PLoS Biology最新文献

{"title":"Horizontal gene transfer of molecular weapons can reshape bacterial competition.","authors":"Elisa T Granato, Jacob D Palmer, Christian Kirk, Connor Sharp, George Shillcock, Kevin R Foster","doi":"10.1371/journal.pbio.3003095","DOIUrl":"10.1371/journal.pbio.3003095","url":null,"abstract":"<p><p>Bacteria commonly use molecular weaponry to kill or inhibit competitors. Genes encoding many weapons and their associated immunity mechanisms can be transmitted horizontally. These transfer events are striking because they appear to undermine bacterial weapons when given to competing strains. Here, we develop an ecological model of bacterial warfare to understand the impacts of horizontal gene transfer. Our model predicts that weapon gene transfer from an attacker to a target strain is possible, but will typically occur at a low rate such that transfer has a negligible impact on competition outcomes. We tested the model empirically using a transmissible plasmid encoding colicin E2, a potent antibacterial toxin produced by Escherichia coli. As predicted by the model, we find that toxin plasmid transfer is feasible during warfare, but the resulting transconjugants remain rare. However, exploring the model further reveals realistic conditions where transfer is predicted to have major impacts. Specifically, the model predicts that whenever competing strains have access to unique nutrients, transconjugants can proliferate and reach high abundances. In support of these predictions, short- and long-term experiments show that transconjugants can thrive when nutrient competition is relaxed. Our work shows how horizontal gene transfer can reshape bacterial warfare in a way that benefits a weapon gene and strains that receive it. Interestingly, we also find that there is little cost to a strain that transfers a weapon gene, which is expected to further enable the horizontal gene transfer of molecular weapons.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003095"},"PeriodicalIF":9.8,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12094771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120700","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":"Inhibition of the nucleolar RNA exosome facilitates adaptation to starvation.","authors":"Xi Feng, Xiaoman Wang, Shouhong Guang, Shanshan Pang, Haiqing Tang","doi":"10.1371/journal.pbio.3003190","DOIUrl":"10.1371/journal.pbio.3003190","url":null,"abstract":"<p><p>In response to nutrient scarcity, cells must reallocate their limited energy for cellular maintenance at the expense of certain processes. How such a tradeoff is achieved remains largely unknown. RNA surveillance is crucial for the integrity of the transcriptome, whose defects are associated with several human diseases. Unexpectedly, we discover that the nucleolar RNA exosome, a key RNA surveillance machine, is inhibited by starvation. This is not merely the cessation of a temporarily non-essential process, but rather a key signal to allocate energy. By rewiring one-carbon metabolism, the inhibition of RNA exosome reduces translation, the most energy-consuming process. Energy is then conserved for fat synthesis to enhance cellular maintenance and starvation survival. Notably, while benefiting starvation fitness, RNA exosome inhibition impairs the life span of well-fed animals, indicating a tradeoff between short-term and long-term fitness. Our findings suggest that the nucleolar RNA surveillance can be temporarily sacrificed to facilitate starvation adaptation.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003190"},"PeriodicalIF":9.8,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12136472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120800","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":"Correction: Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities.","authors":"Joseph A Morton, Carlos Alberto Arnillas, Lori Biedermann, Elizabeth T Borer, Lars A Brudvig, Yvonne M Buckley, Marc W Cadotte, Kendi Davies, Ian Donohue, Anne Ebeling, Nico Eisenhauer, Catalina Estrada, Sylvia Haider, Yann Hautier, Anke Jentsch, Holly Martinson, Rebecca L McCulley, Xavier Raynaud, Christiane Roscher, Eric W Seabloom, Carly J Stevens, Katerina Vesela, Alison Wallace, Ilia J Leitch, Andrew R Leitch, Erika I Hersch-Green","doi":"10.1371/journal.pbio.3003195","DOIUrl":"10.1371/journal.pbio.3003195","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1371/journal.pbio.3002927.].</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003195"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112344","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":"Accredited ocean sanctuaries for transforming captive cetacean care.","authors":"Lori Marino, Charles Vinick, Katy Foster, Jeff Foster, Rob Hicks, Graham McGrath, John Racanelli, Janesse Brewer","doi":"10.1371/journal.pbio.3003166","DOIUrl":"10.1371/journal.pbio.3003166","url":null,"abstract":"<p><p>Increasing concerns over the welfare of captive cetaceans (dolphins, whales, and porpoises) have led to calls for their transfer from marine parks and aquariums to sanctuaries. We describe an unprecedented collaboration to develop the first accreditation guidelines for authentic ocean sanctuaries to transform cetacean care.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003166"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112338","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":"Excitatory projections from the nucleus reuniens to the medial prefrontal cortex modulate pain and depression-like behaviors in mice.","authors":"Shu-Ting Bao, Fang Rao, Cui Yin, Yong Niu, Jun-Li Cao, Cheng Xiao, Chunyi Zhou","doi":"10.1371/journal.pbio.3003170","DOIUrl":"10.1371/journal.pbio.3003170","url":null,"abstract":"<p><p>The medial prefrontal cortex (mPFC) is implicated in emotional processing, cognition, and pain sensation, moreover, its circuitry undergoes neuroplastic changes in chronic pain. Although the nucleus reuniens (RE) of the thalamus provides significant glutamatergic inputs to the mPFC, it remains unclear whether this projection contributes to plasticity changes in the mPFC and pain-related behaviors in chronic pain. Using fiber photometry, we demonstrated that RE neurons responded to pain stimulation and emotional changes. Optogenetic activation of RE neurons and their projections to the mPFC (RE-mPFC projection) elicits hyperalgesia and depression-like behaviors in naïve mice. In a neuropathic pain mouse model, RE neurons were hyperactive, and the RE-mPFC projection was enhanced with a marked preference for the part innervating GABAergic circuits in the mPFC to that controlling mPFC neurons projecting to the ventrolateral periaqueductal gray (vlPAG). Expectedly, optogenetic inhibition of RE neurons and the RE-mPFC projection ameliorated pain-like and depression-like behaviors in neuropathic pain mice. Additionally, chemogenetic inhibition of RE-mPFC neurons conferred analgesia in neuropathic pain mice exposed to both acute and chronic morphine. Our findings highlight the significant role of the RE-mPFC pathway in neuropathic pain comorbid with depression, suggesting its potential as a target for treatment of neuropathic pain.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003170"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112352","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":"Permeability selection of biologically relevant membranes matches the stereochemistry of life on Earth.","authors":"Olivia Goode, Urszula Łapińska, Juliano Morimoto, Georgina Glover, David S Milner, Alyson E Santoro, Stefano Pagliara, Thomas A Richards","doi":"10.1371/journal.pbio.3003155","DOIUrl":"10.1371/journal.pbio.3003155","url":null,"abstract":"<p><p>Early in the evolution of life, a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds could enter the compartment and which compounds could not. One key feature of known life is the utilization of right-handed d-ribose and d-deoxyribose sugars and left-handed l-amino acid stereochemical isomers (enantiomers); however, it is not clear why life adopted this specific chirality. Generally, archaea have l-phospholipid membrane chemistries and bacteria and eukaryotes have d-phospholipid membrane chemistries. We previously demonstrated that an l-archaeal and a d-intermediate membrane mimic, bearing a mixture of bacterial and archaeal lipid characteristics (a 'hybrid' membrane), displayed increased permeability for several key compounds compared to bacterial-like membranes. Here, we investigate if these membranes can drive stereochemical selection on pentose sugars, hexose sugars, and amino acids. Using permeability assays of homogenous unilamellar vesicles, we demonstrate that both membranes select for d-ribose and d-deoxyribose sugars while the hybrid membrane uniquely selects for a reduced alphabet of l-amino acids. This repertoire includes alanine, the plausible first l-amino acid utilized. We conclude such compartments could provide stereochemical compound selection matching those used by the core metabolism of life.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003155"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112498","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":"Rewarding animals based on their subjective percepts is enabled by online Bayesian estimation of perceptual biases.","authors":"Yelin Dong, Gabor Lengyel, Sabyasachi Shivkumar, Akiyuki Anzai, Grace F DiRisio, Ralf M Haefner, Gregory C DeAngelis","doi":"10.1371/journal.pbio.3002764","DOIUrl":"10.1371/journal.pbio.3002764","url":null,"abstract":"<p><p>Elucidating the neural basis of perceptual biases, such as those produced by visual illusions, can provide powerful insights into the neural mechanisms of perceptual inference. However, studying the subjective percepts of animals poses a fundamental challenge: unlike human participants, animals cannot be verbally instructed to report what they see, hear, or feel. Instead, they must be trained to perform a task for reward, and researchers must infer from their responses what the animal perceived. However, animals' responses are shaped by reward feedback, thus raising the major concern that the reward regimen may alter the animal's decision strategy or even their intrinsic perceptual biases. Using simulations of a reinforcement learning agent, we demonstrate that conventional reward strategies fail to allow accurate estimation of perceptual biases. We developed a method that estimates perceptual bias during task performance and then computes the reward for each trial based on the evolving estimate of the animal's perceptual bias. Our approach makes use of multiple stimulus contexts to dissociate perceptual biases from decision-related biases. Starting with an informative prior, our Bayesian method updates a posterior over the perceptual bias after each trial. The prior can be specified based on data from past sessions, thus reducing the variability of the online estimate and allowing it to converge to a stable value over a small number of trials. After validating our method on synthetic data, we apply it to estimate perceptual biases of monkeys in a motion direction discrimination task in which varying background optic flow induces robust perceptual biases. This method overcomes an important challenge to understanding the neural basis of subjective percepts.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3002764"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12129325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112499","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":"Object knowledge representation in the human visual cortex requires a connection with the language system.","authors":"Bo Liu, Xiaosha Wang, Xiaoying Wang, Yan Li, Yang Han, Jiahui Lu, Hui Zhang, Xiaochun Wang, Yanchao Bi","doi":"10.1371/journal.pbio.3003161","DOIUrl":"10.1371/journal.pbio.3003161","url":null,"abstract":"<p><p>How world knowledge is stored in the human brain is a central question in cognitive neuroscience. Object knowledge effects have been commonly observed in higher-order sensory association cortices, with the role of language being highly debated. Using object color as a test case, we investigated whether communication with the language system plays a necessary role in knowledge neural representation in the visual cortex and corresponding behaviors, combining diffusion imaging (measuring white-matter structural integrity), functional MRI (fMRI; measuring functional neural representation of knowledge), and neuropsychological assessments (measuring behavioral integrity) in a group of patients who suffered from stroke (N = 33; 18 with left-hemisphere lesions, 11 with right-hemisphere lesions, and 4 with bilateral lesions). The structural integrity loss of the white-matter connection between the anterior temporal language region and the ventral visual cortex had a significant effect on the neural representation strength of object color knowledge in the ventral visual cortex and on object color knowledge behavior across modalities. These contributions could not be explained by the potential effects of the early visual perception pathway or potential confounding brain or cognitive variables. Our experiments reveal the contribution of the vision-language connection in the ventral occipitotemporal cortex (VOTC) object knowledge neural representation and object knowledge behaviors, highlighting the significance of the language-sensory system interface.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003161"},"PeriodicalIF":9.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112359","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":"The glycosomal ATP-dependent phosphofructokinase of Trypanosoma brucei operates also in the gluconeogenic direction.","authors":"Nicolas Plazolles, Hanna Kulyk, Edern Cahoreau, Marc Biran, Marion Wargnies, Erika Pineda, Mohammad El Kadri, Aline Rimoldi, Perrine Hervé, Corinne Asencio, Loïc Rivière, Paul A M Michels, Daniel Inaoka, Emmanuel Tetaud, Jean-Charles Portais, Frédéric Bringaud","doi":"10.1371/journal.pbio.3002938","DOIUrl":"10.1371/journal.pbio.3002938","url":null,"abstract":"<p><p>In the glucose-free environment of the midgut of the tsetse fly vector, the procyclic forms of Trypanosoma brucei primarily consume proline to feed its central carbon and energy metabolism. In this context, the parasite produces through gluconeogenesis, glucose 6-phosphate (G6P), the precursor of essential metabolic pathways, from proline catabolism. We show here that the parasite uses three different enzymes to perform the key gluconeogenic reaction producing fructose 6-phosphate (F6P) from fructose 1,6-bisphosphate, (i) fructose-1,6-bisphosphatase (FBPase), the canonical enzyme performing this reaction, (ii) sedoheptulose-1,7-bisphosphatase (SBPase), and (iii) more surprisingly ATP-dependent phosphofructokinase (PFK), an enzyme considered to irreversibly catalyze the opposite reaction involved in glycolysis. These three enzymes, as well as six other glycolytic/gluconeogenic enzymes, are located in peroxisome-related organelles, named glycosomes. Incorporation of 13C-enriched glycerol (a more effective alternative to proline for monitoring gluconeogenic activity) into F6P and G6P was more affected in the PFK null mutant than in the FBPase null mutant, suggesting the PFK contributes at least as much as FBPase to gluconeogenesis. We also showed that glucose deprivation did not affect the quantities of PFK substrates and products, whereas an approximately 500-fold increase in the substrate/product ratio was expected for PFK to carry out the gluconeogenic reaction. In conclusion, we show for the first time that ATP-dependent PFK can function in vivo in the gluconeogenic direction, even in the presence of FBPase activity. This particular feature, which precludes loss of ATP through a futile cycle involving PFK and FBPase working simultaneously in the glycolytic and gluconeogenic directions, respectively, is possibly due to the supramolecular organization of the metabolic pathway within glycosomes to overcome thermodynamic barriers through metabolic channeling.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3002938"},"PeriodicalIF":9.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081604","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":"Analysis of gene expression within individual cells reveals spatiotemporal patterns underlying Vibrio cholerae biofilm development.","authors":"Grace E Johnson, Chenyi Fei, Ned S Wingreen, Bonnie L Bassler","doi":"10.1371/journal.pbio.3003187","DOIUrl":"10.1371/journal.pbio.3003187","url":null,"abstract":"<p><p>Bacteria commonly exist in multicellular, surface-attached communities called biofilms. Biofilms are central to ecology, medicine, and industry. The Vibrio cholerae pathogen forms biofilms from single founder cells that, via cell division, mature into three-dimensional structures with distinct, yet reproducible, regional architectures. To define mechanisms underlying biofilm developmental transitions, we establish a single-molecule fluorescence in situ hybridization (smFISH) approach that enables accurate quantitation of spatiotemporal gene-expression patterns in biofilms at cell-scale resolution. smFISH analyses of V. cholerae biofilm regulatory and structural genes demonstrate that, as biofilms mature, overall matrix gene expression decreases, and simultaneously, a pattern emerges in which matrix gene expression becomes largely confined to peripheral biofilm cells. Both quorum sensing and c-di-GMP-signaling are required to generate the proper temporal pattern of matrix gene expression. Quorum sensing signaling is uniform across the biofilm, and thus, c-di-GMP-signaling alone sets the regional matrix gene expression pattern. The smFISH strategy provides insight into mechanisms conferring particular fates to individual biofilm cells.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 5","pages":"e3003187"},"PeriodicalIF":9.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081519","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}