Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway

Løvdok, Linda; Bentele, Kajetan; Vladimirov, Nikita; Müller, Anette; Pop, Ferencz S.; Lebiedz, Dirk; Kollmann, Markus; Sourjik, Victor

doi:10.1371/journal.pbio.1000171

Cited by 56 publications

(93 citation statements)

References 47 publications

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“…This genetic organization differs from that observed in B. subtilis (49), where ohrA and ohrR are transcribed in the opposite direction, but was similar to that observed in other sequenced members of the B. cereus group (see supplemental Table S5). Sequence analysis also showed that the stop codon of ohrR is located close to the start codon of ohrA (2-bp upstream) and overlaps with the Shine-Dalgarno sequence of ohrA, suggesting a putative translational coupling between ohrA and ohrR (50). ohrA encodes a protein of 138 amino acid residues with 65% sequence identity and 74% sequence similarity to B. subtilis OhrA.…”

Section: Analysis Of Central Carbon Metabolism In Early Grown Bmentioning

confidence: 97%

Restricting Fermentative Potential by Proteome Remodeling

Clair¹,

Armengaud²,

Duport³

2012

Molecular & Cellular Proteomics

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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...

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Section: Analysis Of Central Carbon Metabolism In Early Grown Bmentioning

confidence: 97%

Restricting Fermentative Potential by Proteome Remodeling

Clair¹,

Armengaud²,

Duport³

2012

Molecular & Cellular Proteomics

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“…One is the adapted value of the pathway output, CheY-P, which must fall into the narrow sensitive range of the flagellar motor (29,32,46,54). Another parameter is the value of the adaptation rate, i.e., the rate of recovery of the kinase activity through changes in receptor methylation after the rapid initial response.…”

Section: Discussionmentioning

confidence: 99%

“…Increased attractant binding to receptors inhibits CheA activity and thus CheY-P formation, so that swimming up a gradient of attractant results in suppression of tumbling and longer runs in that direction. Receptor methylation by CheR then slowly resets the kinase activity back to steady state, and this delay in adaptation functions as memory (29,30).Several theoretical studies suggested that optimal chemotaxis in a gradient requires a specific adaptation rate that is defined by the gradient steepness and cell swimming velocity (31-34), irrespective of the chemical nature of the ligand or of its receptor specificity. This requirement arises because the time window of temporal comparisons needs to match the typical time (a few seconds) of a straight run of a bacterial cell along the gradient.…”

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confidence: 99%

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Universal Response-Adaptation Relation in Bacterial Chemotaxis

2015

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The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A shortterm memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis. In bacterial chemotaxis, effector stimuli are detected by a set of transmembrane receptors of different specificities (1-4). Escherichia coli has five types of chemoreceptors, with Tar and Tsr being major receptors and Trg, Tap, and Aer being minor chemoreceptors. Together with the histidine kinase CheA and an adaptor protein, CheW, receptors are organized in large sensory complexes that perform most of signal processing in chemotaxis (5-9). Activities of teams of 10 to 20 individual receptors are allosterically coupled within these complexes, enabling amplification and integration of changes in the relative ligand occupancy of receptors (10-17). The integrated signaling output of the receptor complexes is subsequently converted into the stimulation-dependent phosphorylation of the response regulator CheY, which controls cell swimming behavior.The bacterial strategy of chemotaxis relies on temporal comparisons of chemoeffector concentrations. This requires a short-term memory that enables bacteria to detect changes in concentrations along the swimming track and to modify their behavior accordingly, to either continue swimming in this direction or to tumble and reorient (18,19). Memory is provided by the receptor methylation system, consisting of the methyltransferase CheR and the methylesterase CheB, which respectively methylate or demethylate receptors on four or five specific glutamate residues. CheR preferentially recognizes the inactive state of receptors and increases receptor activity through methylation, whereas CheB preferentially demethylates active receptors and thereby lowers their activity (20-26). An additional negative feedback is provided by the CheA-mediated phosphorylation of CheB, which increases its methylesterase activity (27,28). In the absence of a gradient, these feedbacks allow the system to adapt to ambient stimulation, ensuring that t...

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“…Alternatively, the stoichiometry of the MMP0353 subunits in comparison with the other subunits of the proposed complex may be significantly different when mmp0353 is expressed in trans from the nif promoter compared to its natural promoter. Unnatural variation in the stoichiometry of the subunits in a multisubunit complex can lead to formation of a nonfunctional complex (49,50).…”

Section: Figmentioning

confidence: 99%

Evidence that Biosynthesis of the Second and Third Sugars of the Archaellin Tetrasaccharide in the Archaeon Methanococcus maripaludis Occurs by the Same Pathway Used by Pseudomonas aeruginosa To Make a Di-N-Acetylated Sugar

et al. 2015

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Methanococcus maripaludis has two surface appendages, archaella and type IV pili, which are composed of glycoprotein subunits. Archaellins are modified with an N-linked tetrasaccharide with the structure Sug-1,4-␤-ManNAc3NAmA6Thr-1,4-␤-GlcNAc3NAcA-1,3-␤-GalNAc, where Sug is (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-␣-L-erythro-hexos-5-ulo-1,5-pyranose. The pilin glycan has an additional hexose attached to GalNAc. In this study, genes located in two adjacent, divergently transcribed operons (mmp0350-mmp0354 and mmp0359-mmp0355) were targeted for study based on annotations suggesting their involvement in biosynthesis of N-glycan sugars. Mutants carrying deletions in mmp0350, mmp0351, mmp0352, or mmp0353 were nonarchaellated and synthesized archaellins modified with a 1-sugar glycan, as estimated from Western blots. Mass spectroscopy analysis of pili purified from the ⌬mmp0352 strain confirmed a glycan with only GalNAc, suggesting mmp0350 to mmp0353 were all involved in biosynthesis of the second sugar (GlcNAc3NAcA). The ⌬mmp0357 mutant was archaellated and had archaellins with a 2-sugar glycan, as confirmed by mass spectroscopy of purified archaella, indicating a role for MMP0357 in biosynthesis of the third sugar (ManNAc3NAmA6Thr). M. maripaludis mmp0350, mmp0351, mmp0352, mmp0353, and mmp0357 are proposed to be functionally equivalent to Pseudomonas aeruginosa wbpABEDI, involved in converting UDP-N-acetylglucosamine to UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid, an O5-specific antigen sugar. Cross-domain complementation of the final step of the P. aeruginosa pathway with mmp0357 supports this hypothesis. IMPORTANCEThis work identifies a series of genes in adjacent operons that are shown to encode the enzymes that complete the entire pathway for generation of the second and third sugars of the N-linked tetrasaccharide that modifies archaellins of Methanococcus maripaludis. This posttranslational modification of archaellins is important, as it is necessary for archaellum assembly. Pilins are modified with a different N-glycan consisting of the archaellin tetrasaccharide but with an additional hexose attached to the linking sugar. Mass spectrometry analysis of the pili of one mutant strain provided insight into how this different glycan might ultimately be assembled. This study includes a rare example of an archaeal gene functionally replacing a bacterial gene in a complex sugar biosynthesis pathway. While N-linked glycosylation was initially identified as an exclusively eukaryotic process, it is now well established that this pathway is present in the prokaryotic domains of Archaea and Bacteria as well. The posttranslational modification of proteins with N-linked glycans is believed to be much more widespread in Archaea than in Bacteria. In N-linked glycosylation systems, an oligosaccharyltransferase is required for the transfer of assembled oligosaccharides from the lipid carrier onto target proteins; genes encoding this key signature protein of the pathway have been identified in 166 out of 168 sequ...

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Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway

Abstract: Evolutionary selection for robustness of signaling output in the face of stochastic variations in protein expression may explain the organization of bacterial chemotaxis genes.

Cited by 56 publications

References 47 publications

Restricting Fermentative Potential by Proteome Remodeling

Restricting Fermentative Potential by Proteome Remodeling

Universal Response-Adaptation Relation in Bacterial Chemotaxis

Evidence that Biosynthesis of the Second and Third Sugars of the Archaellin Tetrasaccharide in the Archaeon Methanococcus maripaludis Occurs by the Same Pathway Used by Pseudomonas aeruginosa To Make a Di-N-Acetylated Sugar

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