Supplementary materials for the paper:
Dmitry A. Rodionov*1, Inna Dubchak2, Adam Arkin3, Eric Alm3, and Mikhail S. Gelfand1,4
1Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per 19, Moscow, 127994, Russia;
2Genomics and 3Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US;
4State Scientific Center GosNIIGenetika,1st Dorozhny pr. 1, Moscow 117545, Russia
* e-mail: firstname.lastname@example.org
Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. Recent availability of complete finished or draft quality genome sequence for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal ion homeostasis, stress response, and energy metabolism using a combination of the regulatory sequence detection and analysis of the genomic context.
In the genomes of delta-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN, THI, B12 and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions.
Phylogenetically diverse delta-proteobacteria appear to share their regulatory components with other bacteria. This study for the first time shows adaptability of comparative genomics approach for the de novo reconstruction of a regulatory network in poorly studied taxonomic groups of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions.
A. Regulation mediated by DNA-binding transcription factors
B. Regulation mediated by effector-binding RNA structural elements (riboswitches)
P.S. Numerical gene identifiers from the Virtual Institute for Microbial Stress and Survival (VIMSS) Comparative Genomics database (http://escalante.lbl.gov/) are used throughout in the tables and figures.