Department of Plant Biology

- Department of Plant Biology - Devaki Bhaya

My research interests focus on cyanobacteria, the largest and most diverse group of photosynthetic prokaryotes. Cyanobacteria survive and flourish in an amazing range of environments, and are often dominant in marine habitats as well as in microbial mats and biofilms. Their global distribution is reflected, in part, by their ability to cope with wide fluctuations in temperature, nutrient and light levels. I am particularly interested in the ability of cyanobacteria to perceive and move towards or away from a light source, which allows the organism to optimize conditions for photosynthesis. This phenomenon, known as phototaxis, is well known but little understood.

We have recently demonstrated that phototaxis in Synechocystisis a surface-dependent phenomenon that requires type IV pili, which are surface appendages implicated in the association of bacterial pathogens with their hosts and both twitching and social motility. We have taken advantage of the fact that the Synechocystis genome has been entirely sequenced to generate a library of tagged motility-mutants.

Chemotaxis proteins: Several of the tagged-motility mutants mapped to chemotaxis-like (tax) genes. While the roles of the chemotaxis proteins are fairly well-understood in enteric bacteria, it is not clear that the paradigms that have been established extend to the operation of Che-like proteins in other systems. Synechocystis has at least three tax loci, two of which are involved in motility responses. Analysis of these tax loci in much greater detail (i.e by generating specific mutants) will allow us to test a model that we have developed which addresses the regulation of pilus biogenesis and phototactic movement. Major emphasis will also be placed on using molecular and biochemical tools to tag and/or mutate specific proteins such that we can localize them within the cell to understand the interactions between proteins that regulate phototaxis (with Jacky Ng, Carnegie Insitution.

Photoreceptor-like protein (TaxD1): One of the mutants that we have isolated has a lesion in a chemoreceptor-like protein with a domain that is reminiscent of the chromophore-binding domain of phytochrome in vascular plants. This has several interesting implications and we will attempt to prove that this is protein can act like a photoreceptor (to be carried out in collaboration with Clark Lagarias, UC, Davis).

Time lapse video microscopy :To elucidate the elements involved in generating and controlling motility, we will use time-lapse video microscopy to record movement in real time both in wild type cells and in mutant strains. This would allow us to observe, for the first time, movement of single cells and cell populations to ask fundamental questions about the parameters that govern motility.

Novel mutants: 300 tagged motility mutants have been generated so far, and we have only just begun to map these mutants. Many have mapped to novel proteins (such as coiled-coil proteins) as well as to proteins such as an alternative sigma factor, an ABC transporter, an adenylyl cyclase and to a serine threonine kinase. We will focus on a few of these proteins to understand some of the novel interactions that may provide insights into the regulation of motility.

A second area of research interest stems from the several recently completed sequencing projects of a number of different cyanobacterial species. I am interested in analyzing these genomes in a number of ways to make specific predictions of how different organisms are likely to respond to their environment. Coupling this bioinformatic approach with microarray analysis should provide a more robust understanding of how cyanobacteria respond to various environmental stresses and particularly to fluctuations in light and nutrient levels.

So far, six cyanobacterial genomes have been sequenced entirely or in large part. These include fresh water as well as marine strains. Two nitrogen-fixing filamentous strains have also been sequenced. To exploit the full power of this information we will collaborate with Jeff Shrager, Carnegie Institution ) and Daniel Vaulot (Station Biologique, Roscoff, CNRS, France) to analyze gene families etc. In the future predictions based on such analyses can be tested using microarray analysis (the microarray chip for Synechocystis is available). Currently we are analyzing the large hli gene family which appears to be required for acclimation to high light. This gene family has been extensively analyzed in the Grossman laboratory at the genetic and biochemical level and can become a paradigm for functional genomics in cyanobacteria.

Selected Publications: ( = Full text, Adobe Acrobat PDF format)

Ng, W.O., Grossman, A. and Bhaya, D. (2003) Multiple light inputs control phototaxis in Synechocystis PCC6803 Journal of Bacteriology In press

Appendix Figures (in PDF format): Table A1, Fig. A1, Fig. A2 , Fig. A3 , Fig. A4 , Fig. A5
Bhaya, D, Dufresne, A, Vaulot, D, Grossman, A. (2002) Analysis of the hli gene family in marine and freshwater cyanobacteria. FEMS Microbiology Letters 215:209-219
Bhaya D, Takahashi A, Shahi P., and A R. Grossman (2001) Novel motility mutants from Synechocystis PCC6803 generated by in vitro transposon mutagenesis. Journal of Bacteriology 183:6140-6143
Bhaya D, Takahashi, A and A R. Grossman (2001) Light regulation of Type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC 6803. Proc. Natl. Acad. Sci. U.S.A ,98:7540-7545
Grossman, A. R., D.Bhaya and Q. He (2001) Tracking the light environment by cyanobacteria and the dynamic nature of light harvesting Journal of Biological Chemistry276:11449-52
Mrázek, J., D. Bhaya, A. R. Grossman and S. Karlin(2001) Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29:1590-601
Bhaya, D, N. R. Bianco, D. Bryant and A. R. (2000)Type IV pilus biogenesis and motility in the cyanobacterium Synechocystis sp. PCC6803. Mol. Microbiol. 37: 941-951
Bhaya,D., D.Vaulot, P.Amin, A.W. Takahashi and A.R. Grossman (2000) Isolation of regulated genes of the unicellular cyanobacterium Synechocystis sp.strain PCC6803 by differential display. Journal of Bacteriology 182:5692-5699
Bhaya, D., R. Schwarz and A. R. Grossman (2000) "Molecular responses to environmental stresses" in "Ecology of Cyanobacteria: Their diversity in time and space" Ed. B.A.Whitton and M.Potts, Kluwer Academic Publishers Ltd. pp 397-442
Bhaya, D. and A.R. Grossman (1999) The role of an alternative sigma factor in motility and pilus formation in the cyanobacterium Synechocystis sp. strain PCC6803. Proc. Natl. Acad. Sci. U.S.A., 96:3188-3193