scholarly journals CRISPR‐based curing and analysis of metabolic burden of cryptic plasmids inEscherichia coliNissle 1917

2019 ◽  
Vol 19 (6) ◽  
pp. 478-485 ◽  
Author(s):  
Halimatun S. Zainuddin ◽  
Yanfen Bai ◽  
Thomas J. Mansell
Keyword(s):  
Metabolic Burden ◽  
Cryptic Plasmids

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

Nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium Ruegeria isolate PR1b

Plasmid ◽  
2003 ◽  
Vol 49 (3) ◽  
pp. 233-252 ◽  
Author(s):  
Zhenping Zhong ◽  
Ron Caspi ◽  
Donald Helinski ◽  
Vic Knauf ◽  
Sean Sykes ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Marine Bacterium ◽  
Cryptic Plasmids

Global transcriptional analysis of metabolic burden due to plasmid maintenance in Escherichia coli DH5α during batch fermentation

2006 ◽  
Vol 39 (3) ◽  
pp. 391-398 ◽  
Author(s):  
Dave Siak-Wei Ow ◽  
Peter Morin Nissom ◽  
Robin Philp ◽  
Steve Kah-Weng Oh ◽  
Miranda Gek-Sim Yap
Keyword(s):  
Escherichia Coli ◽  
Batch Fermentation ◽  
Transcriptional Analysis ◽  
Plasmid Maintenance ◽  
Metabolic Burden

Rhizobial plasmids — replication, structure and biological role

2012 ◽  
Vol 7 (4) ◽  
pp. 571-586 ◽  
Author(s):  
Andrzej Mazur ◽  
Piotr Koper
Keyword(s):  
Genome Organization ◽  
Soil Bacteria ◽  
Evolutionary History ◽  
Bacterial Genome ◽  
Biological Role ◽  
Genome Architecture ◽  
Genomic Knowledge ◽  
History Of ◽  
Cryptic Plasmids ◽  
Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

Genetic Transformation of Streptococcus sanguis (Challis) with Cryptic Plasmids from Streptococcus ferus

1980 ◽  
Vol 28 (3) ◽  
pp. 692-699 ◽  
Author(s):  
Francis L. Macrina ◽  
Patricia H. Wood ◽  
Kevin R. Jones
Keyword(s):  
Genetic Transformation ◽  
Streptococcus Mutans ◽  
Restriction Enzyme ◽  
Deoxyribonucleic Acid ◽  
Cryptic Plasmid ◽  
Common Ancestry ◽  
Erythromycin Resistance ◽  
Streptococcus Sanguis ◽  
Cryptic Plasmids ◽  
Isogenic Strains

By using the basic methodology initially published by Kretschmer et al. (J. Bacteriol. 124 :225-231, 1975), we have been able to introduce phenotypically cryptic plasmids from Streptococcus ferus (formerly Streptococcus mutans subsp. ferus ) into Streptococcus sanguis by genetic transformation. In this system, the entry of the cryptic plasmids is selected indirectly. This is effected with transforming deoxyribonucleic acid mixtures in which the cryptic plasmid deoxyribonucleic acid is present in an approximate 10-fold molar excess with respect to a plasmid (pVA1) known to confer erythromycin resistance. Under such conditions, 5 to 10% of the pVA1-containing erythromycin-resistant transformants were cotransformed with cryptic plasmid deoxyribonucleic acid. pVA1 may be selectively eliminated by growth of its S. sanguis host strain at 42°C, enabling the construction of isogenic strains with and without S. ferus cryptic plasmids. Comparative physiological studies of such strains have failed to reveal any plasmid-conferred phenotypes in S. sanguis. With this procedure, we have been able to physically separate two small cryptic plasmids (2.4 × 10 6 and 2.8 × 10 6 daltons) of S. ferus. Although these plasmids were found naturally to exist in a single S. ferus host, they were able to replicate independently of one another in S. sanguis. Restriction enzyme fingerprinting indicated that these plasmids did not share a common ancestry.

Metabolic Burden and Disease and Mortality Risk Associated with Impaired Fasting Glucose in Elderly Adults

2015 ◽  
Vol 63 (7) ◽  
pp. 1435-1442 ◽  
Author(s):  
Katherine Samaras ◽  
John Crawford ◽  
Helen L. Lutgers ◽  
Lesley V. Campbell ◽  
Bernhard T. Baune ◽  
...  
Keyword(s):  
Impaired Fasting Glucose ◽  
Mortality Risk ◽  
Fasting Glucose ◽  
Elderly Adults ◽  
Metabolic Burden

Genetic elements of Thermococcales

2004 ◽  
Vol 32 (2) ◽  
pp. 184-187 ◽  
Author(s):  
D. Prieur ◽  
G. Erauso ◽  
C. Geslin ◽  
S. Lucas ◽  
M. Gaillard ◽  
...  
Keyword(s):  
Recent Work ◽  
Deep Sea ◽  
Current Knowledge ◽  
Genetic Tools ◽  
Genetic Elements ◽  
Cryptic Plasmids

This minireview summarizes our current knowledge about archaeal genetic elements in the hyperthermophilic order Thermococcales in the phylum Euryarchaeota. This includes recent work on the first virus of Pyrococcus, PAV1, the discovery of novel unique virus morphotypes in hot deep-sea environments, and preliminary observations on novel cryptic plasmids. We also review the work accomplished over the last 5 years in the development of genetic tools for members of the Pyrococcus and Thermococcus genera, mainly in our laboratories.

Brevibacterium linens pBL33 and Rhodococcus rhodochrous pRC1 cryptic plasmids replicate in Rhodococcus sp. R312 (formerly Brevibacterium sp. R312)

Gene ◽  
1995 ◽  
Vol 154 (1) ◽  
pp. 77-79 ◽  
Author(s):  
F. Bigey ◽  
B. Grossiord ◽  
C.K.N. Chan Kwo Chion ◽  
A. Arnaud ◽  
P. Galzy
Keyword(s):  
Rhodococcus Rhodochrous ◽  
Brevibacterium Linens ◽  
Cryptic Plasmids ◽  
Rhodococcus Sp

scholarly journals Recombinant protein production provoked accumulation of ATP, fructose-1,6-bisphosphate and pyruvate in E. coli K12 strain TG1

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Jan Weber ◽  
Zhaopeng Li ◽  
Ursula Rinas
Keyword(s):  
Recombinant Protein ◽  
Recombinant Protein Production ◽  
Protein Production ◽  
Expression System ◽  
Limiting Factors ◽  
Expression Vectors ◽  
Metabolic Enzyme ◽  
E Coli ◽  
Metabolic Burden ◽  
Fructose 1,6 Bisphosphate

Abstract Background Recently it was shown that production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress comparable to a carbon overfeeding response. Opposite to original expectations generation of energy as well as catabolic provision of precursor metabolites were excluded as limiting factors for growth and protein production. On the contrary, accumulation of ATP and precursor metabolites revealed their ample formation but insufficient withdrawal as a result of protein production mediated constraints in anabolic pathways. Thus, not limitation but excess of energy and precursor metabolites were identified as being connected to the protein production associated metabolic burden. Results Here we show that the protein production associated accumulation of energy and catabolic precursor metabolites is not unique to E. coli BL21(DE3) but also occurs in E. coli K12. Most notably, it was demonstrated that the IPTG-induced production of hFGF-2 using a tac-promoter based expression vector in the E. coli K12 strain TG1 was leading to persistent accumulation of key regulatory molecules such as ATP, fructose-1,6-bisphosphate and pyruvate. Conclusions Excessive energy generation, respectively, accumulation of ATP during recombinant protein production is not unique to the BL21(DE3)/T7 promoter based expression system but also observed in the E. coli K12 strain TG1 using another promoter/vector combination. These findings confirm that energy is not a limiting factor for recombinant protein production. Moreover, the data also show that an accelerated glycolytic pathway flux aggravates the protein production associated “metabolic burden”. Under conditions of compromised anabolic capacities cells are not able to reorganize their metabolic enzyme repertoire as required for reduced carbon processing.

Disappearance of the covalently closed circular cryptic plasmid PO-2 in Salmonella pullorum MS35 containing F77

1974 ◽  
Vol 20 (4) ◽  
pp. 551-557
Author(s):  
Paul W. Stiffler ◽  
D. E. Schoenhard
Keyword(s):  
Salmonella Typhimurium ◽  
Sucrose Gradient ◽  
Buoyant Density ◽  
Sedimentation Coefficient ◽  
Apparent Effect ◽  
Donor Property ◽  
Circular Dna ◽  
Salmonella Pullorum ◽  
Cryptic Plasmids ◽  
Equilibrium Centrifugation

The physical basis of the donor property of Salmonella pullorum donor strains MS8300, MS830, and MS831 carrying the F77 factor from Salmonella typhimurium was investigated by dye-buoyant density equilibrium centrifugation and zonal centrifugation in neutral sucrose gradients. Centrifugation of the MS8300 and MS831 closed circular DNA material in a 20 to 31% neutral sucrose gradient resulted in a profile having one sharp peak of radioactivity with a sedimentation coefficient of 17 S and a broad peak extending from 65 to 70 S. The 17- and 65-S species were isolated from the isogenic F− strain MS83. These appeared identical with those isolated previously in S. pullorum MS53 as the cryptic plasmids PO-1 and PO-2 respectively. Cosedimentation of differentially labeled F77 DNA and the lysate containing the 65-S and 70-S species suggested that the 70-S species is the autonomous F77 factor in strains MS8300 and MS831. Lysates of MS830 similarly treated produced a profile containing the 17-S molecule and possibly some 70-S molecules but no 65-S molecules. It was concluded that the F77 factor was integrated in most cells and that the covalently closed circular state of PO-2 plasmid was lost. The mutation in the cysE gene of the F77 factor carried by MS831 had no apparent effect on the covalently closed circular nature of PO-2 plasmid, although F77 no longer seemed to mobilize the chromosome from the cysE locus.

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