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Department of Molecular Biology

College of Agriculture and Natural Resources


Research Interests

We (i) study bacterial signal transduction (nucleotide second messengers; photosensory transduction) and (ii) engineer synthetic light-regulated proteins and gene circuits for optogenetic applications. We use various bacterial systems and experimental approaches: synthetic biology, genetics, protein-ligand biochemistry, photochemistry, structural biology, metabolic engineering, bioinformatics, transcriptomics.

Cyclic dimeric GMP signaling in bacteria

C-di-GMP is one of the most common bacterial second messengers. It plays a central role in bacterial transition from the motile, single-cellular lifestyle to the sessile, surface-attached, multicellular lifestyle. Surface-attached bacteria form biofilms, communities of cells growing in the self-produced extracellular matrices. The majority of chronic infections involve bacterial pathogens growing in biofilms, where cells are much less susceptible to antibiotics. Therefore, understanding how biofilms are formed and destroyed is of significant medical importance. Current foci of c-di-GMP research involve (i) elucidating molecular mechanisms through which c-di-GMP operates in E. coli and in the intracellular pathogen Listeria monocytogenes, and (ii) using c-di-GMP to control activities of engineered proteins in animals. We also collaborate with several groups worldwide on c-di-GMP signaling mechanisms in diverse bacterial species.

Figure 1Fig. 1. c-di-GMP-dependent signaling pathways in a hypothetical cell affecting flagellum, exopolysaccharide synthesis, and gene expression. Clouds represents local c-di-GMP gradients.
Figure 2Fig. 2. Overview of the enzymes involved in c-di-GMP synthesis and degradation and c-di-GMP receptors.

MMBRTo learn more on c-di-GMP signaling, see:

Römling U, Galperin MY, Gomelsky M. 2013. Cyclic di-GMP: The first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1-52.

Chen LH, Köseoğlu VK, Güvener ZT, Myers-Morales T, Reed JM, D’Orazio SEF, Miller KW, Gomelsky M. 2014. Cyclic di-GMP-dependent signaling pathways in the pathogenic firmicute Listeria monocytogenes. PLoS Pathog 10:e1004301.

Fang X, Ahmad I, Blanka A, Schottkowski M, Cimdins A, Galperin MY, Römling U, Gomelsky M. 2014. GIL, a new c-di-GMP binding protein domain involved in cellulose synthesis regulation in enterobacteria. Mol Microbiol 93:439–452.

Engineering light-activated proteins and gene circuits

Near-infrared light-activated proteins have the potential to revolutionize biomedical research. These proteins can be delivered into model organisms (optogenetics) to control various activities in vivo with the spatiotemporal precision that supersedes that of chemicals (drugs). Near-infrared light penetrates mammalian tissues to the depths of several centimeters. We engineered light-activated enzymes that control synthesis and degradation of nucleotide second messenger (e.g., c-di-GMP, cAMP). Using these enzymes, we are building synthetic signaling pathways for remote photocontrol of biological processes.

Figure 3Fig. 3. Engineered light-controlled bacterial behavior in E. coli (biofilm formation and motility).
Figure 4Fig. 4. Engineered light-activated gene expression.
Figure 5Fig. 5. Remote control of gene expression in bacterial pathogens in murine models of diseases.

Trends in MicrobiologyTo learn more on light-activated systems for optogenetic applications, see:

Ryu MH, Kang IH, Nelson MD, Jensen TM, Lyuksyutova AI, Siltberg-Liberles J, Raizen DM, Gomelsky M. 2014. Engineering adenylate cyclases regulated by near-infrared window light. Proc Natl Acad Sci USA 111:10167-72.

Ryu MH, Gomelsky M. 2014. Synthetic second messenger module controlled by near-infrared window light. ACS Synth Biol Jan 28. doi: 10.1021/sb400182x. [Epub ahead of print].

Gomelsky M, Hoff WH. 2011. Light helps bacteria make important lifestyle decisions. Trends Microbiol 19: 441-448.

Metabolic engineering of Rhodobacter sphaeroides

Anoxygenic phototrophic bacteria are incredibly metabolically versatile. They can utilize solar energy and organic waste products to synthesize hydrogen and liquid biofuels. We use metabolic maps, flux balance analysis and reconstructed global gene regulatory systems of a model bacterium Rhodobacter sphaeroides to engineer biofuel producing strains.

Figure 6a

Fig. 6. Phototrophic production of hydrogen gas by metabolically engineered R. sphaeroides. Left panel, hydrogen accumulation in various constructed mutants (A-C) compared to the wild-type strain (WT). Right panel, experimental setup; hydrogen produced by bacteria pushes water out and accumulates in the inverted tubes.

Figure 6b

Figure 7Fig. 7. Transcriptomic analysis of the AppA -PpsR regulatory system controlling photosynthesis genes in R. sphaeroides


Figure 8To learn more about metabolic engineering of R. sphaeroides, see:

Ryu MH, Hull NC, Gomelsky M. 2014. Metabolic engineering of Rhodobacter sphaeroides for improved hydrogen production. Intl J Hydrogen Energy 39:6384-6390.

Gomelsky M, Zeilstra-Ryalls JH. 2013. The living genome of a purple nonsulfur photosynthetic bacterium: Overview of the Rhodobacter sphaeroides transcriptome landscapes. Adv Botanical Res 66:179-203.

Moskvin OV, Bolotin D, Wang A, Ivanov PS, Gomelsky M. 2011. Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium. BioSystems 103: 125-131.

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