Boonchai Boonyaratanakornkit.

Graduate Student
University of California, Berkeley

B.S. Chemistry, 2000
University of California, Davis

Office Location: 497A Tan Hall
Office Telephone: 510-643-8340
Office Fax: 510-643-1228

Genomic Expression Analysis of Extremophiles

My research involves gene expression profiling of Methanococcus jannaschii, a hyperthermophilic archaeon isolated at a depth of 2,600-m around deep-sea hydrothermal vents in the East Pacific Rise. This organism utilizes a gas substrate consisting of H2:CO2 (4:1 v/v) with CO2 as the only necessary carbon source for growth. The optimal growth temperature of M. jannaschii is 85°C, and its growth rate increases with pressure up to 750 atm. The entire genome of this organism has been sequenced and consists of 1,738 genes, 44% of which are uncharacterized. This goal of my project is to understand the mechanisms M. jannaschii uses to adapt to extremes of temperature and pressure and to identify and characterize new proteins that are responsible for these adaptations.

Using cDNA microarrays, we have identified genes involved in the heat and cold shock response of M. jannaschii at 3 atm, conditions that occur in situ due to the large thermal gradients around the deep-sea vents (Boonyaratanakornkit et al., Environ. Microbiol. 7(6):789-797, 2005). Genes that are up-regulated upon lethal heat shock consist primarily of chaperones including a novel prefoldin (currently being characterized), which suggests that proteins are largely unfolded under these conditions. Upon cold shock, a very different response is observed consisting of up-regulation of genes involved in transcription and translation and genes coding for proteases and transport proteins. A chaperone, peptidyl-prolyl cis/trans isomerase, may also facilitate protein folding at low temperatures.

We are currently cultivating M. jannaschii in a high temperature-pressure bioreactor at conditions reaching up to 500 atm and 95°C. Gas-liquid mass transfer of the gas substrate has been found to mask pressure effects, as pressure effects that typically increased growth rates by about two fold at 500 atm compared to 7 atm under non-limiting conditions did not accelerate growth when gas-liquid mass transfer limited growth. The effects of these mass transfer limitations are currently being examined on the gene-expression level. We are also examining the effects of 500 atm, pressure shock from 7 to 500 atm, and heat shock at 500 atm to understand the changes that are incurred by high pressure on cell physiology.