Faculty Opinions recommendation of Essential genes from Arctic bacteria used to construct stable, temperature-sensitive bacterial vaccines.

Author(s):  
Michael Y Galperin
2010 ◽  
Vol 107 (30) ◽  
pp. 13456-13460 ◽  
Author(s):  
B. N. Duplantis ◽  
M. Osusky ◽  
C. L. Schmerk ◽  
D. R. Ross ◽  
C. M. Bosio ◽  
...  

2008 ◽  
Vol 30 (2) ◽  
pp. 248-258 ◽  
Author(s):  
Shay Ben-Aroya ◽  
Candice Coombes ◽  
Teresa Kwok ◽  
Kathryn A. O'Donnell ◽  
Jef D. Boeke ◽  
...  

2015 ◽  
Vol 5 (9) ◽  
pp. 1879-1887 ◽  
Author(s):  
Megan Kofoed ◽  
Karissa L. Milbury ◽  
Jennifer H. Chiang ◽  
Sunita Sinha ◽  
Shay Ben-Aroya ◽  
...  

2020 ◽  
Author(s):  
Leopold Parts ◽  
Amandine Batté ◽  
Maykel Lopes ◽  
Michael W. Yuen ◽  
Meredith Laver ◽  
...  

AbstractThe consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, but lead to lethality in another. The extent to which mutant phenotypes are malleable, the complexity of the architecture of modifiers, and the identities of causal genes and pathways remain largely unknown. Here, we measure the fitness effects of ~1,500 temperature sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds, and map the modifiers for 19 combinations. Altogether, fitness defects for 183 of the 530 tested genes (35%) could be suppressed by standing genetic variation in at least one wild strain. Suppression was generally driven by gain-of-function of a single, strong modifier gene. The validated causes included both variants in protein interaction partners or pathway members suppressing specific genes, as well as general modifiers altering the effect of many temperature sensitive alleles. The emerging frequency of suppression and range of possible suppression mechanisms suggest that a substantial fraction of monogenic diseases could be repressed by modulating other gene products.


Genetics ◽  
1988 ◽  
Vol 118 (1) ◽  
pp. 61-74
Author(s):  
T M Rogalski ◽  
D L Riddle

Abstract The amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans is encoded by the ama-1 gene, located approximately 0.05 map unit to the right of dpy-13 IV. Using the amanitin-resistant ama-1(m118) strain as a parent, we have isolated amanitin-sensitive mutants that carry recessive-lethal ama-1 alleles. Of the six ethyl methanesulfonate-induced mutants examined, two are arrested late in embryogenesis. One of these is a large deficiency, mDf9, but the second may be a novel point mutation. The four other mutants are hypomorphs, and presumably produce altered RNA polymerase II enzymes with some residual function. Two of these mutants develop into sterile adults at 20 degrees but are arrested as larvae at 25 degrees, and two others are fertile at 20 degrees and sterile at 25 degrees. Temperature-shift experiments performed with the adult sterile mutant, ama-1(m118m238ts), have revealed a temperature-sensitive period that begins late in gonadogenesis and is centered around the initiation of egg-laying. Postembryonic development at 25 degrees is slowed by 30%. By contrast, the amanitin-resistant allele of ama-1 has very little effect on developmental rate or fertility. We have identified 15 essential genes in an interval of 4.5 map units surrounding ama-1, as well as four gamma-ray-induced deficiencies and two duplications that include the ama-1 gene. The larger duplication, mDp1, may include the entire left arm of chromosome IV, and it recombines with the normal homologue at a low frequency. The smallest deficiency, mDf10, complements all but three identified genes: let-278, dpy-13 and ama-1, which define an interval of only 0.1 map unit. The terminal phenotype of mDf10 homozygotes is developmental arrest during the first larval stage, suggesting that there is sufficient maternal RNA polymerase II to complete embryonic development.


1998 ◽  
Vol 29 (3) ◽  
pp. 859-869 ◽  
Author(s):  
Sébastien Pichoff ◽  
Laetitia Alibaud ◽  
Agnès Guédant ◽  
Marie‐Pierre Castanié ◽  
Jean‐Pierre Bouché

2017 ◽  
Author(s):  
CA Mok ◽  
V Au ◽  
OA Thompson ◽  
ML Edgley ◽  
L Gevirtzman ◽  
...  

AbstractTemperature sensitive (TS) alleles are important tools for the genetic and functional analysis of essential genes in many model organisms. While isolating TS alleles is not difficult, determining the TS-conferring mutation can be problematic. Even with whole-genome sequencing (WGS) data there is a paucity of predictive methods for identifying TS alleles from DNA sequence alone. We assembled 173 TS lethal mutants of Caenorhabditis elegans and used WGS to identify several hundred mutations per strain. We leveraged single molecule molecular inversion probes (MIPs) to sequence variant sites at high depth in the cross-progeny of TS mutants and a mapping strain with identified sequence variants but no apparent phenotypic differences from the reference N2 strain. By sampling for variants at ~1Mb intervals across the genome we genetically mapped mutant alleles at a resolution comparable to current standards in a process we call MIP-MAP. The MIP-MAP protocol, however, permits high-throughput sequencing of multiple TS mutation mapping libraries at less than 200K reads per library. Using MIP-MAP on a subset of TS mutants, via a competitive selection assay and standard recombinant mutant selection, we defined TS-associated intervals of 3Mb or less. Our results suggest this collection of strains contains a diverse library of TS alleles for genes involved in development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes. The MIPs protocol should allow high-throughput tracking of genetic variants in any mixed population.


Genetics ◽  
1995 ◽  
Vol 141 (3) ◽  
pp. 889-902 ◽  
Author(s):  
S Loo ◽  
P Laurenson ◽  
M Foss ◽  
A Dillin ◽  
J Rine

Abstract A sensitized genetic screen was carried out to identify essential genes involved in silencing in Saccharomyces cerevisiae. This screen identified temperature-sensitive alleles of ORC2 and ORC5, as described elsewhere, and ABF1, NPL3, and YCL54, as described here. Alleles of ABF1 that caused silencing defects provided the genetic proof of Abflp's role in silencing. The roles of Npl3p and Ycl54p are less clear. These proteins did not act exclusively through any one of the three protein binding sites of the HMR-E silencer. Unlike the orc2, orc5, and abf1 mutations that were isolated in the same (or a similar) screen for silencing mutants, neither temperature-sensitive mutation in NPL3 or YCL54 caused overt replication defects.


Genetics ◽  
1991 ◽  
Vol 127 (2) ◽  
pp. 279-285 ◽  
Author(s):  
S D Harris ◽  
J R Pringle

Abstract In a previous attempt to identify as many as possible of the essential genes on Saccharomyces cerevisiae chromosome I, temperature-sensitive (Ts-) lethal mutations that had been induced by ethyl methane-sulfonate or nitrosoguanidine were analyzed. Thirty-two independently isolated mutations that mapped to chromosome I identified only three complementation groups, all of which had been known previously. In contrast, molecular analyses of segments of the chromosome have suggested the presence of numerous additional essential genes. In order to assess the degree to which problems of mutagen specificity had limited the set of genes detected using Ts- lethal mutations, we isolated a new set of such mutations after mutagenesis with UV or nitrogen mustard. Surprisingly, of 21 independently isolated mutations that mapped to chromosome I, 17 were again in the same three complementation groups as identified previously, and two of the remaining four mutations were apparently in a known gene involved in cysteine biosynthesis. Of the remaining two mutations, one was in one of the essential genes identified in the molecular analyses, and the other was too leaky to be mapped. These results suggest that only a minority of the essential genes in yeast can be identified using Ts- lethal mutations, regardless of the mutagen used, and thus emphasize the need to use multiple genetic strategies in the investigation of cellular processes.


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