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Properties of the Ureaplasma parvum structural maintenance of chromosomes protein related to its interaction with DNA.
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf010
Natalia A Rumyantseva, Vladimir M Shutov, Dina G Belenkaia, Aleksandr A Alekseev, Natalia E Morozova, Alexey D Vedyaykin

SMC (Structural Maintenance of Chromosomes) ATPase proteins are integral components of complexes bearing the same name, crucial for the spatial organization of DNA across diverse life forms, spanning bacteria, archaea, and eukaryotes. It is proposed that in bacteria, SMC complexes facilitate DNA compaction through loop extrusion and aid in the segregation of daughter nucleoids. In this paper, the properties of the SMC ATPase protein from Ureaplasma parvum were investigated by using a spectrum of methods, including conventional biochemical methods as well as advanced single-molecule techniques. Our findings reveal distinctive properties of this protein compared to its extensively studied homologue from Bacillus subtilis. Notably, our results suggest that U. parvum Smc ATPase facilitates DNA compaction even in the absence of ATP.

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引用次数: 0
Effects of phyto-phenolic compounds on ammonia production by select amino acid fermenting bacteria.
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf018
Jourdan E Lakes, Leah I Ramos, Maedean L Cardenas, Natasha L Mast, Michael D Flythe

Bacteria that ferment amino acids to ammonia can be categorized as generalists or specialist hyper-ammonia-producing bacteria. In the rumens of ruminant animals, most of the ammonia produced is eventually excreted as urea in urine. This process can be controlled with off-label use of antibiotics, but the practice can lead to antibiotic resistance; therefore, discovery of antibiotic alternatives is pertinent. Plant-derived phenolic compounds have demonstrated antimicrobial efficacy for such purposes. This study investigated the antimicrobial and metabolic suppressive potential of six phenolic compounds on five amino acid fermenting bacteria: Clostridium sporogenes MD1, C. aminophilum F, Acetoanaerobium sticklandii SR, Peptostreptococcus sp. BG1, and Prevotella bryantii B14. Inhibitory action of the compounds was determined using a 10% v/v serial dilution method in basal media. Carvacrol (1 mM), thymol (1 mM), and eugenol (10 mM) demonstrated the greatest antimicrobial potential, where carvacrol and eugenol inhibited growth of all five species and thymol four species except BG1. The cinnamic acids (trans and hydro) demonstrated variable activity against all organisms. Suppression of metabolic activity was determined via colorimetric assay quantifying ammonia in washed stationary phase culture supernatant after 24 h of metabolism on fresh substrate. Carvacrol and eugenol yielded the greatest reduction of ammonia by all organisms except B14, which produced no ammonia under the growth conditions. Thymol greatly reduced ammonia production of four organisms except F. These data demonstrate that eugenol, carvacrol, and thymol may be worthy antimicrobial candidates for the control of ammonia-producing organisms.

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引用次数: 0
Determination of bacteriocin genes and antimicrobial activity of Lactiplantibacillus plantarum isolated from feta cheese samples. 菲达干酪植物乳杆菌细菌素基因及抑菌活性测定。
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf002
Sumeyye Akbulut, Elanur Dasdemir, Hakan Ozkan, Ahmet Adiguzel

In this study designed to isolate lactic acid bacteria (LAB) with bacteriocin production potential, white cheese samples were collected from different provinces of Turkey and isolation was carried out. A series of experiments were carried out for the main purpose and the actual bacteriocin producers were identified by detecting the genes encoding this bacteriocin. The experiments carried out in this direction were initially carried out with 20 isolates and as a result of various experiments, the number of isolates was reduced to 8 and the study was continued with 8 isolates. In order to determine that the eight isolates identified as a result of a phenotypic and biochemical characterization study were true bacteriocin-producing strains, their antibacterial activity was investigated and then the presence of bacteriocin genes was examined by specific polymerase chain reaction (PCR) using gene-specific primers. As a result, MS16 coded Lactiplantibacillus plantarum OR922652 was found to have strong antibacterial activity against Escherichia coli, Klebsiella pneumonia, Yersinia enterocolitica, Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus; the isolate was susceptible to clinically important antibiotics (ciprofloxacin, gentamicin, penicillin G, ampicillin, chloramphenicol, and vancomycin) and resistant to erythromycin, had no hemolytic activity and possessed plnA and plnD genes encoding bacteriocin production. In conclusion, the MS16 coded L. plantarum isolate has emerged as a promising strain that can be used especially in the health field and in the food industry related to LAB.

本研究旨在分离具有细菌素生产潜力的乳酸菌(LAB),对土耳其不同省份的白奶酪样品进行了分离。为此进行了一系列实验,并通过检测编码该细菌素的基因,确定了实际的细菌素产生者。在这个方向上进行的实验最初是用20株分离株进行的,由于各种实验,分离株数量减少到8株,并继续用8株分离株进行研究。为了确定表型和生化鉴定结果鉴定的8株菌株是真正的细菌素产生菌株,研究了它们的抗菌活性,然后使用基因特异性引物通过特异性PCR检测了细菌素基因的存在。结果发现MS16编码的植物乳杆菌OR922652对大肠埃希菌、肺炎克雷伯菌、小肠结肠炎耶尔森菌、单核增生李斯特菌、蜡样芽孢杆菌和金黄色葡萄球菌具有较强的抑菌活性,对临床重要抗生素(环丙沙星、庆大霉素、青霉素G、氨苄西林、氯霉素、万古霉素)敏感,对红霉素耐药;无溶血活性,具有编码细菌素产生的plnA和plnD基因。综上所述,MS16编码的植物乳杆菌分离株已成为一种有前景的菌株,特别是在卫生领域和与LAB相关的食品工业中具有重要的应用价值。
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引用次数: 0
Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs.
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf017
Ifigeneia Kyrkou, Jennifer Bartell, Ana Lechuga, Cédric Lood, Rasmus L Marvig, Rob Lavigne, Søren Molin, Helle Krogh Johansen

Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.

{"title":"Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs.","authors":"Ifigeneia Kyrkou, Jennifer Bartell, Ana Lechuga, Cédric Lood, Rasmus L Marvig, Rob Lavigne, Søren Molin, Helle Krogh Johansen","doi":"10.1093/femsle/fnaf017","DOIUrl":"10.1093/femsle/fnaf017","url":null,"abstract":"<p><p>Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Comparison of crystal violet staining, microscopy with image analysis, and quantitative PCR to examine biofilm dynamics. 比较结晶紫染色,显微镜与图像分析,定量PCR检查生物膜动力学。
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnae115
So-Yeon Jeong, Ji Won Lee, Eun Ji Kim, Chi Won Lee, Tae Gwan Kim

Crystal-violet staining, microscopy with image analysis, and quantitative PCR (qPCR) were compared to examine biofilm dynamics. Biofilms of 30 polycultures comprising 15 bacterial species were monitored for 14 days. Collectively, qPCR (representing population) revealed a different growth pattern compared to staining (biomass) and microscopy (colonization): biomass and colonization gradually increased over time, whereas population increased rapidly for the first seven days and leveled off. Temporal forms were categorized into two growth patterns: continuous increase (CI) and non-continuous increase. Staining and microscopy showed similar odds of detecting the CI pattern (27 and 23 polycultures, respectively) across polycultures, greater than that of qPCR (14 polycultures) (P < 0.05). All three methods revealed the identical patterns for 13 polycultures. Staining with microscopy, staining with qPCR, and microscopy with qPCR found the same patterns in 22, 15, and 19 polycultures, respectively. Additionally, staining was quantitatively agreed with microscopy (P < 0.05; R2 > 0.50), whereas neither staining nor microscopy strongly agreed with qPCR (P < 0.05; R2 ≤ 0.22). Collectively, staining was more compatible with microscopy than qPCR in characterizing biofilm dynamics and quantifying biofilms owing to the difference between population growth and biofilm expansion. The concurrent use of qPCR with biomass estimations allows for accurate and comprehensive biofilm quantification.

比较结晶紫染色,显微镜图像分析和定量PCR (qPCR)来检测生物膜动力学。对包含15种细菌的30种复培养物的生物膜进行了14天的监测。总体而言,与染色(生物量)和显微镜(定植)相比,qPCR(代表种群)揭示了不同的生长模式:生物量和定植随着时间的推移逐渐增加,而种群在前7天迅速增加并趋于平稳。时间形态分为连续增长(CI)和非连续增长(NCI)两种增长模式。染色法和显微镜法在多培养中检测CI模式(分别为27和23个多培养)的几率相似,高于qPCR法(14个多培养)(P 0.50),而染色法和显微镜法都与qPCR法不一致(P .50)
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引用次数: 0
About two French cases of disseminated Cryptococcus neoformans infection associated with COVID-19.
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf012
Wendy Pulby, Jérémy Lafolie, Chloé Belot, Loïc Dopeux, Sébastien Loiseau, Maxime Moniot, Philippe Poirier, Céline Nourrisson

SARS-CoV-2 infection is an acute respiratory distress syndrome associated with immune dysfunction, causing coronavirus disease 2019 (COVID-19) disease. The use of immunosuppressive drugs in its treatment increases the risk of opportunistic infections. In particular, opportunistic fungal infections have been described in initially non-immunocompromised patients with severe COVID-19 disease. Among them, rare cases of cryptococcosis have been described. Here we present the first two French cases of non-HIV non-transplant patients who developed disseminated Cryptococcus neoformans fungal infection in the setting of severe COVID-19 disease. Blood cultures appear to be an interesting diagnostic tool for post-COVID-19 cryptococcosis, which is an often fatal complication.

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引用次数: 0
Reach of the Instagram profile @microbioworld in popularizing mycology and microbiology.
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnaf019
Jefferson Brendon Almeida Dos Reis, Sofia Coradini Schirmer

Online social networks have revolutionized scientific communication, making platforms like Instagram indispensable for sharing complex topics, including mycology. This study evaluated three key factors in assessing the impact of social media on scientific dissemination: follower profiles, reach, and engagement levels. We used the professional Instagram account @microbioworld as a case study. Account performance data were collected over a 90-day period (12 August-9 November 2024). Post performance was evaluated using data from selected posts published between 11 January and 11 November 2024. By the end of our sampling period, the account reached a total of 45 959 followers, with the majority aged 25-34 years (44.8%). It reached 108 631 unique accounts, with 22.4% being followers and 77.6% non-followers, generating 236 860 impressions and 15 750 interactions. Likes accounted for 83.3% of engagement. Posts featuring microorganism cultures achieved the highest engagement and reach. Sentiment analysis, using Bing and AFINN lexicons, revealed that over 89% of sentiments expressed in comments were positive. These findings demonstrate how Instagram can disseminate microbial content, foster positive perceptions of microorganisms, and emphasize their ecological importance, encouraging audience involvement with mycology and microbiology.

在线社交网络彻底改变了科学传播方式,使Instagram等平台成为分享复杂话题(包括真菌学)不可或缺的工具。本研究评估了社交媒体对科学传播影响的三个关键因素:追随者资料、覆盖面和参与度。我们以专业 Instagram 帐户 @microbioworld 为案例进行研究。我们收集了账户在 90 天内(2024 年 8 月 12 日至 11 月 9 日)的表现数据。我们使用 2024 年 1 月 11 日至 11 月 11 日期间发布的部分帖子数据对帖子性能进行了评估。在取样期结束时,该账户共有 45 959 名粉丝,其中大部分年龄在 25-34 岁之间(44.8%)。独立账户达到 108 631 个,其中 22.4% 为关注者,77.6% 为非关注者,产生了 236 860 个印象和 15 750 个互动。点赞占互动的 83.3%。以微生物培养为主题的帖子获得了最高的参与度和覆盖率。使用 Bing 和 AFINN 词库进行的情感分析表明,评论中表达的情感有 89% 以上是积极的。这些研究结果表明,Instagram 可以传播微生物内容,培养人们对微生物的积极看法,强调其生态重要性,鼓励受众参与真菌学和微生物学研究。
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引用次数: 0
Functionally important components of the transcription elongation complex involved in Rho-dependent termination. 转录延伸复合体的重要功能组分参与rho依赖性终止。
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnae111
Ajay Khatri, Ranjan Sen

Bacterial transcription terminator, Rho is an RNA (Ribonucleic Acid)-dependent ATPase that terminates transcription. Several structures of pretermination complexes of the Rho-transcription elongation complex (EC) revealed a static picture of components of the EC that come close to the nascent RNA-bound Rho, where many of the residues of EC reside ≤10 Å from the Rho residues. However, the in vitro-formed Rho-EC complexes do not reveal the in vivo Rho-EC dynamic interaction patterns during the termination process. Here we report synthetic defect analyses of various combinations of the mutations in RNAP β, β' and ω-subunits, NusA, NusG, and Rho proteins to delineate the functional network of this process. Several mutations in the β-flap and β'-Zn-finger and -Clamp helices domains of RNAP are synthetically defective in the presence of Rho mutants indicating functional involvement of these domains. Mutations in the NusA RNA-binding domains were synthetically defective with the Rho mutants suggesting its involvement. Our genetic analyses also revealed functional antagonisms between the ω-subunit of RNAP and the NusG-CTD (c-terminal domain) during termination. We concluded that the regions surrounding the RNA exit channel, the RNA-binding domains of NusA, the RNAP ω-subunit, and NusG-CTD constitute a functional network with Rho just before the onset of in vivo Rho-dependent termination.

细菌转录终止酶,Rho是一种终止转录的rna依赖性atp酶。Rho转录延伸复合物(EC)的几个预终止复合物的结构揭示了接近新生rna结合Rho的EC组分的静态图像,其中EC的许多残基位于Rho残基≤10 Å处。然而,体外形成的Rho-EC复合物在终止过程中不显示体内Rho-EC的动态相互作用模式。在这里,我们报道了RNAP β, β'和ω-亚基,NusA, NusG和Rho蛋白突变的各种组合的合成缺陷分析,以描述该过程的功能网络。在Rho突变体的存在下,RNAP的β-flap和β'-Zn-finger和-Clamp螺旋结构域的一些突变是合成缺陷的,表明这些结构域的功能参与。NusA rna结合域的突变是合成缺陷,Rho突变表明其参与。我们的遗传分析还发现RNAP的ω-亚基与NusG-CTD在终止过程中存在功能拮抗。我们得出结论,RNA出口通道周围的区域、NusA的RNA结合域、RNAP ω-亚基和NusG-CTD在体内Rho依赖性终止开始之前与Rho构成了一个功能网络。
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引用次数: 0
Contributions of hemolytic proteins in virulent Aeromonas hydrophila to motile Aeromonas septicemia disease of channel catfish (Ictalurus punctatus). 嗜水气单胞菌毒力溶血蛋白在海峡鲶鱼运动性气单胞菌败血症中的作用。
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnae108
Dunhua Zhang, Jun Feng, Yi Wang, Craig A Shoemaker, Allison A Wise, Benjamin H Beck

Hemolytic proteins are a major group of virulence factors in pathogenic Aeromonas hydrophila. Six genes encoding presumable hemolytic proteins were revealed from the genome of virulent A. hydrophila (vAh) that caused severe disease in channel catfish. The aim of this study was to assess the contribution of these hemolytic proteins to the virulence of this bacterium. Genes coding for following six proteins were investigated: aerolysin (Arl), 21-kDa hemolysin (Hly1), thermostable hemolysin (Hly2), phospholipase/lecithinase-related hemolysin (Hly3), membrane-associated hemolysin III (Hly4), and cytolysin-associated hemolysin (Hly5). Individual genes were deleted from the bacterium using CRISPR-Cas9 mediated methods. Assessment showed that deletion of Arl gene (Δarl) completely abolished hemolytic activity of this mutant while Δhly1-Δhly5 mutants had the same activity as the wild vAh. Extracellular proteins (ECPs) of the Δarl mutant caused significantly (p < 0.01) less cell death in vitro with viability increased by approximately 20%, compared to the wild vAh. ECPs of mutants Δhly1-Δhly5 remained the same cell toxicity as the wild vAh. A second deletion of hly5 from the Δarl mutant further lowered the cell toxicity of the ECP of the mutant (Δarl + Δhly5). Assays in vivo showed that both Δarl and Δhly5 mutants caused less fish mortality with reduction of 57% and 16%, respectively, compared to the wild vAh; the Δarl + Δhly5 mutant caused the least mortality with approximately 87% of reduction; and other mutants had the same virulence as the wild vAh. Analyses of SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and Western blotting evidently indicate that both Arl and Hly5 proteins formed hexamer-like stable structures post secretion from the bacterium. Arl and Hly5 apparently had synergistic action in cytotoxicity and causing disease and were the major virulence factors among the six hemolytic proteins analyzed in this study.

溶血蛋白是致病性嗜水气单胞菌的主要毒力因子。从引起通道鲶鱼严重疾病的毒力嗜水A. (vAh)基因组中发现了6个编码可能溶血蛋白的基因。本研究的目的是评估这些溶血蛋白对这种细菌的毒力的贡献。研究了航空溶血素(Arl)、21-kDa溶血素(Hly1)、耐热溶血素(Hly2)、磷脂酶/卵磷脂酶相关溶血素(Hly3)、膜相关溶血素III (Hly4)和细胞溶血素相关溶血素(Hly5)等6种蛋白的基因编码。使用CRISPR-Cas9介导的方法从细菌中删除单个基因。评估表明,Arl基因(Δarl)的缺失完全消除了该突变体的溶血活性,而Δhly1-Δhly5突变体与野生vAh具有相同的活性。Δarl突变体的细胞外蛋白(ECP)显著(p
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引用次数: 0
SoxR-dependent regulation of sodA1 and its impact on Stenotrophomonas maltophilia survival under external oxidative stress. soxr依赖性sodA1调控及其对嗜麦芽窄养单胞菌外部氧化应激存活的影响
IF 2.2 4区 生物学 Q3 MICROBIOLOGY Pub Date : 2025-01-10 DOI: 10.1093/femsle/fnae112
Suparat Giengkam, Nisanart Charoenlap, Wirongrong Whangsuk, Kisana Bhinija, Skorn Mongkolsuk, Paiboon Vattanaviboon

Stenotrophomonas maltophilia is an emerging global opportunistic pathogen that causes nosocomial infections. We demonstrated that the superoxide stress-sensing transcriptional regulator SoxR directly modulated the expression of an operon encompassing sodA1 (encoding manganese-containing superoxide dismutase) and fre (encoding putative flavin reductase) by directly binding to the operator site, which was located between the -35 and -10 motifs of the sodA1 promoter. It is known that upon exposure to the superoxide generators/redox-cycling drugs, the SoxR, which is bound to the operator site, became oxidized. This oxidation causes a conformational change of SoxR to an active form, enabling the upregulation of sodA1-fre gene expression. A ΔsodA1 was constructed, and the mutant showed enhanced sensitivity to the redox-cycling drugs, including menadione, plumbagin, and methyl viologen (paraquat), relative to its parental strain K279a. Thus, sodA1 may play a role in the survival of S. maltophilia under superoxide stress during either its saprophyte stage (e.g. exposure to redox-cycling drugs) or host-pathogen interactions.

嗜麦芽窄养单胞菌是一种新兴的全球性机会性病原体,可引起医院感染。我们证明了超氧化物应激感应转录调节剂SoxR通过直接结合位于sodA1启动子- 35和-10基元之间的操作子位点,直接调节包含sodA1(编码含锰超氧化物歧化酶)和fre(编码推测的黄素还原酶)的操纵子的表达。众所周知,暴露于超氧化物发生器/氧化还原循环药物后,与操作位点结合的SoxR被氧化。这种氧化导致SoxR的构象改变为活性形式,使soda1 - free基因表达上调。构建ΔsodA1,与亲本菌株K279a相比,该突变体对氧化还原循环药物,包括美萘醌、白丹素和甲基紫草酮(百草枯)的敏感性增强。因此,sodA1可能在嗜麦芽葡萄球菌腐生期(例如暴露于氧化还原循环药物)或宿主-病原体相互作用下的超氧胁迫下的存活中发挥作用。
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Fems Microbiology Letters
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