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Functional omics of ORP7 in primary endothelial cells.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-18 DOI: 10.1186/s12915-024-02087-6
Juuso H Taskinen, Minna Holopainen, Hanna Ruhanen, Miesje van der Stoel, Reijo Käkelä, Elina Ikonen, Salla Keskitalo, Markku Varjosalo, Vesa M Olkkonen
{"title":"Functional omics of ORP7 in primary endothelial cells.","authors":"Juuso H Taskinen, Minna Holopainen, Hanna Ruhanen, Miesje van der Stoel, Reijo Käkelä, Elina Ikonen, Salla Keskitalo, Markku Varjosalo, Vesa M Olkkonen","doi":"10.1186/s12915-024-02087-6","DOIUrl":"https://doi.org/10.1186/s12915-024-02087-6","url":null,"abstract":"<p><strong>Background: </strong>Many members of the oxysterol-binding protein-related protein (ORP) family have been characterized in detail over the past decades, but the lipid transport and other functions of ORP7 still remain elusive. What is known about ORP7 points toward an endoplasmic reticulum and plasma membrane-localized protein, which also interacts with GABA type A receptor-associated protein like 2 (GABARAPL2) and unlipidated Microtubule-associated proteins 1A/1B light chain 3B (LC3B), suggesting a further autophagosomal/lysosomal association. Functional roles of ORP7 have been suggested in cholesterol efflux, hypercholesterolemia, and macroautophagy. We performed a hypothesis-free multi-omics analysis of chemical ORP7 inhibition utilizing transcriptomics and lipidomics as well as proximity biotinylation interactomics to characterize ORP7 functions in a primary cell type, human umbilical vein endothelial cells (HUVECs). Moreover, assays on angiogenesis, cholesterol efflux, and lipid droplet quantification were conducted.</p><p><strong>Results: </strong>Pharmacological inhibition of ORP7 leads to an increase in gene expression related to lipid metabolism and inflammation, while genes associated with cell cycle and cell division were downregulated. Lipidomic analysis revealed increases in ceramides and lysophosphatidylcholines as well as saturated and monounsaturated triacylglycerols. Significant decreases were seen in all cholesteryl ester and in some unsaturated triacylglycerol species, compatible with the detected decrease of mean lipid droplet area. Along with the reduced lipid stores, ATP-binding cassette subfamily G member 1 (ABCG1)-mediated cholesterol efflux and angiogenesis decreased. Interactomics revealed an interaction of ORP7 with AKT1, a central metabolic regulator.</p><p><strong>Conclusions: </strong>The transcriptomics results suggest an increase in prostanoid as well as oxysterol synthesis, which could be related to the observed upregulation of proinflammatory genes. We envision that the defective angiogenesis in HUVECs subjected to ORP7 inhibition could be the result of an unfavorable plasma membrane lipid composition and/or reduced potential for cell division. To conclude, the present study suggests multifaceted functions of ORP7 in lipid homeostasis, angiogenic tube formation, and gene expression of lipid metabolism, inflammation, and cell cycle in primary endothelial cells.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"292"},"PeriodicalIF":4.4,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-18 DOI: 10.1186/s12915-024-02085-8
Zhaoyang Huang, Xinyang Guo, Jie Qin, Lin Gao, Fen Ju, Chenguang Zhao, Liang Yu
{"title":"Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data.","authors":"Zhaoyang Huang, Xinyang Guo, Jie Qin, Lin Gao, Fen Ju, Chenguang Zhao, Liang Yu","doi":"10.1186/s12915-024-02085-8","DOIUrl":"https://doi.org/10.1186/s12915-024-02085-8","url":null,"abstract":"<p><p>RNA velocity, as an extension of trajectory inference, is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. However, existing RNA velocity methods are limited by the batch effect because they cannot directly correct for batch effects in the input data, which comprises spliced and unspliced matrices in a proportional relationship. This limitation can lead to an incorrect velocity stream. This paper introduces VeloVGI, which addresses this issue innovatively in two key ways. Firstly, it employs an optimal transport (OT) and mutual nearest neighbor (MNN) approach to construct neighbors in batch data. This strategy overcomes the limitations of existing methods that are affected by the batch effect. Secondly, VeloVGI improves upon VeloVI's velocity estimation by incorporating the graph structure into the encoder for more effective feature extraction. The effectiveness of VeloVGI is demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb tissue, as well as on several public datasets. The results show that VeloVGI outperformed other methods in terms of metric performance.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"290"},"PeriodicalIF":4.4,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The 24-kDa subunit of mitochondrial complex I regulates growth, microsclerotia development, stress tolerance, and virulence in Verticillium dahliae.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-18 DOI: 10.1186/s12915-024-02084-9
Huan Li, Ying Liu, Dan Wang, Ya-Hong Wang, Ruo-Cheng Sheng, Zhi-Qiang Kong, Steven J Klosterman, Jie-Yin Chen, Krishna V Subbarao, Feng-Mao Chen, Dan-Dan Zhang
{"title":"The 24-kDa subunit of mitochondrial complex I regulates growth, microsclerotia development, stress tolerance, and virulence in Verticillium dahliae.","authors":"Huan Li, Ying Liu, Dan Wang, Ya-Hong Wang, Ruo-Cheng Sheng, Zhi-Qiang Kong, Steven J Klosterman, Jie-Yin Chen, Krishna V Subbarao, Feng-Mao Chen, Dan-Dan Zhang","doi":"10.1186/s12915-024-02084-9","DOIUrl":"https://doi.org/10.1186/s12915-024-02084-9","url":null,"abstract":"<p><strong>Background: </strong>The complete mitochondrial respiratory chain is a precondition for maintaining cellular energy supply, development, and metabolic balance. Due to the evolutionary differentiation of complexes and the semi-autonomy of mitochondria, respiratory chain subunits have become critical targets for crop improvement and fungal control. In fungi, mitochondrial complex I mediates growth and metabolism. However, the role of this complex in the pathogenesis of phytopathogenic fungi is largely unknown.</p><p><strong>Results: </strong>In this study, we identified the NADH: ubiquinone oxidoreductase 24-kDa subunit (VdNuo1) of complex in vascular wilt pathogen, Verticillium dahliae, and examined its functional conservation in phytopathogenic fungi. Based on the treatments with respiratory chain inhibitors, the mitochondria-localized VdNuo1 was confirmed to regulate mitochondrial morphogenesis and homeostasis. VdNuo1 was induced during the different developmental stages in V. dahliae, including hyphal growth, conidiation, and melanized microsclerotia development. The VdNuo1 mutants displayed variable sensitivity to stress factors and decreased pathogenicity in multiple hosts, indicating that VdNuo1 is necessary in stress tolerance and full virulence. Comparative transcriptome analysis demonstrated that VdNuo1 mediates global transcriptional effects, including oxidation and reduction processes, fatty acid, sugar, and energy metabolism. These defects are partly attributed to impairments of mitochondrial morphological integrity, complex assembly, and related functions. Its homologue (CgNuo1) functions in the vegetative growth, melanin biosynthesis, and pathogenicity of Colletotrichum gloeosporioides; however, CgNuo1 does not restore the VdNuo1 mutant to normal phenotypes.</p><p><strong>Conclusions: </strong>Our results revealed that VdNuo1 plays important roles in growth, metabolism, microsclerotia development, stress tolerance, and virulence of V. dahliae, sharing novel insight into the function of complex I and a potential fungicide target for pathogenic fungi.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"289"},"PeriodicalIF":4.4,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Type-B response regulator RRB12 regulates nodule formation in Lotus japonicus.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-18 DOI: 10.1186/s12915-024-02088-5
Jingjing Cao, Yu Zhou, Tao Tian, Jie Ji, Yan Deng, Yuhao Guan, Yongmei Qi, Longxiang Wang, Longlong Wang, Yibo Huang, Qiuling Fan, Deqiang Duanmu
{"title":"Type-B response regulator RRB12 regulates nodule formation in Lotus japonicus.","authors":"Jingjing Cao, Yu Zhou, Tao Tian, Jie Ji, Yan Deng, Yuhao Guan, Yongmei Qi, Longxiang Wang, Longlong Wang, Yibo Huang, Qiuling Fan, Deqiang Duanmu","doi":"10.1186/s12915-024-02088-5","DOIUrl":"https://doi.org/10.1186/s12915-024-02088-5","url":null,"abstract":"<p><strong>Background: </strong>The mutualistic beneficial relationship between legume plants and rhizobia enables the growth of plants in nitrogen-limiting conditions. Rhizobia infect legumes through root hairs and trigger nodule organogenesis in the cortex. The plant hormone cytokinin plays a pivotal role in regulating both rhizobial infection and the initiation of nodule development. However, the mechanism used by the cytokinin output module to control symbiosis remains poorly documented.</p><p><strong>Results: </strong>In this study, we identified a cytokinin signaling output component encoded by the Type-B RESPONSE REGULATOR (RRB) gene, LjRRB12, which is expressed in Lotus japonicus nodule primordia and young nodules. Disruption of LjRRB12 leads to a reduction in nodulation and to an increase in the number of infection threads. Overexpression of LjRRB12<sup>D76E</sup>, an active form of the LjRRB12 protein, induces nodule-like structures in wild type and hit1 (hyperinfected 1/lotus histidine kinase 1) mutants but not in nin2 (nodule inception 2) mutants. Additionally, we utilized nCUT&Tag and EMSA to demonstrate that LjRRB12 can bind a CE (cytokinin response element) from the LjNIN promoter.</p><p><strong>Conclusions: </strong>Our results provide a deeper understanding of nodule organogenesis by establishing a link between the cytokinin signal and the transcriptional regulation of LjNIN.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"293"},"PeriodicalIF":4.4,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Author Correction: Novel function of single-target regulator NorR involved in swarming motility and biofilm formation revealed in Vibrio alginolyticus.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-16 DOI: 10.1186/s12915-024-02095-6
Tongxian Chen, Xiaoling Zhou, Ruonan Feng, Shuhao Shi, Xiyu Chen, Bingqi Wei, Zhong Hu, Tao Peng
{"title":"Author Correction: Novel function of single-target regulator NorR involved in swarming motility and biofilm formation revealed in Vibrio alginolyticus.","authors":"Tongxian Chen, Xiaoling Zhou, Ruonan Feng, Shuhao Shi, Xiyu Chen, Bingqi Wei, Zhong Hu, Tao Peng","doi":"10.1186/s12915-024-02095-6","DOIUrl":"https://doi.org/10.1186/s12915-024-02095-6","url":null,"abstract":"","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"285"},"PeriodicalIF":4.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-05 DOI: 10.1186/s12915-024-02025-6
Zhanshan Sam Ma
{"title":"Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes.","authors":"Zhanshan Sam Ma","doi":"10.1186/s12915-024-02025-6","DOIUrl":"10.1186/s12915-024-02025-6","url":null,"abstract":"<p><strong>Background: </strong>Microgenderome or arguably more accurately microsexome refers to studies on sexual dimorphism of human microbiomes aimed at investigating bidirectional interactions between human microbiomes, sex hormones, and immune systems. It is important because of its implications to disease susceptibility and therapy, in which men and women demonstrate divergence in many diseases especially autoimmune diseases. In a previous report [1], we presented analyses of several key ecological aspects of microgenderome by leveraging the large datasets of the HMP (human microbiome project) but failed to offer species-level composition differences such as sexually unique species (US) and enriched species (ES). Existing approaches, for such tasks, including differential species relative abundance analysis and differential network analysis, possess certain limitations given that virtually all rely on species abundance alone or are univariate, while ignoring species distribution information across samples. Obviously, it is both species abundance and distribution that shape/drive the structure and dynamics of human microbiomes, and both should be equally responsible for the universal heterogeneity of microbiomes including the sexual dimorphism.</p><p><strong>Results: </strong>Here, we fill the gap by taking advantages of a recently developed computational algorithm, species specificity, and specificity diversity (SSD) framework (refer to the companion article) to reanalyze the HMP and complementary seminovaginal microbiome datasets. The SSD framework can randomly search and catalogue the sexually specific unique/enriched species with statistical rigor, guided by species specificity (a synthetic metric of abundance and distribution) and specificity diversity (SD). The SSD framework reveals that men seem to have more unique species than women in their gut and reproductive system microbiomes, but women seem to have more unique species than men in the airway, oral, and skin microbiomes, which is likely due to sexual dimorphism in the hormone and immune systems. We further investigate co-dependency and heterogeneity of those sexually unique/enriched species across 15 body sites, with core/periphery network analyses.</p><p><strong>Conclusions: </strong>This study not only produced sexually unique/enriched species in the human microbiomes and analyzed their codependency and heterogeneity but also further validated the robustness of the SSD framework presented in the companion article, by performing all negative control tests based on the HMP gut microbiome samples.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"284"},"PeriodicalIF":4.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784002","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
Species specificity and specificity diversity (SSD) framework: a novel method for detecting the unique and enriched species associated with disease by leveraging the microbiome heterogeneity.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-05 DOI: 10.1186/s12915-024-02024-7
Zhanshan Sam Ma
{"title":"Species specificity and specificity diversity (SSD) framework: a novel method for detecting the unique and enriched species associated with disease by leveraging the microbiome heterogeneity.","authors":"Zhanshan Sam Ma","doi":"10.1186/s12915-024-02024-7","DOIUrl":"10.1186/s12915-024-02024-7","url":null,"abstract":"<p><strong>Background: </strong>Differentiating the microbiome changes associated with diseases is challenging but critically important. Majority of existing efforts have been focused on a community level, but the discerning power of community or holistic metrics such as diversity analysis seems limited. This prompts many researchers to believe that the promise should be downward to species or even strain level-effectively and efficiently identifying unique or enriched species in diseased microbiomes with statistical rigor. Nevertheless, virtually, all species-level approaches such as differential abundance and differential network analysis methods exclusively rely on species abundances without considering species distribution information, while it can be said that distribution is equally, if not more, important than abundance in shaping the spatiotemporal heterogeneity of community compositions.</p><p><strong>Results: </strong>Here, we fill the gap by developing a novel framework-species specificity and specificity diversity (SSD)-that synthesizes both abundance and distribution information to differentiate microbiomes, at both species and community scales, under different environmental gradients such as the healthy and diseased treatments. The proposed SSD framework consists of three essential elements. The first is species specificity (SS), a concept that reincarnates the traditional specialist-generalist continuum and is defined by Mariadassou et al. (Ecol Lett 18:974-82, 2015). The SS synthesizes a species' local prevalence (distribution) and global abundance information and attaches specificity measure to each species in a specific habitat (e.g., healthy or diseased treatment). The second element is a new concept to introduce here, the (species) specificity diversity (SD), which is inspired by traditional species (abundance) diversity in community ecology and measures the diversity of specificity (a proxy for metacommunity heterogeneity, essentially) with Renyi's entropy. The third element is a pair of statistical tests based on the principle of permutation tests.</p><p><strong>Conclusions: </strong>The SSD framework can (i) identify and catalogue lists of unique species (US), significantly enriched species (ES) in each treatment based on SS and specificity permutation (SP) test and (ii) measure the holistic differences between assemblages (or treatments) based on SD and specificity diversity permutation (SDP) test. Both capacities can be enabling technologies for general comparative microbiome research including risk assessment, diagnosis, and treatment of microbiome-associated diseases.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"283"},"PeriodicalIF":4.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784119","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
CRISPR/Cas9-induced double-strand breaks in the huntingtin locus lead to CAG repeat contraction through DNA end resection and homology-mediated repair.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-03 DOI: 10.1186/s12915-024-02079-6
Pawel Sledzinski, Mateusz Nowaczyk, Marianna Iga Smielowska, Marta Olejniczak
{"title":"CRISPR/Cas9-induced double-strand breaks in the huntingtin locus lead to CAG repeat contraction through DNA end resection and homology-mediated repair.","authors":"Pawel Sledzinski, Mateusz Nowaczyk, Marianna Iga Smielowska, Marta Olejniczak","doi":"10.1186/s12915-024-02079-6","DOIUrl":"10.1186/s12915-024-02079-6","url":null,"abstract":"<p><strong>Background: </strong>The expansion of CAG/CTG repeats in functionally unrelated genes is a causative factor in many inherited neurodegenerative disorders, including Huntington's disease (HD), spinocerebellar ataxias (SCAs), and myotonic dystrophy type 1 (DM1). Despite many years of research, the mechanism responsible for repeat instability is unknown, and recent findings indicate the key role of DNA repair in this process. The repair of DSBs induced by genome editing tools results in the shortening of long CAG/CTG repeats in yeast models. Understanding this mechanism is the first step in developing a therapeutic strategy based on the controlled shortening of repeats. The aim of this study was to characterize Cas9-induced DSB repair products at the endogenous HTT locus in human cells and to identify factors affecting the formation of specific types of sequences.</p><p><strong>Results: </strong>The location of the cleavage site and the surrounding sequence influence the outcome of DNA repair. DSBs within CAG repeats result in shortening of the repeats in frame in ~ 90% of products. The mechanism of this contraction involves MRE11-CTIP and RAD51 activity and DNA end resection. We demonstrated that a DSB located upstream of CAG repeats induces polymerase theta-mediated end joining, resulting in deletion of the entire CAG tract. Furthermore, using proteomic analysis, we identified novel factors that may be involved in CAG sequence repair.</p><p><strong>Conclusions: </strong>Our study provides new insights into the complex mechanisms of CRISPR/Cas9-induced shortening of CAG repeats in human cells.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"282"},"PeriodicalIF":4.4,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766454","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
Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-03 DOI: 10.1186/s12915-024-02080-z
Alexei Yu Kostygov, Karolína Skýpalová, Natalia Kraeva, Elora Kalita, Cameron McLeod, Vyacheslav Yurchenko, Mark C Field, Julius Lukeš, Anzhelika Butenko
{"title":"Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote.","authors":"Alexei Yu Kostygov, Karolína Skýpalová, Natalia Kraeva, Elora Kalita, Cameron McLeod, Vyacheslav Yurchenko, Mark C Field, Julius Lukeš, Anzhelika Butenko","doi":"10.1186/s12915-024-02080-z","DOIUrl":"10.1186/s12915-024-02080-z","url":null,"abstract":"<p><strong>Background: </strong>In trypanosomatids, a group of unicellular eukaryotes that includes numerous important human parasites, cis-splicing has been previously reported for only two genes: a poly(A) polymerase and an RNA helicase. Conversely, trans-splicing, which involves the attachment of a spliced leader sequence, is observed for nearly every protein-coding transcript. So far, our understanding of splicing in this protistan group has stemmed from the analysis of only a few medically relevant species. In this study, we used an extensive dataset encompassing all described trypanosomatid genera to investigate the distribution of intron-containing genes and the evolution of splice sites.</p><p><strong>Results: </strong>We identified a new conserved intron-containing gene encoding an RNA-binding protein that is universally present in Kinetoplastea. We show that Perkinsela sp., a kinetoplastid endosymbiont of Amoebozoa, represents the first eukaryote completely devoid of cis-splicing, yet still preserving trans-splicing. We also provided evidence for reverse transcriptase-mediated intron loss in Kinetoplastea, extensive conservation of 5' splice sites, and the presence of non-coding RNAs within a subset of retained trypanosomatid introns.</p><p><strong>Conclusions: </strong>All three intron-containing genes identified in Kinetoplastea encode RNA-interacting proteins, with a potential to fine-tune the expression of multiple genes, thus challenging the perception of cis-splicing in these protists as a mere evolutionary relic. We suggest that there is a selective pressure to retain cis-splicing in trypanosomatids and that this is likely associated with overall control of mRNA processing. Our study provides new insights into the evolution of introns and, consequently, the regulation of gene expression in eukaryotes.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"281"},"PeriodicalIF":4.4,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766451","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
Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.
IF 4.4 1区 生物学
BMC Biology Pub Date : 2024-12-02 DOI: 10.1186/s12915-024-02077-8
Abigail J Perrin, Richard G Dorrell
{"title":"Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.","authors":"Abigail J Perrin, Richard G Dorrell","doi":"10.1186/s12915-024-02077-8","DOIUrl":"10.1186/s12915-024-02077-8","url":null,"abstract":"<p><p>Eukaryotic microorganisms, or \"protists,\" while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"22 1","pages":"279"},"PeriodicalIF":4.4,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766456","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
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