Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea

Abstract

Background: Differential expression of genes can be regulated on many different levels. Most global studies of gene regulation concentrate on transcript level regulation, and very few global analyses of differential translational efficiencies exist. The studies have revealed that in Saccharomyces cerevisiae, Arabidopsis thaliana, and human cell lines translational regulation plays a significant role. Additional species have not been investigated yet. Particularly, until now no global study of translational control with any prokaryotic species was available.

Results: A global analysis of translational control was performed with two haloarchaeal model species, Halobacterium salinarum and Haloferax volcanii. To identify differentially regulated genes, exponentially growing and stationary phase cells were compared. More than 20% of H. salinarum transcripts are translated with non-average efficiencies. By far the largest group is comprised of genes that are translated with above-average efficiency specifically in exponential phase, including genes for many ribosomal proteins, RNA polymerase subunits, enzymes, and chemotaxis proteins. Translation of 1% of all genes is specifically repressed in either of the two growth phases. For comparison, DNA microarrays were also used to identify differential transcriptional regulation in H. salinarum, and 17% of all genes were found to have non-average transcript levels in exponential versus stationary phase. In H. volcanii, 12% of all genes are translated with non-average efficiencies. The overlap with H. salinarum is negligible. In contrast to H. salinarum, 4.6% of genes have non-average translational efficiency in both growth phases, and thus they might be regulated by other stimuli than growth phase.

Conclusion: For the first time in any prokaryotic species it was shown that a significant fraction of genes is under differential translational control. Groups of genes with different regulatory patterns were discovered. However, neither the fractions nor the identity of regulated genes are conserved between H. salinarum and H. volcanii, indicating that prokaryotes as well as eukaryotes use differential translational control for the regulation of gene expression, but that the identity of regulated genes is not conserved. For 70 H. salinarum genes potentiation of regulation was observed, but for the majority of regulated genes either transcriptional or translational regulation is employed.

Figure 1

Global analysis of translational regulation. A. Schematic overview of the experimental approach. B. An agarose gel showing the RNAs contained in the fractions of a typical density gradient. The numbers 1 – 8 denote the fractions from top to bottom. Fractions 1 and 2 and fractions 6–8 were pooled to yield the fractions of "free transcripts" and "ribosome-bound transcripts", respectively.

Figure 2

Comparison of groups of translationally regulated genes in Halobacterium salinarum and Haloferax volcanii. The relative fractions of regulated genes, compared to the total number of expressed genes, were calculated for six groups of genes with different patterns of translational efficiencies in exponential phase and stationary phase, as indicated in the inset. The six groups with non-average translational efficiencies and the group of averagely-translated genes are graphically represented for H. salinarum and H. volcanii.