Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase

Adenylate kinases play a crucial role in cellular energy homeostasis through the interconversion of ATP, AMP, and ADP in all living organisms. Here, we explore how adenylate kinase (AdK) from Escherichia coli interacts with diadenosine tetraphosphate (AP4A), a putative alarmone associated with transcriptional regulation, stress, and DNA damage response. From a combination of EPR and NMR spectroscopy together with X-ray crystallography, we found that AdK interacts with AP4A with two distinct modes that occur on disparate time scales. First, AdK dynamically interconverts between open and closed states with equal weights in the presence of AP4A. On a much slower time scale, AdK hydrolyses AP4A, and we suggest that the dynamically accessed substrate-bound open AdK conformation enables this hydrolytic activity. The partitioning of the enzyme into open and closed states is discussed in relation to a recently proposed linkage between active site dynamics and collective conformational dynamics.

Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages

A hallmark of Listeria (L.) monocytogenes pathogenesis is bacterial escape from maturing entry vacuoles, which is required for rapid bacterial replication in the host cell cytoplasm and cell-to-cell spread. The bacterial transcriptional activator PrfA controls expression of key virulence factors that enable exploitation of this intracellular niche. The transcriptional activity of PrfA within infected host cells is controlled by allosteric coactivation. Inhibitory occupation of the coactivator site has been shown to impair PrfA functions, but consequences of PrfA inhibition for L. monocytogenes infection and pathogenesis are unknown. Here we report the crystal structure of PrfA with a small molecule inhibitor occupying the coactivator site at 2.0 Å resolution. Using molecular imaging and infection studies in macrophages, we demonstrate that PrfA inhibition prevents the vacuolar escape of L. monocytogenes and enables extensive bacterial replication inside spacious vacuoles. In contrast to previously described spacious Listeria-containing vacuoles, which have been implicated in supporting chronic infection, PrfA inhibition facilitated progressive clearance of intracellular L. monocytogenes from spacious vacuoles through lysosomal degradation. Thus, inhibitory occupation of the PrfA coactivator site facilitates formation of a transient intravacuolar L. monocytogenes replication niche that licenses macrophages to effectively eliminate intracellular bacteria. Our findings encourage further exploration of PrfA as a potential target for antimicrobials and highlight that intra-vacuolar residence of L. monocytogenes in macrophages is not inevitably tied to bacterial persistence.

Structural basis for transthyretin amyloid formation in vitreous body of the eye

Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form.

Control of Bacterial Virulence through the Peptide Signature of the Habitat

To optimize fitness, pathogens selectively activate their virulence program upon host entry. Here, we report that the facultative intracellular bacterium Listeria monocytogenes exploits exogenous oligopeptides, a ubiquitous organic N source, to sense the environment and control the activity of its virulence transcriptional activator, PrfA. Using a genetic screen in adsorbent-treated (PrfA-inducing) medium, we found that PrfA is functionally regulated by the balance between activating and inhibitory nutritional peptides scavenged via the Opp transport system. Activating peptides provide essential cysteine precursor for the PrfA-inducing cofactor glutathione (GSH). Non-cysteine-containing peptides cause promiscuous PrfA inhibition. Biophysical and co-crystallization studies reveal that peptides inhibit PrfA through steric blockade of the GSH binding site, a regulation mechanism directly linking bacterial virulence and metabolism. L. monocytogenes mutant analysis in macrophages and our functional data support a model in which changes in the balance of antagonistic Opp-imported oligopeptides promote PrfA induction intracellularly and PrfA repression outside the host.

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Listeria PrfA virulence regulation is controlled by antagonistic nutritional peptides

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Opp-imported peptides regulate PrfA upstream of the activating cofactor GSH

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PrfA is activated by peptides that provide essential cysteine for GSH biosynthesis

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Blockade of PrfA’s GSH binding site by peptides inhibits virulence gene activation

Serum adenosine deaminase in the early diagnosis of typhoid fever

To study the usefulness of the enzyme adenosine deaminase for the early diagnosis of typhoid fever, its activity in serum was assayed in 277 children admitted to the Hospital Guillermo Grant Benavente at Concepción, Chile, from March, 1988, to December, 1990. The children were distributed into seven groups: control, N = 82; bacteremia, N = 8; acute viral respiratory infection, N = 43; febrile children with miscellaneous etiologies, N = 49; pulmonary tuberculosis, N = 3; hepatitis A virus infection, N = 30; and typhoid fever, N = 62. The medium serum adenosine deaminase values were significantly higher in children with typhoid fever (P < 0.0001) in relation to the values in the control group (122.2 +/- 40.7 vs 28.1 +/- 8.4 units/liter at 37 degrees C). This test had a sensitivity of 91.9% and a specificity of 92.5% in identifying the patient with typhoid fever when using 80 units/liter as the cutoff values. The positive predictive value of the test was 83.8% and the negative predictive value was 96%. Determination of adenosine deaminase values in serum could be helpful in the early diagnosis of typhoid fever.

[Adenosine deaminase in typhoid fever and other febrile diseases]

The contribution of serum adenosine deaminase (ADA) activity to the diagnosis of typhoid fever was assessed in 246 children and in 46 adults, by Giusti's original technique. Children included otherwise healthy patients admitted for elective surgical conditions or under follow up for epilepsy which were considered to be a control group (n: 81), presumptive viral diseases (n: 31), miscellaneous febrile diseases except for typhoid fever (n: 41), different kinds of bacteremia (n: 6), diarrhea due to Salmonella typhimurium (n: 14), viral hepatitis (n: 24), and culture proven typhoid fever (n: 49). Adult's group included 39 healthy controls and 7 patients with culture proven typhoid fever. Among children mean ADA activity was as follows: control group 28 +/- 7.8, viral disease 35.3 +/- 13.1, miscellaneous febrile disease 36.1 +/- 15.6, bacteremia group: 30.3 +/- 10.3, salmonellosis group 51.6 +/- 9, hepatitis group 68.3 +/- 34.5, typhoid fever group 124.4 +/- 40.8 U/I 37 degrees C. Among adults, values were 18.4 +/- 7.5 for controls and 112.8 +/- 19.2 U/I 37 degrees C in typhoid fever patients. In both adults and children ADA activity was significantly higher in the typhoid fever group (p < 0.0001). Untreated typhoid fever patients had their higher ADA activity between 10th and 15th day of illness. When ADA cut point was set at 80 U/I, sensitivity of the test was 91.8% and specificity was 91.4% as a preliminary clue to the recognition of typhoid fever.