PLoS Biology最新文献

{"title":"Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.","authors":"Lanxiang Wang, Yue Liu, Haoran Ni, Wenlong Zuo, Haimei Shi, Weixin Liao, Hongbin Liu, Jiajia Chen, Yang Bai, Hong Yue, Ancheng Huang, Jonathan Friedman, Tong Si, Yinggao Liu, Moxian Chen, Lei Dai","doi":"10.1371/journal.pbio.3002921","DOIUrl":"10.1371/journal.pbio.3002921","url":null,"abstract":"<p><p>Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002921"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733614","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":"Biofilm dispersal patterns revealed using far-red fluorogenic probes.","authors":"Jojo A Prentice, Sandhya Kasivisweswaran, Robert van de Weerd, Andrew A Bridges","doi":"10.1371/journal.pbio.3002928","DOIUrl":"10.1371/journal.pbio.3002928","url":null,"abstract":"<p><p>Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious due to the limitations of traditional fluorescent proteins, which lose functionality in large, oxygen-deprived biofilms. To overcome this challenge, we developed a cell-labeling strategy utilizing fluorogen-activating proteins (FAPs) and cognate far-red dyes, which remain functional throughout biofilm development, enabling long-term imaging. Using this approach, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae. We reveal that dispersal initiates at the biofilm periphery and approximately 25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression during cell departure and regional heterogeneity in cell motions. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate. Moreover, we demonstrate the broad applicability of FAPs as a powerful tool for high-resolution studies of microbial dynamics in complex environments.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002928"},"PeriodicalIF":9.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717502","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":"Reconstructing the last common ancestor of all eukaryotes.","authors":"Thomas A Richards, Laura Eme, John M Archibald, Guy Leonard, Susana M Coelho, Alex de Mendoza, Christophe Dessimoz, Pavel Dolezal, Lillian K Fritz-Laylin, Toni Gabaldón, Vladimír Hampl, Geert J P L Kops, Michelle M Leger, Purificacion Lopez-Garcia, James O McInerney, David Moreira, Sergio A Muñoz-Gómez, Daniel J Richter, Iñaki Ruiz-Trillo, Alyson E Santoro, Arnau Sebé-Pedrós, Berend Snel, Courtney W Stairs, Eelco C Tromer, Jolien J E van Hooff, Bill Wickstead, Tom A Williams, Andrew J Roger, Joel B Dacks, Jeremy G Wideman","doi":"10.1371/journal.pbio.3002917","DOIUrl":"10.1371/journal.pbio.3002917","url":null,"abstract":"<p><p>Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002917"},"PeriodicalIF":9.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717506","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":"Queer- and trans-inclusive faculty hiring-A call for change.","authors":"J L Weissman, Callie R Chappell, Bruno Francesco Rodrigues de Oliveira, Natalya Evans, Anna C Fagre, Desiree Forsythe, Steven A Frese, Rachel Gregor, Suzanne L Ishaq, Juliet Johnston, Bittu K R, Shayle B Matsuda, Sam McCarren, Melanie Ortiz Alvarez de la Campa, Troy A Roepke, Nasa Sinnott-Armstrong, Cora S Stobie, Lauren Talluto, José M Vargas-Muñiz","doi":"10.1371/journal.pbio.3002919","DOIUrl":"10.1371/journal.pbio.3002919","url":null,"abstract":"<p><p>As queer and trans scientists, we face varied and systemic barriers to our professional success, resulting in our relative absence from faculty ranks at many institutions. In this Perspective, we call for a change in faculty hiring practices and present concrete guidance to make it a more inclusive process.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002919"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693862","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":"CD74 promotes the formation of an immunosuppressive tumor microenvironment in triple-negative breast cancer in mice by inducing the expansion of tolerogenic dendritic cells and regulatory B cells.","authors":"Bianca Pellegrino, Keren David, Stav Rabani, Bar Lampert, Thuy Tran, Edward Doherty, Marta Piecychna, Roberto Meza-Romero, Lin Leng, Dov Hershkovitz, Arthur A Vandenbark, Richard Bucala, Shirly Becker-Herman, Idit Shachar","doi":"10.1371/journal.pbio.3002905","DOIUrl":"10.1371/journal.pbio.3002905","url":null,"abstract":"<p><p>CD74 is a cell-surface receptor for the cytokine macrophage migration inhibitory factor (MIF). MIF binding to CD74 induces a signaling cascade resulting in the release of its cytosolic intracellular domain (CD74-ICD), which regulates transcription in naïve B and chronic lymphocytic leukemia (CLL) cells. In the current study, we investigated the role of CD74 in the regulation of the immunosuppressive tumor microenvironment (TME) in triple-negative breast cancer (TNBC). TNBC is the most aggressive breast cancer subtype and is characterized by massive infiltration of immune cells to the tumor microenvironment, making this tumor a good candidate for immunotherapy. The tumor and immune cells in TNBC express high levels of CD74; however, the function of this receptor in the tumor environment has not been extensively characterized. Regulatory B cells (Bregs) and tolerogenic dendritic cells (tol-DCs) were previously shown to attenuate the antitumor immune response in TNBC. Here, we demonstrate that CD74 enhances tumor growth by inducing the expansion of tumor-infiltrating tol-DCs and Bregs. Utilizing CD74-KO mice, Cre-flox mice lacking CD74 in CD23+ mature B cells, mice lacking CD74 in the CD11c+ population, and a CD74 inhibitor (DRQ), we elucidate the mechanism by which CD74 inhibits antitumor immunity. MIF secreted from the tumor cells activates CD74 expressed on DCs. This activation induces the binding of CD74-ICD to the SP1 promotor, resulting in the up-regulation of SP1 expression. SP1 binds the IL-1β promotor, leading to the down-regulation of its transcription. The reduced levels of IL-1β lead to decreased antitumor activity by allowing expansion of the tol-DC, which induces the expansion of the Breg population, supporting the cross-talk between these 2 populations. Taken together, these results suggest that CD74+ CD11c+ DCs are the dominant cell type involved in the regulation of TNBC progression. These findings indicate that CD74 might serve as a novel therapeutic target in TNBC.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002905"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693858","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 call for research to address the threat of paper mills.","authors":"Jennifer A Byrne, Anna Abalkina, Olufolake Akinduro-Aje, Jana Christopher, Sarah E Eaton, Nitin Joshi, Ulf Scheffler, Nick H Wise, Jennifer Wright","doi":"10.1371/journal.pbio.3002931","DOIUrl":"10.1371/journal.pbio.3002931","url":null,"abstract":"<p><p>Research paper mills are covert organizations that provide low-quality or fabricated manuscripts to paying clients. As members of the United2Act Research Working Group, we propose 5 key research questions on paper mills that require resourcing and support.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002931"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693856","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":"How do mammals convert dynamic odor information into neural maps for landscape navigation?","authors":"Anantu Sunil, Olivia Pedroncini, Andreas T Schaefer, Tobias Ackels","doi":"10.1371/journal.pbio.3002908","DOIUrl":"10.1371/journal.pbio.3002908","url":null,"abstract":"<p><p>Odors are transported by seemingly chaotic plumes, whose spatiotemporal structure contains rich information about space, with olfaction serving as a gateway for obtaining and processing this spatial information. Beyond tracking odors, olfaction provides localization and chemical communication cues for detecting conspecifics and predators, and linking external environments to internal cognitive maps. In this Essay, we discuss recent physiological, behavioral, and methodological advancements in mammalian olfactory research to present our current understanding of how olfaction can be used to navigate the environment. We also examine potential neural mechanisms that might convert dynamic olfactory inputs into environmental maps along this axis. Finally, we consider technological applications of odor dynamics for developing bio-inspired sensor technologies, robotics, and computational models. By shedding light on the principles underlying the processing of odor dynamics, olfactory research will pave the way for innovative solutions that bridge the gap between biology and technology, enriching our understanding of the natural world.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002908"},"PeriodicalIF":9.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11581409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689338","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 human posterior parietal cortices orthogonalize the representation of different streams of information concurrently coded in visual working memory.","authors":"Yaoda Xu","doi":"10.1371/journal.pbio.3002915","DOIUrl":"10.1371/journal.pbio.3002915","url":null,"abstract":"<p><p>The key to adaptive visual processing lies in the ability to maintain goal-directed visual representation in the face of distraction. In visual working memory (VWM), distraction may come from the coding of distractors or other concurrently retained targets. This fMRI study reveals a common representational geometry that our brain uses to combat both types of distractions in VWM. Specifically, using fMRI pattern decoding, the human posterior parietal cortex is shown to orthogonalize the representations of different streams of information concurrently coded in VWM, whether they are targets and distractors, or different targets concurrently held in VWM. The latter is also seen in the human occipitotemporal cortex. Such a representational geometry provides an elegant and simple solution to enable independent information readout, effectively combating distraction from the different streams of information, while accommodating their concurrent representations. This representational scheme differs from mechanisms that actively suppress or block the encoding of distractors to reduce interference. It is likely a general neural representational principle that supports our ability to represent information beyond VWM in other situations where multiple streams of visual information are tracked and processed simultaneously.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002915"},"PeriodicalIF":9.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689364","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":"Stochastic models allow improved inference of microbiome interactions from time series data.","authors":"Román Zapién-Campos, Florence Bansept, Arne Traulsen","doi":"10.1371/journal.pbio.3002913","DOIUrl":"10.1371/journal.pbio.3002913","url":null,"abstract":"<p><p>How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic. Starting from a stochastic model, we derive dynamical equations not only for the average, but also for higher statistical moments of the microbial abundances. We use these equations to infer distributions of the interaction parameters that best describe the biological experimental data-improving identifiability and precision. The inferred distributions allow us to make predictions but also to distinguish between fairly certain parameters and those for which the available experimental data does not give sufficient information. Compared to related approaches, we derive expressions that also work for the relative abundance of microbes, enabling us to use conventional metagenome data, and account for cases where not a single host, but only replicate hosts, can be tracked over time.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002913"},"PeriodicalIF":9.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689362","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":"Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila.","authors":"Cécile Courret, Lucas W Hemmer, Xiaolu Wei, Prachi D Patel, Bryce J Chabot, Nicholas J Fuda, Xuewen Geng, Ching-Ho Chang, Barbara G Mellone, Amanda M Larracuente","doi":"10.1371/journal.pbio.3002911","DOIUrl":"10.1371/journal.pbio.3002911","url":null,"abstract":"<p><p>Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within the Drosophila simulans clade-D. simulans, D. sechellia, and D. mauritiana-and their relative, D. melanogaster. Using chromatin profiling combined with high-resolution fluorescence in situ hybridization on stretched chromatin fibers, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes in D. sechellia, where the X and fourth centromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002911"},"PeriodicalIF":9.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689368","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}