Dissection of the Bradyrhizobium japonicum NifAσ54 regulon, and identification of a ferredoxin gene ( fdxN ) for symbiotic nitrogen fixation.

Autor: Felix Hauser, Gabriella Pessi, Markus Friberg, Christoph Weber, Nicola Rusca, Andrea Lindemann, Hans-Martin Fischer, Hauke Hennecke
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Zdroj: Molecular Genetics & Genomics; Sep2007, Vol. 278 Issue 3, p255-271, 17p
Abstrakt: Abstract  Hierarchically organized regulatory proteins form a complex network for expression control of symbiotic and accessory genes in the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum. A genome-wide survey of regulatory interactions was made possible with the design of a custom-made gene chip. Here, we report the first use of the microarray in a comprehensive and complete characterization of the B. japonicum NifAσ54 regulon which forms an important node in the entire network. Comparative transcript profiles of anaerobically grown wild-type, nifA, and rpoN 1/2 mutant cells were complemented with a position-specific frequency matrix-based search for NifA- and σ54-binding sites plus a simple operon definition. One of the newly identified NifAσ54-dependent genes, fdxN, encodes a ferredoxin required for efficient symbiotic nitrogen fixation, which makes it a candidate for being a direct electron donor to nitrogenase. The fdxN gene has an unconventional, albeit functional σ54 promoter with the dinucleotide GA instead of the consensus GC motif at position −12. A GC-containing mutant promoter and the atypical GA-containing promoter of the wild type were disparately activated. Expression analyses were also carried out with two other NifAσ54 targets (ectC; ahpC). Incidentally, the tiling-like design of the microarray has helped to arrive at completely revised annotations of the ectC- and ahpC-upstream DNA regions, which are now compatible with promoter locations. Taken together, the approaches used here led to a substantial expansion of the NifAσ54 regulon size, culminating in a total of 65 genes for nitrogen fixation and diverse other processes. [ABSTRACT FROM AUTHOR]
Databáze: Complementary Index
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