FEBS Open Bio最新文献

Matrix: a complex amalgam of structures and functions in tumor microenvironment. 基质：肿瘤微环境中结构和功能的复杂混合体。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-21 DOI: 10.1002/2211-5463.70074

Spyros S Skandalis, Evgenia Tsoukala, Theodora D Sarantopoulou, Maria-Elpida Christopoulou

引用次数: 0

Current trends in single-cell RNA sequencing applications in diabetes mellitus. 单细胞RNA测序在糖尿病研究中的应用现状。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-19 DOI: 10.1002/2211-5463.70061

Seyed Sajjad Zadian, Khodakaram Jahanbin, Shekoofeh Nikooei, Marzieh Rostaminejad, Arezoo Rahimi, Pedram Abdizadeh, Behnam Alipoor

引用次数: 0

Interaction of class III cellobiose dehydrogenase with lytic polysaccharide monooxygenase. III类纤维素二糖脱氢酶与水解多糖单加氧酶的相互作用。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-18 DOI: 10.1002/2211-5463.70067

Angela Giorgianni, Florian Csarman, Peicheng Sun, Mirjam Kabel, Roland Ludwig

{"title":"Interaction of class III cellobiose dehydrogenase with lytic polysaccharide monooxygenase.","authors":"Angela Giorgianni, Florian Csarman, Peicheng Sun, Mirjam Kabel, Roland Ludwig","doi":"10.1002/2211-5463.70067","DOIUrl":"https://doi.org/10.1002/2211-5463.70067","url":null,"abstract":"The genome of Fusarium solani, a well-known plant pathogen, encodes various lytic polysaccharide monooxygenases (LPMOs) involved in plant biomass degradation in combination with cellobiose dehydrogenase (CDH). To investigate the auxiliary role of the recently expressed and characterized class III CDH from F. solani (FsCDH), this enzyme was tested in combination with the well-characterized AA9C from Neurospora crassa (NcAA9C). Steady-state and stopped-flow methods as well as electrochemical measurements demonstrate how FsCDH efficiently transfers electrons to NcAA9C, with a rapid, observed heme reoxidation rate constant of 129 s-1. In comparison to ascomycete class II CDHs, the H2O2 production by FsCDH is insufficient to promote LPMO activity. However, a cyclic cascade between NcAA9C and FsCDH was found. NcAA9C reaction products showed a high catalytic efficiency as FsCDH substrates, with KM values close to its natural substrate cellobiose. This reaction was further investigated by a real time measurement, where FsCDH and NcAA9C were incubated with phosphoric acid-swollen cellulose and the reaction was sustained over a long period without the addition of an external reductant. The new class III CDH is similar to other CDH classes, except its very low reactivity with molecular oxygen, pointing towards a different function in Ascomycota than class II CDH. These findings contribute to the better understanding of oxidative cellulose degradation by fungi and thus, to potential biotechnological applications for the sustainable use of biomass.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Gut alterations in a chronic kidney disease rat model with diet-induced vascular calcification. 饮食诱导血管钙化的慢性肾病大鼠模型的肠道改变。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-17 DOI: 10.1002/2211-5463.70043

Piotr Bartochowski, Irene Cortijo, Shruti Bhargava, Bernard Jover, Fabrice Raynaud, Juliana H Boukhaled, Anne-Dominique Lajoix, Vera Jankowski, Joachim Jankowski, Magali Cordaillat-Simmons, Àngel Argilés, Nathalie Gayrard, Flore Duranton, Jonas Laget

{"title":"Gut alterations in a chronic kidney disease rat model with diet-induced vascular calcification.","authors":"Piotr Bartochowski, Irene Cortijo, Shruti Bhargava, Bernard Jover, Fabrice Raynaud, Juliana H Boukhaled, Anne-Dominique Lajoix, Vera Jankowski, Joachim Jankowski, Magali Cordaillat-Simmons, Àngel Argilés, Nathalie Gayrard, Flore Duranton, Jonas Laget","doi":"10.1002/2211-5463.70043","DOIUrl":"https://doi.org/10.1002/2211-5463.70043","url":null,"abstract":"Intestinal disorders and vascular calcification (VC) are often associated with chronic kidney disease (CKD). While gut barrier alterations have been reported in CKD (such as abnormal intestinal permeability, bacterial overgrowth, and inflammation), it is not clear if vascular calcification influences these alterations. To investigate whether the bidirectional relationships between VC and gut dysfunction could be mediated by increased inflammation and uremic toxin generation, we used the SNx-VC model of uremic vascular calcification (rats undergoing subtotal 5/6th nephrectomy and fed a procalcifying high-phosphate and vitamin D diet). We confirmed the presence of CKD and VC by von Kossa staining and observed increased gut-origin uremic toxin, indoxyl sulfate (IS), in SNx-VC animals compared to controls. In SNx-VC rats, we observed decreased mucus production (Alcian blue, Mucin 2 staining) in the colon and ileum which was correlated with the level of calcification. There was no change in inflammation markers or tight junction protein expression. We assessed intestinal levels in the NOD-like receptor family pyrin domain containing 6 (NLRP6) protein, known to regulate mucus secretion, and found no change in the colon or ileum. Nlrp6 mRNA was, however, decreased in the colon of SNx-VC rats, along with other mRNA (Ly96, Sod1), while Tlr2 was increased compared to controls. Our observations of low mucus, low Nlrp6 mRNA, and high IS in SNx-VC rats confirm a link between gut barrier alterations and uremic VC. This suggests that alterations in the mucus layer could favor the generation of gut-origin uremic toxins and promote VC in CKD. Thus, improving the gut mucus barrier function in the context of uremic VC could be considered as a possible therapeutic strategy in CKD patients.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Genetic diversity and population structure of the Taigan dog breed. 太干犬品种的遗传多样性和种群结构。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-17 DOI: 10.1002/2211-5463.70065

Kira Bespalova, Anastassiya Perfilyeva, Мamura Begmanova, Assel Zhaxylykova, Arailym Yerzhan, Kanagat Yergali, Almazbek Akunov, Marat Munarbek Uulu, Anna Khamchukova, Almira Amirgaliyeva, Yelena Kuzovleva

{"title":"Genetic diversity and population structure of the Taigan dog breed.","authors":"Kira Bespalova, Anastassiya Perfilyeva, Мamura Begmanova, Assel Zhaxylykova, Arailym Yerzhan, Kanagat Yergali, Almazbek Akunov, Marat Munarbek Uulu, Anna Khamchukova, Almira Amirgaliyeva, Yelena Kuzovleva","doi":"10.1002/2211-5463.70065","DOIUrl":"https://doi.org/10.1002/2211-5463.70065","url":null,"abstract":"The Taigan is an ancient sighthound breed native to the Tien Shan Mountains in Kyrgyzstan and adapted to hunting at high altitudes and in rough terrain. Previous studies have provided insights into its phylogenetic relationships, but more data are needed to determine whether the Taigan is genetically distinct from related sighthounds. In the present study, we conducted a comprehensive genetic analysis using short tandem repeat markers and high-density single nucleotide polymorphism array data to assess genetic diversity, population structure and differentiation from other sighthound breeds. The analysis showed high polymorphism and an excess of heterozygosity (F = -0.013), indicating a balanced genetic structure. Bayesian clustering identified five genetic clusters among the Taigans, with no dominant lineage, suggesting a diverse gene pool. Principal component analysis and admixture analyses assigned the Taigan to the eastern sighthound group, closely clustered with the Kazakh Tazy. A pairwise FST analysis showed only 17 highly divergent single nucleotide polymorphisms. This number is significantly lower than in recognized and well-differentiated breed pairs and suggests that genetic differentiation between Kazakh Tazy and Taigan breeds is minimal under current sampling conditions. Further studies with larger data sets are needed to determine the genetic divergence between the Taigan and the Kazakh Tazy.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Biophysical characterization and ion transport with cell-based and proteoliposome reconstitution assays of invertebrate K⁺-Cl^- cotransporters. 无脊椎动物K+- cl -共转运体的生物物理特性和离子转运与细胞和蛋白脂质体重建分析。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-13 DOI: 10.1002/2211-5463.70063

Satoshi Fudo, Marina Verkhovskaya, Coralie Di Scala, Claudio Rivera, Tommi Kajander

{"title":"Biophysical characterization and ion transport with cell-based and proteoliposome reconstitution assays of invertebrate K+-Cl- cotransporters.","authors":"Satoshi Fudo, Marina Verkhovskaya, Coralie Di Scala, Claudio Rivera, Tommi Kajander","doi":"10.1002/2211-5463.70063","DOIUrl":"https://doi.org/10.1002/2211-5463.70063","url":null,"abstract":"The cation-chloride cotransporter (CCC) family includes ion symporters that cotransport monovalent cations and Cl-, playing a crucial role in controlling cytoplasmic ion content. K+-Cl- cotransporters (KCCs) facilitate the symport of ions across the plasma membrane. The CCCs participate in various physiological processes, such as transepithelial ion transport and regulation of cell volume. Among KCCs, KCC2 has unique and essential functions in the central nervous system. KCC from Drosophila melanogaster (DmKCC) is an ortholog of mammalian KCCs. Its critical role in neuronal transmission has been demonstrated. Also, the cnidarian Hydra vulgaris has a functional KCC (HvKCC). Comparative analyses of these transporters with vertebrate counterparts can provide insights into the mechanism of KCC ion transport, regulation, and evolution. Thus, here we purified DmKCC and HvKCC and characterized their biophysical properties using differential scanning fluorimetry and light scattering. We evaluated their functionality in cells and developed a method to study ion transport with flame photometry. Further, a fluorescence-based assay for DmKCC reconstituted into proteoliposomes was developed. The activity of DmKCC was found to be dependent on Ca2+, which is reminiscent of some other chloride transport protein families and potentially important for the KCC protein family overall.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144283091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Earthing effects on mitochondrial function: ATP production and ROS generation. 接地对线粒体功能的影响：ATP的产生和ROS的产生。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-13 DOI: 10.1002/2211-5463.70062

Cecilia Giulivi, Richard Kotz

引用次数: 0

Analysis of the regulation of undecaprenyl diphosphate dephosphorylation in Escherichia coli. 十一戊烯基二磷酸在大肠杆菌中的脱磷酸化调控分析。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-13 DOI: 10.1002/2211-5463.70066

Tomotaka Jitsukawa, Yasushi Shigeri, Shingo Fujisaki

{"title":"Analysis of the regulation of undecaprenyl diphosphate dephosphorylation in Escherichia coli.","authors":"Tomotaka Jitsukawa, Yasushi Shigeri, Shingo Fujisaki","doi":"10.1002/2211-5463.70066","DOIUrl":"https://doi.org/10.1002/2211-5463.70066","url":null,"abstract":"Undecaprenyl phosphate (C55P) is an essential sugar carrier for bacterial cell wall synthesis, which has gained importance in recent years as a promising target for new antibiotic development. In Escherichia coli, C55P is produced by dephosphorylation of undecaprenyl diphosphate (C55PP) by BacA and two type 2 phosphatidic acid phosphatase (PAP2) family enzymes, PgpB and YbjG, in the periplasmic space. To clarify the regulatory mechanism of C55PP dephosphorylation, we quantified C55P and C55PP using a new high-performance liquid chromatography method, conducted susceptibility tests against bacitracin, and analyzed the gene expression of bacA, pgpB, and ybjG in E. coli single- and double-disruption strains of those genes. C55P levels were similar in all strains, but C55PP levels increased only in the bacA, ybjG double-disruption strain. The double-disruption strains containing bacA disruption and the bacA single-disruption strain were more susceptible to bacitracin than the other strains. In the double-disruption strains containing bacA disruption, the expression of the remaining genes pgpB and ybjG increased. These results indicate that the transcription of the PAP2 family enzyme genes, pgpB and ybjG, was activated under conditions where C55PP dephosphorylation activity in cells was reduced. This transcriptional regulation might contribute to the maintenance of C55P levels in cells.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144283090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

An efficient strategy for producing RNA-free Nucleocapsid protein of SARS-CoV-2 for biochemical and structural investigations. 用于生化和结构研究的SARS-CoV-2无rna核衣壳蛋白的高效制备策略

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-09 DOI: 10.1002/2211-5463.70064

Shweta Singh, Gagan D Gupta

{"title":"An efficient strategy for producing RNA-free Nucleocapsid protein of SARS-CoV-2 for biochemical and structural investigations.","authors":"Shweta Singh, Gagan D Gupta","doi":"10.1002/2211-5463.70064","DOIUrl":"https://doi.org/10.1002/2211-5463.70064","url":null,"abstract":"The SARS-CoV-2 Nucleocapsid (N) protein plays a crucial role in genome packaging, replication, transcription, and pathogenesis, making it a promising target for antiviral drug development. However, its large intrinsically disordered regions and propensity to form RNA condensates pose significant challenges for recombinant expression and purification. In this study, we successfully expressed and purified full-length N protein with a cleavable N-terminal Thioredoxin (Trx) fusion to enhance solubility and stability. The acidic Trx tag helped in the efficient binding of basic N protein to an anion-exchange column, enabling complete removal of bound RNA. Through a four-step process-immobilized metal affinity chromatography (IMAC), anion exchange, TEV protease-mediated tag cleavage followed by a second IMAC to remove cleaved fragments, and final polishing by size-exclusion chromatography (SEC)-we obtained highly homogeneous, RNA-free N protein. A single well-defined peak on SEC and dynamic light scattering confirmed the homogeneity of the purified protein. Electrophoretic mobility shift assays revealed strong RNA-binding activity, as a nearly complete RNA shift was observed at N protein concentrations as low as 0.25 μm. Fluorescence polarization assays further quantified RNA-binding affinity, yielding a dissociation constant of ~28 nm. These results establish an effective strategy for obtaining nucleic acid-free N protein suitable for biochemical and structural studies. Ultimately, this work provides a foundation for high-resolution structural investigations and the development of novel antiviral therapeutics targeting the N protein to combat COVID-19.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Construction of hyperthermostable d-allulose 3-epimerase from Arthrobacter globiformis M30 using the sequence information from Arthrobacter psychrolactophilus. 利用嗜冷嗜酸节杆菌序列信息构建球状节杆菌M30超耐热d-allulose 3- epimase。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2025-06-09 DOI: 10.1002/2211-5463.70060

Kensaku Shimada, Kouhei Ohtani, Pushpa Kiran Gullapalli, Kazuhiko Ishikawa

{"title":"Construction of hyperthermostable d-allulose 3-epimerase from Arthrobacter globiformis M30 using the sequence information from Arthrobacter psychrolactophilus.","authors":"Kensaku Shimada, Kouhei Ohtani, Pushpa Kiran Gullapalli, Kazuhiko Ishikawa","doi":"10.1002/2211-5463.70060","DOIUrl":"https://doi.org/10.1002/2211-5463.70060","url":null,"abstract":"d-Allulose is one of the rare monosaccharides and is considered as a safe ingredient in foods. It can be enzymatically produced from d-fructose by the enzyme d-allulose 3-epimerase. More stable enzymes can operate effectively for longer durations, reducing the need for frequent replacements and thereby lowering costs. In addition, the preparation of the recombinant Arthrobacter globiformis M30 (AgDAE) enzyme requires heat treatment at 60-70 °C to remove host cell debris and potential microbial contaminants. Therefore, to address the need for more thermostable enzymes in d-allulose production, we aimed to create thermostable mutants of AgDAE using the protein engineering method. We cloned d-allulose identified from A. globiformis M30 and, using sequence homology, we constructed thermostable mutants by protein engineering. Each effect of the five mutations used was independent and additive. By integrating positive mutations, we succeeded in the construction of a chimeric enzyme exhibiting hyperthermostability without loss of enzymatic activity. The constructed chimera mutant was highly functional above 95 °C and remained stable under 80 °C. Our approach using structural information for the chimeric construction experiments also suggested that incorporating mutations from other homologous enzymes can impart advantages in enzymes in a simple and effective manner.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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