mSystems最新文献

{"title":"Proteomic insights into extracellular matrix dynamics in the intestine of Labeo rohita during Aeromonas hydrophila infection","authors":"Mehar Un NissaNevil PintoBiplab GhoshAnwesha BanerjeeUrvi SinghMukunda GoswamiSanjeeva Srivastava1Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India2Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra, India3German Cancer Research Center (DKFZ), Heidelberg, Germany4Indian Institute of Science Bangalore, Bangalore, Karnataka, India5Friedrich Alexander University Erlangen Nuremberg, Erlangen, GermanyJoshua E. EliasLeonard J. Foster","doi":"10.1128/msystems.00247-24","DOIUrl":"https://doi.org/10.1128/msystems.00247-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy","authors":"Ying XuMin YuXin HuangGuixiang WangHua WangFengzhen ZhangJie ZhangXuemei Gao1Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China2Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China3Department of Otolaryngology, Head and Neck Surgery, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, ChinaNeha Sachdeva","doi":"10.1128/msystems.00968-24","DOIUrl":"https://doi.org/10.1128/msystems.00968-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting <i>Pseudomonas aeruginosa</i> drug resistance using artificial intelligence and clinical MALDI-TOF mass spectra.","authors":"Hoai-An Nguyen, Anton Y Peleg, Jiangning Song, Bhavna Antony, Geoffrey I Webb, Jessica A Wisniewski, Luke V Blakeway, Gnei Z Badoordeen, Ravali Theegala, Helen Zisis, David L Dowe, Nenad Macesic","doi":"10.1128/msystems.00789-24","DOIUrl":"10.1128/msystems.00789-24","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories for bacterial identification but its use for detection of antimicrobial resistance (AMR) remains limited. Here, we used MALDI-TOF MS with artificial intelligence (AI) approaches to successfully predict AMR in <i>Pseudomonas aeruginosa</i>, a priority pathogen with complex AMR mechanisms. The highest performance was achieved for modern β-lactam/β-lactamase inhibitor drugs, namely, ceftazidime/avibactam and ceftolozane/tazobactam. For these drugs, the model demonstrated area under the receiver operating characteristic curve (AUROC) of 0.869 and 0.856, specificity of 0.925 and 0.897, and sensitivity of 0.731 and 0.714, respectively. As part of this work, we developed dynamic binning, a feature engineering technique that effectively reduces the high-dimensional feature set and has wide-ranging applicability to MALDI-TOF MS data. Compared to conventional feature engineering approaches, the dynamic binning method yielded highest performance in 7 of 10 antimicrobials. Moreover, we showcased the efficacy of transfer learning in enhancing the AUROC performance for 8 of 11 antimicrobials. By assessing the contribution of features to the model's prediction, we identified proteins that may contribute to AMR mechanisms. Our findings demonstrate the potential of combining AI with MALDI-TOF MS as a rapid AMR diagnostic tool for <i>Pseudomonas aeruginosa</i>.IMPORTANCE<i>Pseudomonas aeruginosa</i> is a key bacterial pathogen that causes significant global morbidity and mortality. Antimicrobial resistance (AMR) emerges rapidly in <i>P. aeruginosa</i> and is driven by complex mechanisms. Drug-resistant <i>P. aeruginosa</i> is a major challenge in clinical settings due to limited treatment options. Early detection of AMR can guide antibiotic choices, improve patient outcomes, and avoid unnecessary antibiotic use. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid species identification in clinical microbiology. In this study, we repurposed mass spectra generated by MALDI-TOF and used them as inputs for artificial intelligence approaches to successfully predict AMR in <i>P. aeruginosa</i> for multiple key antibiotic classes. This work represents an important advance toward using MALDI-TOF as a rapid AMR diagnostic for <i>P. aeruginosa</i> in clinical settings.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.","authors":"Marwan E Majzoub, Laurence D W Luu, Craig Haifer, Sudarshan Paramsothy, Thomas J Borody, Rupert W Leong, Torsten Thomas, Nadeem O Kaakoush","doi":"10.1128/msystems.00746-24","DOIUrl":"10.1128/msystems.00746-24","url":null,"abstract":"<p><p>Characterization of microbial community metabolic output is crucial to understanding their functions. Construction of genome-scale metabolic models from metagenome-assembled genomes (MAG) has enabled prediction of metabolite production by microbial communities, yet little is known about their accuracy. Here, we examined the performance of two approaches for metabolite prediction from metagenomes, one that is MAG-guided and another that is taxonomic reference-guided. We applied both on shotgun metagenomics data from human and environmental samples, and validated findings in the human samples using untargeted metabolomics. We found that in human samples, where taxonomic profiling is optimized and reference genomes are readily available, when number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach. The two approaches showed significant overlap but each identified metabolites not predicted in the other. Pathway enrichment analyses identified significant differences in inferences derived from data based on the approach, highlighting the need for caution in interpretation. In environmental samples, when the number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach for total metabolites in both sample types and non-redundant metabolites in seawater samples. Nonetheless, as was observed for the human samples, the approaches overlapped substantially but also predicted metabolites not observed in the other. Our findings report on utility of a complementary input to genome-scale metabolic model construction that is less computationally intensive forgoing MAG assembly and refinement, and that can be applied on shallow shotgun sequencing where MAGs cannot be generated.IMPORTANCELittle is known about the accuracy of genome-scale metabolic models (GEMs) of microbial communities despite their influence on inferring community metabolic outputs and culture conditions. The performance of GEMs for metabolite prediction from metagenomes was assessed by applying two approaches on shotgun metagenomics data from human and environmental samples, and validating findings in the human samples using untargeted metabolomics. The performance of the approach was found to be dependent on sample type, but collectively, the reference-guided approach predicted more metabolites than the MAG-guided approach. Despite the differences, the predictions from the approaches overlapped substantially but each identified metabolites not predicted in the other. We found significant differences in biological inferences based on the approach, with some examples of uniquely enriched pathways in one group being invalidated when using the alternative approach, highlighting the need for caution in interpretation of GEMs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141971448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combinatorial control of <i>Pseudomonas aeruginosa</i> biofilm development by quorum-sensing and nutrient-sensing regulators.","authors":"Gong Chen, Georgia Fanouraki, Aathmaja Anandhi Rangarajan, Bradford T Winkelman, Jared T Winkelman, Christopher M Waters, Sampriti Mukherjee","doi":"10.1128/msystems.00372-24","DOIUrl":"10.1128/msystems.00372-24","url":null,"abstract":"<p><p>The human pathogen <i>Pseudomonas aeruginosa</i>, a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways-the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system-intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the Δ<i>rhlR</i>Δ<i>cbrA</i> double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent Δ<i>rhlR</i> and Δ<i>cbrA</i> mutants indicating codominance of each signaling pathway. The Δ<i>rhlR</i>Δ<i>cbrA</i> mutant gains suppressor mutations that allow biofilm expansion; these mutations map to the <i>crc</i> gene resulting in loss of function of the carbon catabolite repression protein Crc. Furthermore, the combined absence of RhlR and CbrA leads to a drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. We find that in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components-Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies.IMPORTANCEBacteria often form multicellular communities encased in an extracytoplasmic matrix called biofilms. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. To understand how information from two distinct stimuli is integrated, we used biofilm formation in the human pathogen <i>Pseudomonas aeruginosa</i> as a model and studied the intersection of two global sensory signaling pathways-quorum sensing and nutritional adaptation. Global transcriptomics on biofilm cells and reporter assays suggest parallel regulation of biofilms by each pathway that converges on the abundance of a small RNA antagonist of the carbon catabolite repression protein, Crc. We find a new role of Crc as it modulates the expression of biofilm matrix components in response to the environment. These results expand our understanding of the genetic regulatory strategies that allow <i>P. aeruginosa</i> to successfully develop biofilm communities.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses.","authors":"Lauren M Lui, Torben N Nielsen","doi":"10.1128/msystems.00242-24","DOIUrl":"10.1128/msystems.00242-24","url":null,"abstract":"<p><p>Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.</p><p><strong>Importance: </strong>Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and genomic analysis of the hypervirulent methicillin-resistant <i>Staphylococcus aureus</i> ST630 clone in China.","authors":"Junhong Shi, Yanghua Xiao, Li Shen, Cailing Wan, Bingjie Wang, Peiyao Zhou, Jiao Zhang, Weihua Han, Fangyou Yu","doi":"10.1128/msystems.00664-24","DOIUrl":"10.1128/msystems.00664-24","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) sequence type 630 (ST630) is a rarely reported lineage worldwide. This study aimed to trace the dissemination of the emerging MRSA ST630 clones in China and investigate their virulence potential. We collected 22 ST630-MRSA isolates from across China and performed whole-genome sequencing analysis and virulence characterization on these isolates. Epidemiological results showed that MRSA ST630 isolates were primarily isolated from pus/wound secretions, mainly originating from Jiangxi province, and carried diverse virulence and drug resistance genes. Staphylococcal cassette chromosome mec type V (SCCmec V) predominated (11/22, 50.0%) among the MRSA ST630 isolates. Interestingly, nearly half (45.5%) of the 22 ST630-MRSA isolates tested lacked intact SCCmec elements. Phylogenetic analysis demonstrated that ST630-MRSA could be divided into two distinct clades, with widespread dissemination mainly in Chinese regions. Five representative isolates were selected for phenotypic assays, including hemolysin activity, real-time fluorescence quantitative PCR, western blot analysis, hydrogen peroxide killing assay, blood killing assay, cell adhesion and invasion assay, and mouse skin abscess model. The results showed that, compared to the USA300-LAC strain, ST630 isolates exhibited particularly strong invasiveness and virulence in the aforementioned phenotypic assays. This study described the emergence of a highly virulent ST630-MRSA lineage and improved our insight into the molecular epidemiology of ST630 clones in China.IMPORTANCEMethicillin-resistant <i>Staphylococcus aureus</i> (MRSA) sequence type 630 (ST630) is an emerging clone with an increasing isolation rate in China. This study raises awareness of the hypervirulent MRSA ST630 clones in China and alerts people to their widespread dissemination. ST630-staphylococcal cassette chromosome mec V is a noteworthy clone in China, and we present the first comprehensive genetic and phenotypic analysis of this lineage. Our findings provide valuable insights for the prevention and control of infections caused by this emerging MRSA clone.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity and impact of single-stranded RNA viruses in Czech Heterobasidion populations","authors":"László Benedek DályaMartin ČernýMarcos de la PeñaAnna PoimalaEeva J. VainioJarkko HantulaLeticia Botella1Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia2Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia3Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain4Natural Resources Institute Finland (Luke), Helsinki, FinlandLiyuan Maİkbal Agah İnce","doi":"10.1128/msystems.00506-24","DOIUrl":"https://doi.org/10.1128/msystems.00506-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of <i>Streptococcus pyogenes</i>.","authors":"Yujiro Hirose, Daniel C Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O Palsson, Victor Nizet","doi":"10.1128/msystems.00736-24","DOIUrl":"10.1128/msystems.00736-24","url":null,"abstract":"<p><p><i>Streptococcus pyogenes</i> is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of <i>S. pyogenes</i>, serotype M1 strains hold the greatest clinical relevance due to their high prevalence in severe human infections. To enhance our understanding of pathogenesis and discovery of potential therapeutic approaches, we have developed the first genome-scale metabolic model (GEM) for a serotype M1 <i>S. pyogenes</i> strain, which we name iYH543. The curation of iYH543 involved cross-referencing a draft GEM of <i>S. pyogenes</i> serotype M1 from the AGORA2 database with gene essentiality and autotrophy data obtained from transposon mutagenesis-based and growth screens. We achieved a 92.6% (503/543 genes) accuracy in predicting gene essentiality and a 95% (19/20 amino acids) accuracy in predicting amino acid auxotrophy. Additionally, Biolog Phenotype microarrays were employed to examine the growth phenotypes of <i>S. pyogenes,</i> which further contributed to the refinement of iYH543. Notably, iYH543 demonstrated 88% accuracy (168/190 carbon sources) in predicting growth on various sole carbon sources. Discrepancies observed between iYH543 and the actual behavior of living <i>S. pyogenes</i> highlighted areas of uncertainty in the current understanding of <i>S. pyogenes</i> metabolism. iYH543 offers novel insights and hypotheses that can guide future research efforts and ultimately inform novel therapeutic strategies.IMPORTANCEGenome-scale models (GEMs) play a crucial role in investigating bacterial metabolism, predicting the effects of inhibiting specific metabolic genes and pathways, and aiding in the identification of potential drug targets. Here, we have developed the first GEM for the <i>S. pyogenes</i> highly virulent serotype, M1, which we name iYH543. The iYH543 achieved high accuracy in predicting gene essentiality. We also show that the knowledge obtained by substituting actual measurement values for iYH543 helps us gain insights that connect metabolism and virulence. iYH543 will serve as a useful tool for rational drug design targeting <i>S. pyogenes</i> metabolism and computational screening to investigate the interplay between inhibiting virulence factor synthesis and growth.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium <i>Gemmatimonas phototrophica</i>.","authors":"Karel Kopejtka, Jürgen Tomasch, Sahana Shivaramu, Mohit Kumar Saini, David Kaftan, Michal Koblížek","doi":"10.1128/msystems.00706-24","DOIUrl":"10.1128/msystems.00706-24","url":null,"abstract":"<p><p>The first phototrophic member of the bacterial phylum <i>Gemmatimonadota</i>, <i>Gemmatimonas phototrophica</i> AP64^T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. <i>G. phototrophica</i> grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of <i>G. phototrophica</i> was optimal at 80 µmol photon m^-2 s^-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m^-2 s^-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that <i>G. phototrophica</i> possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, <i>G. phototrophica</i> has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.</p><p><strong>Importance: </strong>Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. <i>Gemmatimonas phototrophica</i>, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that <i>G. phototrophica</i> lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}