PLoS Biology最新文献

{"title":"Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution.","authors":"Rekha Gopalan-Nair, Aurore Coissac, Ludovic Legrand, Céline Lopez-Roques, Yann Pécrix, Céline Vandecasteele, Olivier Bouchez, Xavier Barlet, Anne Lanois, Alain Givaudan, Julien Brillard, Stéphane Genin, Alice Guidot","doi":"10.1371/journal.pbio.3002792","DOIUrl":"10.1371/journal.pbio.3002792","url":null,"abstract":"<p><p>Adaptation is usually explained by beneficial genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, genetic mutation analysis alone is not sufficient to fully explain the adaptive processes, and several studies report the existence of nongenetic (or epigenetic) inheritance that can enable adaptation to new environments. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia pseudosolanacearum to the host during experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones obtained after serial passages on 5 different plant species during 300 generations. Comparison with the methylome of the ancestral clone revealed a list of 50 differential methylated sites (DMSs) at the GTWWAC motif. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential expression of the corresponding genes. Only 1 gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR technology, used as an alternative approach for DNA methylation analysis, also found the 2 DMSs upstream RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these 2 DMSs in host adaptation. As these DMSs appeared very early in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. In addition, we found that the change in DNA methylation upstream RSp0338 remains stable at least for 100 generations outside the host and thus can contribute to long-term adaptation to the host plant. To our knowledge, this is the first study showing a direct link between bacterial epigenetic variation and adaptation to a new environment.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002792"},"PeriodicalIF":9.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a highly efficient chloroplast-targeting peptide for plastid engineering.","authors":"Chonprakun Thagun, Masaki Odahara, Yutaka Kodama, Keiji Numata","doi":"10.1371/journal.pbio.3002785","DOIUrl":"10.1371/journal.pbio.3002785","url":null,"abstract":"<p><p>Plastids are pivotal target organelles for comprehensively enhancing photosynthetic and metabolic traits in plants via plastid engineering. Plastidial proteins predominantly originate in the nucleus and must traverse membrane-bound multiprotein translocons to access these organelles. This import process is meticulously regulated by chloroplast-targeting peptides (cTPs). Whereas many cTPs have been employed to guide recombinantly expressed functional proteins to chloroplasts, there is a critical need for more efficient cTPs. Here, we performed a comprehensive exploration and comparative assessment of an advanced suite of cTPs exhibiting superior targeting capabilities. We employed a multifaceted approach encompassing computational prediction, in planta expression, fluorescence tracking, and in vitro chloroplast import studies to identify and analyze 88 cTPs associated with Arabidopsis thaliana mutants with phenotypes linked to chloroplast function. These polypeptides exhibited distinct abilities to transport green fluorescent protein (GFP) to various compartments within leaf cells, particularly chloroplasts. A highly efficient cTP derived from Arabidopsis plastid ribosomal protein L35 (At2g24090) displayed remarkable effectiveness in chloroplast localization. This cTP facilitated the activities of chloroplast-targeted RNA-processing proteins and metabolic enzymes within plastids. This cTP could serve as an ideal transit peptide for precisely targeting biomolecules to plastids, leading to advancements in plastid engineering.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002785"},"PeriodicalIF":9.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Promoting reusable and open methods and protocols (PRO-MaP) can improve methodological reporting in the life sciences.","authors":"Sofia Batista Leite, Matthew A Brooke, Annamaria Carusi, Andy Collings, Pierre Deceuninck, Jean-François Dechamp, Bronwen Dekker, Elisa De Ranieri, Emma Ganley, Annalisa Gastaldello, Fanglian He, Marcel LaFlamme, Ingrid Langezaal, James Morris, David Pamies, Monica Piergiovanni, Bernd Pulverer, David Sadler, Caroline Shamu, Vivian Siegel, Marco Straccia, Tracey L Weissgerber","doi":"10.1371/journal.pbio.3002835","DOIUrl":"10.1371/journal.pbio.3002835","url":null,"abstract":"<p><p>Detailed method descriptions are essential for reproducibility, research evaluation, and effective data reuse. We summarize the key recommendations for life sciences researchers and research institutions described in the European Commission PRO-MaP report.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002835"},"PeriodicalIF":9.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11441691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A taxon-rich and genome-scale phylogeny of Opisthokonta.","authors":"Hongyue Liu, Jacob L Steenwyk, Xiaofan Zhou, Darrin T Schultz, Kevin M Kocot, Xing-Xing Shen, Antonis Rokas, Yuanning Li","doi":"10.1371/journal.pbio.3002794","DOIUrl":"10.1371/journal.pbio.3002794","url":null,"abstract":"<p><p>Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002794"},"PeriodicalIF":9.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new lineage nomenclature to aid genomic surveillance of dengue virus.","authors":"Verity Hill, Sara Cleemput, James Siqueira Pereira, Robert J Gifford, Vagner Fonseca, Houriiyah Tegally, Anderson F Brito, Gabriela Ribeiro, Vinicius Carius de Souza, Isabela Carvalho Brcko, Igor Santana Ribeiro, Iago Trezena Tavares De Lima, Svetoslav Nanev Slavov, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Vi Thuy Tran, Duong Thi Hue Kien, Tuyen Huynh, Sophie Yacoub, Idrissa Dieng, Richard Salvato, Gabriel Luz Wallau, Tatiana S Gregianini, Fernanda M S Godinho, Chantal B F Vogels, Mallery I Breban, Mariana Leguia, Suraj Jagtap, Rahul Roy, Chanditha Hapuarachchi, Gaspary Mwanyika, Marta Giovanetti, Luiz C J Alcantara, Nuno R Faria, Christine V F Carrington, Kathryn A Hanley, Edward C Holmes, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D Grubaugh","doi":"10.1371/journal.pbio.3002834","DOIUrl":"10.1371/journal.pbio.3002834","url":null,"abstract":"<p><p>Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present assignment tools to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002834"},"PeriodicalIF":9.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142299306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LXR-dependent enhancer activation regulates the temporal organization of the liver's response to refeeding leading to lipogenic gene overshoot.","authors":"Noga Korenfeld, Tali Gorbonos, Maria C Romero Florian, Dan Rotaro, Dana Goldberg, Talia Radushkevitz-Frishman, Meital Charni-Natan, Meirav Bar-Shimon, Carolyn L Cummins, Ido Goldstein","doi":"10.1371/journal.pbio.3002735","DOIUrl":"10.1371/journal.pbio.3002735","url":null,"abstract":"<p><p>Transitions between the fed and fasted state are common in mammals. The liver orchestrates adaptive responses to feeding/fasting by transcriptionally regulating metabolic pathways of energy usage and storage. Transcriptional and enhancer dynamics following cessation of fasting (refeeding) have not been explored. We examined the transcriptional and chromatin events occurring upon refeeding in mice, including kinetic behavior and molecular drivers. We found that the refeeding response is temporally organized with the early response focused on ramping up protein translation while the later stages of refeeding drive a bifurcated lipid synthesis program. While both the cholesterol biosynthesis and lipogenesis pathways were inhibited during fasting, most cholesterol biosynthesis genes returned to their basal levels upon refeeding while most lipogenesis genes markedly overshoot above pre-fasting levels. Gene knockout, enhancer dynamics, and ChIP-seq analyses revealed that lipogenic gene overshoot is dictated by LXRα. These findings from unbiased analyses unravel the mechanism behind the long-known phenomenon of refeeding fat overshoot.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002735"},"PeriodicalIF":9.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11379474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Syllable processing is organized in discrete subregions of the human superior temporal gyrus.","authors":"Daniel R Cleary, Youngbin Tchoe, Andrew Bourhis, Charles W Dickey, Brittany Stedelin, Mehran Ganji, Sang Heon Lee, Jihwan Lee, Dominic A Siler, Erik C Brown, Burke Q Rosen, Erik Kaestner, Jimmy C Yang, Daniel J Soper, Seunggu Jude Han, Angelique C Paulk, Sydney S Cash, Ahmed M Raslan, Shadi A Dayeh, Eric Halgren","doi":"10.1371/journal.pbio.3002774","DOIUrl":"10.1371/journal.pbio.3002774","url":null,"abstract":"<p><p>Modular organization at approximately 1 mm scale could be fundamental to cortical processing, but its presence in human association cortex is unknown. Using custom-built, high-density electrode arrays placed on the cortical surface of 7 patients undergoing awake craniotomy for tumor excision, we investigated receptive speech processing in the left (dominant) human posterior superior temporal gyrus. Responses to consonant-vowel syllables and noise-vocoded controls recorded with 1,024 channel micro-grids at 200 μm pitch demonstrated roughly circular domains approximately 1.7 mm in diameter, with sharp boundaries observed in 128 channel linear arrays at 50 μm pitch, possibly consistent with a columnar organization. Peak latencies to syllables in different modules were bimodally distributed centered at 252 and 386 ms. Adjacent modules were sharply delineated from each other by their distinct time courses and stimulus selectivity. We suggest that receptive language cortex may be organized in discrete processing modules.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002774"},"PeriodicalIF":9.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11410217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Centrosome amplification primes ovarian cancer cells for apoptosis and potentiates the response to chemotherapy.","authors":"Frances Edwards, Giulia Fantozzi, Anthony Y Simon, Jean-Philippe Morretton, Aurelie Herbette, Andrea E Tijhuis, Rene Wardenaar, Stacy Foulane, Simon Gemble, Diana C J Spierings, Floris Foijer, Odette Mariani, Anne Vincent-Salomon, Sergio Roman-Roman, Xavier Sastre-Garau, Oumou Goundiam, Renata Basto","doi":"10.1371/journal.pbio.3002759","DOIUrl":"10.1371/journal.pbio.3002759","url":null,"abstract":"<p><p>Centrosome amplification is a feature of cancer cells associated with chromosome instability and invasiveness. Enhancing chromosome instability and subsequent cancer cell death via centrosome unclustering and multipolar divisions is an aimed-for therapeutic approach. Here, we show that centrosome amplification potentiates responses to conventional chemotherapy in addition to its effect on multipolar divisions and chromosome instability. We perform single-cell live imaging of chemotherapy responses in epithelial ovarian cancer cell lines and observe increased cell death when centrosome amplification is induced. By correlating cell fate with mitotic behaviors, we show that enhanced cell death can occur independently of chromosome instability. We identify that cells with centrosome amplification are primed for apoptosis. We show they are dependent on the apoptotic inhibitor BCL-XL and that this is not a consequence of mitotic stresses associated with centrosome amplification. Given the multiple mechanisms that promote chemotherapy responses in cells with centrosome amplification, we assess such a relationship in an epithelial ovarian cancer patient cohort. We show that high centrosome numbers associate with improved treatment responses and longer overall survival. Our work identifies apoptotic priming as a clinically relevant consequence of centrosome amplification, expanding our understanding of this pleiotropic cancer cell feature.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002759"},"PeriodicalIF":9.8,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11441705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Keeping time: How musical training may boost cognition.","authors":"M Florencia Assaneo, Fernando Lizcano-Cortés, Pablo Ripolles","doi":"10.1371/journal.pbio.3002810","DOIUrl":"10.1371/journal.pbio.3002810","url":null,"abstract":"<p><p>The relationship between musical training and intellect is controversial. A new hypothesis may help resolve the debate by proposing an explanation for how training in rhythmic skills can improve cognitive abilities in some individuals, but not others.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002810"},"PeriodicalIF":9.8,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11407654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142141489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A flexible loop in the paxillin LIM3 domain mediates its direct binding to integrin β subunits.","authors":"Timo Baade, Marcus Michaelis, Andreas Prestel, Christoph Paone, Nikolai Klishin, Marleen Herbinger, Laura Scheinost, Ruslan Nedielkov, Christof R Hauck, Heiko M Möller","doi":"10.1371/journal.pbio.3002757","DOIUrl":"10.1371/journal.pbio.3002757","url":null,"abstract":"<p><p>Integrins are fundamental for cell adhesion and the formation of focal adhesions (FA). Accordingly, these receptors guide embryonic development, tissue maintenance, and haemostasis but are also involved in cancer invasion and metastasis. A detailed understanding of the molecular interactions that drive integrin activation, FA assembly, and downstream signalling cascades is critical. Here, we reveal a direct association of paxillin, a marker protein of FA sites, with the cytoplasmic tails of the integrin β1 and β3 subunits. The binding interface resides in paxillin's LIM3 domain, where based on the NMR structure and functional analyses, a flexible, 7-amino acid loop engages the unstructured part of the integrin cytoplasmic tail. Genetic manipulation of the involved residues in either paxillin or integrin β3 compromises cell adhesion and motility of murine fibroblasts. This direct interaction between paxillin and the integrin cytoplasmic domain identifies an alternative, kindlin-independent mode of integrin outside-in signalling particularly important for integrin β3 function.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 9","pages":"e3002757"},"PeriodicalIF":9.8,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11374337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}