mLife最新文献 - Book学术

Heme homeostasis and its regulation by hemoproteins in bacteria 细菌的血红素平衡及其受血红蛋白的调节

mLife Pub Date : 2024-07-11 DOI: 10.1002/mlf2.12120

Yingxi Li, Sirui Han, Haichun Gao

引用次数: 0

Impact of the gut microbiome on atherosclerosis 肠道微生物群对动脉粥样硬化的影响

mLife Pub Date : 2024-04-01 DOI: 10.1002/mlf2.12110

Yuqin Mao, Chao Kong, Tongtong Zang, Lingsen You, Li‐Shun Wang, Li Shen, Jun‐Bo Ge

引用次数: 0

Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus 无限制 pRN1 衍生物的合理设计及其在构建岛酵母双质粒载体系统中的应用

mLife Pub Date : 2024-03-20 DOI: 10.1002/mlf2.12107

Pengpeng Zhao, Xiaonan Bi, Xiaoning Wang, Xu Feng, Yulong Shen, Guanhua Yuan, Q. She

{"title":"Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus","authors":"Pengpeng Zhao, Xiaonan Bi, Xiaoning Wang, Xu Feng, Yulong Shen, Guanhua Yuan, Q. She","doi":"10.1002/mlf2.12107","DOIUrl":"https://doi.org/10.1002/mlf2.12107","url":null,"abstract":"Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools, which include efficient genome editing, gene silencing, and robust protein expression systems. However, plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic plasmid. Although this plasmid coexists with pRN1 in its original host, early attempts to test pRN1‐based vectors consistently failed to yield any stable host–vector system for Sa. islandicus. We hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this archaeon. We identified a putative target sequence in orf904 encoding a putative replicase on pRN1 (target N1). Mutated targets (N1a, N1b, and N1c) were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid interference assay. The results revealed that the original target triggered CRISPR immunity in this archaeon, whereas all three mutated targets did not, indicating that all the designed target mutations evaded host immunity. These mutated targets were then incorporated into orf904 individually, yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed (pN1aSD, pN1bSD, and pN1cSD). Sa. islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors, but pN1cSD lost the capability for replication. These results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the replicase. We further showed that pRN1‐based and pRN2‐based vectors were stably maintained in the archaeal cells either alone or in combination, and this yielded a dual plasmid system for genetic study with this important archaeal model.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"9 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140225623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Understanding the rapid spread of antimicrobial resistance genes mediated by IS26 了解由 IS26 介导的抗菌药耐药性基因的快速传播

mLife Pub Date : 2024-03-18 DOI: 10.1002/mlf2.12114

Na Tang, Dawei Wei, Yuan Zeng, Gang Zhang, Chao Wang, Jie Feng, Yuqin Song

{"title":"Understanding the rapid spread of antimicrobial resistance genes mediated by IS26","authors":"Na Tang, Dawei Wei, Yuan Zeng, Gang Zhang, Chao Wang, Jie Feng, Yuqin Song","doi":"10.1002/mlf2.12114","DOIUrl":"https://doi.org/10.1002/mlf2.12114","url":null,"abstract":"Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656 \u0000translocatable \u0000IS26\u0000‐bounded \u0000units with \u0000ARGs (tIS26‐bUs‐ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that \u0000IS26\u0000‐bounded \u0000units (IS26‐bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26‐bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of “passenger” genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140234708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RsaL is a self‐regulatory switch that controls alternative biosynthesis of two AHL‐type quorum sensing signals in Pseudomonas aeruginosa PA1201 RsaL 是一种自我调节开关，可控制铜绿假单胞菌 PA1201 中两种 AHL 型法定量传感信号的替代生物合成

mLife Pub Date : 2024-03-18 DOI: 10.1002/mlf2.12113

Ya‐Wen He, Zi-Jing Jin, Ying Cui, Kai Song, Bo Chen, Lian Zhou

{"title":"RsaL is a self‐regulatory switch that controls alternative biosynthesis of two AHL‐type quorum sensing signals in Pseudomonas aeruginosa PA1201","authors":"Ya‐Wen He, Zi-Jing Jin, Ying Cui, Kai Song, Bo Chen, Lian Zhou","doi":"10.1002/mlf2.12113","DOIUrl":"https://doi.org/10.1002/mlf2.12113","url":null,"abstract":"Pseudomonas aeruginosa is a ubiquitous and metabolically versatile microorganism naturally found in soil and water. It is also an opportunistic pathogen in plants, insects, animals, and humans. In response to increasing cell density, P. aeruginosa uses two acyl‐homoserine lactone (AHL) quorum‐sensing (QS) signals (i.e., N‐3‐oxo‐dodecanoyl homoserine lactone [3‐oxo‐C12‐HSL] and N‐butanoyl‐homoserine lactone [C4‐HSL]), which regulate the expression of hundreds of genes. However, how the biosynthesis of these two QS signals is coordinated remains unknown. We studied the regulation of these two QS signals in the rhizosphere strain PA1201. PA1201 sequentially produced 3‐oxo‐C12‐HSL and C4‐HSL at the early and late growth stages, respectively. The highest 3‐oxo‐C12‐HSL‐dependent elastase activity was observed at the early stage, while the highest C4‐HSL‐dependent rhamnolipid production was observed at the late stage. The atypical regulator RsaL played a pivotal role in coordinating 3‐oxo‐C12‐HSL and C4‐HSL biosynthesis and QS‐associated virulence. RsaL repressed lasI transcription by binding the –10 and –35 boxes of the lasI promoter. In contrast, RsaL activated rhlI transcription by binding the region encoding the 5′‐untranslated region of the rhlI mRNA. Further, RsaL repressed its own expression by binding a nucleotide motif located in the –35 box of the rsaL promoter. Thus, RsaL acts as a molecular switch that coordinates the sequential biosynthesis of AHL QS signals and differential virulence in PA1201. Finally, C4‐HSL activation by RsaL was independent of the Las and Pseudomonas quinolone signal (PQS) QS signaling systems. Therefore, we propose a new model of the QS regulatory network in PA1201, in which RsaL represents a superior player acting at the top of the hierarchy.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"35 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140232558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The global regulation of c‐di‐GMP and cAMP in bacteria 细菌中 c-di-GMP 和 cAMP 的全球调控

mLife Pub Date : 2024-03-11 DOI: 10.1002/mlf2.12104

Cong Liu, Rui Shi, Marcus S. Jensen, Jingrong Zhu, Jiawen Liu, Xiaobo Liu, Di Sun, Weijie Liu

{"title":"The global regulation of c‐di‐GMP and cAMP in bacteria","authors":"Cong Liu, Rui Shi, Marcus S. Jensen, Jingrong Zhu, Jiawen Liu, Xiaobo Liu, Di Sun, Weijie Liu","doi":"10.1002/mlf2.12104","DOIUrl":"https://doi.org/10.1002/mlf2.12104","url":null,"abstract":"Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria. The best‐studied examples are cyclic AMP (cAMP) and bis‐(3′–5′)‐cyclic dimeric guanosine monophosphate (c‐di‐GMP), which both act as global regulators. Global regulatory frameworks of c‐di‐GMP and cAMP in bacteria show several parallels but also significant variances. In this review, we illustrate the global regulatory models of the two nucleotide second messengers, compare the different regulatory frameworks between c‐di‐GMP and cAMP, and discuss the mechanisms and physiological significance of cross‐regulation between c‐di‐GMP and cAMP. c‐di‐GMP responds to numerous signals dependent on a great number of metabolic enzymes, and it regulates various signal transduction pathways through its huge number of effectors with varying activities. In contrast, due to the limited quantity, the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals. cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein (CRP) in most bacteria. This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes, providing theoretical guidelines for future research.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"32 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140253998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fight or flee, a vital choice for Clostridioides difficile 战斗或逃跑，艰难梭菌的重要选择

mLife Pub Date : 2024-02-09 DOI: 10.1002/mlf2.12102

Ji Zeng, Shuying Fang, Jinquan Guo, Min Dong, Guo-bao Tian, Liang Tao

引用次数: 0

Fight or flee, a vital choice for Clostridioides difficile 战斗或逃跑，艰难梭菌的重要选择

mLife Pub Date : 2024-02-09 DOI: 10.1002/mlf2.12102

Ji Zeng, Shuying Fang, Jinquan Guo, Min Dong, Guo-bao Tian, Liang Tao

引用次数: 0

Why and how to use the SeqCode 为什么以及如何使用 SeqCode

mLife Pub Date : 2024-02-07 DOI: 10.1002/mlf2.12092

William B. Whitman, M. Chuvochina, B. Hedlund, Konstantinos T. Konstantinidis, M. Palmer, Luis M. Rodriguez‐R, Iain Sutcliffe, Fengping Wang

{"title":"Why and how to use the SeqCode","authors":"William B. Whitman, M. Chuvochina, B. Hedlund, Konstantinos T. Konstantinidis, M. Palmer, Luis M. Rodriguez‐R, Iain Sutcliffe, Fengping Wang","doi":"10.1002/mlf2.12092","DOIUrl":"https://doi.org/10.1002/mlf2.12092","url":null,"abstract":"The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"60 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139796848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Why and how to use the SeqCode 为什么以及如何使用 SeqCode

mLife Pub Date : 2024-02-07 DOI: 10.1002/mlf2.12092

William B. Whitman, M. Chuvochina, B. Hedlund, Konstantinos T. Konstantinidis, M. Palmer, Luis M. Rodriguez‐R, Iain Sutcliffe, Fengping Wang

{"title":"Why and how to use the SeqCode","authors":"William B. Whitman, M. Chuvochina, B. Hedlund, Konstantinos T. Konstantinidis, M. Palmer, Luis M. Rodriguez‐R, Iain Sutcliffe, Fengping Wang","doi":"10.1002/mlf2.12092","DOIUrl":"https://doi.org/10.1002/mlf2.12092","url":null,"abstract":"The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.","PeriodicalId":508070,"journal":{"name":"mLife","volume":"82 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139856739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0