Adjustment of physiology in response to changes in oxygen availability is
Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. a variety of different sources. Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific 41044-12-6 manufacture instances of post-transcriptional regulation. Adaptation to varying levels of oxygen is critical for the survival of all organisms since this element is required for energy production in aerobic organisms, but is a dangerous poison for obligate anaerobes. Thus, diverse strategies have evolved for optimizing fitness under conditions of fluctuating oxygen availability. For example, anaerobic microbes have evolved specialized anoxic physiologies, including mechanisms to exclude and scavenge traces of oxygen (Imlay 2002). In contrast, facultative anaerobes such as flexibly transition between oxidative metabolism and anaerobic growth, using alternate respiratory enzymes when oxygen becomes limiting (Nakano and Zuber 1998). Anoxia-tolerant eukaryotes such as enter a state of suspended animation in which energy supply and demand are drastically reduced in a regulated manner during oxygen starvation (Hochachka et al. 1996). Understanding cellular responses to oxygen at the molecular systems level requires comprehensive and quantitative measurements of changes in parameters such as transcription, translation, and metabolism. Transcriptome measurements are quite comprehensive (Lander 1999), whereas current technology limits the detection of the complete microbial proteome and metabolome; e.g., the highest reported coverage for microbial shotgun proteomics is 60% (Lipton et al. 2002; Brauer et al. 2006). Furthermore, in addition to this disparity in technical tractability, the dynamic nature of information processing at all of these levels further complicates the collective comparative analysis of global changes in transcriptome, proteome, and metabolome (Gygi et al. 1999; Ideker et al. 2001; Beyer et al. 2004). Consequently, the global dynamic relationships across these distinct but interconnected processes remain to be characterized to build a physiological model of systems behavior. We chose the haloarchaeon as a model organism to investigate the systems-level oxygen response. This organism, found in the Great Salt Lake, the Dead Sea, and other waters with high salt concentration, requires an environment with a high concentration of salt for survival (4.0 M) TSPAN32 (Robb et al. 1995). Our choice of this organism was guided by (1) the relative simplicity afforded by the small genome size (2.6 Mb) and lack of compartmentalization of prokaryotes, and (2) capability to effect metabolic changes within a remarkably narrow range of oxygen availability. Rapid shifts to low environmental oxygen tension is a frequent challenge to utilizes metabolic strategies similar to other facultative anaerobic microbes such as to alternate between four modes within a narrow range (0C5 M) of oxygen concentration: (1) aerobic respiration via the tricarboxylic acid (TCA) cycle (Ng et al. 2000); (2) anaerobic fermentation via the arginine deiminase (ADI) pathway (Hartmann et al. 1980; Ruepp and Soppa 1996; Baliga et al. 2002); (3) anaerobic dimethyl sulfoxide (DMSO) and trimethylamine shifts from a state of anoxic quiescence to active growth when the oxygen supply is replenished. During quiescence, the organism appears to remain poised for a rapid transition to alternative metabolic states. We were able to significantly improve the concordance between changes in 41044-12-6 manufacture transcription and translation when a time lag was considered during data analysis. In addition, this analysis suggested several possible post-transcriptional strategies enabling adaptation to changes in oxygen. From this standpoint, the dynamic temporal model of has shed new insights into general principles of the oxygen response. Results and Discussion Experimental design and rationale Cellular responses to changes in the environment require coordinated signal processing and other physiological adjustments at the transcriptional, translational, and metabolic levels. Therefore, to capture a systems perspective of cellular responses to oxygen, global changes in relative abundance of transcripts, proteins, ATP, and growth were measured in continuous chemostat cultures. In the chemostat, pH, cell density, light, and temperature were kept constant, whereas oxygen was perturbed in a controlled manner (Fig. 1; Table 1; Methods). Sampling was temporally more frequent close to perturbations to ensure that all rapid responses were measured, and less frequent farther from perturbations as cultures equilibrated to the new condition (Table 1). This 41044-12-6 manufacture experiment was conducted in triplicate, varying oxygen appropriately to assess the reproducibility of growth and molecular response characteristics (Fig. 1; Table 1; Methods). The results and conclusions from these oxygen response.