Abstract
Oxalobacter formigenes is a unique intestinal organism that relies on oxalate degradation to meet most of its energy and carbon needs. A lack of colonization is a risk factor for calcium oxalate kidney stone disease. The release of the genome sequence of O. formigenes has provided an opportunity to increase our understanding of the biology of O. formigenes. This study used mass spectrometry based shotgun proteomics to examine changes in protein levels associated with the transition of growth from log to stationary phase. Of the 1867 unique protein coding genes in the genome of O. formigenes strain OxCC13, 1822 proteins were detected, which is at the lower end of the range of 1500–7500 proteins found in free-living bacteria. From the protein datasets presented here it is clear that O. formigenes contains a repertoire of metabolic pathways expected of an intestinal microbe that permit it to survive and adapt to new environments. Although further experimental testing is needed to confirm the physiological and regulatory processes that mediate adaptation with nutrient shifts, the O. formigenes protein datasets presented here can be used as a reference for studying proteome dynamics under different conditions and have significant potential for hypothesis development.
Highlights
Oxalobacter formigenes is a Gram-negative, obligate anaerobic bacterium that commonly inhabits the human gut and degrades oxalate as its major energy and carbon source [1,2]
The proteomic approach was used to identify proteome changes associated with the transition from log phase growth to stationary phase, offering a dynamic view of the different processes associated with entry into stationary phase
As an initial approach to both enrich the annotation of the O. formigenes genome and identify proteins important for growth and survival, mass spectrometry based global shotgun proteomics was performed on O. formigenes OxCC13 cultures harvested from log phase and stationary phase
Summary
Oxalobacter formigenes is a Gram-negative, obligate anaerobic bacterium that commonly inhabits the human gut and degrades oxalate as its major energy and carbon source [1,2]. Protection against calcium oxalate stone disease appears to be due to the oxalate degradation that occurs in the gut on low calcium diets [6] with a possible further contribution from intestinal oxalate secretion [7,8,9]. Despite the role this organism may play in reducing oxalate levels in the host and reducing the risk of calcium oxalate stone disease, there is scant information on how this organism colonizes the host and adapts to new environments. These proteomic analyses of O. formigenes cultures provide insight into the physiological response associated with nutrient shifts and entry into stationary phase growth
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