{"title":"Discovery of β-nitrostyrene derivatives as potential quorum sensing inhibitors for biofilm inhibition and antivirulence factor therapeutics against <i>Serratia marcescens</i>.","authors":"Jiang Wang, Jingyi Yang, Pradeepraj Durairaj, Wei Wang, Dongyan Wei, Shi Tang, Haiqing Liu, Dayong Wang, Ai-Qun Jia","doi":"10.1002/mlf2.12135","DOIUrl":"10.1002/mlf2.12135","url":null,"abstract":"<p><p>Quorum sensing (QS) inhibition has emerged as a promising target for directed drug design, providing an appealing strategy for developing antimicrobials, particularly against infections caused by drug-resistant pathogens. In this study, we designed and synthesized a total of 33 β-nitrostyrene derivatives using 1-nitro-2-phenylethane (NPe) as the lead compound, to target the facultative anaerobic bacterial pathogen <i>Serratia marcescens</i>. The QS-inhibitory effects of these compounds were evaluated using <i>S. marcescens</i> NJ01 and the reporter strain <i>Chromobacterium violaceum</i> CV026. Among the 33 new β-nitrostyrene derivatives, (<i>E</i>)-1-methyl-4-(2-nitrovinyl)benzene (m-NPe, compound 28) was proven to be a potent inhibitor that reduced biofilm formation of <i>S. marcescens</i> NJ01 by 79%. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) results revealed that treatment with m-NPe (50 μg/ml) not only enhanced the susceptibility of the formed biofilms but also disrupted the architecture of biofilms by 84%. m-NPe (50 μg/ml) decreased virulence factors in <i>S. marcescens</i> NJ01, reducing the activity of protease, prodigiosin, and extracellular polysaccharide (EPS) by 36%, 72%, and 52%, respectively. In <i>S. marcescens</i> 4547, the activities of hemolysin and EPS were reduced by 28% and 40%, respectively, outperforming the positive control, vanillic acid (VAN). The study also found that the expression levels of QS- and biofilm-related genes (<i>flhD, fimA, fimC, sodB, bsmB, pigA, pigC</i>, and <i>shlA</i>) were downregulated by 1.21- to 2.32-fold. Molecular dynamics analysis showed that m-NPe could bind stably to SmaR, RhlI, RhlR, LasR, and CviR proteins in a 0.1 M sodium chloride solution. Importantly, a microscale thermophoresis (MST) test revealed that SmaR could be a target protein for the screening of a quorum sensing inhibitor (QSI) against <i>S. marcescens</i>. Overall, this study highlights the efficacy of m-NPe in suppressing the virulence factors of <i>S. marcescens</i>, identifying it as a new potential QSI and antibiofilm agent capable of restoring or improving antimicrobial drug sensitivity.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 3","pages":"445-458"},"PeriodicalIF":4.5,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-09-04eCollection Date: 2024-09-01DOI: 10.1002/mlf2.12138
Feiyue Cheng, Aici Wu, Zhihua Li, Jing Xu, Xifeng Cao, Haiying Yu, Zhenquan Liu, Rui Wang, Wenyuan Han, Hua Xiang, Ming Li
{"title":"Catalytically active prokaryotic Argonautes employ phospholipase D family proteins to strengthen immunity against different genetic invaders.","authors":"Feiyue Cheng, Aici Wu, Zhihua Li, Jing Xu, Xifeng Cao, Haiying Yu, Zhenquan Liu, Rui Wang, Wenyuan Han, Hua Xiang, Ming Li","doi":"10.1002/mlf2.12138","DOIUrl":"10.1002/mlf2.12138","url":null,"abstract":"<p><p>Prokaryotic Argonautes (pAgos) provide bacteria and archaea with immunity against plasmids and viruses. Catalytically active pAgos utilize short oligonucleotides as guides to directly cleave foreign nucleic acids, while inactive pAgos lacking catalytic residues employ auxiliary effectors, such as nonspecific nucleases, to trigger abortive infection upon detection of foreign nucleic acids. Here, we report a unique group of catalytically active pAgo proteins that frequently associate with a phospholipase D (PLD) family protein. We demonstrate that this particular system employs the catalytic center of the associated PLD protein rather than that of pAgo to restrict plasmid DNA, while interestingly, its immunity against a single-stranded DNA virus relies on the pAgo catalytic center and is enhanced by the PLD protein. We also find that this system selectively suppresses viral DNA propagation without inducing noticeable abortive infection outcomes. Moreover, the pAgo protein alone enhances gene editing, which is unexpectedly inhibited by the PLD protein. Our data highlight the ability of catalytically active pAgo proteins to employ auxiliary proteins to strengthen the targeted eradication of different genetic invaders and underline the trend of PLD nucleases to participate in host immunity.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 3","pages":"403-416"},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-06-28eCollection Date: 2024-06-01DOI: 10.1002/mlf2.12132
Pan Zhang, Biliang Zhang, Yuan-Yuan Ji, Jian Jiao, Ziding Zhang, Chang-Fu Tian
{"title":"Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome.","authors":"Pan Zhang, Biliang Zhang, Yuan-Yuan Ji, Jian Jiao, Ziding Zhang, Chang-Fu Tian","doi":"10.1002/mlf2.12132","DOIUrl":"10.1002/mlf2.12132","url":null,"abstract":"<p><p>Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for <i>Sinorhizobium</i> strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in <i>Sinorhizobium</i> pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"277-290"},"PeriodicalIF":4.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of 3-ketocapnine reductase activity within the human microbiota.","authors":"Xiaotong Wu, Lukuan Hou, Haili Zhang, Yi Ma, Jufang Wang, Mingwei Cai, Xiaoyu Tang","doi":"10.1002/mlf2.12134","DOIUrl":"10.1002/mlf2.12134","url":null,"abstract":"<p><p>The microbial synthesis of sulfonolipids within the human body is likely involved in maintaining human health or causing diseases. However, the enzymes responsible for their biosynthesis remain largely unknown. In this study, we identified and verified the role of 3-ketocapnine reductase, the third-step enzyme, in the four-step conversion of l-phosphoserine into sulfobacin B both in vivo and in vitro. This finding builds upon our previous research into sulfonolipid biosynthesis, which focused on the vaginal bacterium <i>Chryseobacterium gleum</i> DSM 16776 and the gut bacterium <i>Alistipes finegoldii</i> DSM 17242. Through comprehensive gene mapping, we demonstrate the widespread presence of potential sulfonolipid biosynthetic genes across diverse bacterial species inhabiting various regions of the human body. These findings shed light on the prevalence of sulfonolipid-like metabolites within the human microbiota, suggesting a potential role for these lipid molecules in influencing the intricate biointeractions within the complex microbial ecosystem of the human body.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"307-316"},"PeriodicalIF":4.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-06-28eCollection Date: 2024-06-01DOI: 10.1002/mlf2.12126
Ching Tse, Kesen Ma
{"title":"A novel alcohol dehydrogenase in the hyperthermophilic crenarchaeon <i>Hyperthermus butylicus</i>.","authors":"Ching Tse, Kesen Ma","doi":"10.1002/mlf2.12126","DOIUrl":"10.1002/mlf2.12126","url":null,"abstract":"<p><p><i>Hyperthermus butylicus</i> is a hyperthermophilic crenarchaeon that produces 1-butanol as an end product. A thermostable alcohol dehydrogenase (ADH) must be present in <i>H. butylicus</i> to act as the key enzyme responsible for this production; however, the gene that encodes the ADH has not yet been identified. A novel ADH, HbADH2, was purified from a cell-free extract of <i>H. butylicus</i>, and its characteristics were determined. The gene that encodes HbADH2 was demonstrated to be <i>HBUT_RS04850</i> and annotated as a hypothetical protein in <i>H. butylicus</i>. HbADH2 was found to be a primary-secondary ADH capable of using a wide range of substrates, including butyraldehyde and butanol. Butyraldehyde had the highest specificity constant, calculated as <i>k</i> <sub>c</sub> <sub>at</sub>/<i>K</i> <sub>m</sub>, with <i>k</i> <sub>cat</sub> and apparent <i>K</i> <sub>m</sub> values of 8.00 ± 0.22 s<sup>-1</sup> and 0.59 ± 0.07 mM, respectively. The apparent <i>K</i> <sub>m</sub> values for other substrates, including ethanol, 1-propanol, 2-propanol, butanol, acetaldehyde, propanal, and acetone, were 4.36 ± 0.42, 4.69 ± 0.41, 3.74 ± 0.46, 2.44 ± 0.30, 1.27 ± 0.18, 1.55 ± 0.20, and 0.68 ± 0.04 mM, respectively. The optimal pH values for catalyzing aldehyde reduction and alcohol oxidation were 6.0 and 9.0, respectively, while the optimal temperature was higher than 90°C due to the increase in enzymatic activity from 60°C to 90°C. Based on its substrate specificity, enzyme kinetics, and thermostability, HbADH2 may be the ADH that catalyzes the production of 1-butanol in <i>H. butylicus</i>. The putative conserved motif sites for NAD(P)<sup>+</sup> and iron binding were identified by aligning HbADH2 with previously characterized Fe-containing ADHs.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"317-325"},"PeriodicalIF":4.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-06-28eCollection Date: 2024-06-01DOI: 10.1002/mlf2.12133
Di Wang, Toshiyuki Ueki, Peiyu Ma, Dake Xu, Derek R Lovley
{"title":"Elucidating microbial iron corrosion mechanisms with a hydrogenase-deficient strain of <i>Desulfovibrio vulgaris</i>.","authors":"Di Wang, Toshiyuki Ueki, Peiyu Ma, Dake Xu, Derek R Lovley","doi":"10.1002/mlf2.12133","DOIUrl":"10.1002/mlf2.12133","url":null,"abstract":"<p><p>Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure. There is substantial debate over their corrosion mechanisms. We investigated Fe<sup>0</sup> corrosion with <i>Desulfovibrio vulgaris</i>, the sulfate reducer most often employed in corrosion studies. Cultures were grown with both lactate and Fe<sup>0</sup> as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes. Fe<sup>0</sup> was corroded in cultures of a <i>D. vulgaris</i> hydrogenase-deficient mutant with the 1:1 correspondence between Fe<sup>0</sup> loss and H<sub>2</sub> accumulation expected for Fe<sup>0</sup> oxidation coupled to H<sup>+</sup> reduction to H<sub>2</sub>. This result and the extent of sulfate reduction indicated that <i>D. vulgaris</i> was not capable of direct Fe<sup>0</sup>-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous sulfide. Corrosion in the hydrogenase-deficient mutant cultures was greater than in sterile controls, demonstrating that H<sub>2</sub> removal was not necessary for the enhanced corrosion observed in the presence of microbes. The parental H<sub>2</sub>-consuming strain corroded more Fe<sup>0</sup> than the mutant strain, which could be attributed to H<sub>2</sub> oxidation coupled to sulfate reduction, producing sulfide that further stimulated Fe<sup>0</sup> oxidation. The results suggest that H<sub>2</sub> consumption is not necessary for microbially enhanced corrosion, but H<sub>2</sub> oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction. The finding that <i>D. vulgaris</i> was incapable of direct electron uptake from Fe<sup>0</sup> reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"269-276"},"PeriodicalIF":4.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-05-27eCollection Date: 2024-06-01DOI: 10.1002/mlf2.12123
Tao Wang, Peng Tan, Qi Tang, Chenlong Zhou, Yakun Ding, Shenrui Xu, Mengda Song, Huiyang Fu, Yucheng Zhang, Xiaohui Zhang, Yueyu Bai, Zhihong Sun, Xi Ma
{"title":"Phage-displayed heptapeptide sequence conjugation significantly improves the specific targeting ability of antimicrobial peptides against <i>Staphylococcus aureus</i>.","authors":"Tao Wang, Peng Tan, Qi Tang, Chenlong Zhou, Yakun Ding, Shenrui Xu, Mengda Song, Huiyang Fu, Yucheng Zhang, Xiaohui Zhang, Yueyu Bai, Zhihong Sun, Xi Ma","doi":"10.1002/mlf2.12123","DOIUrl":"10.1002/mlf2.12123","url":null,"abstract":"<p><p>Broad-spectrum antibacterial drugs often lack specificity, leading to indiscriminate bactericidal activity, which can disrupt the normal microbial balance of the host flora and cause unnecessary cytotoxicity during systemic administration. In this study, we constructed a specifically targeted antimicrobial peptide against <i>Staphylococcus aureus</i> by introducing a phage-displayed peptide onto a broad-spectrum antimicrobial peptide and explored its structure-function relationship through one-factor modification. SFK2 obtained by screening based on the selectivity index and the targeting index showed specific killing ability against <i>S. aureus</i>. Moreover, SFK2 showed excellent biocompatibility in mice and piglet, and demonstrated significant therapeutic efficacy against <i>S. aureus</i> infection. In conclusion, our screening of phage-derived heptapeptides effectively enhances the specific bactericidal ability of the antimicrobial peptides against <i>S. aureus</i>, providing a theoretical basis for developing targeted antimicrobial peptides.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"251-268"},"PeriodicalIF":4.5,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
mLifePub Date : 2024-05-27eCollection Date: 2024-06-01DOI: 10.1002/mlf2.12118
Yunxuan Guan, Di Wu, Hui Wang, Ning-Ning Liu
{"title":"Microbiome-driven anticancer therapy: A step forward from natural products.","authors":"Yunxuan Guan, Di Wu, Hui Wang, Ning-Ning Liu","doi":"10.1002/mlf2.12118","DOIUrl":"10.1002/mlf2.12118","url":null,"abstract":"<p><p>Human microbiomes, considered as a new emerging and enabling cancer hallmark, are increasingly recognized as critical effectors in cancer development and progression. Manipulation of microbiome revitalizing anticancer therapy from natural products shows promise toward improving cancer outcomes. Herein, we summarize our current understanding of the human microbiome-driven molecular mechanisms impacting cancer progression and anticancer therapy. We highlight the potential translational and clinical implications of natural products for cancer prevention and treatment by developing targeted therapeutic strategies as adjuvants for chemotherapy and immunotherapy against tumorigenesis. The challenges and opportunities for future investigations using modulation of the microbiome for cancer treatment are further discussed in this review.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"219-230"},"PeriodicalIF":4.5,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}