IF 4.5

mLife Pub Date : 2024-07-31 eCollection Date: 2024-09-01 DOI: 10.1002/mlf2.12127

Wenchen Song

引用次数: 0

Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. 协同网络连通性决定了开放细菌泛基因组的模糊基本区。

IF 4.5

mLife Pub Date : 2024-06-28 eCollection Date: 2024-06-01 DOI: 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":"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 Sinorhizobium 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 Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.","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}

引用次数: 0

Identification of 3-ketocapnine reductase activity within the human microbiota. 鉴定人体微生物群中的 3-Ketocapnine 还原酶活性。

IF 4.5

mLife Pub Date : 2024-06-28 eCollection Date: 2024-06-01 DOI: 10.1002/mlf2.12134

Xiaotong Wu, Lukuan Hou, Haili Zhang, Yi Ma, Jufang Wang, Mingwei Cai, Xiaoyu Tang

引用次数: 0

A novel alcohol dehydrogenase in the hyperthermophilic crenarchaeon Hyperthermus butylicus. 高热嗜温性丁香菌（Hyperthermus butylicus）中的一种新型醇脱氢酶。

IF 4.5

mLife Pub Date : 2024-06-28 eCollection Date: 2024-06-01 DOI: 10.1002/mlf2.12126

Ching Tse, Kesen Ma

{"title":"A novel alcohol dehydrogenase in the hyperthermophilic crenarchaeon Hyperthermus butylicus.","authors":"Ching Tse, Kesen Ma","doi":"10.1002/mlf2.12126","DOIUrl":"10.1002/mlf2.12126","url":null,"abstract":"Hyperthermus butylicus is a hyperthermophilic crenarchaeon that produces 1-butanol as an end product. A thermostable alcohol dehydrogenase (ADH) must be present in H. butylicus 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 H. butylicus, and its characteristics were determined. The gene that encodes HbADH2 was demonstrated to be HBUT_RS04850 and annotated as a hypothetical protein in H. butylicus. 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 k c at/K m, with k cat and apparent K m values of 8.00 ± 0.22 s-1 and 0.59 ± 0.07 mM, respectively. The apparent K m 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 H. butylicus. The putative conserved motif sites for NAD(P)+ and iron binding were identified by aligning HbADH2 with previously characterized Fe-containing ADHs.","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}

引用次数: 0

Elucidating microbial iron corrosion mechanisms with a hydrogenase-deficient strain of Desulfovibrio vulgaris. 利用氢化酶缺陷的普通脱硫弧菌菌株阐明微生物的铁腐蚀机制。

IF 4.5

mLife Pub Date : 2024-06-28 eCollection Date: 2024-06-01 DOI: 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 Desulfovibrio vulgaris.","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":"Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure. There is substantial debate over their corrosion mechanisms. We investigated Fe0 corrosion with Desulfovibrio vulgaris, the sulfate reducer most often employed in corrosion studies. Cultures were grown with both lactate and Fe0 as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes. Fe0 was corroded in cultures of a D. vulgaris hydrogenase-deficient mutant with the 1:1 correspondence between Fe0 loss and H2 accumulation expected for Fe0 oxidation coupled to H+ reduction to H2. This result and the extent of sulfate reduction indicated that D. vulgaris was not capable of direct Fe0-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 H2 removal was not necessary for the enhanced corrosion observed in the presence of microbes. The parental H2-consuming strain corroded more Fe0 than the mutant strain, which could be attributed to H2 oxidation coupled to sulfate reduction, producing sulfide that further stimulated Fe0 oxidation. The results suggest that H2 consumption is not necessary for microbially enhanced corrosion, but H2 oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction. The finding that D. vulgaris was incapable of direct electron uptake from Fe0 reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.","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}

引用次数: 0

Phage-displayed heptapeptide sequence conjugation significantly improves the specific targeting ability of antimicrobial peptides against Staphylococcus aureus. 噬菌体显示的七肽序列连接显著提高了抗菌肽对金黄色葡萄球菌的特异性靶向能力。

IF 4.5

mLife Pub Date : 2024-05-27 eCollection Date: 2024-06-01 DOI: 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 Staphylococcus aureus.","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":"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 Staphylococcus aureus 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 S. aureus. Moreover, SFK2 showed excellent biocompatibility in mice and piglet, and demonstrated significant therapeutic efficacy against S. aureus infection. In conclusion, our screening of phage-derived heptapeptides effectively enhances the specific bactericidal ability of the antimicrobial peptides against S. aureus, providing a theoretical basis for developing targeted antimicrobial peptides.","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}

引用次数: 0

Harnessing marine microbiomes to develop a sustainable, all-Atlantic bioeconomy. 利用海洋微生物群发展可持续的全大西洋生物经济。

IF 4.5

mLife Pub Date : 2024-05-27 eCollection Date: 2024-06-01 DOI: 10.1002/mlf2.12124

Cristiane Thompson, Alice C Ortmann, Henk Bolhuis, Thulani Makhalanyane, Fabiano Thompson

引用次数: 0

Microbiome-driven anticancer therapy: A step forward from natural products. 微生物驱动的抗癌疗法：从天然产品向前迈进。

IF 4.5

mLife Pub Date : 2024-05-27 eCollection Date: 2024-06-01 DOI: 10.1002/mlf2.12118

Yunxuan Guan, Di Wu, Hui Wang, Ning-Ning Liu

引用次数: 0

Filamentation and inhibition of prokaryotic CTP synthase with ligands. 原核生物 CTP 合酶的成丝和配体抑制作用。

IF 4.5

mLife Pub Date : 2024-05-02 eCollection Date: 2024-06-01 DOI: 10.1002/mlf2.12119

Chenjun Guo, Zixuan Wang, Ji-Long Liu

{"title":"Filamentation and inhibition of prokaryotic CTP synthase with ligands.","authors":"Chenjun Guo, Zixuan Wang, Ji-Long Liu","doi":"10.1002/mlf2.12119","DOIUrl":"10.1002/mlf2.12119","url":null,"abstract":"Cytidine triphosphate synthase (CTPS) plays a pivotal role in the de novo synthesis of cytidine triphosphate (CTP), a fundamental building block for RNA and DNA that is essential for life. CTPS is capable of directly binding to all four nucleotide triphosphates: adenine triphosphate, uridine triphosphate, CTP, and guanidine triphosphate. Furthermore, CTPS can form cytoophidia in vivo and metabolic filaments in vitro, undergoing regulation at multiple levels. CTPS is considered a potential therapeutic target for combating invasions or infections by viral or prokaryotic pathogens. Utilizing cryo-electron microscopy, we determined the structure of Escherichia coli CTPS (ecCTPS) filament in complex with CTP, nicotinamide adenine dinucleotide (NADH), and the covalent inhibitor 6-diazo-5-oxo- l-norleucine (DON), achieving a resolution of 2.9 Å. We constructed a phylogenetic tree based on differences in filament-forming interfaces and designed a variant to validate our hypothesis, providing an evolutionary perspective on CTPS filament formation. Our computational analysis revealed a solvent-accessible ammonia tunnel upon DON binding. Through comparative structural analysis, we discern a distinct mode of CTP binding of ecCTPS that differs from eukaryotic counterparts. Combining biochemical assays and structural analysis, we determined and validated the synergistic inhibitory effects of CTP with NADH or adenine on CTPS. Our results expand our comprehension of the diverse regulatory aspects of CTPS and lay a foundation for the design of specific inhibitors targeting prokaryotic CTPS.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 2","pages":"240-250"},"PeriodicalIF":4.5,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474095","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}

引用次数: 0

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus. 通过酵母人工染色体转移二硫键形成模块可促进马氏假丝酵母中异源蛋白的表达。

mLife Pub Date : 2024-03-22 eCollection Date: 2024-03-01 DOI: 10.1002/mlf2.12115

Pingping Wu, Wenjuan Mo, Tian Tian, Kunfeng Song, Yilin Lyu, Haiyan Ren, Jungang Zhou, Yao Yu, Hong Lu

{"title":"Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus.","authors":"Pingping Wu, Wenjuan Mo, Tian Tian, Kunfeng Song, Yilin Lyu, Haiyan Ren, Jungang Zhou, Yao Yu, Hong Lu","doi":"10.1002/mlf2.12115","DOIUrl":"10.1002/mlf2.12115","url":null,"abstract":"Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins. Improving the yield in K. marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering. To address these issues, linear and circular yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K. marxianus. These modules contained up to seven genes with a maximum size of 15 kb. KmYACs carried telomeres either from K. marxianus or Tetrahymena. KmYACs were transferred successfully into K. marxianus and stably propagated without affecting the normal growth of the host, regardless of the type of telomeres and configurations of KmYACs. KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins. In high-density fermentation, the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l, the highest reported level to date in K. marxianus. Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis, enhanced flux entering the tricarboxylic acid cycle, and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins. Consistently, supplementing lysine or arginine further improved the yield. Therefore, KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research. Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins, and this strategy may be applied to optimize other microbial cell factories.","PeriodicalId":94145,"journal":{"name":"mLife","volume":"3 1","pages":"129-142"},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11139206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201209","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}

引用次数: 0

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