion homeostasis. The influence of Hrk1 on S. cerevisiae adaptation to acetic acid-induced stress was explored by employing a physiological approach based on previous phosphoproteomics analyses. The results from this study reflect the multifunctional roles of Hrk1 in maintaining proton and potassium homeostasis during different phases of acetic acid-stressed cultivation. Hrk1 is shown to play a role in the activation of plasma membrane H+-ATPase, maintaining pH homeostasis, and in the modulation of plasma membrane potential under acetic acid stressed cultivation. Potassium (K+) supplementation of the growth medium, particularly when provided at limiting concentrations, led to a notable improvement in acetic acid stress tolerance of the hrk1Δ strain. Moreover, abrogation of this kinase expression is shown to confer a physiological advantage to growth under K+ limitation also in the absence of acetic acid stress. The involvement of the alkali metal cation/H+ exchanger Nha1, another proposed molecular target of Hrk1, in improving yeast growth under K+ limitation or acetic acid stress, is proposed.
{"title":"The Hrk1 kinase is a determinant of acetic acid tolerance in yeast by modulating H<sup>+</sup> and K<sup>+</sup> homeostasis.","authors":"Miguel Antunes, Deepika Kale, Hana Sychrová, Isabel Sá-Correia","doi":"10.15698/mic2023.12.809","DOIUrl":"10.15698/mic2023.12.809","url":null,"abstract":"<p><p>Acetic acid-induced stress is a common challenge in natural environments and industrial bioprocesses, significantly affecting the growth and metabolic performance of <i>Saccharomyces cerevisiae</i>. The adaptive response and tolerance to this stress involves the activation of a complex network of molecular pathways. This study aims to delve deeper into these mechanisms in <i>S. cerevisiae</i>, particularly focusing on the role of the Hrk1 kinase. Hrk1 is a key determinant of acetic acid tolerance, belonging to the NPR/Hal family, whose members are implicated in the modulation of the activity of plasma membrane transporters that orchestrate nutrient uptake and ion homeostasis. The influence of Hrk1 on <i>S. cerevisiae</i> adaptation to acetic acid-induced stress was explored by employing a physiological approach based on previous phosphoproteomics analyses. The results from this study reflect the multifunctional roles of Hrk1 in maintaining proton and potassium homeostasis during different phases of acetic acid-stressed cultivation. Hrk1 is shown to play a role in the activation of plasma membrane H<sup>+</sup>-ATPase, maintaining pH homeostasis, and in the modulation of plasma membrane potential under acetic acid stressed cultivation. Potassium (K<sup>+</sup>) supplementation of the growth medium, particularly when provided at limiting concentrations, led to a notable improvement in acetic acid stress tolerance of the <i>hrk1</i>Δ strain. Moreover, abrogation of this kinase expression is shown to confer a physiological advantage to growth under K<sup>+</sup> limitation also in the absence of acetic acid stress. The involvement of the alkali metal cation/H<sup>+</sup> exchanger Nha1, another proposed molecular target of Hrk1, in improving yeast growth under K<sup>+</sup> limitation or acetic acid stress, is proposed.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138487935","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}