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University of Wyoming


 

Research Interests

Novel protein domains in
microbial sensory transduction

In a broad sense, we are interested in understanding how single-cellular organisms sense their environment and adapt to it. Why are we interested in microbial sensory transduction?

(i) All living organisms sense major environmental parameters, e.g. oxygen or light, by the finite number of ways. Therefore, understanding how they do it is of fundamental importance in biology. Some of these sensory mechanisms are conserved throughout evolution, therefore knowledge about bacterial sensors (which are easier to study) can be applied to sensors from higher organisms.

(ii) Certain sensors have the potential to be used in the artificially designed molecular switches that regulate desired outputs by specific signals, e.g. photoswitches.

(iii) Some sensory transduction pathways are unique to bacteria and can be used as potential targets for antibacterial intervention. 

We use a variety of approaches in our research, including bioinformatics, genetics, biochemistry, photobiology, transcriptomics, and we collaborate with structural biologists and biophysicists in order to elucidate structures of sensors at the atomic level and mechanisms of their operation.

There are two major ongoing projects.

1.  Novel oxygen and light sensors.

We have identified novel protein domains sensing light (BLUF) and oxygen (SHIC). We are studying how they sense these signals, how they transfer information about these signals to their downstream partners and how bacteria respond to these signals. One of our favorite model organisms is a metabolically versatile photosynthetic bacterium Rhodobacter sphaeroides that regulates production of its photosynthetic apparatus in response to fluctuations in oxygen concentration and illumination. On this project we’re closely collaborating with Ilme Schlichting (Max Planck Institute for Medical Research – Heidelberg, Germany), Gabriele Klug (University of Giessen, Germany), Kevin Gardner and Marie-Alda Gilles-Gonzalez (both from University of Texas Southwestern Medical Center - Dallas).

To learn more about this project read these selected papers:

Gomelsky, M. and S. Kaplan. 1995. appA, a novel gene encoding a trans-acting factor involved in the regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 177: 4609-4618.

Gomelsky, M.  and  S. Kaplan.  1997. Molecular genetic evidence suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 179: 128-134.

Gomelsky, M. and S. Kaplan. 1998. AppA, a redox regulator of photosystem formation in Rhodobacter sphaeroides 2.4.1 is a flavoprotein. Identification of a novel FAD binding domain. J Biol Chem 273: 35319-35325

Braatsch, S., M. Gomelsky, S. Kuphal, and G. Klug. 2002. The single flavoprotein, AppA, from Rhodobacter sphaeroides integrates both redox and light signals. Mol Microbiol 45: 827-836.

Gomelsky, M. and G. Klug. 2002. BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem Sci 27: 497-500.

Braatsch, S., O.V. Moskvin, G. Klug and M. Gomelsky. 2004. Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J Bacteriol 186: 7726-7735.

Moskvin, O.V., L. Gomelsky and M. Gomelsky. 2005. Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development. J Bacteriol 187: 2148-2156.

Jung, A., T. Domratcheva, M. Tarutina, Q. Wu, W.-H. Ko, R.L. Shoeman, M. Gomelsky, K.H. Gardner and I. Schlichting. 2005. Structure of a bacterial BLUF photoreceptor: Insights into blue light-mediated signal transduction. Proc Natl Acad Sci USA 102: 12350-12355.

 Project 1 figures/graphs

2.  Cyclic dimeric GMP, c-di-GMP, a novel second messenger in Bacteria.

We are studying a signal transduction system centered around unusual cyclic dinucleotide, c-di-GMP. c-di-GMP has emerged in the last few years as a ubiquitous second messenger in Bacteria. It controls exopolysaccharide synthesis, biofilm formation and structure, flagella- and pili-based motility, and gene expression. c-di-GMP plays a key role in bacterial transition from the motile, single-cellular lifestyle to a sessile, often multicellular (biofilm) lifestyle. In addition, c-di-GMP plays an important role in bacterial virulence. Significant progress has been achieved in understanding how c-di-GMP is synthesized and broken down. However, mechanisms of c-di-GMP action and its end-targets remain essentially unknown. This represents the key unresolved problem in the field of c-di-GMP signaling and one of our objectives. We are also interested in understanding how various environmental signals regulate c-di-GMP level in the cell. On this project we’re closely collaborating with Ute Romling’s group (Karolinska Institutet, Sweden) and Michael Galperin (NCBI, NIH).

To learn more about this project read these selected papers:                  

Romling, U., M. Gomelsky and M.Y. Galperin. 2005. C-di-GMP: the dawning of a novel bacterial signaling system. MicroReview. Mol Microbiol 57: 629-639.

Galperin, M.Y. and M. Gomelsky. 2005. Bacterial signal transduction modules: From genomics to biology. Features. ASM News 71: 326-333.

Ryjenkov, D.A., M. Tarutina, O.V. Moskvin and M. Gomelsky. 2005. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: Insights into the biochemistry of the GGDEF protein domain. J Bacteriol 187: 1792-1798.

Schmidt, A.J., D.A. Ryjenkov and M. Gomelsky. 2005. The ubiquitous protein domain EAL is a c-di-GMP-specific phosphodiesterase: Enzymatically active and inactive EAL domains. J Bacteriol 187: 4774-4781.

Tarutina, M., D.A. Ryjenkov and M. Gomelsky. 2006. The unorthodox bacteriophytochrome from Rhodobacter sphaeroides involved in turnover of the second messenger c-di-GMP. J Biol Chem /in press/

Project 2 figures/graphs

Additional ongoing collaborative projects include:

Various Rhodobacter sphaeroides transcriptomics studies (with G. Klug, University of Giessen, Germany; with Dr. M. Abo and M. Tsuzuki, University of Tokyo, Japan; with F.R. Tabita, The Ohio State Univerisy; with J. Zeilstra-Ryalls, Bowling Green University; J.K. Lee, Sogan University, S. Korea).

To learn more about some of these project read these selected papers:

Braatsch, S., O.V. Moskvin, G. Klug and M. Gomelsky. 2004. Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J Bacteriol 186: 7726-7735.

Zeller, T., O.V. Moskvin, K. Li, G. Klug and M. Gomelsky. 2005. Transcriptome and physiological responses to hydrogen peroxide in the facultatively phototrophic bacterium Rhodobacter sphaeroides. J Bacteriol 187: 7232-7242.

Role of c-di-GMP in various bacteria (with J. O’Gara, University College-Dublin, Ireland, F. Yildiz, University of California – Santa Cruz, F. Yang, Indiana University School of Medicine; L. Claret, Université d'Auvergne, France; D. Karaolis, University of Maryland).

Antioxidants in cyanobacteria (with S. Herbert and F. Basile, University of Wyoming).

Microarray data analysis and modeling of transcriptional regulation (with P. Ivanov, Moscow State University, Russia)

This site is maintained by Randy L. Anderson.