Restricting Fermentative Potential by Proteome Remodeling

Abstract

Pathogenesis hinges on successful colonization of the gastrointestinal (GI) tract by pathogenic facultative anaerobes. The GI tract is a carbohydrate-limited environment with varying oxygen availability and oxidoreduction potential (ORP). How pathogenic bacteria are able to adapt and grow in these varying conditions remains a key fundamental question. Here, we designed a system biologyinspired approach to pinpoint the key regulators allowing Bacillus cereus to survive and grow efficiently under low ORP anoxic conditions mimicking those encountered in the intestinal lumen. We assessed the proteome components using high throughput nanoLC-MS/MS techniques, reconstituted the main metabolic circuits, constructed ⌬ohrA and ⌬ohrR mutants, and analyzed the impacts of ohrA and ohrR disruptions by a novel round of shotgun proteomics. Our study revealed that OhrR and OhrA are crucial to the successful adaptation of B. cereus to the GI tract environment. Specifically, we showed that B. cereus restricts its fermentative growth under low ORP anaerobiosis and sustains efficient aerobic respiratory metabolism, motility, and stress response via OhrRA-dependent proteome remodeling. Finally, our results introduced a new adaptive strategy where facultative anaerobes prefer to restrict their fermentative potential for a long term benefit. Molecular & Cellular Proteomics 11: 10.1074/ mcp.M111.013102, 1-13, 2012.Facultative anaerobes encompass all the major pathogens of the human gastrointestinal (GI) 1 tract. The GI tract poses several challenges for pathogens because it is sliced into distinct niches with different oxygen concentrations and different oxidoreduction potentials (ORP) (1-3). Although much is known about gene expression and metabolism under fully aerobic and high ORP anaerobic condition (4, 5), our knowledge about the physiological impact of low ORP anoxic conditions and the underlying molecular mechanisms is scarce (6).Bacillus cereus is a notorious food-borne pathogenic bacterium. Like the closely related Bacillus anthracis (7,8), it is a recognized agent of GI tract infections (9 -11). The critical step of infection takes place in the small intestine, where B. cereus has to grow and produce virulence factors to induce diarrheal disease (11, 12). Thus, how B. cereus adapts its catabolism and regulates its proteome across the range of physiologically relevant ORP and oxygen availabilities is important for its survival and growth. In B. cereus, anaerobic and aerobic catabolism work through different pathways. In the presence of oxygen, reducing equivalents generated by glycolysis and the TCA cycle (NADH and FADH) are reoxidized by the respiratory chain, resulting in the buildup of a proton motive force and the subsequent synthesis of ATP. Acetate excretion can occur aerobically when carbon flux into the cells exceeds TCA cycle capacity. In the absence of oxygen or other external electron acceptors (such as nitrate), NADH is reoxidized in terminal step fermentative reactions from pyruvate. When grown in pH-controlled ana...

Time dynamics of the Bacillus cereus exoproteome are shaped by cellular oxidation

“…Figure 1 shows the B. cereus growth curves and the extracellular ORP profiles established for the three culture conditions. As reported previously (Clair et al, 2012 ), B. cereus cells grew more slowly and produced less biomass in anoxic fermentative conditions than in oxic respiratory conditions. Changes in the initial extracellular ORP did not alter the growth rate and biomass production under fermentative anoxic conditions (Table S1 in Supplementary Material).…”

“…B. cereus adjusts its primary metabolism to grow efficiently under aerobic respiratory and anaerobic fermentative conditions and to adapt to low-ORP conditions (Duport et al, 2006 ; Clair et al, 2012 ). In addition, as for all other bacteria, B. cereus undergoes a major metabolic switch from primary metabolism (exponential growth) to secondary metabolism (stationary phase) in response to nutrient starvation or oxidative stress (Nieselt et al, 2010 ).…”

“…Under anaerobiosis, B. cereus catabolizes glucose-using, fermentative pathways, which are not recognized as high-ROS-producing pathways under normal conditions. However, low-ORP conditions can induce ROS production in response to reductive stress (Clair et al, 2012 ). Bacteria use a large spectrum of ROS scavenging systems, including low-molecular-weight molecules, metabolites, and antioxidant enzymes, to maintain ROS at non-toxic levels and to prevent macromolecule damage (Chi et al, 2011 ; Mailloux et al, 2011 ).…”

Bacillus cereus Fnr binds a [4Fe-4S] cluster and forms a ternary complex with ResD and PlcR

“…We demonstrated that CsdA from E. coli was capable of assembling the B. cereus Fnr Fe-S cluster. Interestingly, B. cereus synthesizes [13]one pyridoxal 5-phosphate-containing enzyme (NP_834652) [13] that might be involved in Fe-S cluster biogenesis. When anaerobically reconstituted B. cereus Fnr was exposed to O 2 , we observed a rapid loss of the Fe-S cluster, demonstrating that Fnr functions as an oxygen sensor via its Fe-S cluster.…”

Titanium Dioxide Nanoparticles Alter the Cellular Phosphoproteome in A549 Cells

“…Peak lists were generated with the MASCOT DAEMON software (Matrix Science, London, UK, version 2.3.2) using the extract_msn.exe data import filter from the Xcalibur FT package (version 2.0.7) (ThermoFisher Scientific, Les Ulis, France). The filtering options were, as previously [41]: minimum mass: 400, maximum mass: 5000, grouping tolerance: 0, intermediate scans: 0, minimum peaks: 10, extract MSn: 2 and threshold: 1000. Peptides were assigned from MS/MS spectra according to the SwissProt database with the MASCOT 2.3.02 software (Matrix Science, London, UK), by searching the database with the following parameters: Mammalia taxonomy (65,476 sequences), SwissProt_2012_02, maximum number of miss-cleavages: 2; mass tolerances: 5 ppm (parent ion) and 0.5 Da (MS/MS); carbamidomethylated Cys: fixed modification; and oxidized Met and phosphorylated Ser, Thr and Tyr residues: variable modification.…”