Biochimie最新文献_第10页

Among the recombinant TSPOs, the BcTSPO 在重组 TSPOs 中，BcTSPO

IF 3.3 3区生物学

Biochimie Pub Date : 2024-01-25 DOI: 10.1016/j.biochi.2024.01.011

{"title":"Among the recombinant TSPOs, the BcTSPO","authors":"","doi":"10.1016/j.biochi.2024.01.011","DOIUrl":"10.1016/j.biochi.2024.01.011","url":null,"abstract":"<div>Overexpression of recombinant Bacillus cereus TSPO (BcTSPO) in E. coli bacteria leads to its recovery with a bound hemin both in bacterial membrane (MB) and inclusion bodies (IB). Unlike mouse TSPO, BcTSPO purified in SDS detergent from IB is well structured and can bind various ligands such as high-affinity PK 11195, protoporphyrin IX (PPIX) and δ-aminolevulinic acid (ALA). For each of the three ligands, 1H–15N HSQC titration NMR experiments suggest that different amino acids of BcTSPO binding cavity are involved in the interaction. PPIX, an intermediate of heme biosynthesis, binds to the cavity of BcTSPO and its fluorescence can be significantly reduced in the presence of light and oxygen. The light irradiation leads to two products that have been isolated and characterized as photoporphyrins. They result from the addition of singlet oxygen to the two vinyl groups hence leading to the formation of hydroxyaldehydes. The involvement of water molecules, recently observed along with the binding of heme in Rhodobacter sphaeroides (RsTSPO) is highly probable. Altogether, these results raise the question of the role of TSPO in heme biosynthesis regulation as a possible scavenger of reactive intermediates.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"224 ","pages":"Pages 16-28"},"PeriodicalIF":3.3,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0300908424000294/pdfft?md5=f60dea544285655bf51b2d49d8344540&pid=1-s2.0-S0300908424000294-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139556346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Inside front cover-EDB 封面内页-EDB

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-23 DOI: 10.1016/S0300-9084(24)00017-8

引用次数: 0

The rise of RNA: From fundamental research to therapeutic applications RNA 的崛起：从基础研究到治疗应用

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-23 DOI: 10.1016/j.biochi.2024.01.005

Marie Sissler, Fabien Darfeuille

引用次数: 0

Amplifying PCR productivity and environmental sustainability through shortened cycling protocols 通过缩短循环方案提高 PCR 生产率和环境可持续性

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-21 DOI: 10.1016/j.biochi.2024.01.013

Matthew Pedlar , Matthew J. Emery , Philip J. Warburton

{"title":"Amplifying PCR productivity and environmental sustainability through shortened cycling protocols","authors":"Matthew Pedlar , Matthew J. Emery , Philip J. Warburton","doi":"10.1016/j.biochi.2024.01.013","DOIUrl":"10.1016/j.biochi.2024.01.013","url":null,"abstract":"<div>Since its inception in the 1980s, advancements in PCR technology using improved thermal cyclers, engineered DNA polymerases and commercial master mixes, have led to increased PCR productivity. Despite these advancements, PCR cycling protocols have largely remained unchanged over the same period. This study aimed to systemically evaluate the effect of reduced PCR cycling parameters on amplicon production. The 1466bp fragment from the 16S rRNA gene present in low-, medium- and high-CG bacteria was amplified using three commercially available PCR master mixes. The shortest cycling parameters required to successfully amplify the 16S fragment from all bacteria and master mixes comprised 30-cycles of 5 s denaturation, 25 s annealing, and 25 s extension. While all produced an amplicon with sufficient yield to enable downstream sequence analysis, the PCRBIO Ultra Mix in conjunction with the shortened parameters was found to achieve the highest amplicon yield across low-, medium- and high CG bacteria. Comparing the run times to that of a typical 16S PCR protocol, the shortened cycling parameters reduced the program duration by 46 % and consumed 50 % less electricity, translating into increased productivity and helping to improve laboratory environmental sustainability.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 60-64"},"PeriodicalIF":3.9,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0300908424000312/pdfft?md5=611751bcc2e6e2f9ae6166201d625756&pid=1-s2.0-S0300908424000312-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139518569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Deciphering the Akt1-HuD interaction in HuD-mediated neuronal differentiation 解密HuD介导的神经元分化过程中Akt1与HuD的相互作用

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-18 DOI: 10.1016/j.biochi.2024.01.010

Hikari Nishisaka , Takumi Tomohiro , Kako Fukuzumi, Akira Fukao, Yoshinori Funakami, Toshinobu Fujiwara

{"title":"Deciphering the Akt1-HuD interaction in HuD-mediated neuronal differentiation","authors":"Hikari Nishisaka , Takumi Tomohiro , Kako Fukuzumi, Akira Fukao, Yoshinori Funakami, Toshinobu Fujiwara","doi":"10.1016/j.biochi.2024.01.010","DOIUrl":"10.1016/j.biochi.2024.01.010","url":null,"abstract":"<div>The RNA-binding protein HuD/ELAVL4 is essential for neuronal development and synaptic plasticity by governing various post-transcriptional processes of target mRNAs, including stability, translation, and localization. We previously showed that the linker region and poly(A)-binding domain of HuD play a pivotal role in promoting translation and inducing neurite outgrowth. In addition, we found that HuD interacts exclusively with the active form of Akt1, through the linker region. Although this interaction is essential for neurite outgrowth, HuD is not a substrate for Akt1, raising questions about the dynamics between HuD-mediated translational stimulation and its association with active Akt1.Here, we demonstrate that active Akt1 interacts with the cap-binding complex via HuD. We identify key amino acids in linker region of HuD responsible for Akt1 interaction, leading to the generation of two point-mutated HuD variants: one that is incapable of binding to Akt1 and another that can interact with Akt1 regardless of its phosphorylation status. In vitro translation assays using these mutants reveal that HuD-mediated translation stimulation is independent of its binding to Akt1. In addition, it is evident that the interaction between HuD and active Akt1 is essential for HuD-induced neurite outgrowth, whereas a HuD mutant capable of binding to any form of Akt1 leads to aberrant neurite development.Collectively, our results revisit the understanding of the HuD-Akt1 interaction in translation and suggest that this interaction contributes to HuD-mediated neurite outgrowth via a unique molecular mechanism distinct from translation regulation.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 20-26"},"PeriodicalIF":3.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139498740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Discovery and characterization of the α-amylases cDNAs from Enchytraeus albidus shed light on the evolution of “Enchytraeus-Eisenia type” Amy homologs in Annelida 白尾 Enchytraeus α 淀粉酶 cDNA 的发现和特征描述揭示了无脊椎动物中 "Enchytraeus-Eisenia 型 "淀粉酶同源物的进化过程。

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-17 DOI: 10.1016/j.biochi.2024.01.008

Łukasz Gajda, Agata Daszkowska-Golec, Piotr Świątek

{"title":"Discovery and characterization of the α-amylases cDNAs from Enchytraeus albidus shed light on the evolution of “Enchytraeus-Eisenia type” Amy homologs in Annelida","authors":"Łukasz Gajda, Agata Daszkowska-Golec, Piotr Świątek","doi":"10.1016/j.biochi.2024.01.008","DOIUrl":"10.1016/j.biochi.2024.01.008","url":null,"abstract":"<div>Although enchytraeids have gained popularity in scientific research, fundamental questions regarding their feeding ecology and biology remain largely unexplored. This study investigates α-amylases, major digestive enzymes responsible for hydrolyzing starch and similar polysaccharides into sugars, in Enchytraeus albidus. Genetic data related to α-amylases is currently lacking for the family Enchytraeidae but also for the entire Annelida. To detect and identify coding sequences of the expressed α-amylase genes in COI-monohaplotype culture (PL-A strain) of E. albidus, we used classical “gene fishing” and transcriptomic approaches. We also compared coding sequence variants of α-amylase retrieved from transcriptomic data related to freeze-tolerant strains. Our results reveal that E. albidus possesses two distinct α-amylase genes (Amy I and Amy II) that are homologs to earthworm Eisenia fetida Ef-Amy genes. Different strains of E. albidus possess distinctive alleles of α-amylases with unique SNP patterns specific to a particular strain. Unlike Amy II, Amy I seems to be a highly polymorphic and multicopy gene. The domain architecture of the putative Amy proteins was found the same as for classical animal α-amylases with ABC-domains. A characteristic feature of Amy II is the lack of GHGA motif in the flexible loop region, similarly to many insect amylases. We identified “Enchytraeus-Eisenia type” α-amylase homologs in other clitellates and polychaetes, indicating the ancestral origin of Amy I/II proteins in Annelida. This study provides the first insight into the endogenous non-proteolytic digestive enzyme genes in potworms, discusses the evolution of Amy α-amylases in Annelida, and explores phylogenetic implications.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 38-59"},"PeriodicalIF":3.9,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139502049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Dynamic modulation of transthylakoid electric potential by chloroplast ATP synthases 叶绿体 ATP 合成酶对跨叶绿体电动势的动态调节

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-13 DOI: 10.1016/j.biochi.2024.01.007

Hui Lyu, Yong-Song Zuo

{"title":"Dynamic modulation of transthylakoid electric potential by chloroplast ATP synthases","authors":"Hui Lyu, Yong-Song Zuo","doi":"10.1016/j.biochi.2024.01.007","DOIUrl":"10.1016/j.biochi.2024.01.007","url":null,"abstract":"<div>The light-induced transthylakoid membrane potential (ΔΨm) can function as a driving force to help catalyzing the formation of ATP molecules, proving a tight connection between ΔΨm and the ATP synthase. Naturally, a question can be raised on the effects of altered functioning of ATP synthases on regulating ΔΨm, which is attractive in the area of photosynthetic research. Lots of findings, when making efforts of solving this difficulty, can offer an in-depth understanding into the mechanism behind. However, the functional network on modulating ΔΨm is highly interdependent. It is difficult to comprehend the consequences of altered activity of ATP synthases on adjusting ΔΨm because parameters that have influences on ΔΨm would themselves be affected by ΔΨm. In this work, a computer model was applied to check the kinetic changes in polarization/depolarization across the thylakoid membrane (TM) regulated by the modified action of ATP synthases. The computing data revealed that under the extreme condition by numerically “switching off” the action of the ATP synthase, the complete inactivation of ATP synthase would markedly impede proton translocation at the cytb6f complex. Concurrently, the KEA3 (CLCe) porter, actively pumping protons into the stroma, further contributes to achieving a sustained low level of ΔΨm. Besides, the quantitative consequences on every particular component of ΔΨm adjusted by the modified functioning of ATP synthases were also explored. By employing the model, we bring evidence from the theoretical perspective that the ATP synthase is a key factor in forming a transmembrane proton loop thereby maintaining a propriate steady-state ΔΨm to meet variable environmental conditions.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 27-37"},"PeriodicalIF":3.9,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139462817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Cell-penetrating peptide and cationic liposomes mediated siRNA delivery to arrest growth of chronic myeloid leukemia cells in vitro 细胞穿透肽和阳离子脂质体介导的 siRNA 体外递送可阻止慢性髓性白血病细胞生长

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-10 DOI: 10.1016/j.biochi.2024.01.006

Vera Vysochinskaya , Yana Zabrodskaya , Olesya Dovbysh , Anton Emelyanov , Vladimir Klimenko , Nikolay Knyazev , Ivan Terterov , Marya Egorova , Alexey Bogdanov , Michael Maslov , Andrey Vasin , Michael Dubina

{"title":"Cell-penetrating peptide and cationic liposomes mediated siRNA delivery to arrest growth of chronic myeloid leukemia cells in vitro","authors":"Vera Vysochinskaya , Yana Zabrodskaya , Olesya Dovbysh , Anton Emelyanov , Vladimir Klimenko , Nikolay Knyazev , Ivan Terterov , Marya Egorova , Alexey Bogdanov , Michael Maslov , Andrey Vasin , Michael Dubina","doi":"10.1016/j.biochi.2024.01.006","DOIUrl":"10.1016/j.biochi.2024.01.006","url":null,"abstract":"<div>Gene silencing through RNA interference (RNAi) is a promising therapeutic approach for a wide range of disorders, including cancer. Non-viral gene therapy, using specific siRNAs against BCR-ABL1, can be a supportive or alternative measure to traditional chronic myeloid leukemia (CML) tyrosine kinase inhibitor (TKIs) therapies, given the prevalence of clinical TKI resistance. The main challenge for such approaches remains the development of the effective delivery system for siRNA tailored to the specific disease model.The purpose of this study was to examine and compare the efficiency of endosomolytic cell penetrating peptide (CPP) EB1 and PEG2000-decorated cationic liposomes composed of polycationic lipid 1,26-bis(cholest-5-en-3-yloxycarbonylamino)-7,11,16,20-tetraazahexacosane tetrahydrochloride (2Х3) and helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) for anti-bcr-abl siRNA delivery into the K562 human CML cell line. We show that both EB1 and 2Х3-DOPE-DSPE-PEG2000 (0.62 % mol.) liposomes effectively deliver siRNA into K562 cells by endocytic mechanisms, and the use of liposomes leads to more effective inhibition of expression of the targeted gene (BCR-ABL1) and cancer cell proliferation. Taken together, these findings suggest that PEG-decorated cationic liposomes mediated siRNA delivery allows an effective antisense suppression of certain oncogenes, and represents a promising new class of therapies for CML.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 1-12"},"PeriodicalIF":3.9,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139412347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Sucrose phosphorylase from Alteromonas mediterranea: Structural insight into the regioselective α-glucosylation of (+)-catechin 来自地中海单胞菌的蔗糖磷酸化酶：对(+)-儿茶素的区域选择性α-葡萄糖基化的结构洞察

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-09 DOI: 10.1016/j.biochi.2024.01.004

Marine Goux , Marie Demonceaux , Johann Hendrickx , Claude Solleux , Emilie Lormeau , Folmer Fredslund , David Tezé , Bernard Offmann , Corinne André-Miral

{"title":"Sucrose phosphorylase from Alteromonas mediterranea: Structural insight into the regioselective α-glucosylation of (+)-catechin","authors":"Marine Goux , Marie Demonceaux , Johann Hendrickx , Claude Solleux , Emilie Lormeau , Folmer Fredslund , David Tezé , Bernard Offmann , Corinne André-Miral","doi":"10.1016/j.biochi.2024.01.004","DOIUrl":"10.1016/j.biochi.2024.01.004","url":null,"abstract":"<div>Sucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate their solubility and bioactivity. Here, we report for the first time the structure of sucrose phosphorylase from the marine bacteria Alteromonas mediterranea (AmSP) and its enzymatic properties. Kinetics of sucrose hydrolysis and transglucosylation capacities on (+)-catechin were investigated. Wild-type enzyme (AmSP-WT) displayed high hydrolytic activity on sucrose and was devoid of transglucosylation activity on (+)-catechin. Two variants, AmSP-Q353F and AmSP-P140D catalysed the regiospecific transglucosylation of (+)-catechin: 89 % of a novel compound (+)-catechin-4′-O-α-d-glucopyranoside (CAT-4′) for AmSP-P140D and 92 % of (+)-catechin-3′-O-α-d-glucopyranoside (CAT-3′) for AmSP-Q353F. The compound CAT-4′ was fully characterized by NMR and mass spectrometry. An explanation for this difference in regiospecificity was provided at atomic level by molecular docking simulations: AmSP-P140D was found to preferentially bind (+)-catechin in a mode that favours glucosylation on its hydroxyl group in position 4′ while the binding mode in AmSP-Q353F favoured glucosylation on its hydroxyl group in position 3’.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"221 ","pages":"Pages 13-19"},"PeriodicalIF":3.9,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S030090842400004X/pdfft?md5=42e43335b2df48c3f434f3f13832e47b&pid=1-s2.0-S030090842400004X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139412343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The determinants of metabolic discrepancies in aerobic glycolysis: Providing potential targets for breast cancer treatment 有氧糖酵解代谢差异的决定因素：为乳腺癌治疗提供潜在靶点

IF 3.9 3区生物学

Biochimie Pub Date : 2024-01-04 DOI: 10.1016/j.biochi.2024.01.003

Ajeesh Babu Littleflower, Sulfath Thottungal Parambil, Gisha Rose Antony, Lakshmi Subhadradevi

{"title":"The determinants of metabolic discrepancies in aerobic glycolysis: Providing potential targets for breast cancer treatment","authors":"Ajeesh Babu Littleflower, Sulfath Thottungal Parambil, Gisha Rose Antony, Lakshmi Subhadradevi","doi":"10.1016/j.biochi.2024.01.003","DOIUrl":"10.1016/j.biochi.2024.01.003","url":null,"abstract":"<div>Altered aerobic glycolysis is the robust mechanism to support cancer cell survival and proliferation beyond the maintenance of cellular energy metabolism. Several investigators portrayed the important role of deregulated glycolysis in different cancers, including breast cancer. Breast cancer is the most ubiquitous form of cancer and the primary cause of cancer death in women worldwide. Breast cancer with increased glycolytic flux is hampered to eradicate with current therapies and can result in tumor recurrence. In spite of the low order efficiency of ATP production, cancer cells are highly addicted to glycolysis. The glycolytic dependency of cancer cells provides potential therapeutic strategies to preferentially kill cancer cells by inhibiting glycolysis using antiglycolytic agents. The present review emphasizes the most recent research on the implication of glycolytic enzymes, including glucose transporters (GLUTs), hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), lactate dehydrogenase-A (LDHA), associated signalling pathways and transcription factors, as well as the antiglycolytic agents that target key glycolytic enzymes in breast cancer. The potential activity of glycolytic inhibitors impinges cancer prevalence and cellular resistance to conventional drugs even under worse physiological conditions such as hypoxia. As a single agent or in combination with other chemotherapeutic drugs, it provides the feasibility of new therapeutic modalities against a wide spectrum of human cancers.</div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"220 ","pages":"Pages 107-121"},"PeriodicalIF":3.9,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139096584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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