Pub Date : 2023-06-05eCollection Date: 2023-01-01DOI: 10.1093/femsml/uqad027
Chris van der Does, Frank Braun, Hongcheng Ren, Sonja-Verena Albers
Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.
{"title":"Putative nucleotide-based second messengers in archaea.","authors":"Chris van der Does, Frank Braun, Hongcheng Ren, Sonja-Verena Albers","doi":"10.1093/femsml/uqad027","DOIUrl":"10.1093/femsml/uqad027","url":null,"abstract":"<p><p>Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/90/0b/uqad027.PMC10249747.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9612316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-11eCollection Date: 2023-01-01DOI: 10.1093/femsml/uqad009
Andrea Salzer, Christiane Wolz
The stringent response and its signalling nucleotides, pppGpp and ppGpp, have been the subject of intense research since the discovery of (p)ppGpp in 1969. Recent studies have revealed that the downstream events that follow (p)ppGpp accumulation vary among species. Consequently, the stringent response as initially characterized in Escherichia coli largely differs from the response in Firmicutes (Bacillota), wherein synthesis and degradation of the messengers (p)ppGpp are orchestrated by the bifunctional Rel enzyme with synthetase and hydrolase activity and the two synthetases SasA/RelP and SasB/RelQ. Here we will summarize recent studies supporting the role of (p)ppGpp in the development of antibiotic resistance and tolerance as well as survival under adverse environmental conditions in Firmicutes. We will also discuss the impact of elevated (p)ppGpp levels on the development of persister cells and the establishment of persistent infections. (p)ppGpp levels are usually tightly controlled to allow optimal growth under non-stressed conditions. Upon the onset of certain 'stringent conditions' the sudden increase in (p)ppGpp levels limits growth while exerting protective effects. In Firmicutes, the (p)ppGpp-mediated restriction of GTP accumulation is one major mechanism of protection and survival under stresses such as antibiotic exposure.
{"title":"Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes.","authors":"Andrea Salzer, Christiane Wolz","doi":"10.1093/femsml/uqad009","DOIUrl":"10.1093/femsml/uqad009","url":null,"abstract":"<p><p>The stringent response and its signalling nucleotides, pppGpp and ppGpp, have been the subject of intense research since the discovery of (p)ppGpp in 1969. Recent studies have revealed that the downstream events that follow (p)ppGpp accumulation vary among species. Consequently, the stringent response as initially characterized in <i>Escherichia coli</i> largely differs from the response in Firmicutes (Bacillota), wherein synthesis and degradation of the messengers (p)ppGpp are orchestrated by the bifunctional Rel enzyme with synthetase and hydrolase activity and the two synthetases SasA/RelP and SasB/RelQ. Here we will summarize recent studies supporting the role of (p)ppGpp in the development of antibiotic resistance and tolerance as well as survival under adverse environmental conditions in Firmicutes. We will also discuss the impact of elevated (p)ppGpp levels on the development of persister cells and the establishment of persistent infections. (p)ppGpp levels are usually tightly controlled to allow optimal growth under non-stressed conditions. Upon the onset of certain 'stringent conditions' the sudden increase in (p)ppGpp levels limits growth while exerting protective effects. In Firmicutes, the (p)ppGpp-mediated restriction of GTP accumulation is one major mechanism of protection and survival under stresses such as antibiotic exposure.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9570012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-10eCollection Date: 2023-01-01DOI: 10.1093/femsml/uqad012
Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H Ahrens, Cynthia M Sharma, Elena Evguenieva-Hackenberg
The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.
{"title":"Unraveling the small proteome of the plant symbiont <i>Sinorhizobium meliloti</i> by ribosome profiling and proteogenomics.","authors":"Lydia Hadjeras, Benjamin Heiniger, Sandra Maaß, Robina Scheuer, Rick Gelhausen, Saina Azarderakhsh, Susanne Barth-Weber, Rolf Backofen, Dörte Becher, Christian H Ahrens, Cynthia M Sharma, Elena Evguenieva-Hackenberg","doi":"10.1093/femsml/uqad012","DOIUrl":"10.1093/femsml/uqad012","url":null,"abstract":"<p><p>The soil-dwelling plant symbiont <i>Sinorhizobium meliloti</i> is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for <i>S. meliloti</i> 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of <i>S. meliloti</i> was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from <i>Rhizobiaceae</i> to Bacteria, suggesting important physiological functions.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-10eCollection Date: 2023-01-01DOI: 10.1093/femsml/uqad013
Kenneth Timmis
In this short piece, I connect the dots between the pervasive influence of microbial activities on our health and that of the planet, including their positive and negative roles in current polycrises, our ability to influence microbes to promote their positive influences and mitigate their negative impacts, the roles of everyone as stewards and stakeholders in personal, family, community, national, and global wellbeing, the need for stewards and stakeholders to possess relevant information in order to fulfil their roles and obligations, and the compelling case for microbiology literacy and introduction of a societally relevant microbiology curriculum in school.
{"title":"Microbiology education: a significant path to sustainably improve the human and biosphere condition.","authors":"Kenneth Timmis","doi":"10.1093/femsml/uqad013","DOIUrl":"10.1093/femsml/uqad013","url":null,"abstract":"<p><p>In this short piece, I connect the dots between the pervasive influence of microbial activities on our health and that of the planet, including their positive and negative roles in current polycrises, our ability to influence microbes to promote their positive influences and mitigate their negative impacts, the roles of everyone as stewards and stakeholders in personal, family, community, national, and global wellbeing, the need for stewards and stakeholders to possess relevant information in order to fulfil their roles and obligations, and the compelling case for microbiology literacy and introduction of a societally relevant microbiology curriculum in school.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-16eCollection Date: 2023-01-01DOI: 10.1093/femsml/uqad001
Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M Sharma, Anita Marchfelder
In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea.
与广泛研究的原核生物 "小 "转录组(包括所有小的非编码 RNA)相比,小蛋白质组(这里定义为包括小于 70 aa 的蛋白质)现在才进入人们的视野。由于大多数原核生物缺乏完整的小蛋白质目录,我们无法了解这些分子是如何影响生理机能的。迄今为止,我们还没有专门针对小蛋白对古生菌基因组进行广泛分析。在这里,我们介绍了一种组合方法,它整合了小蛋白优化质谱(MS)和核糖体分析(Ribo-seq)的实验数据,生成了模型古菌 Haloferax volcanii 的高置信度小蛋白清单。我们通过质谱和核糖体分析(Ribo-seq)证明,在标准生长条件下,317 个已注释的小开放阅读框(sORFs)中有 67% 被翻译。此外,独立于注释的 Ribo-seq 数据分析显示,在基因间区域有 47 个新的 sORF 被核糖体参与。蛋白质组学也检测到了其中的 7 个,此外还有第 8 个新型小蛋白是通过 MS 唯一鉴定到的。我们还利用表位标记和 Western 印迹法提供了 12 个 sORF(已注释和新的)在体内翻译的独立实验证据,强调了我们鉴定方案的有效性。几个新的 sORFs 在 Haloferax 物种中是保守的,可能具有重要功能。根据我们的研究结果,我们得出结论:H. volcanii 的小蛋白质组比以前认识到的要大,结合 MS 与 Ribo-seq 是发现古细菌中新型小蛋白质编码基因的有效方法。
{"title":"Revealing the small proteome of <i>Haloferax volcanii</i> by combining ribosome profiling and small-protein optimized mass spectrometry.","authors":"Lydia Hadjeras, Jürgen Bartel, Lisa-Katharina Maier, Sandra Maaß, Verena Vogel, Sarah L Svensson, Florian Eggenhofer, Rick Gelhausen, Teresa Müller, Omer S Alkhnbashi, Rolf Backofen, Dörte Becher, Cynthia M Sharma, Anita Marchfelder","doi":"10.1093/femsml/uqad001","DOIUrl":"10.1093/femsml/uqad001","url":null,"abstract":"<p><p>In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon <i>Haloferax volcanii</i>. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence <i>in vivo</i> for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in <i>Haloferax</i> species and might have important functions. Based on our findings, we conclude that the small proteome of <i>H. volcanii</i> is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/78/30/uqad001.PMC10117724.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Benedikt H Wimmer, Sarah Moraïs, Ran Zalk, Itzhak Mizrahi, Ohad Medalia
Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the Family level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems.
{"title":"Phylogenetic diversity of core rumen microbiota as described by cryo-ET.","authors":"Benedikt H Wimmer, Sarah Moraïs, Ran Zalk, Itzhak Mizrahi, Ohad Medalia","doi":"10.1093/femsml/uqad010","DOIUrl":"https://doi.org/10.1093/femsml/uqad010","url":null,"abstract":"<p><p>Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the <i>Family</i> level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/96/0c/uqad010.PMC10117717.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tom Luthe, Larissa Kever, Sebastian Hänsch, Aël Hardy, Natalia Tschowri, Stefanie Weidtkamp-Peters, Julia Frunzke
The formation of plaques represents the hallmark of phage infection visualizing the clearance of the bacterial lawn in structured environments. In this study, we have addressed the impact of cellular development on phage infection in Streptomyces undergoing a complex developmental life cycle. Analysis of plaque dynamics revealed, after a period of plaque size enlargement, a significant regrowth of transiently phage-resistant Streptomyces mycelium into the lysis zone. Analysis of Streptomyces venezuelae mutant strains defective at different stages of cellular development indicated that this regrowth was dependent on the onset of the formation of aerial hyphae and spores at the infection interface. Mutants restricted to vegetative growth (ΔbldN) featured no significant constriction of plaque area. Fluorescence microscopy further confirmed the emergence of a distinct zone of cells/spores with reduced cell permeability towards propidium iodide staining at the plaque periphery. Mature mycelium was further shown to be significantly less susceptible to phage infection, which is less pronounced in strains defective in cellular development. Transcriptome analysis revealed the repression of cellular development at the early stages of phage infection probably facilitating efficient phage propagation. We further observed an induction of the chloramphenicol biosynthetic gene cluster highlighting phage infection as a trigger of cryptic metabolism in Streptomyces. Altogether, our study emphasizes cellular development and the emergence of transient phage resistance as an important layer of Streptomyces antiviral immunity.
{"title":"<i>Streptomyces</i> development is involved in the efficient containment of viral infections.","authors":"Tom Luthe, Larissa Kever, Sebastian Hänsch, Aël Hardy, Natalia Tschowri, Stefanie Weidtkamp-Peters, Julia Frunzke","doi":"10.1093/femsml/uqad002","DOIUrl":"https://doi.org/10.1093/femsml/uqad002","url":null,"abstract":"<p><p>The formation of plaques represents the hallmark of phage infection visualizing the clearance of the bacterial lawn in structured environments. In this study, we have addressed the impact of cellular development on phage infection in <i>Streptomyces</i> undergoing a complex developmental life cycle. Analysis of plaque dynamics revealed, after a period of plaque size enlargement, a significant regrowth of transiently phage-resistant <i>Streptomyces</i> mycelium into the lysis zone. Analysis of <i>Streptomyces venezuelae</i> mutant strains defective at different stages of cellular development indicated that this regrowth was dependent on the onset of the formation of aerial hyphae and spores at the infection interface. Mutants restricted to vegetative growth (Δ<i>bldN</i>) featured no significant constriction of plaque area. Fluorescence microscopy further confirmed the emergence of a distinct zone of cells/spores with reduced cell permeability towards propidium iodide staining at the plaque periphery. Mature mycelium was further shown to be significantly less susceptible to phage infection, which is less pronounced in strains defective in cellular development. Transcriptome analysis revealed the repression of cellular development at the early stages of phage infection probably facilitating efficient phage propagation. We further observed an induction of the chloramphenicol biosynthetic gene cluster highlighting phage infection as a trigger of cryptic metabolism in <i>Streptomyces</i>. Altogether, our study emphasizes cellular development and the emergence of transient phage resistance as an important layer of <i>Streptomyces</i> antiviral immunity.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
When Sabine Ehrt first got into contact with bacteria in University lectures, she almost disregarded them as being too simple. But soon she realised that ‘they are actually not that simple; they are quite complicated, adapting to different environments, niches, and hosts.’ After finishing her Ph.D. on adaptation strategies of Acinetobacter calcoaceticus at the University of Erlangen in Germany, Sabine switched to human pathogens for her postdoc positions at Cornell University Medical College in New York and the University of California at Berkeley. She took the chance to work on bacteria that require a biosafety 3 lab set up and deep dived into the question of how the death-causing pathogen Mycobacterium tuberculosis adapts to humans. As an Assistant Professor in the Department of Microbiology and Immunology at Weill Medical College of Cornell University, Sabine started a substantial collaboration with Dirk Schnappinger to investigate the pathogen’s adaptation mechanisms. Mycobacterium tuberculosis comes into contact with a host via inhalation and infects macrophages in the lung. Within the macrophage cytosol, the pathogen resides within phagosomes, but prevents them from fusing with lysosomes and thereby from clearing the pathogen. To investigate how the pathogen adjusts to the macrophage environment and how macrophages respond to the infection, Sabine and her team set up two major studies ‘that used microarray techniques for the first time in tuberculosis research’. They found that M. tuberculosis senses the intraphagosomal environment through the presence of fatty acids and low pH. Hence, the pathogen responds by inducing anaerobic respiration, degradation of fatty acids, remodelling of its cell envelope and by producing siderophores for efficient iron acquisition (Schnappinger et al. 2003). Similarly, macrophages upregulate genes with functions related to immunity and inflammation to clear the invading pathogen. About 25% of the macrophage genome showed altered expression levels upon infection mainly driven by the macrophage-activating factor Interferon-γ (Ehrt et al. 2001). Her collaborative spirit became even more profound when Sabine was appointed Professor in 2010. She got involved in several global scientific projects, e.g. as chair of the Tuberculosis/Leprosy Panel of the USA–Japan Cooperative Medical Science Program, which fosters engagement between US and Asian scientists. Sabine was also involved on scientific advisory boards of several international research programs, including the Translational & Clinical Research Flagship Program Medical Research Council Singapore and the Research Unit at the University of Witwatersrand in Johannesburg. Being a member of the European Academy of Microbiology and section editor of their journal microLife fosters her belief that ‘science is and should not be limited to a single country or continent as it is important to collaborate with other scientists globally and exchange knowledge’.
{"title":"Working together to fighting the bad guys.","authors":"Sarah Wettstadt","doi":"10.1093/femsml/uqad022","DOIUrl":"https://doi.org/10.1093/femsml/uqad022","url":null,"abstract":"When Sabine Ehrt first got into contact with bacteria in University lectures, she almost disregarded them as being too simple. But soon she realised that ‘they are actually not that simple; they are quite complicated, adapting to different environments, niches, and hosts.’ After finishing her Ph.D. on adaptation strategies of Acinetobacter calcoaceticus at the University of Erlangen in Germany, Sabine switched to human pathogens for her postdoc positions at Cornell University Medical College in New York and the University of California at Berkeley. She took the chance to work on bacteria that require a biosafety 3 lab set up and deep dived into the question of how the death-causing pathogen Mycobacterium tuberculosis adapts to humans. As an Assistant Professor in the Department of Microbiology and Immunology at Weill Medical College of Cornell University, Sabine started a substantial collaboration with Dirk Schnappinger to investigate the pathogen’s adaptation mechanisms. Mycobacterium tuberculosis comes into contact with a host via inhalation and infects macrophages in the lung. Within the macrophage cytosol, the pathogen resides within phagosomes, but prevents them from fusing with lysosomes and thereby from clearing the pathogen. To investigate how the pathogen adjusts to the macrophage environment and how macrophages respond to the infection, Sabine and her team set up two major studies ‘that used microarray techniques for the first time in tuberculosis research’. They found that M. tuberculosis senses the intraphagosomal environment through the presence of fatty acids and low pH. Hence, the pathogen responds by inducing anaerobic respiration, degradation of fatty acids, remodelling of its cell envelope and by producing siderophores for efficient iron acquisition (Schnappinger et al. 2003). Similarly, macrophages upregulate genes with functions related to immunity and inflammation to clear the invading pathogen. About 25% of the macrophage genome showed altered expression levels upon infection mainly driven by the macrophage-activating factor Interferon-γ (Ehrt et al. 2001). Her collaborative spirit became even more profound when Sabine was appointed Professor in 2010. She got involved in several global scientific projects, e.g. as chair of the Tuberculosis/Leprosy Panel of the USA–Japan Cooperative Medical Science Program, which fosters engagement between US and Asian scientists. Sabine was also involved on scientific advisory boards of several international research programs, including the Translational & Clinical Research Flagship Program Medical Research Council Singapore and the Research Unit at the University of Witwatersrand in Johannesburg. Being a member of the European Academy of Microbiology and section editor of their journal microLife fosters her belief that ‘science is and should not be limited to a single country or continent as it is important to collaborate with other scientists globally and exchange knowledge’.","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/59/dd/uqad022.PMC10167628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
{"title":"Epigenetic effects of short-chain fatty acids from the large intestine on host cells.","authors":"Richard A Stein, Leise Riber","doi":"10.1093/femsml/uqad032","DOIUrl":"https://doi.org/10.1093/femsml/uqad032","url":null,"abstract":"<p><p>Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, <i>the gut microbiota</i>, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5e/b1/uqad032.PMC10335734.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9817978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eduard Fadeev, Cécile Carpaneto Bastos, Jennifer H Hennenfeind, Steven J Biller, Daniel Sher, Matthias Wietz, Gerhard J Herndl
Bacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of Alteromonas macleodii, a cosmopolitan marine bacterium. Alteromonas macleodii strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that A. macleodii MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that A. macleodii MVs may support its growth through generation of extracellular 'hotspots' that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria.
{"title":"Characterization of membrane vesicles in <i>Alteromonas macleodii</i> indicates potential roles in their copiotrophic lifestyle.","authors":"Eduard Fadeev, Cécile Carpaneto Bastos, Jennifer H Hennenfeind, Steven J Biller, Daniel Sher, Matthias Wietz, Gerhard J Herndl","doi":"10.1093/femsml/uqac025","DOIUrl":"https://doi.org/10.1093/femsml/uqac025","url":null,"abstract":"<p><p>Bacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of <i>Alteromonas macleodii</i>, a cosmopolitan marine bacterium. <i>Alteromonas macleodii</i> strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that <i>A. macleodii</i> MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that <i>A. macleodii</i> MVs may support its growth through generation of extracellular 'hotspots' that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/33/5a/uqac025.PMC10117737.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}