The effects of extremes of ph on the growth and transcriptomic profiles of three haloarchaea

Abstract

The Archaea represent a fascinating domain of life where each species comprises a hybrid of bacterial and eukaryal features. Unfortunately, there have been few investigations of the Archaea and many fundamental questions remain regarding their biochemistry, genetics, and genomics. One reason for this is that few archaea are amenable to detailed experimental analysis; however, a few halophilic archaea (haloarchaea) can be easily manipulated in the laboratory and contain a sequenced genome, allowing for bioinformatics studies, such as recording changes in the transcriptomes. Haloarchaea are found wherever seawater is concentrated above 2 M NaCl and contain a similarly high concentration of salts internally, without producing compatible solutes. They exhibit a variety of novel molecular characteristics, including acidic proteins that resist the denaturing effects of salts, and DNA repair systems that minimize the deleterious effects of desiccation and intense solar radiation. In addition, haloarchaea are metabolically versatile and respond to a wide variety of environmental signals, including extremes of radiation, salinity, temperature, heavy metals, pollutants, and pH by modulating the activity of key genes.

Of the above naturally occurring stresses, all have been previously studied but one, pH. Haloarchaea are routinely isolated from both acidic and alkaline saline lakes; however, their ability to thrive under these conditions still remains an unexplored mystery. Therefore, I have endeavored to unlock a few of these secrets by growing sequenced haloarchaeal strains at extremes of pH and cataloging the changes in their transcriptomes compared to growth at optimal pH. For my experiments, RNA was isolated at the end of logarithmic growth and labeled cDNA was generated and hybridized to custom-designed microarray slides that I designed. Changes in the transcriptomes were cataloged and compared to each other as well as to changes from previously studied bacteria. The results from my experiments showed that haloarchaea are primarily responding to extremes of pH in a manner similar to known bacterial cells, making these responses similar across two domains of life. However, there are a few differences, compared to bacteria, due to the unique nature of the Archaea.