Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

Abstract

BackgroundRapidly characterizing the operational interrelationships among all genes in a given organism is a critical bottleneck to significantly advancing our understanding of thousands of newly sequenced microbial and eukaryotic species. While evolving technologies for global profiling of transcripts, proteins, and metabolites are making it possible to comprehensively survey cellular physiology in newly sequenced organisms, these experimental techniques have not kept pace with sequencing efforts. Compounding these technological challenges is the fact that individual experiments typically only stimulate relatively small-scale cellular responses, thus requiring numerous expensive experiments to survey the operational relationships among nearly all genetic elements. Therefore, a relatively quick and inexpensive strategy for observing changes in large fractions of the genetic elements is highly desirable.ResultsWe have discovered in the model organism Halobacterium salinarum NRC-1 that batch culturing in complex medium stimulates meaningful changes in the expression of approximately two thirds of all genes. While the majority of these changes occur during transition from rapid exponential growth to the stationary phase, several transient physiological states were detected beyond what has been previously observed. In sum, integrated analysis of transcript and metabolite changes has helped uncover growth phase-associated physiologies, operational interrelationships among two thirds of all genes, specialized functions for gene family members, waves of transcription factor activities, and growth phase associated cell morphology control.ConclusionsSimple laboratory culturing in complex medium can be enormously informative regarding the activities of and interrelationships among a large fraction of all genes in an organism. This also yields important baseline physiological context for designing specific perturbation experiments at different phases of growth. The integration of such growth and perturbation studies with measurements of associated environmental factor changes is a practical and economical route for the elucidation of comprehensive systems-level models of biological systems.

Expression of multiple tfb genes in different Halobacterium salinarum strains and interaction of TFB with transcriptional activator GvpE

“…salinarum PHH1 and PHH4 lack one or even Wve tbp genes and are devoid of tfbC and tfbE, it was interesting to investigate both strains in comparison to NRC-1 with respect to their growth behavior. Growth at diVerent temperatures was chosen, since global transcriptomic studies have been performed with NRC-1 Koide et al 2009;Facciotti et al 2010) and tfb and/or tbp gene knockouts help to determine the importance of the GTFs . The single-knockout strains tbpD and tfbA grow more slowly at 49°C and show a reduced viability at 56°C leading to the suggestion that TbpD and TfbA are important for heat shock response .…”

“…The simultaneous expression of these GTFs suggests that the members of each group could function together. Additional studies on the expression imply that TbpE and TfbF are the dominant GTFs during exponential growth in NRC-1 (Facciotti et al , 2010Bonneau et al 2007), and the expression of tbpF and of the alternative tfbA, B, D, E, and G genes is increased during the stationary growth phase (Facciotti et al 2010).…”

“…Multiple and divergent GTF genes are present in the genome sequences of the haloarchaeon Halobacterium salinarum NRC-1 and the gas vesicle negative mutant strain R1 PfeiVer et al 2008a, b). The possession of multiple GTFs led to the hypothesis that the formation of diVerent TFB-TBP complexes plays a role in the regulation of transcription initiation and the GTFs constitute a regulatory network Facciotti et al 2007Facciotti et al , 2010.…”

Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

“…From these data, we identified genes with expression responsive to growth rate and genes with expression responsive to salinity. H. salinarum is known to display several growth phase-associated transitions in cell physiology and gene expression (29). In the transition from active growth in log phase to stationary phase, H. salinarum is known to switch from aerobic to anaerobic metabolism in anticipation of nutrient limitation, generating gas vesicles to vertically relocate in the water column (29).…”

“…H. salinarum is known to display several growth phase-associated transitions in cell physiology and gene expression (29). In the transition from active growth in log phase to stationary phase, H. salinarum is known to switch from aerobic to anaerobic metabolism in anticipation of nutrient limitation, generating gas vesicles to vertically relocate in the water column (29). In the current experiments, genes involved in these processes were significantly correlated with , including the phototrophy genes for light-driven energy production under anaerobic conditions (specifically, the bacteriorhodopsin pump components bacterioopsin [bop] and retinal chromophore synthesizing phytoene synthase [crtB1]) and gas vesicle genes for flotation (gvpA1, gvpC1, gvpA2, and gvpV1).…”