By elucidating

The major coinducer is usually a unique metabolite of the pathway regulated by the specific LTTR.

Coinducers confer altered DNA binding properties to the LTTR protein, possibly due to a conformation change to the tertiary structure of the protein (13).

The two atypical response regulators (Cbb RR1 [response regulator 1 of the Cbb RRS system] and Cbb RR2) are unique in that they contain domains that are normally part of hybrid sensor kinases; response regulator 1 (Cbb RR1) contains a phosphate receiver domain and a histidine phosphotransfer domain, while response regulator 2 (Cbb RR2) contains two phosphate receiver domains (18, 19).

In addition, these regulators do not contain traditional DNA binding domains and are not able to bind to any discernible target DNA sequences, and yet they are able to interact and modify the properties of Cbb R (11) and influence Cbb R-mediated transcription under specialized growth conditions (10, 11, 18).

Gel mobility shift assays and surface plasmon resonance analyses together indicated that biosynthetic intermediates such as Ru BP, ATP, fructose 1,6-bisphosphate, and NADPH enhanced DNA binding by Cbb R.

These coinducers did not yield identical Cbb R-dependent DNase I footprints, indicating that the coinducers caused significant changes in DNA structure. The hybrid sensor kinase Cbb SR contains an N-terminal sensor domain, a central transmitter domain, and a C-terminal receiver domain.

Cbb R-DNA interactions were determined as described previously (11).(B) Comparison of the promoter region, DNase I footprinting was performed using fluorescently labeled DNA and an automated fluorescent DNA analyzer to resolve the digestion products, as described by Zianni et al. Plasmid p GSJFP, which contains the intergenic region between , was used as the template to generate the 459-bp probe (FP).The probe was generated by PCR amplification with the primers Fpcbb1-VIC [5′-(VIC)-AAGCTCGATCACGAGGCG-3′] and Fpcbb2-FAM [5′-6-carboxyfluorescein (FAM)-GACTTGTAGCGTTCCTTGC-3′] from Applied Biosystems.Following drying, the gel was analyzed by autoradiography and visualized with a Storm 840 Phosphor Imager (Molecular Dynamics, Sunnyvale, CA). Putative Cbb R binding sites (1 and 2) are highlighted in red.This region was used to generate DNA targets SP, SP90, SP2, SPΔ1, and SPΔ2, sequences of which are indicated, for gel mobility shift analyses.

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As a member of the well-studied Lys R-type transcriptional regulator (LTTR) family of regulators, Cbb R has been shown to positively regulate -A, located anywhere between 65 and 100 bp upstream of the transcription start (8, 13, 21, 31).

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