FEBS Journal最新文献_第4页

Systematic investigation of PRMT6 substrate recognition reveals broad specificity with a preference for an RG motif or basic and bulky residues. 对PRMT6底物识别的系统研究揭示了广泛的特异性，偏爱RG基序或基本的大块残基。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-04-14 DOI: 10.1111/febs.15837

Joshua J Hamey, Sinja Rakow, Caroline Bouchard, Johanna M Senst, Peter Kolb, Uta-Maria Bauer, Marc R Wilkins, Gene Hart-Smith

{"title":"Systematic investigation of PRMT6 substrate recognition reveals broad specificity with a preference for an RG motif or basic and bulky residues.","authors":"Joshua J Hamey, Sinja Rakow, Caroline Bouchard, Johanna M Senst, Peter Kolb, Uta-Maria Bauer, Marc R Wilkins, Gene Hart-Smith","doi":"10.1111/febs.15837","DOIUrl":"https://doi.org/10.1111/febs.15837","url":null,"abstract":"Protein arginine methyltransferase 6 (PRMT6) catalyses the asymmetric dimethylation of arginines on numerous substrate proteins within the human cell. In particular, PRMT6 methylates histone H3 arginine 2 (H3R2) which affects both gene repression and activation. However, the substrate specificity of PRMT6 has not been comprehensively analysed. Here, we systematically characterise the substrate recognition motif of PRMT6, finding that it has broad specificity and recognises the RG motif. Working with a H3 tail peptide as a template, on which we made 204 amino acid substitutions, we use targeted mass spectrometry to measure their effect on PRMT6 in vitro activity. We first show that PRMT6 methylates R2 and R8 in the H3 peptide, although H3R8 is methylated with lower efficiency and is not an in vivo PRMT6 substrate. We then quantify the effect of 194 of these amino acid substitutions on methylation at both H3R2 and H3R8. In both cases, we find that PRMT6 tolerates essentially any amino acid substitution in the H3 peptide, but that positively charged and bulky residues are preferred near the target arginine. We show that PRMT6 also has preference for glycine, but only in the position immediately following the target arginine. This indicates that PRMT6 recognises the RG motif rather than the RGG motif. We further confirm this preference for the RG motif on another PRMT6 substrate, histone H4R3. This broad specificity and recognition of RG rather than RGG are distinctive among the PRMT family and has implications for the development of drugs to selectively target PRMT6. DATABASES: Panorama Public (https://panoramaweb.org/PRMT6motif.url); ProteomeXchange (PXD016711).","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5668-5691"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15837","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25525198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 5

Conserved residues Glu37 and Trp229 play an essential role in protein folding of β-lactamase. 保守残基Glu37和Trp229在β-内酰胺酶的蛋白折叠中起重要作用。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-05-02 DOI: 10.1111/febs.15854

Aleksandra Chikunova, Max P Manley, Misbha Ud Din Ahmad, Tuğçe Bilman, Anastassis Perrakis, Marcellus Ubbink

{"title":"Conserved residues Glu37 and Trp229 play an essential role in protein folding of β-lactamase.","authors":"Aleksandra Chikunova, Max P Manley, Misbha Ud Din Ahmad, Tuğçe Bilman, Anastassis Perrakis, Marcellus Ubbink","doi":"10.1111/febs.15854","DOIUrl":"https://doi.org/10.1111/febs.15854","url":null,"abstract":"Evolutionary robustness requires that the number of highly conserved amino acid residues in proteins is minimized. In enzymes, such conservation is observed for catalytic residues but also for some residues in the second shell or even further from the active site. β-Lactamases evolve in response to changing antibiotic selection pressures and are thus expected to be evolutionarily robust, with a limited number of highly conserved amino acid residues. As part of the effort to understand the roles of conserved residues in class A β-lactamases, we investigate the reasons leading to the conservation of two amino acid residues in the β-lactamase BlaC, Glu37, and Trp229. Using site-directed mutagenesis, we have generated point mutations of these residues and observed a drastic decrease in the levels of soluble protein produced in Escherichia coli, thus abolishing completely the resistance of bacteria against β-lactam antibiotics. However, the purified proteins are structurally and kinetically very similar to the wild-type enzyme, only differing by exhibiting a slightly lower melting temperature. We conclude that conservation of Glu37 and Trp229 is solely caused by an essential role in the folding process, and we propose that during folding Glu37 primes the formation of the central β-sheet and Trp229 contributes to the hydrophobic collapse into a molten globule. ENZYME: EC 3.5.2.6. DATABASE: Structural data are available in PDB database under the accession number 7A5U.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5708-5722"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15854","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25537480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 6

A liquid culture cancer spheroid model reveals low PI3K/Akt pathway activity and low adhesiveness to the extracellular matrix. 液体培养癌球体模型显示低PI3K/Akt通路活性和对细胞外基质的低粘附性。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-05-02 DOI: 10.1111/febs.15867

Natsuki Abe-Fukasawa, Rina Watanabe, Yuki Gen, Taito Nishino, Nobue Itasaki

{"title":"A liquid culture cancer spheroid model reveals low PI3K/Akt pathway activity and low adhesiveness to the extracellular matrix.","authors":"Natsuki Abe-Fukasawa, Rina Watanabe, Yuki Gen, Taito Nishino, Nobue Itasaki","doi":"10.1111/febs.15867","DOIUrl":"https://doi.org/10.1111/febs.15867","url":null,"abstract":"Three-dimensional (3D) cultures of cancer cells in liquid without extracellular matrix (ECM) offer in vitro models for metastasising conditions such as those in vessels and effusion. However, liquid culturing is often hindered by cell adhesiveness, which causes large cell clumps. We previously described a liquid culture material, LA717, which prevents nonclonal cell adhesion and subsequent clumping, thus allowing clonal growth of spheroids in an anchorage-independent manner. Here, we examined such liquid culture cancer spheroids for the acquisition of apical-basal polarity, sensitivity to an Akt inhibitor (anticancer drug MK-2206) and interaction with ECM. The spheroids present apical plasma membrane on the surface, which originated from the failure of polarisation at the single-cell stage and subsequent defects in phosphorylated ezrin accumulation at the cell boundary during the first cleavage, failing internal lumen formation. At the multicellular stage, liquid culture spheroids presented bleb-like protrusion on the surface, which was enhanced by the activation of the PI3K/Akt pathway and reduced by PI3K/Akt inhibitors. Liquid culture spheroids exhibited slow proliferation speed and low endogenous pAkt levels compared with gel-cultured spheroids and 2D-cultured cells, explaining the susceptibility to the Akt-inhibiting anticancer drug. Subcutaneous xenografting and in vitro analysis demonstrated low viability and adhesive property of liquid culture spheroids to ECM, while migratory and invasive capacities were comparable with gel-cultured spheroids. These features agree with the low efficacy of circulating tumour spheroids in the settling step of metastasis. This study demonstrates the feature of anchorage-independent spheroids and validates liquid cultures as a useful method in cancer spheroid research.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5650-5667"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15867","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25576343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 5

Crystal structure of an inulosucrase from Halalkalicoccus jeotgali B3T, a halophilic archaeal strain. 嗜盐古菌嗜盐球菌jotgali B3T的菊糖酶晶体结构。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-04-22 DOI: 10.1111/febs.15843

Komal Ghauri, Tjaard Pijning, Nayla Munawar, Hazrat Ali, Muhammad A Ghauri, Munir A Anwar, Russell Wallis

{"title":"Crystal structure of an inulosucrase from Halalkalicoccus jeotgali B3T, a halophilic archaeal strain.","authors":"Komal Ghauri, Tjaard Pijning, Nayla Munawar, Hazrat Ali, Muhammad A Ghauri, Munir A Anwar, Russell Wallis","doi":"10.1111/febs.15843","DOIUrl":"https://doi.org/10.1111/febs.15843","url":null,"abstract":"Several archaea harbor genes that code for fructosyltransferase (FTF) enzymes. These enzymes have not been characterized yet at structure-function level, but are of extreme interest in view of their potential role in the synthesis of novel compounds for food, nutrition, and pharmaceutical applications. In this study, 3D structure of an inulin-type fructan producing enzyme, inulosucrase (InuHj), from the archaeon Halalkalicoccus jeotgali was resolved in its apo form and with bound substrate (sucrose) molecule and first transglycosylation product (1-kestose). This is the first crystal structure of an FTF from halophilic archaea. Its overall five-bladed β-propeller fold is conserved with previously reported FTFs, but also shows some unique features. The InuHj structure is closer to those of Gram-negative bacteria, with exceptions such as residue E266, which is conserved in FTFs of Gram-positive bacteria and has possible role in fructan polymer synthesis in these bacteria as compared to fructooligosaccharide (FOS) production by FTFs of Gram-negative bacteria. Highly negative electrostatic surface potential of InuHj, due to a large amount of acidic residues, likely contributes to its halophilicity. The complex of InuHj with 1-kestose indicates that the residues D287 in the 4B-4C loop, Y330 in 4D-5A, and D361 in the unique α2 helix may interact with longer FOSs and facilitate the binding of longer FOS chains during synthesis. The outcome of this work will provide targets for future structure-function studies of FTF enzymes, particularly those from archaea.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5723-5736"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15843","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25530102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 3

CCCP-induced mitochondrial dysfunction - characterization and analysis of integrated stress response to cellular signaling and homeostasis. cccp诱导的线粒体功能障碍-细胞信号和体内平衡的综合应激反应的表征和分析。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-04-27 DOI: 10.1111/febs.15868

Ramagopal Reddy Koncha, Gayatri Ramachandran, Naresh Babu V Sepuri, Kolluru V A Ramaiah

{"title":"CCCP-induced mitochondrial dysfunction - characterization and analysis of integrated stress response to cellular signaling and homeostasis.","authors":"Ramagopal Reddy Koncha, Gayatri Ramachandran, Naresh Babu V Sepuri, Kolluru V A Ramaiah","doi":"10.1111/febs.15868","DOIUrl":"https://doi.org/10.1111/febs.15868","url":null,"abstract":"Mitochondrial dysfunction mediated by CCCP (carbonyl cyanide m-chlorophenyl hydrazone), an inhibitor of mitochondrial oxidative phosphorylation, evokes the integrated stress response (ISR), which is analyzed here by eIF2α phosphorylation and expression profiles of ATF4 and CHOP proteins. Our findings suggest that the CCCP-induced ISR pathway is mediated by activation of HRI kinase, but not by GCN2, PERK, or PKR. Also, CCCP activates AMPK, a cellular energy sensor, and AKT, a regulator implicated in cell survival, and suppresses phosphorylation of mTORC1 substrates eIF4E-BP1 and S6K. CCCP also downregulates translation and promotes autophagy, leading to noncaspase-mediated cell death in HepG2 cells. All these events are neutralized by NAC, an anti-ROS, suggesting that CCCP-induced mitochondrial dysfunction promotes oxidative stress. ISRIB, an inhibitor of the ISR pathway, mitigates CCCP-induced expression of ATF4 and CHOP, activation of AKT, and autophagy, similar to NAC. However, it fails to reverse CCCP-induced AMPK activation, suggesting that CCCP-induced autophagy is dependent on ISR and independent of AMPK activation. ISRIB restores partly, inhibition in eIF4E-BP1 phosphorylation, promotes eIF2α phosphorylation, albeit slowly, and mitigates suppression of translation accordingly, in CCCP-treated cells. These findings are consistent with the idea that CCCP-induced oxidative stress leading to eIF2α phosphorylation and ATF4 expression, which is known to stimulate genes involved in autophagy, play a pro-survival role together with AKT activation and regulate mTOR-mediated eIF4E-BP1 phosphorylation.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5737-5754"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15868","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25575956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 18

Table of Contents. 目录。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 DOI: 10.1111/febs.15413

引用次数: 0

Structural basis for substrate specificity of the peroxisomal acyl-CoA hydrolase MpaH' involved in mycophenolic acid biosynthesis. 参与霉酚酸生物合成的过氧化物酶体酰基辅酶a水解酶MpaH'底物特异性的结构基础。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-04-23 DOI: 10.1111/febs.15874

Cai You, Fengwei Li, Xingwang Zhang, Li Ma, Yu-Zhong Zhang, Wei Zhang, Shengying Li

{"title":"Structural basis for substrate specificity of the peroxisomal acyl-CoA hydrolase MpaH' involved in mycophenolic acid biosynthesis.","authors":"Cai You, Fengwei Li, Xingwang Zhang, Li Ma, Yu-Zhong Zhang, Wei Zhang, Shengying Li","doi":"10.1111/febs.15874","DOIUrl":"https://doi.org/10.1111/febs.15874","url":null,"abstract":"Mycophenolic acid (MPA) is a fungal natural product and first-line immunosuppressive drug for organ transplantations and autoimmune diseases. In the compartmentalized biosynthesis of MPA, the acyl-coenzyme A (CoA) hydrolase MpaH' located in peroxisomes catalyzes the highly specific hydrolysis of MPA-CoA to produce the final product MPA. The strict substrate specificity of MpaH' not only averts undesired hydrolysis of various cellular acyl-CoAs, but also prevents MPA-CoA from further peroxisomal β-oxidation catabolism. To elucidate the structural basis for this important property, in this study, we solve the crystal structures of the substrate-free form of MpaH' and the MpaH'S139A mutant in complex with the product MPA. The MpaH' structure reveals a canonical α/β-hydrolase fold with an unusually large cap domain and a rare location of the acidic residue D163 of catalytic triad after strand β6. MpaH' also forms an atypical dimer with the unique C-terminal helices α13 and α14 arming the cap domain of the other protomer and indirectly participating in the substrate binding. With these characteristics, we propose that MpaH' and its homologs form a new subfamily of α/β hydrolase fold protein. The crystal structure of MpaH'S139A /MPA complex and the modeled structure of MpaH'/MPA-CoA, together with the structure-guided mutagenesis analysis and isothermal titration calorimetry (ITC) measurements, provide important mechanistic insights into the high substrate specificity of MpaH'.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5768-5780"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15874","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25580885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 3

The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector. 铜绿假单胞菌PAAR2簇编码一个假定的含VRR-NUC结构域的效应物。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-04-25 DOI: 10.1111/febs.15870

Shuangyue Wang, Zhi Geng, Heng Zhang, Zhun She, Yuhui Dong

{"title":"The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector.","authors":"Shuangyue Wang, Zhi Geng, Heng Zhang, Zhun She, Yuhui Dong","doi":"10.1111/febs.15870","DOIUrl":"https://doi.org/10.1111/febs.15870","url":null,"abstract":"The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in inter-bacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from the virulence of their own effectors. The T6SS injects its inner-needle Hcp tube, the sharpening tip complex -consisting of VgrG and proline-alanine-alanine-arginine repeats (PAAR) proteins- and toxic effectors into neighboring cells. Its functions are largely determined by the activities of its delivered effectors. Five PAAR proteins were found in the Pseudomonas aeruginosa PAO1 genome with three of them shown to facilitate the delivery of various effectors. Here, we report a putative virus-type replication-repair nuclease domain-containing effector TseV encoded by the least investigated P. aeruginosa PAAR2 cluster. The crystal structure of its putative cognate effector TsiV is presented at 1.6 Å resolution. Through structure and sequence comparisons, we propose TseV-TsiV to be a putative novel effector-immunity (E-I) pair and we discuss the roles of other PAAR2 cluster encoded proteins.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5755-5767"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15870","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25593948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 6

Model-based robustness and bistability analysis for methylation-based, epigenetic memory systems. 甲基化表观遗传记忆系统的模型鲁棒性和双稳定性分析。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-10-01 Epub Date: 2021-05-01 DOI: 10.1111/febs.15838

Viviane Klingel, Jakob Kirch, Timo Ullrich, Sara Weirich, Albert Jeltsch, Nicole E Radde

{"title":"Model-based robustness and bistability analysis for methylation-based, epigenetic memory systems.","authors":"Viviane Klingel, Jakob Kirch, Timo Ullrich, Sara Weirich, Albert Jeltsch, Nicole E Radde","doi":"10.1111/febs.15838","DOIUrl":"https://doi.org/10.1111/febs.15838","url":null,"abstract":"In recent years, epigenetic memory systems have been developed based on DNA methylation and positive feedback systems. Achieving a robust design for these systems is generally a challenging and multifactorial task. We developed and validated a novel mathematical model to describe methylation-based epigenetic memory systems that capture switching dynamics of methylation levels and methyltransferase amounts induced by different inputs. A bifurcation analysis shows that the system operates in the bistable range, but in its current setup is not robust to changes in parameters. An expansion of the model captures heterogeneity of cell populations by accounting for distributed cell division rates. Simulations predict that the system is highly sensitive to variations in temperature, which affects cell division and the efficiency of the zinc finger repressor. A moderate decrease in temperature leads to a highly heterogeneous response to input signals and bistability on a single-cell level. The predictions of our model were confirmed by flow cytometry experiments conducted in this study. Overall, the results of our study give insights into the functional mechanisms of methylation-based memory systems and demonstrate that the switching dynamics can be highly sensitive to experimental conditions.","PeriodicalId":12261,"journal":{"name":"FEBS Journal","volume":"288 19","pages":"5692-5707"},"PeriodicalIF":5.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/febs.15838","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25533832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 3

Table of Contents. 目录。

IF 5.4 2区生物学

FEBS Journal Pub Date : 2021-09-16 DOI: 10.2307/j.ctv28bqknj.2

S. Taie

引用次数: 0