Genome-related datasets within the<i>E.coli</i>Genetic Stock Center database

Berlyn, Mary B.; Letovsky, Stanley

doi:10.1093/nar/20.23.6143

Cited by 24 publications

(13 citation statements)

References 37 publications

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“…71 The MG1655 strain was selected for analysis because its genome has been completely sequenced and is well annotated. 72 The two strains can be easily differentiated on MacConkey agar medium by colony color.…”

Section: Methodsmentioning

confidence: 99%

“…An isogenic pair of E. coli strains, namely NCM520 (designated genotype F − , Δ ( lacA-lacZ ) 880 ( FRT ), λ − , rph -1; CGSC # 8252) a lac minus strain derived from MG1655 in which the entire lac operon was deleted and the well characterized MG1655 (a lac plus strain; CGSC # 6300) 70 were obtained from the E. coli Genetic Stock Center at Yale University. 71 The MG1655 strain was selected for analysis because its genome has been completely sequenced and is well annotated. 72 The two strains can be easily differentiated on MacConkey agar medium by colony color.…”

Section: Methodsmentioning

confidence: 99%

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The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

et al. 2017

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Microorganisms impact spaceflight in a variety of ways. They play a positive role in biological systems, such as waste water treatment but can be problematic through buildups of biofilms that can affect advanced life support. Of special concern is the possibility that during extended missions, the microgravity environment will provide positive selection for undesirable genomic changes. Such changes could affect microbial antibiotic sensitivity and possibly pathogenicity. To evaluate this possibility, Escherichia coli (lac plus) cells were grown for over 1000 generations on Luria Broth medium under low-shear modeled microgravity conditions in a high aspect rotating vessel. This is the first study of its kind to grow bacteria for multiple generations over an extended period under low-shear modeled microgravity. Comparisons were made to a non-adaptive control strain using growth competitions. After 1000 generations, the final low-shear modeled microgravity-adapted strain readily outcompeted the unadapted lac minus strain. A portion of this advantage was maintained when the low-shear modeled microgravity strain was first grown in a shake flask environment for 10, 20, or 30 generations of growth. Genomic sequencing of the 1000 generation strain revealed 16 mutations. Of the five changes affecting codons, none were neutral. It is not clear how significant these mutations are as individual changes or as a group. It is concluded that part of the long-term adaptation to low-shear modeled microgravity is likely genomic. The strain was monitored for acquisition of antibiotic resistance by VITEK analysis throughout the adaptation period. Despite the evidence of genomic adaptation, resistance to a variety of antibiotics was never observed.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

et al. 2017

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“…One was a lac minus strain derived from MG1655 (in which the entire lac operon was deleted) and the other a lac plus strain (MG1655; CGSC 6300) (111). Both strains were obtained from the E. coli Genetic Stock Center at Yale University (112). The two strains are distinguishable on MacConkey agar media, with the lac plus strain producing red/pink colonies and the lac minus strain producing white colonies (113).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Acquired Antibiotic Resistance in Escherichia coli Exposed to Long-Term Low-Shear Modeled Microgravity and Background Antibiotic Exposure

Tirumalai

Karouia

Tran

et al. 2019

mBio

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The long-term response of microbial communities to the microgravity environment of space is not yet fully understood. Of special interest is the possibility that members of these communities may acquire antibiotic resistance. In this study, Escherichia coli cells were grown under low-shear modeled microgravity (LSMMG) conditions for over 1,000 generations (1000G) using chloramphenicol treatment between cycles to prevent contamination. The results were compared with data from an earlier control study done under identical conditions using steam sterilization between cycles rather than chloramphenicol. The sensitivity of the final 1000G-adapted strain to a variety of antibiotics was determined using Vitek analysis. In addition to resistance to chloramphenicol, the adapted strain acquired resistance to cefalotin, cefuroxime, cefuroxime axetil, cefoxitin, and tetracycline. In fact, the resistance to chloramphenicol and cefalotin persisted for over 110 generations despite the removal of both LSMMG conditions and trace antibiotic exposure. Genome sequencing of the adapted strain revealed 22 major changes, including 3 transposon-mediated rearrangements (TMRs). Two TMRs disrupted coding genes (involved in bacterial adhesion), while the third resulted in the deletion of an entire segment (14,314 bp) of the genome, which includes 14 genes involved with motility and chemotaxis. These results are in stark contrast with data from our earlier control study in which cells grown under the identical conditions without antibiotic exposure never acquired antibiotic resistance. Overall, LSMMG does not appear to alter the antibiotic stress resistance seen in microbial ecosystems not exposed to microgravity. IMPORTANCE Stress factors experienced during space include microgravity, sleep deprivation, radiation, isolation, and microbial contamination, all of which can promote immune suppression (1, 2). Under these conditions, the risk of infection from opportunistic pathogens increases significantly, particularly during long-term missions (3). If infection occurs, it is important that the infectious agent should not be antibiotic resistant. Minimizing the occurrence of antibiotic resistance is, therefore, highly desirable. To facilitate this, it is important to better understand the long-term response of bacteria to the microgravity environment. This study demonstrated that the use of antibiotics as a preventive measure could be counterproductive and would likely result in persistent resistance to that antibiotic. In addition, unintended resistance to other antimicrobials might also occur as well as permanent genome changes that might have other unanticipated and undesirable consequences.

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“…EcoliWiki gene pages contain >16 000 entries for alleles or phenotypes for E. coli genes. These alleles and phenotypes are a combination of alleles imported from the records of the E. coli Genetic Stock Center ( 21 ) and information from manual curation of the E. coli genetics literature. As part of EcoliWiki, these pages are available for community curation.…”

Section: Porteco Data: Collection Processing and Curationmentioning

confidence: 99%

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Sherlock

Siegele

et al. 2013

Nucl. Acids Res.

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PortEco (http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a ‘virtual’ model organism database that provides a single unified interface to the user, while integrating information from a variety of sources. The main focus of PortEco is to enable broad use of the growing number of high-throughput experiments available for E. coli, and to leverage community annotation through the EcoliWiki and GONUTS systems. Currently, PortEco includes curated data from hundreds of genome-wide RNA expression studies, from high-throughput phenotyping of single-gene knockouts under hundreds of annotated conditions, from chromatin immunoprecipitation experiments for tens of different DNA-binding factors and from ribosome profiling experiments that yield insights into protein expression. Conditions have been annotated with a consistent vocabulary, and data have been consistently normalized to enable users to find, compare and interpret relevant experiments. PortEco includes tools for data analysis, including clustering, enrichment analysis and exploration via genome browsers. PortEco search and data analysis tools are extensively linked to the curated gene, metabolic pathway and regulation content at its sister site, EcoCyc.

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Genome-related datasets within theE.coliGenetic Stock Center database

Cited by 24 publications

References 37 publications

The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

Evaluation of Acquired Antibiotic Resistance in Escherichia coli Exposed to Long-Term Low-Shear Modeled Microgravity and Background Antibiotic Exposure

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

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