The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus

We report here the characterization of the first agmatine/cadaverine aminopropyl transferase (ACAPT), the enzyme responsible for polyamine biosynthesis from an archaeon. The gene PF0127 encoding ACAPT in the hyperthermophile Pyrococcus furiosus was cloned and expressed in Escherichia coli, and the recombinant protein was purified to homogeneity. P. furiosus ACAPT is a homodimer of 65 kDa. The broad substrate specificity of the enzyme toward the amine acceptors is unique, as agmatine, 1,3-diaminopropane, putrescine, cadaverine, and sym-nor-spermidine all serve as substrates. While maximal catalytic activity was observed with cadaverine, agmatine was the preferred substrate on the basis of the k(cat)/K(m) value. P. furiosus ACAPT is thermoactive and thermostable with an apparent melting temperature of 108 degrees C that increases to 112 degrees C in the presence of cadaverine. Limited proteolysis indicated that the only proteolytic cleavage site is localized in the C-terminal region and that the C-terminal peptide is not necessary for the integrity of the active site. The crystal structure of the enzyme determined to 1.8-A resolution confirmed its dimeric nature and provided insight into the proteolytic analyses as well as into mechanisms of thermal stability. Analysis of the polyamine content of P. furiosus showed that spermidine, cadaverine, and sym-nor-spermidine are the major components, with small amounts of sym-nor-spermine and N-(3-aminopropyl)cadaverine (APC). This is the first report in Archaea of an unusual polyamine APC that is proposed to play a role in stress adaptation.     

Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis

Yersinia pestis, the causative agent of plague, utilizes a type III secretion system (T3SS) to inject effector proteins directly into the cytosol of mammalian cells where they interfere with signal transduction pathways that regulate actin cytoskeleton dynamics and inflammation, thereby enabling the bacterium to avoid engulfment and destruction by macrophages. Type III secretion normally does not occur in the absence of close contact with eukaryotic cells. Negative regulation is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. Here, we report two crystal structures of YopN in complex with its heterodimeric secretion chaperone SycN-YscB and the co-regulatory protein TyeA, respectively. By merging these two overlapping structures, it was possible to construct a credible theoretical model of the YopN-SycN-YscB-TyeA complex. The modeled assembly features the secretion signaling elements of YopN at one end of an elongated structure and the secretion regulating TyeA binding site at the other. A patch of highly conserved residues on the surface of the C-terminal alpha-helix of TyeA may mediate its interaction with structural components of the secretion apparatus. Conserved arginine residues that reside inside a prominent cavity at the dimer interface of SycN-YscB were mutated in order to investigate whether they play a role in targeting the YopN-chaperone complex to the type III secretion apparatus. One of the mutants exhibited a phenotype that is consistent with this hypothesis.     

Phosphorylation and Dephosphorylation among Dif Chemosensory Proteins Essential for Exopolysaccharide Regulation in Myxococcus xanthus

Myxococcus xanthus social gliding motility, which is powered by type IV pili, requires the presence of exopolysaccharides (EPS) on the cell surface. The Dif chemosensory system is essential for the regulation of EPS production. It was demonstrated previously that DifA (methyl-accepting chemotaxis protein [MCP]-like), DifC (CheW-like), and DifE (CheA-like) stimulate whereas DifD (CheY-like) and DifG (CheC-like) inhibit EPS production. DifD was found not to function downstream of DifE in EPS regulation, as a difD difE double mutant phenocopied the difE single mutant. It has been proposed that DifA, DifC, and DifE form a ternary signaling complex that positively regulates EPS production through the kinase activity of DifE. DifD was proposed as a phosphate sink of phosphorylated DifE (DifE∼P), while DifG would augment the function of DifD as a phosphatase of phosphorylated DifD (DifD∼P). Here we report in vitro phosphorylation studies with all the Dif chemosensory proteins that were expressed and purified from Escherichia coli. DifE was demonstrated to be an autokinase. Consistent with the formation of a DifA-DifC-DifE complex, DifA and DifC together, but not individually, were found to influence DifE autophosphorylation. DifD, which did not inhibit DifE autophosphorylation directly, was found to accept phosphate from autophosphorylated DifE. While DifD∼P has an unusually long half-life for dephosphorylation in vitro, DifG efficiently dephosphorylated DifD∼P as a phosphatase. These results support a model where DifE complexes with DifA and DifC to regulate EPS production through phosphorylation of a downstream target, while DifD and DifG function synergistically to divert phosphates away from DifE∼P.The proper regulation of bacterial motility is critical for the survival of bacteria in their natural environment. One such form of regulation is bacterial chemotaxis, which enables organisms to move toward more favorable niches and away from hazardous ones. Chemotaxis regulation in flagellated swimming bacteria has been well studied in model organisms such as Escherichia coli and Bacillus subtilis (2, 36). In general, environmental changes are detected and transduced to the cytoplasmic side of the cell by a transmembrane ternary signaling complex composed of methyl-accepting chemotaxis proteins (MCPs), CheW, and CheA. Typically, MCPs anchor the complex to the membrane through their two transmembrane (TM) domains. Chemical changes in the environment are detected by the periplasmic domain of an MCP, resulting in conformational changes in the conserved cytoplasmic signaling domain. These changes can modulate the activity of the CheA kinase via interactions with CheW in the signaling complex. The response regulator CheY, another essential component of the bacterial chemotaxis pathway, is a substrate of the CheA kinase that accepts a phosphate from autophosphorylated CheA. Phosphorylated CheY (CheY∼P) interacts with the flagellar motor complex to effect bacterial swimming behavior. Although the dephosphorylation of CheY∼P can occur spontaneously, it is accelerated by phosphatases such as CheZ in E. coli and CheC as well as FliY in B. subtilis. The dephosphorylation of CheY∼P is critical for chemotaxis since it is one of the mechanisms for the desensitization of a stimulated chemotaxis pathway. This basic architecture of chemotaxis pathways is generally conserved in all the flagellated swimming bacteria examined to date (31, 36).Myxococcus xanthus is a gliding Gram-negative bacterium that encodes eight chemosensory systems based on the genome sequence (18, 54). This bacterium, which develops fruiting bodies under nutrient deprivation (25), is motile on surfaces by adventurous (A) and social (S) gliding motility (22). While A motility enables the movement of a cell that is well separated from others, S motility is functional only when cells are in close proximity. S motility is analogous to bacterial twitching in that both are powered by retraction of the type 4 pilus (Tfp) (24, 30, 38). M. xanthus S motility additionally requires exopolysaccharides (EPS) to function (29). For S motility, EPS on one cell is thought to provide the anchor and trigger for the retraction of Tfp from a neighboring cell, thus explaining the proximity requirement. Chemotaxis regulation in M. xanthus has also been investigated extensively (27, 54). One of the surprises from these investigations was that among the eight chemosensory systems, only Frz signal transduction plays a primary role in chemotaxis regulation and mutants in other systems have no or only specific defects in chemotaxis under certain experimental conditions.The M. xanthus Dif chemosensory system, while also important for tactic responses to certain species of phosphatidylethanolamine (PE) (8), plays a primary role in the regulation of EPS production (7, 53). difA, difC, and difE mutants produce no detectable levels of EPS, whereas difD and difG mutants overproduce EPS (3, 7, 53). Mutations in difD and difG have additive effects on EPS production but failed to suppress mutations in difE (6). Additional analysis, including the use of yeast two- and three-hybrid (Y2H and Y3H, respectively) systems, led to a working model for the regulation of EPS by the Dif system (6, 52). DifA (MCP-like), DifC (CheW-like), and DifE (CheA-like) were projected to form a ternary signaling complex as do the MCPs, CheW, and CheA in bacterial chemotaxis. DifE is proposed to be an autokinase whose activity is modulated by DifA in combination with DifC (6, 52). The output of the signaling complex is the phosphorylation of an unidentified downstream component by DifE. DifD (CheY-like) and DifG (CheC-like), negative regulators of EPS production, are proposed to be ancillary modulators of the output of DifE by partially diverting phosphate from the DifE kinase and thus away from its downstream target(s) (6). That is, DifD may accept phosphate from autophosphorylated DifE (DifE∼P) and DifG may function as a phosphatase to accelerate the autodephosphorylation of phosphorylated DifD (DifD∼P). Phosphorylation and dephosphorylation events, which are obviously critical to this model, had not been examined prior to this present report.In this study, we used purified Dif proteins expressed in E. coli to examine the autophosphorylation, phosphotransfer, and dephosphorylation properties of the Dif proteins in vitro. Our results provide strong evidence for most of the proposed biochemical and physical interactions among the Dif proteins. Necessary modifications of the model based on the results here are also discussed.     

Properties of microtubule sliding disintegration in isolated tetrahymena cilia

Properties of the sliding disintegration response of demembranated tetrahymena cilia have been studied by measuring the spectrophotomeric response or turbidity of cilia suspensions at a wavelength of 350 nm relative to changes in the dynein substrate (MgATP(2-)) concentration. The maximum decrease in turbidity occurs in 20 muM ATP, and 90 percent of the decrease occurs in approximately 5.9 s. At lower ATP concentrations (1-20 muM), both the velocity and magnitude of the turbidity decreases are proportional to ATP concentration. The velocity data for 20 muM ATP permit construction of a reaction velocity curve suggesting that changes in turbidity are directly proportional to the extent and velocity of disintegration. At ATP concentrations more than 20 muM (50muM to 5mM), both velocity and magnitude of the turbidimetric response are reduced by approximately 50 percent. This apparent inhibition results in a biphasic response curve that may be related to activation of residual shear resistance or regulatory components at the higher ATP concentrations. The inhibitory effects of elevated ATP can be eliminated by mild trypsin proteolysis, whereupon the reaction goes to completion at any ATP concentration. The turbidimetric responses of the axoneme-substrate suspensions are consistent with the extent and type of axoneme disintegration revealed by electron microscope examination of the various suspensions, suggesting that the turbidimetric assay may prove to be a reliable means for assessing the state of axoneme integrity.     

New protein fold revealed by a 1.65 A resolution crystal structure of Francisella tularensis pathogenicity island protein IglC

Francisella tularensis is a highly infectious Gram-negative intracellular pathogen that causes the fulminating disease tularemia and is considered to be a potential bioweapon. F. tularensis pathogenicity island proteins play a key role in modulating phagosome biogenesis and subsequent bacterial escape into the cytoplasm of macrophages. The 23 kDa pathogenicity island protein IglC is essential for the survival and proliferation of F. tularensis in macrophages. Seeking to gain some insight into its function, we determined the crystal structure of IglC at 1.65 A resolution. IglC adopts a beta-sandwich conformation that exhibits no similarity with any known protein structure.     

RetS inhibits Pseudomonas aeruginosa biofilm formation by disrupting the canonical histidine kinase dimerization interface of GacS

Bacterial signaling histidine kinases (HKs) have long been postulated to function exclusively through linear signal transduction chains. However, several HKs have recently been shown to form complex multikinase networks (MKNs). The most prominent MKN, involving the enzymes RetS and GacS, controls the switch between the motile and biofilm lifestyles in the pathogenic bacterium Pseudomonas aeruginosa. While GacS promotes biofilm formation, RetS counteracts GacS using three distinct mechanisms. Two are dephosphorylating mechanisms. The third, a direct binding between the RetS and GacS HK regions, blocks GacS autophosphorylation. Focusing on the third mechanism, we determined the crystal structure of a cocomplex between the HK region of RetS and the dimerization and histidine phosphotransfer (DHp) domain of GacS. This is the first reported structure of a complex between two distinct bacterial signaling HKs. In the complex, the canonical HK homodimerization interface is replaced by a strikingly similar heterodimeric interface between RetS and GacS. We further demonstrate that GacS autophosphorylates in trans, thus explaining why the formation of a RetS-GacS complex inhibits GacS autophosphorylation. Using mutational analysis in conjunction with bacterial two-hybrid and biofilm assays, we not only corroborate the biological role of the observed RetS-GacS interactions, but also identify a residue critical for the equilibrium between the RetS-GacS complex and the respective RetS and GacS homodimers. Collectively, our findings suggest that RetS and GacS form a domain-swapped hetero-oligomer during the planktonic growth phase of P. aeruginosa before unknown signals cause its dissociation and a relief of GacS inhibition to promote biofilm formation.