EcoSal Plus最新文献_第10页

Systems Metabolic Engineering of Escherichia coli. 大肠杆菌系统代谢工程。

EcoSal Plus Pub Date : 2017-03-01 DOI: 10.1128/ecosalplus.ESP-0088-2015

Kyeong Rok Choi, Jae Ho Shin, Jae Sung Cho, Dongsoo Yang, Sang Yup Lee

{"title":"Systems Metabolic Engineering of Escherichia coli.","authors":"Kyeong Rok Choi, Jae Ho Shin, Jae Sung Cho, Dongsoo Yang, Sang Yup Lee","doi":"10.1128/ecosalplus.ESP-0088-2015","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0088-2015","url":null,"abstract":"Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34801437","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: 24

Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family. I 型蛋白质分泌--看似简单，但在整个家族中具有广泛的机制变异性。

EcoSal Plus Pub Date : 2016-12-01 DOI: 10.1128/ecosalplus.ESP-0019-2015

I Barry Holland, Sandra Peherstorfer, Kerstin Kanonenberg, Michael Lenders, Sven Reimann, Lutz Schmitt

{"title":"Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family.","authors":"I Barry Holland, Sandra Peherstorfer, Kerstin Kanonenberg, Michael Lenders, Sven Reimann, Lutz Schmitt","doi":"10.1128/ecosalplus.ESP-0019-2015","DOIUrl":"10.1128/ecosalplus.ESP-0019-2015","url":null,"abstract":"A very large type I polypeptide begins to reel out from a ribosome; minutes later, the still unidentifiable polypeptide, largely lacking secondary structure, is now in some cases a thousand or more residues longer. Synthesis of the final hundred C-terminal residues commences. This includes the identity code, the secretion signal within the last 50 amino acids, designed to dock with a waiting ATP binding cassette (ABC) transporter. What happens next is the subject of this review, with the main, but not the only focus on hemolysin HlyA, an RTX protein toxin secreted by the type I system. Transport substrates range from small peptides to giant proteins produced by many pathogens. These molecules, without detectable cellular chaperones, overcome enormous barriers, crossing two membranes before final folding on the cell surface, involving a unique autocatalytic process.Unfolded HlyA is extruded posttranslationally, C-terminal first. The transenvelope \"tunnel\" is formed by HlyB (ABC transporter), HlyD (membrane fusion protein) straddling the inner membrane and periplasm and TolC (outer membrane). We present a new evaluation of the C-terminal secretion code, and the structure function of HlyD and HlyB at the heart of this nanomachine. Surprisingly, key details of the secretion mechanism are remarkably variable in the many type I secretion system subtypes. These include alternative folding processes, an apparently distinctive secretion code for each type I subfamily, and alternative forms of the ABC transporter; most remarkably, the ABC protein probably transports peptides or polypeptides by quite different mechanisms. Finally, we suggest a putative structure for the Hly-translocon, HlyB, the multijointed HlyD, and the TolC exit.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64031511","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

Live Attenuated Human Salmonella Vaccine Candidates: Tracking the Pathogen in Natural Infection and Stimulation of Host Immunity. 人类沙门氏菌减毒活疫苗候选者：追踪自然感染中的病原体并刺激宿主免疫。

EcoSal Plus Pub Date : 2016-11-01 DOI: 10.1128/ecosalplus.ESP-0010-2016

James E Galen, Amanda D Buskirk, Sharon M Tennant, Marcela F Pasetti

{"title":"Live Attenuated Human Salmonella Vaccine Candidates: Tracking the Pathogen in Natural Infection and Stimulation of Host Immunity.","authors":"James E Galen, Amanda D Buskirk, Sharon M Tennant, Marcela F Pasetti","doi":"10.1128/ecosalplus.ESP-0010-2016","DOIUrl":"10.1128/ecosalplus.ESP-0010-2016","url":null,"abstract":"Salmonellosis, caused by members of the genus Salmonella, is responsible for considerable global morbidity and mortality in both animals and humans. In this review, we will discuss the pathogenesis of Salmonella enterica serovar Typhi and Salmonella enterica serovar Typhimurium, focusing on human Salmonella infections. We will trace the path of Salmonella through the body, including host entry sites, tissues and organs affected, and mechanisms involved in both pathogenesis and stimulation of host immunity. Careful consideration of the natural progression of disease provides an important context in which attenuated live oral vaccines can be rationally designed and developed. With this in mind, we will describe a series of attenuated live oral vaccines that have been successfully tested in clinical trials and demonstrated to be both safe and highly immunogenic. The attenuation strategies summarized in this review offer important insights into further development of attenuated vaccines against other Salmonella for which live oral candidates are currently unavailable.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64031447","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

Anaerobic Formate and Hydrogen Metabolism. 厌氧甲酸盐和氢代谢。

EcoSal Plus Pub Date : 2016-10-01 DOI: 10.1128/ecosalplus.ESP-0011-2016

Constanze Pinske, R Gary Sawers

{"title":"Anaerobic Formate and Hydrogen Metabolism.","authors":"Constanze Pinske, R Gary Sawers","doi":"10.1128/ecosalplus.ESP-0011-2016","DOIUrl":"10.1128/ecosalplus.ESP-0011-2016","url":null,"abstract":"Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64031529","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

Animal Enterotoxigenic Escherichia coli. 动物肠毒性大肠杆菌。

EcoSal Plus Pub Date : 2016-10-01 DOI: 10.1128/ecosalplus.ESP-0006-2016

J Daniel Dubreuil, Richard E Isaacson, Dieter M Schifferli

{"title":"Animal Enterotoxigenic Escherichia coli.","authors":"J Daniel Dubreuil, Richard E Isaacson, Dieter M Schifferli","doi":"10.1128/ecosalplus.ESP-0006-2016","DOIUrl":"10.1128/ecosalplus.ESP-0006-2016","url":null,"abstract":"Enterotoxigenic Escherichia coli (ETEC) is the most common cause of E. coli diarrhea in farm animals. ETEC are characterized by the ability to produce two types of virulence factors: adhesins that promote binding to specific enterocyte receptors for intestinal colonization and enterotoxins responsible for fluid secretion. The best-characterized adhesins are expressed in the context of fimbriae, such as the F4 (also designated K88), F5 (K99), F6 (987P), F17, and F18 fimbriae. Once established in the animal small intestine, ETEC produce enterotoxin(s) that lead to diarrhea. The enterotoxins belong to two major classes: heat-labile toxins that consist of one active and five binding subunits (LT), and heat-stable toxins that are small polypeptides (STa, STb, and EAST1). This review describes the disease and pathogenesis of animal ETEC, the corresponding virulence genes and protein products of these bacteria, their regulation and targets in animal hosts, as well as mechanisms of action. Furthermore, vaccines, inhibitors, probiotics, and the identification of potential new targets by genomics are presented in the context of animal ETEC.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64031821","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

The Mosaic Type IV Secretion Systems. 马赛克IV型分泌系统。

EcoSal Plus Pub Date : 2016-08-04 DOI: 10.1128/ecosalplus.ESP-0020-2015

P. Christie

{"title":"The Mosaic Type IV Secretion Systems.","authors":"P. Christie","doi":"10.1128/ecosalplus.ESP-0020-2015","DOIUrl":"https://doi.org/10.1128/ecosalplus.ESP-0020-2015","url":null,"abstract":"Escherichia coli and other Gram-negative and -positive bacteria employ type IV secretion systems (T4SSs) to translocate DNA and protein substrates, generally by contact-dependent mechanisms, to other cells. The T4SSs functionally encompass two major subfamilies, the conjugation systems and the effector translocators. The conjugation systems are responsible for interbacterial transfer of antibiotic resistance genes, virulence determinants, and genes encoding other traits of potential benefit to the bacterial host. The effector translocators are used by many Gram-negative pathogens for delivery of potentially hundreds of virulence proteins termed effectors to eukaryotic cells during infection. In E. coli and other species of Enterobacteriaceae, T4SSs identified to date function exclusively in conjugative DNA transfer. In these species, the plasmid-encoded systems can be classified as the P, F, and I types. The P-type systems are the simplest in terms of subunit composition and architecture, and members of this subfamily share features in common with the paradigmatic Agrobacterium tumefaciens VirB/VirD4 T4SS. This review will summarize our current knowledge of the E. coli systems and the A. tumefaciens P-type system, with emphasis on the structural diversity of the T4SSs. Ancestral P-, F-, and I-type systems were adapted throughout evolution to yield the extant effector translocators, and information about well-characterized effector translocators also is included to further illustrate the adaptive and mosaic nature of these highly versatile machines.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/ecosalplus.ESP-0020-2015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64031609","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: 109

The Enterobacterial Genotoxins: Cytolethal Distending Toxin and Colibactin. 肠杆菌基因毒素：细胞致死膨胀毒素和 Colibactin。

EcoSal Plus Pub Date : 2016-07-01 DOI: 10.1128/ecosalplus.ESP-0008-2016

Frederic Taieb, Claude Petit, Jean-Philippe Nougayrède, Eric Oswald

{"title":"The Enterobacterial Genotoxins: Cytolethal Distending Toxin and Colibactin.","authors":"Frederic Taieb, Claude Petit, Jean-Philippe Nougayrède, Eric Oswald","doi":"10.1128/ecosalplus.ESP-0008-2016","DOIUrl":"10.1128/ecosalplus.ESP-0008-2016","url":null,"abstract":"While the DNA damage induced by ionizing radiation and by many chemical compounds and drugs is well characterized, the genotoxic insults inflicted by bacteria are only scarcely documented. However, accumulating evidence indicates that we are exposed to bacterial genotoxins. The prototypes of such bacterial genotoxins are the Cytolethal Distending Toxins (CDTs) produced by Escherichia coli and Salmonella enterica serovar Typhi. CDTs display the DNase structure fold and activity, and induce DNA strand breaks in the intoxicated host cell nuclei. E. coli and certain other Enterobacteriaceae species synthesize another genotoxin, colibactin. Colibactin is a secondary metabolite, a hybrid polyketide/nonribosomal peptide compound synthesized by a complex biosynthetic machinery. In this review, we summarize the current knowledge on CDT and colibactin produced by E. coli and/or Salmonella Typhi. We describe their prevalence, genetic determinants, modes of action, and impact in infectious diseases or gut colonization, and discuss the possible involvement of these genotoxigenic bacteria in cancer.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34672540","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

C4-Dicarboxylate Utilization in Aerobic and Anaerobic Growth. 有氧和无氧生长中的 C4-二羧酸利用。

EcoSal Plus Pub Date : 2016-06-01 DOI: 10.1128/ecosalplus.ESP-0021-2015

Gottfried Unden, Alexander Strecker, Alexandra Kleefeld, Ok Bin Kim

{"title":"C4-Dicarboxylate Utilization in Aerobic and Anaerobic Growth.","authors":"Gottfried Unden, Alexander Strecker, Alexandra Kleefeld, Ok Bin Kim","doi":"10.1128/ecosalplus.ESP-0021-2015","DOIUrl":"10.1128/ecosalplus.ESP-0021-2015","url":null,"abstract":"C4-dicarboxylates and the C4-dicarboxylic amino acid l-aspartate support aerobic and anaerobic growth of Escherichia coli and related bacteria. In aerobic growth, succinate, fumarate, D- and L-malate, L-aspartate, and L-tartrate are metabolized by the citric acid cycle and associated reactions. Because of the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of C4-dicarboxylates depends on fumarate reduction to succinate (fumarate respiration). In some related bacteria (e.g., Klebsiella), utilization of C4-dicarboxylates, such as tartrate, is independent of fumarate respiration and uses a Na+-dependent membrane-bound oxaloacetate decarboxylase. Uptake of the C4-dicarboxylates into the bacteria (and anaerobic export of succinate) is achieved under aerobic and anaerobic conditions by different sets of secondary transporters. Expression of the genes for C4-dicarboxylate metabolism is induced in the presence of external C4-dicarboxylates by the membrane-bound DcuS-DcuR two-component system. Noncommon C4-dicarboxylates like l-tartrate or D-malate are perceived by cytoplasmic one-component sensors/transcriptional regulators. This article describes the pathways of aerobic and anaerobic C4-dicarboxylate metabolism and their regulation. The citric acid cycle, fumarate respiration, and fumarate reductase are covered in other articles and discussed here only in the context of C4-dicarboxylate metabolism. Recent aspects of C4-dicarboxylate metabolism like transport, sensing, and regulation will be treated in more detail. This article is an updated version of an article published in 2004 in EcoSal Plus. The update includes new literature, but, in particular, the sections on the metabolism of noncommon C4-dicarboxylates and their regulation, on the DcuS-DcuR regulatory system, and on succinate production by engineered E. coli are largely revised or new.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34670127","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

Systems Metabolic Engineering of Escherichia coli. 大肠杆菌的系统代谢工程。

EcoSal Plus Pub Date : 2016-05-01 DOI: 10.1128/ecosalplus.ESP-0010-2015

Kyeong Rok Choi, Jae Ho Shin, Jae Sung Cho, Dongsoo Yang, Sang Yup Lee

{"title":"Systems Metabolic Engineering of Escherichia coli.","authors":"Kyeong Rok Choi, Jae Ho Shin, Jae Sung Cho, Dongsoo Yang, Sang Yup Lee","doi":"10.1128/ecosalplus.ESP-0010-2015","DOIUrl":"10.1128/ecosalplus.ESP-0010-2015","url":null,"abstract":"Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34516103","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

Aminoacyl-tRNA Synthetases in the Bacterial World. 细菌世界中的氨基酰-tRNA 合成酶

EcoSal Plus Pub Date : 2016-05-01 DOI: 10.1128/ecosalplus.ESP-0002-2016

Richard Giegé, Mathias Springer

{"title":"Aminoacyl-tRNA Synthetases in the Bacterial World.","authors":"Richard Giegé, Mathias Springer","doi":"10.1128/ecosalplus.ESP-0002-2016","DOIUrl":"10.1128/ecosalplus.ESP-0002-2016","url":null,"abstract":"Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.","PeriodicalId":11500,"journal":{"name":"EcoSal Plus","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34516100","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