scholarly journals Rewiring the specificity of extra-cytoplasmic function sigma factors

2020 ◽  
Author(s):  
Horia Todor ◽  
Hendrik Osadnik ◽  
Elizabeth A. Campbell ◽  
Kevin S. Myers ◽  
Timothy J. Donohue ◽  
...  

SUMMARYBacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators’ DNA binding and precise determination of biologically significant binding sites. Here, we address these challenges by solving the DNA-specificity code of extra-cytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the auto-regulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid – nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic foot-printing pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that ECF σs play varied roles: some are global regulators controlling many genes throughout the genome that are important under many conditions, while others are local regulators, controlling few closely linked genes in response to specific stimuli. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.

2020 ◽  
Vol 117 (52) ◽  
pp. 33496-33506
Author(s):  
Horia Todor ◽  
Hendrik Osadnik ◽  
Elizabeth A. Campbell ◽  
Kevin S. Myers ◽  
Hao Li ◽  
...  

Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators’ DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid–nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.


2010 ◽  
Vol 46 (4) ◽  
pp. 411-417 ◽  
Author(s):  
Yang MENG ◽  
Lin GU ◽  
Wenzheng ZHANG

1968 ◽  
Vol 12 ◽  
Author(s):  
R. Goossens

A precise method for the determination of the increment of the  basal area using the PressIer bore. Refering to  previous research showing that the basal area of the corsica pine could be  characterized by an ellips, we present in this paper a precise method for the  determination of the increment of the basal area. In this method we determine  the direction of the maximum diameter, we measure this diameter and we take a  core in one of the points of tangency of the caliper with the measured tree.  The determination of the diameter perpendicular to the maximum diameter  finishes the work wich is to be done in the forest. From the classical  measurements effectuated on the core and from the measured diameters we can  then determine the form (V) and the excentricity (e). Substituting these two  parameters in the formula 2 or 2', we can also calculate the error of a  radius measured on the core with respect to the representative radius, This  error with them allow us to correct the measured value of the minimum or the  maximum radius and we will be able to do a precise determination of the  increment.


1980 ◽  
Vol 45 (8) ◽  
pp. 2364-2370 ◽  
Author(s):  
Antonín Holý ◽  
Erik De Clercq

Reaction of 3',5'-di-O-benzoyl-6-methyl-2'-deoxyuridine (IIa) with elementary bromine or iodine afforded 5-halogeno derivatives IIc and IId which on methanolysis gave 5-bromo-6-methyl-2'-deoxyurine (Ic) and 5-iodo-6-methyl-2'-deoxyurine (Id), respectively. The CD spectra of Ic, Id and 6-methyl-2'-deoxyuridine (Ia) are compared and discussed with regard to determination of the nucleoside conformation. Unlike 5-bromo- and 5-iodo-2'-deoxyuridine, the 6-methyl derivatives Ic and Id exhibit neither antibacterial nor antiviral activity. Nor do they exert any antimetabolic effect on the de novo DNA synthesis in primary rabbit kidney cells.


1995 ◽  
Vol 269 (2) ◽  
pp. E247-E252 ◽  
Author(s):  
H. O. Ajie ◽  
M. J. Connor ◽  
W. N. Lee ◽  
S. Bassilian ◽  
E. A. Bergner ◽  
...  

To determine the contributions of preexisting fatty acid, de novo synthesis, and chain elongation in long-chain fatty acid (LCFA) synthesis, the synthesis of LCFAs, palmitate (16:0), stearate (18:0), arachidate (20:0), behenate (22:0), and lignocerate (24:0), in the epidermis, liver, and spinal cord was determined using deuterated water and mass isotopomer distribution analysis in hairless mice and Sprague-Dawley rats. Animals were given 4% deuterated water for 5 days or 8 wk in their drinking water. Blood was withdrawn at the end of these times for the determination of deuterium enrichment, and the animals were killed to isolate the various tissues for lipid extraction for the determination of the mass isotopomer distributions. The mass isotopomer distributions in LCFA were incompatible with synthesis from a single pool of primer. The synthesis of palmitate, stearate, arachidate, behenate, and lignocerate followed the expected biochemical pathways for the synthesis of LCFAs. On average, three deuterium atoms were incorporated for every addition of an acetyl unit. The isotopomer distribution resulting from chain elongation and de novo synthesis can be described by the linear combination of two binomial distributions. The proportions of preexisting, chain elongation, and de novo-synthesized fatty acids as a percentage of the total fatty acids were determined using multiple linear regression analysis. Fractional synthesis was found to vary, depending on the tissue type and the fatty acid, from 47 to 87%. A substantial fraction (24-40%) of the newly synthesized molecules was derived from chain elongation of unlabeled (recycled) palmitate.


Author(s):  
Ferrari Colin ◽  
Resongles Eléonore ◽  
Freydier Rémi ◽  
Casiot Corinne

Thiol-functionalized silica powder allowed single-step purification of antimony for exploring stable Sb isotope signatures in the environment.


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