An E. coli-yeast shuttle cosmid with positive selection for inserted fragments

1985 ◽  
Vol 10 (1) ◽  
pp. 29-33 ◽  
Author(s):  
Manda E. Gent ◽  
Patrick Crowley ◽  
J. Richard Ludwig ◽  
Rashida Anwar ◽  
David A. Sugden ◽  
...  
Keyword(s):  
Positive Selection ◽  
E Coli ◽  
Selection For

scholarly journals TRANSITORY DEREPRESSION AND THE MAINTENANCE OF CONJUGATIVE PLASMIDS

Genetics ◽  
1986 ◽  
Vol 113 (3) ◽  
pp. 483-497
Author(s):  
Peter D Lundquist ◽  
Bruce R Levin
Keyword(s):  
Population Dynamics ◽  
Positive Selection ◽  
Low Frequencies ◽  
E Coli ◽  
Conjugative Plasmids ◽  
Bacterial Plasmids ◽  
Naturally Occurring ◽  
Chemostat Cultures ◽  
Selection For ◽  
K 12

ABSTRACT It has been proposed that bacterial plasmids cannot be maintained by infectious transfer alone and that their persistence requires positive selection for plasmid-borne genes. To test this hypothesis, the population dynamics of two laboratory and five naturally occurring conjugative plasmids were examined in chemostat cultures of E. coli K-12. Both laboratory plasmids and three of the five wild plasmids failed to increase in frequency when introduced at low frequencies. However, two of the naturally occurring plasmids rapidly increased in frequency, and bacteria carrying them achieved dominance in the absence of selection for known plasmid-borne genes. Three hypotheses for the invasion and persistence of these two plasmids were examined. It is concluded that although these two extrachromsomal genetic elements are repressed for conjugative pili synthesis, as a consequence of high rates of transfer during periods of transitory derepression in newly formed transconjugants, they become established and are maintained by infectious transfer alone. The implications of these observations to the theory of plasmid maintenance and the evolution of repressible conjugative pili synthesis are discussed.

scholarly journals A Positive Selection for Nucleoside Kinases in E. coli

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0162921 ◽  
Author(s):  
Nirav Y. Shelat ◽  
Sidhartha Parhi ◽  
Marc Ostermeier
Keyword(s):  
Positive Selection ◽  
E Coli ◽  
Selection For

scholarly journals Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate

2014 ◽  
Vol 81 (1) ◽  
pp. 130-138 ◽  
Author(s):  
James Kirby ◽  
Minobu Nishimoto ◽  
Ruthie W. N. Chow ◽  
Edward E. K. Baidoo ◽  
George Wang ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Xylose Reductase ◽  
Pentose Phosphate ◽  
Terpene Biosynthesis ◽  
Content Type ◽  
E Coli ◽  
Pathway Expression ◽  
Terpene Synthesis ◽  
Selection For

ABSTRACTTerpene synthesis in the majority of bacterial species, together with plant plastids, takes place via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. The first step of this pathway involves the condensation of pyruvate and glyceraldehyde 3-phosphate by DXP synthase (Dxs), with one-sixth of the carbon lost as CO2. A hypothetical novel route from a pentose phosphate to DXP (nDXP) could enable a more direct pathway from C5sugars to terpenes and also circumvent regulatory mechanisms that control Dxs, but there is no enzyme known that can convert a sugar into its 1-deoxy equivalent. Employing a selection for complementation of adxsdeletion inEscherichia coligrown on xylose as the sole carbon source, we uncovered two candidate nDXP genes. Complementation was achieved either via overexpression of the wild-typeE. coliyajOgene, annotated as a putative xylose reductase, or via various mutations in the nativeribBgene.In vitroanalysis performed with purified YajO and mutant RibB proteins revealed that DXP was synthesized in both cases from ribulose 5-phosphate (Ru5P). We demonstrate the utility of these genes for microbial terpene biosynthesis by engineering the DXP pathway inE. colifor production of the sesquiterpene bisabolene, a candidate biodiesel. To further improve flux into the pathway from Ru5P, nDXP enzymes were expressed as fusions to DXP reductase (Dxr), the second enzyme in the DXP pathway. Expression of a Dxr-RibB(G108S) fusion improved bisabolene titers more than 4-fold and alleviated accumulation of intracellular DXP.

scholarly journals A novel positive selection for identifying cold-sensitive myosin II mutants in Dictyostelium.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 505-515 ◽  
Author(s):  
B Patterson ◽  
J A Spudich
Keyword(s):  
Positive Selection ◽  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Time Scale ◽  
Myosin Ii ◽  
Rapid Onset ◽  
Chemical Mutagenesis ◽  
Wild Type ◽  
Cold Sensitive ◽  
Selection For

Abstract We developed a positive selection for myosin heavy chain mutants in Dictyostelium. This selection is based on the fact that brief exposure to azide causes wild-type cells to release from the substrate, whereas myosin null cells remain adherent. This procedure assays myosin function on a time scale of minutes and has therefore allowed us to select rapid-onset cold-sensitive mutants after random chemical mutagenesis of Dictyostelium cells. We developed a rapid technique for determining which mutations lie in sequences of the myosin gene that encode the head (motor) domain and localized 27 of 34 mutants to this domain. We recovered the appropriate sequences from five of the mutants and demonstrated that they retain their cold-sensitive properties when expressed from extrachromosomal plasmids.

scholarly journals Is formal employment sector hereditary? Determinants of formal/informal sector choice for Mexican male workers

2019 ◽  
pp. 91-121
Author(s):  
Adelaido García-Andrés ◽  
Ernesto Aguayo-Téllez ◽  
Jose N. Martínez
Keyword(s):  
Positive Selection ◽  
Social Mobility ◽  
Informal Sector ◽  
Formal Sector ◽  
Strong Connection ◽  
Employment Sector ◽  
Formal Employment ◽  
Selection For ◽  
The Relationship ◽  
Employment Choices

Understanding the relationship between parents’ and sons’ formal employment is essential for promoting social mobility in Mexico. Using the 2011 Survey of Social Mobility in Mexico (EMOVI), this paper contributes to the literature by addressing the intergenerational mobility of employment. Findings show a strong connection between intergenerational employment choices and suggest a positive selection for workers. Individuals with parents who worked in the formal sector are more likely to be enrolled in formal work and vice versa. Also, after controlling for parent’s employment sector, schooling remains as a significant vehicle to transit to the formal sector.

scholarly journals Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

2020 ◽  
Author(s):  
Asma Awadi ◽  
Hichem Ben Slimen ◽  
Helmut Schaschl ◽  
Felix Knauer ◽  
Franz Suchentrunk
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Protein Function ◽  
Transmembrane Domain ◽  
Proton Translocation ◽  
Introgressive Hybridization ◽  
Vibrational Entropy ◽  
Mutant Type ◽  
Selection For ◽  
Protein Variants

Abstract Background: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. Results: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, the PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. The statistical model runs indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgresson.Conclusions: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.

scholarly journals Stable neutralization of virulent bacteria using temperate phage in the mammalian gut

2019 ◽  
Author(s):  
Bryan B. Hsu ◽  
Jeffrey C. Way ◽  
Pamela A. Silver
Keyword(s):  
Temperate Phage ◽  
Cascading Effects ◽  
E Coli ◽  
Bacterial Action ◽  
Exogenous Genes ◽  
Selection For ◽  
Mouse Model Of Infection ◽  
Bacterial Concentrations ◽  
New Framework ◽  
Lambdoid Phages

ABSTRACTElimination or alteration of select members of the gut microbiota is key to therapeutic efficacy. However, the complexity of these microbial inhabitants makes it challenging to precisely target bacteria without unexpected cascading effects. Here, we use bacteriophage to deliver exogenous genes to specific bacteria by genomic integration of temperate phage for long-lasting modification. As a real-world therapeutic test, we engineered λ phage to transcriptionally-repress shigatoxin by using genetic hybrids between λ and other lambdoid phages to overcome resistance encoded by the virulent prophage derived from enterohemorrhagic E. coli. We show that a single dose of engineered phage propagates throughout the bacterial community and reduces shigatoxin production in an enteric mouse model of infection without markedly affecting bacterial concentrations. We thus minimize the selection for resistance by relying on anti-virulence and not anti-bacterial action. Our work reveals a new framework for transferring functions to bacteria within their native environment.

scholarly journals Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

2018 ◽  
Vol 50 (6) ◽  
pp. 849-856 ◽  
Author(s):  
Kathryn E. Holt ◽  
Paul McAdam ◽  
Phan Vuong Khac Thai ◽  
Nguyen Thuy Thuong Thuong ◽  
Dang Thi Minh Ha ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Positive Selection ◽  
Selection For

Molecular Cloning of the gyrA andgyrB Genes of Bacteroides fragilis Encoding DNA Gyrase

1999 ◽  
Vol 43 (10) ◽  
pp. 2423-2429 ◽  
Author(s):  
Yoshikuni Onodera ◽  
Kenichi Sato
Keyword(s):  
Hot Spot ◽  
Bacteroides Fragilis ◽  
Dna Gyrase ◽  
E Coli ◽  
Important Target ◽  
Mutant Strains ◽  
Genes Encoding ◽  
Gyrase A ◽  
Selection For

ABSTRACT The genes encoding the DNA gyrase A and B subunits ofBacteroides fragilis were cloned and sequenced. ThegyrA and gyrB genes code for proteins of 845 and 653 amino acids, respectively. These proteins were expressed inEscherichia coli, and the combination of GyrA and GyrB exhibited ATP-dependent supercoiling activity. To analyze the role of DNA gyrase in quinolone resistance of B. fragilis, we isolated mutant strains by stepwise selection for resistance to increasing concentrations of levofloxacin. We analyzed the resistant mutants and showed that Ser-82 of GyrA, equivalent to resistance hot spot Ser-83 of GyrA in E. coli, was in each case replaced with Phe. These results suggest that DNA gyrase is an important target for quinolones in B. fragilis.

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