Communications Biology最新文献_第3页

MatE transporter affects methane metabolism in Methermicoccus shengliensis and is modulated by methoxylated aromatic compounds.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07583-1

Huan Leng, Dong Wang, Qing Yang, Shuxin Wang, Leizhou Guo, Pengyan Zhao, Yi Chen, Lirong Dai, Guihong Cha, Liping Bai, Frank Delvigne

{"title":"MatE transporter affects methane metabolism in Methermicoccus shengliensis and is modulated by methoxylated aromatic compounds.","authors":"Huan Leng, Dong Wang, Qing Yang, Shuxin Wang, Leizhou Guo, Pengyan Zhao, Yi Chen, Lirong Dai, Guihong Cha, Liping Bai, Frank Delvigne","doi":"10.1038/s42003-025-07583-1","DOIUrl":"10.1038/s42003-025-07583-1","url":null,"abstract":"Methoxylated aromatic compounds, are abundant in subsurface ecosystems. Recently, it was discovered that Methermicoccus shengliensis can convert methoxylated aromatics to methane. Specifically, the MATE family transporters (MatE) and transduction-like protein (Tlp) were hypothesized to play a crucial role in substrate transport. However, their biological function and the transporting model remained unclear. To address this knowledge gap, we employed bacterial two-hybrid and structural model assays to investigate the interaction between Tlp and MatE. Our results revealed that Tlp senses 2-methoxybenzoate and interacts with MatE to facilitate substrate transport. Furthermore, we observed that the matE knock-out mutant significantly impaired the growth and methane production of M. shengliensis when using 2-methoxybenzoate as a substrate, highlighting the essential role of MatE in methoxydotrophic methanogenesis. Overall, our findings suggest that the MatE-Tlp system regulates substrate uptake and methane metabolism in M. shengliensis, providing new avenues for reducing global methane emissions caused by methanogens.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"183"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254631","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}

引用次数: 0

CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07570-6

Jerome J Choi, John Svaren, Daifeng Wang

{"title":"CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics.","authors":"Jerome J Choi, John Svaren, Daifeng Wang","doi":"10.1038/s42003-025-07570-6","DOIUrl":"10.1038/s42003-025-07570-6","url":null,"abstract":"Oligodendrocytes are the myelinating cells within the central nervous system, but the mechanisms by which transcription factors (TFs) cooperate for gene regulation in oligodendrocytes remain unclear. We introduce coTF-reg, an analytical framework that integrates scRNA-seq and scATAC-seq data to identify cooperative TFs co-regulating the target gene (TG). First, we identify co-binding TF pairs in the same oligodendrocyte-specific regulatory regions. Next, we train a deep learning model to predict each TG expression using the co-binding TFs' expressions. Shapley interaction scores reveal high interactions between co-binding TF pairs, such as SOX10-TCF12. Validation using oligodendrocyte eQTLs and their eGenes that are regulated by these cooperative TFs show potential regulatory roles for genetic variants. Experimental validation using ChIP-seq data confirms some cooperative TF pairs, such as SOX10-OLIG2. Prediction performance of our models is evaluated through holdout data and additional datasets, and an ablation study is also conducted. The results demonstrate stable and consistent performance.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"181"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254419","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}

引用次数: 0

A review of quorum-sensing and its role in mediating interkingdom interactions in the ocean.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07608-9

Megan Coolahan, Kristen E Whalen

引用次数: 0

Single-cell RNA sequencing reveals tumor heterogeneity in small cell neuroendocrine cervical carcinoma.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07605-y

Xuesong Xiang, Xiang Tao, Keqin Hua, Hua Jiang, Jingxin Ding

{"title":"Single-cell RNA sequencing reveals tumor heterogeneity in small cell neuroendocrine cervical carcinoma.","authors":"Xuesong Xiang, Xiang Tao, Keqin Hua, Hua Jiang, Jingxin Ding","doi":"10.1038/s42003-025-07605-y","DOIUrl":"10.1038/s42003-025-07605-y","url":null,"abstract":"Small cell neuroendocrine cervical carcinoma (SCNECC) is an aggressive gynecological malignancy with poor prognosis. The precision therapeutic strategies for SCNECC are severely limited by the complex tumor microenvironment. Here, we mapped the single-cell landscape of a total of six samples from matched SCNECC cancerous foci and normal adjacent cervical tissues. Through analysis of 68,455 high-quality cells, malignant epithelial cells were identified with increased neuroendocrine differentiation and reduced keratinization. Within four epithelial cell clusters, the key transcription factors ASCL1, NEUROD1, POU2F3, and YAP1 defined molecular subtypes. Transitional trajectory among subtypes characterized two distinct carcinogenesis pathways in SCNECC. The P-type SCNECC showed potentially enhanced immune infiltration over other subtypes. Intercellular communication analysis identified several immune checkpoints and differentially expressed signaling pathways among subtypes. Through western blotting, the TC-YIK cell line was identified as an N-type SCNECC cell with high expression of SLFN11 and mTOR. Based on immunohistochemical staining of malignant subtyping markers, a cohort of 66 SCNECC patients from our hospital were divided into five subtypes. We further combined YAP1 expression with other clinicopathological factors (Cox p < 0.05) to establish a prognostic nomogram. Overall, these findings provide clues for tumorigenesis, precision treatments and prognostic prediction in SCNECC.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"184"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254795","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}

引用次数: 0

Motion-tolerant 3D volumetric multimodality microscopy imaging of human skin with subcellular resolution and extended field-of-view.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07614-x

Zhenguo Wu, Yunxian Tian, Jianhua Zhao, Yimei Huang, Harvey Lui, Sunil Kalia, Haishan Zeng

{"title":"Motion-tolerant 3D volumetric multimodality microscopy imaging of human skin with subcellular resolution and extended field-of-view.","authors":"Zhenguo Wu, Yunxian Tian, Jianhua Zhao, Yimei Huang, Harvey Lui, Sunil Kalia, Haishan Zeng","doi":"10.1038/s42003-025-07614-x","DOIUrl":"10.1038/s42003-025-07614-x","url":null,"abstract":"The skin, the body's largest organ, has a heterogeneous structure with various cell types and tissue layers. In vivo noninvasive 3D volumetric imaging with multi-contrast, high resolution, a large field-of-view (FOV), and no-motion artifacts is crucial for studying skin biology and diagnosing/evaluating diseases. Traditionally high-resolution in vivo skin microscopy methods capture images in the en-face (xy) plane parallel to the skin surface but are affected by involuntary motion, particularly during large-area volumetric data acquisition using xy-z mosaicking. In this work, we developed an xz-y imaging method that acquires images in the vertical (xz) plane and extends the FOV by moving the skin laterally along the y-direction. This approach is conceived based on our observation that involuntary skin movements are mostly along the vertical direction. Combined with a unique motion correction method, it enables 3D image reconstruction with subcellular resolution and an extended FOV close to a centimeter (8 mm). A multimodality microscopy system using this method provides simultaneous reflectance confocal, two-photon excited fluorescence, and second harmonic generation imaging, enabling multi-contrast capabilities. Using this system, we captured histology-like features of normal skin, vitiligo, and melanoma, demonstrating its potential for in vivo skin biology studies, clinical diagnosis, treatment planning and monitoring.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"186"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254721","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}

引用次数: 0

A multimodal characterization of low-dimensional thalamocortical structural connectivity patterns.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07528-8

Alexandra John, Meike D Hettwer, H Lina Schaare, Amin Saberi, Şeyma Bayrak, Bin Wan, Jessica Royer, Boris C Bernhardt, Sofie L Valk

{"title":"A multimodal characterization of low-dimensional thalamocortical structural connectivity patterns.","authors":"Alexandra John, Meike D Hettwer, H Lina Schaare, Amin Saberi, Şeyma Bayrak, Bin Wan, Jessica Royer, Boris C Bernhardt, Sofie L Valk","doi":"10.1038/s42003-025-07528-8","DOIUrl":"10.1038/s42003-025-07528-8","url":null,"abstract":"The human thalamus is a heterogeneous subcortical structure coordinating whole-brain activity. Investigations of its internal organization reveal differentiable subnuclei, however, a consensus on subnuclei boundaries remains absent. Recent work suggests that thalamic organization additionally reflects continuous axes transcending nuclear boundaries. Here, we study how low-dimensional axes of thalamocortical structural connectivity relate to intrathalamic microstructural features, functional connectivity, and structural covariance. Using diffusion MRI, we compute a thalamocortical structural connectome and derive two main axes of thalamic organization. The principal axis, extending from medial to lateral, relates to intrathalamic myelin, and functional connectivity organization. The secondary axis corresponds to the core-matrix cell distribution. Lastly, exploring multimodal associations globally, we observe the principal axis consistently differentiating limbic, frontoparietal, and default mode network nodes from dorsal and ventral attention networks across modalities. However, the link with sensory modalities varies. In sum, we show the coherence between lower dimensional patterns of thalamocortical structural connectivity and various modalities, shedding light on multiscale thalamic organization.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"185"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254321","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}

引用次数: 0

Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07610-1

Arni Thorlacius, Maksim Rulev, Oscar Sundberg, Anna Sundborger-Lunna

{"title":"Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers.","authors":"Arni Thorlacius, Maksim Rulev, Oscar Sundberg, Anna Sundborger-Lunna","doi":"10.1038/s42003-025-07610-1","DOIUrl":"10.1038/s42003-025-07610-1","url":null,"abstract":"Bin/Amphiphysin/Rvs167 (BAR) domain containing proteins are peripheral membrane proteins that regulate intracellular membrane curvature. BAR protein endophilin B1 plays a key role in multiple cellular processes critical for oncogenesis, including autophagy and apoptosis. Amphipathic regions in endophilin B1 drive membrane association and tubulation through membrane scaffolding. Our understanding of exactly how BAR proteins like endophilin B1 promote highly diverse intracellular membrane remodeling events in the cell is severely limited due to lack of high-resolution structural information. Here we present the highest resolution cryo-EM structure of a BAR protein to date and the first structures of a BAR protein bound to a lipid bicelle. Using neural networks, we can effectively sort particle species of different stoichiometries, revealing the tremendous flexibility of post-membrane binding, pre-polymer BAR dimer organization and membrane deformation. We also show that endophilin B1 efficiently permeabilizes negatively charged liposomes that contain mitochondria-specific lipid cardiolipin and propose a new model for Bax-mediated cell death.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"182"},"PeriodicalIF":5.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11799418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254790","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}

引用次数: 0

A listening advantage for native speech is reflected by attention-related activity in auditory cortex.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-05 DOI: 10.1038/s42003-025-07601-2

Meng Liang, Johannes Gerwien, Alexander Gutschalk

引用次数: 0

Engineering a phi15-based expression system for stringent gene expression in Pseudomonas putida.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-04 DOI: 10.1038/s42003-025-07508-y

Eveline-Marie Lammens, Daniel C Volke, Alison Kerremans, Yannick Aerts, Maarten Boon, Pablo I Nikel, Rob Lavigne

{"title":"Engineering a phi15-based expression system for stringent gene expression in Pseudomonas putida.","authors":"Eveline-Marie Lammens, Daniel C Volke, Alison Kerremans, Yannick Aerts, Maarten Boon, Pablo I Nikel, Rob Lavigne","doi":"10.1038/s42003-025-07508-y","DOIUrl":"10.1038/s42003-025-07508-y","url":null,"abstract":"The T7 phage RNA polymerase (RNAP) is a widely used expression platform, but its implementation in non-model microbial hosts poses significant challenges due to cytotoxicity. We constructed an optimized phage phi15-based expression system as alternative to the T7 platform for a wide range of applications in Pseudomonas putida. The new system employs the small phi15 RNAP, driving expression from an orthogonal phi15 promoter. By finetuning expression levels of phi15rnap and introducing a phi15 lysozyme mutant that inhibits phi15 RNAP in uninduced conditions, a stringent system was created with 200-fold inducibility. Moreover, by successfully decoupling cell growth and protein production using phi15 gp16, a host RNAP inhibitor, expression levels could be enhanced further (20%). Apart from creating four optimized platform P. putida hosts and a set of Golden Gate-compatible vectors, we demonstrate the extensive flexibility of the phi15 system. A proof-of-concept expression for industrially relevant fluorinase resulted in 2.5- and 5-fold increased yield compared to other widely-adopted expression systems. The system functions well in combination with several inducer systems, and in a variety of vector-based and genomically integrated set-ups. In conclusion, the phi15 RNAP, promoter, lysozyme and growth-decoupler provide a valuable plug-and-play set of genetic parts for the P. putida toolbox.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"171"},"PeriodicalIF":5.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188561","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}

引用次数: 0

A cyanobacteria-derived intermolecular salt bridge stabilizes photosynthetic NDH-1 and prevents oxidative stress.

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-02-04 DOI: 10.1038/s42003-025-07556-4

Mei Zheng, Yuanyuan Jiang, Zhaoxing Ran, Shengjun Liang, Tingting Xiao, Xiafei Li, Weimin Ma

{"title":"A cyanobacteria-derived intermolecular salt bridge stabilizes photosynthetic NDH-1 and prevents oxidative stress.","authors":"Mei Zheng, Yuanyuan Jiang, Zhaoxing Ran, Shengjun Liang, Tingting Xiao, Xiafei Li, Weimin Ma","doi":"10.1038/s42003-025-07556-4","DOIUrl":"10.1038/s42003-025-07556-4","url":null,"abstract":"Throughout evolution, addition of numerous cyanobacteria-derived subunits to the photosynthetic NDH-1 complex stabilizes the complex and facilitates cyclic electron transfer around photosystem I (PSI CET), a critical antioxidant mechanism for efficient photosynthesis, but its stabilization mechanism remains elusive. Here, a cyanobacteria-derived intermolecular salt bridge is found to form between the two conserved subunits, NdhF1 and NdhD1. Its disruption destabilizes photosynthetic NDH-1 and impairs PSI CET, resulting in the production of more reactive oxygen species under high light conditions. The salt bridge and transmembrane helix 16, both situated at the C-terminus of NdhF1, collaboratively secure the linkage between NdhD1 and NdhB, akin to a cramping mechanism. The linkage is also stabilized by cyanobacteria-derived NdhP and NdhQ subunits, but their stabilization mechanisms are distinctly different. Collectively, to the best of our knowledge, this is the first study to unveil the stabilization mechanism of photosynthetic NDH-1 by incorporating photosynthetic components into its conserved subunits during evolution.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"172"},"PeriodicalIF":5.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188557","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}

引用次数: 0