{"title":"YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.","authors":"Jingjing Li, Fabienne Göbel, Hsun Yun Hsu, Julian Nikolaus Koch, Natalie Hager, Wanda Antonia Flegler, Tomohisa Sebastian Tanabe, Christiane Dahl","doi":"10.1038/s42003-024-07270-7","DOIUrl":"10.1038/s42003-024-07270-7","url":null,"abstract":"<p><p>Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1548"},"PeriodicalIF":5.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686193","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":"Finding the sweet spot in the deep ocean.","authors":"Linn Hoffmann","doi":"10.1038/s42003-024-07220-3","DOIUrl":"10.1038/s42003-024-07220-3","url":null,"abstract":"","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1544"},"PeriodicalIF":5.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686169","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}
Ying Xu, Wen Yin, Yibin Cheng, Wei Zeng, Wenqiang Li, Wanping Chen, Fei Wang, Nan Peng, Lixin Ma, Tao Liu
{"title":"Collateral nuclease activity of TnpB triggered by high temperature enables fast and sensitive nucleic acid detection.","authors":"Ying Xu, Wen Yin, Yibin Cheng, Wei Zeng, Wenqiang Li, Wanping Chen, Fei Wang, Nan Peng, Lixin Ma, Tao Liu","doi":"10.1038/s42003-024-07123-3","DOIUrl":"10.1038/s42003-024-07123-3","url":null,"abstract":"<p><p>TnpB proteins encoded in the IS200/IS605 family are RNA-guided endonuclease which can be harnessed in genome editing. However, the collateral nuclease activity of TnpB remains poorly understood, which limits the development of TnpB-based diagnostic tools. Here we showed that TnpB from a thermophilic archaeon exhibits enhanced collateral ssDNA cleavage activity (trans-cleavage) activated by high temperature. Mutations either in the TAM or seed sequences of the target DNA impair the trans-cleavage activity, which indicates its potential to be employed in molecular diagnostic. Importantly, by optimizing the length and the sequences of the collateral substrates, we have developed a new nucleic acid detection method based on TnpB with a sensitivity of 29 cp μl<sup>-1</sup> in 30 min, which we name it TESD (TnpB Enable fast and Sensitive Detection). In summary, our findings illustrate the collateral nuclease activity of a TnpB from thermophiles and provide a novel platform for molecular diagnostics.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1541"},"PeriodicalIF":5.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681213","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":"PLGA/BK microspheres targeting the bradykinin signaling pathway as a therapeutic strategy to delay intervertebral disc degeneration.","authors":"Xiaoming Qiu, Yizhi Zhang, Ziyan Wei, Zhangbin Luo, Zhuanping Wang, Xuewen Kang","doi":"10.1038/s42003-024-07196-0","DOIUrl":"10.1038/s42003-024-07196-0","url":null,"abstract":"<p><p>Intervertebral disc degeneration(IVDD) is a common spinal condition with limited effective treatments available. This study aims to investigate the impact of poly(lactic-co-glycolic acid)/Bradykinin (PLGA/BK) microspheres on IVDD and its underlying mechanisms. We collected nucleus pulposus samples from both healthy and degenerated human intervertebral disks and conducted immunohistochemical analyses, revealing reduced BK expression in degenerated tissues. Subsequently, we used BK to treat nucleus pulposus cells and conducted Bulk RNA sequencing (RNA-seq), identifying BK's involvement in cellular senescence, extracellular matrix metabolism, and the PI3K signaling pathway. Further experiments using tert-butyl hydroperoxide (TBHP)-induced cell senescence showed that BK treatment reduced senescence, enhanced extracellular matrix synthesis, and inhibited degradation, along with activation of the PI3K pathway. These effects were mediated through B2R (BK receptor 2) and the downstream PI3K pathway. Following this, we developed sustained-release BK microspheres with an optimized manufacturing process. In vitro co-culture experiments showed no observable toxicity. We established an IVDD model in rat tail vertebrae through fine needle puncture, administering local injections of BK sustained-release microspheres. Using various experimental methods, including X-ray, MRI, histopathology, and immunohistochemistry, we found that these microspheres could slow the progression of IVDD. This study highlights the potential of injectable PLGA/BK microspheres to regulate cellular senescence and extracellular matrix metabolism via the B2R and PI3K pathways, ultimately delaying IVDD.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1540"},"PeriodicalIF":5.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681142","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}
Vivek Jadhav, Roberto Pasqua, Christophe Zanon, Matthieu Roy, Gilles Tredan, Richard Bon, Vishwesha Guttal, Guy Theraulaz
{"title":"Collective responses of flocking sheep (Ovis aries) to a herding dog (border collie).","authors":"Vivek Jadhav, Roberto Pasqua, Christophe Zanon, Matthieu Roy, Gilles Tredan, Richard Bon, Vishwesha Guttal, Guy Theraulaz","doi":"10.1038/s42003-024-07245-8","DOIUrl":"10.1038/s42003-024-07245-8","url":null,"abstract":"<p><p>Group-living organisms commonly exhibit collective escape responses, yet how information flows among group members in these events remains an open question. Here, we study the collective responses of a sheep flock (Ovis aries) to a shepherd dog (border collie) in a driving task between two well-defined target points. We collected high-resolution spatiotemporal data from 14 sheep and the dog, using Ultra-Wide-Band tags attached to each individual. We find that the spatial positions of sheep along the front-back axis of the group's velocity strongly correlate with their impact on the collective movement. Our analyses reveal that, even though the dog chases the sheep flock from behind, directional information on shorter time scales propagates from the front of the group towards the rear; further, the dog adjusts its movement in response to the flock's dynamics. We introduce an agent-based model that captures key data features. Specifically, in response to chasing, the sheep change their spatial relative positions less frequently and exhibit a transfer of directional information flow from front to back; this pattern disappears in the absence of chasing. Our study reveals some general insights into how directional information propagates in escaping animal groups.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1543"},"PeriodicalIF":5.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681139","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}
Qi Wang, Meidi Huang Yang, Shuangting Yu, Yingjie Chen, Kaikuo Wang, Yan Zhang, Ran Zhao, Jiongtang Li
{"title":"An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp.","authors":"Qi Wang, Meidi Huang Yang, Shuangting Yu, Yingjie Chen, Kaikuo Wang, Yan Zhang, Ran Zhao, Jiongtang Li","doi":"10.1038/s42003-024-07177-3","DOIUrl":"10.1038/s42003-024-07177-3","url":null,"abstract":"<p><p>In allotetraploid common carp, protein-coding homoeologs presented divergent expression levels between the two subgenomes. However, whether subgenome dominance occurs in other transcriptional and post-transcriptional events remains unknown. Using Illumina RNA sequencing and PacBio full-length sequencing, we refined the common carp transcriptome annotation and explored differences in four transcriptional and post-transcriptional events between the two subgenomes. The results revealed that the B subgenome presented more alternative splicing events, as did lncRNAs and circRNAs. However, the expression levels, tissue specificity, sequence features, and functions of lncRNAs and circRNAs did not significantly differ between the two subgenomes, suggesting a common regulatory mechanism shared by the two subgenomes. Furthermore, both the number and base substitution frequency of RNA editing events were greater in the B subgenome. Functional analyses of these transcriptional events also revealed subgenome bias. Genes that undergo alternative splicing in the A subgenome participate in more biological processes, and lncRNA targets show a preference between subgenomes. CircRNA host genes in the B subgenome were associated with more biological functions, and RNA editing preferentially occurred in noncoding regions or led to nonsynonymous mutations in the B subgenome. Taken together, the refined transcriptome annotation revealed complicated and imbalanced expression strategies in allotetraploid common carp.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1542"},"PeriodicalIF":5.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681206","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}
James J Valdés, Daniel A Petrash, Kurt O Konhauser
{"title":"A novel in-silico model explores LanM homologs among Hyphomicrobium spp.","authors":"James J Valdés, Daniel A Petrash, Kurt O Konhauser","doi":"10.1038/s42003-024-07258-3","DOIUrl":"10.1038/s42003-024-07258-3","url":null,"abstract":"<p><p>Investigating microorganisms in metal-enriched environments holds the potential to revolutionize the sustainable recovery of critical metals such as lanthanides (Ln<sup>3+</sup>). We observe Hyphomicrobium spp. as part of a Fe<sup>2+</sup>/Mn<sup>2+</sup>-oxidizing consortia native to the ferruginous bottom waters of a Ln<sup>3+</sup>-enriched lake in Czechia. Notably, one species shows similarities to recently discovered bacteria expressing proteins with picomolar Ln<sup>3+</sup> affinity. This finding was substantiated by developing an in-silico ionic competition model and recombinant expression of a homolog protein (Hm-LanM) from Hyphomicrobium methylovorum. Biochemical assays validate Hm-LanM preference for lighter Ln<sup>3+</sup> ions (from lanthanum to gadolinium). This is comparable to established prototypes. Bioinformatics analyses further uncover additional H. methylovorum metabolic biomolecules in genomic proximity to Hm-LanM analogously dependent on Ln<sup>3+</sup>, including an outer membrane receptor that binds Ln<sup>3+</sup>-chelating siderophores. These combined observations underscore the remarkable strategy of Hyphomicrobium spp. for thriving in relatively Ln<sup>3+</sup> enriched zones of metal-polluted environments.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1539"},"PeriodicalIF":5.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675371","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}
Matthew Hunt, Monica Torres, Etty Bachar-Wikstrom, Jakob D Wikstrom
{"title":"Cellular and molecular roles of reactive oxygen species in wound healing.","authors":"Matthew Hunt, Monica Torres, Etty Bachar-Wikstrom, Jakob D Wikstrom","doi":"10.1038/s42003-024-07219-w","DOIUrl":"10.1038/s42003-024-07219-w","url":null,"abstract":"<p><p>Wound healing is a highly coordinated spatiotemporal sequence of events involving several cell types and tissues. The process of wound healing requires strict regulation, and its disruption can lead to the formation of chronic wounds, which can have a significant impact on an individual's health as well as on worldwide healthcare expenditure. One essential aspect within the cellular and molecular regulation of wound healing pathogenesis is that of reactive oxygen species (ROS) and oxidative stress. Wounding significantly elevates levels of ROS, and an array of various reactive species are involved in modulating the wound healing process, such as through antimicrobial activities and signal transduction. However, as in many pathologies, ROS play an antagonistic pleiotropic role in wound healing, and can be a pathogenic factor in the formation of chronic wounds. Whilst advances in targeting ROS and oxidative stress have led to the development of novel pre-clinical therapeutic methods, due to the complex nature of ROS in wound healing, gaps in knowledge remain concerning the specific cellular and molecular functions of ROS in wound healing. In this review, we highlight current knowledge of these functions, and discuss the potential future direction of new studies, and how these pathways may be targeted in future pre-clinical studies.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1534"},"PeriodicalIF":5.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675391","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}
Natalia P Biscola, Petra M Bartmeyer, Youssef Beshay, Esther Stern, Plamen V Mihaylov, Terry L Powley, Matthew P Ward, Leif A Havton
{"title":"Laterality, sexual dimorphism, and human vagal projectome heterogeneity shape neuromodulation to vagus nerve stimulation.","authors":"Natalia P Biscola, Petra M Bartmeyer, Youssef Beshay, Esther Stern, Plamen V Mihaylov, Terry L Powley, Matthew P Ward, Leif A Havton","doi":"10.1038/s42003-024-07222-1","DOIUrl":"10.1038/s42003-024-07222-1","url":null,"abstract":"<p><p>Neuromodulation by vagus nerve stimulation (VNS) provides therapeutic benefits in multiple medical conditions, including epilepsy and clinical depression, but underlying mechanisms of action are not well understood. Cervical vagus nerve biopsies were procured from transplant organ donors for high resolution light microscopy (LM) and transmission electron microscopy (TEM) to map the human fascicular and sub-fascicular organization. Cervical vagal segments show laterality with right sided dominance in fascicle numbers and cross-sectional areas as well as sexual dimorphism with female dominance in fascicle numbers. The novel and unprecedented detection of numerous small fascicles by high resolution LM and TEM expand the known fascicle size range and morphological diversity of the human vagus nerve. Ground truth TEM quantification of all myelinated and unmyelinated axons within individual nerve fascicles show marked sub-fascicular heterogeneity of nerve fiber numbers, size, and myelination. A heuristic action potential interpreter (HAPI) tool predicts VNS-evoked compound nerve action potentials (CNAPs) generated by myelinated and unmyelinated nerve fibers and validates functional dissimilarity between fascicles. Our findings of laterality, sexual dimorphism, and an expanded range of fascicle size heterogeneity provide mechanistic insights into the varied therapeutic responses and off-target effects to VNS and may guide new refinement strategies for neuromodulation.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1536"},"PeriodicalIF":5.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675413","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}
Ferdinand Althammer, Ranjan K Roy, Matthew K Kirchner, Yuval Podpecan, Jemima Helen, Shaina McGrath, Elba Campos Lira, Javier E Stern
{"title":"Angiotensin-II drives changes in microglia-vascular interactions in rats with heart failure.","authors":"Ferdinand Althammer, Ranjan K Roy, Matthew K Kirchner, Yuval Podpecan, Jemima Helen, Shaina McGrath, Elba Campos Lira, Javier E Stern","doi":"10.1038/s42003-024-07229-8","DOIUrl":"10.1038/s42003-024-07229-8","url":null,"abstract":"<p><p>Activation of microglia, the resident immune cells of the central nervous system, leading to the subsequent release of pro-inflammatory cytokines, has been linked to cardiac remodeling, autonomic disbalance, and cognitive deficits in heart failure (HF). While previous studies emphasized the role of hippocampal Angiotensin II (AngII) signaling in HF-induced microglial activation, unanswered mechanistic questions persist. Evidence suggests significant interactions between microglia and local microvasculature, potentially affecting blood-brain barrier integrity and cerebral blood flow regulation. Still, whether the microglial-vascular interface is affected in the brain during HF remains unknown. Using a well-established ischemic HF rat model, we demonstrate the increased abundance of vessel-associated microglia (VAM) in HF rat hippocampi, along with an increased expression of AngII AT1a receptors. Acute AngII administration to sham rats induced microglia recruitment to brain capillaries, along with increased expression of TNFα. Conversely, administering an AT1aR blocker to HF rats prevented the recruitment of microglia to blood vessels, normalizing their levels to those in healthy rats. These results highlight the critical importance of a rather understudied phenomenon (i.e., microglia-vascular interactions in the brain) in the context of the pathophysiology of a highly prevalent cardiovascular disease, and unveil novel potential therapeutic avenues aimed at mitigating neuroinflammation in cardiovascular diseases.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"7 1","pages":"1537"},"PeriodicalIF":5.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675388","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}