Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity

Structural Basis of Nucleotide Selectivity in Pyruvate Kinase

Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures of Streptococcus pneumoniae PYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.

Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs

Acetylation is a protein post-translational modification (PTM) that can affect a variety of cellular processes. In bacteria, two PTM Nε-acetylation mechanisms have been identified: non-enzymatic/chemical acetylation via acetyl phosphate or acetyl coenzyme A and enzymatic acetylation via protein acetyltransferases. Prior studies have shown that extensive acetylation of Nε-lysine residues of numerous proteins from a variety of bacteria occurs via non-enzymatic acetylation. In Escherichia coli, new Nε-lysine acetyltransferases (KATs) that enzymatically acetylate other proteins have been identified, thus expanding the repertoire of protein substrates that are potentially regulated by acetylation. Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. Five E. coli KAT substrate proteins that were previously identified as being acetylated by YiaC and had 3D structures in the PDB were selected for further analysis: adenylate kinase (Adk), isocitrate dehydrogenase (Icd), catalase HPII (KatE), methionyl-tRNA formyltransferase (Fmt), and a peroxide stress resistance protein (YaaA). We methodically compared over 350 protein structures of these E. coli enzymes and their homologs; to accurately determine lysine residue conservation requires a strategy that incorporates both flexible structural alignments and visual inspection. Moreover, our results revealed discrepancies in conclusions about lysine residue conservation in homologs when examining linear amino acid sequences compared to 3D structures.

An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

In theoretical modeling of a physical system, a crucial step consists of the identification of those degrees of freedom that enable a synthetic yet informative representation of it. While in some cases this selection can be carried out on the basis of intuition and experience, straightforward discrimination of the important features from the negligible ones is difficult for many complex systems, most notably heteropolymers and large biomolecules. We here present a thermodynamics-based theoretical framework to gauge the effectiveness of a given simplified representation by measuring its information content. We employ this method to identify those reduced descriptions of proteins, in terms of a subset of their atoms, that retain the largest amount of information from the original model; we show that these highly informative representations share common features that are intrinsically related to the biological properties of the proteins under examination, thereby establishing a bridge between protein structure, energetics, and function.

Enzymatic characteristics of two adenylate kinases, AdkA and AdkB, from Myxococcus xanthus

Adenylate kinase (Adk) plays a critical role in energy metabolism and adaptation of bacteria to environmental stresses. We have previously shown that Myxococcus xanthus expresses polyphosphate kinase 1 (Ppk1) that also has Adk activity in the absence of polyphosphates. In this study, we investigated the Adk activity of the other two M. xanthus enzymes, AdkA and AdkB. The activity of AdkA was increased by dithiothreitol (DTT), which also enhanced enzyme stability. Site-directed mutagenesis of three cysteine residues (C130, C150, and C153) present in the LID domain of AdkA revealed that the Adk activity and stability of C150S and C153S mutants were not affected by DTT addition, suggesting formation of a disulfide bond between C150 and C153 in AdkA. The Km of AdkA for AMP was 8 and 17 times lower than that for ADP and ATP, respectively. AdkB is a polyphosphate kinase 2 (Ppk2) homolog lacking the Ppk2 middle region and, consequently, Ppk activity. According to our analysis, AdkB also had Adk activity and its affinity for substrates was higher than that of AdkA. Thus, M. xanthus expresses three enzymes, AdkA, AdkB, and Ppk1, with Adk activity, which may function to support energy metabolism of the bacteria in different environmental conditions.

Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase

Adenylate kinase is a monomeric phosphotransferase with important biological function in regulating concentration of adenosine triphosphate (ATP) in cells, by transferring the terminal phosphate group from ATP to adenosine monophosphate (AMP) and forming two adenosine diphosphate (ADP) molecules. During this reaction, the kinase may undergo a large conformational transition, forming different states with its substrates. Although many structures of the protein are available, atomic details of the whole process remain unclear. In this article, we use both conventional molecular dynamics (MD) simulation and an enhanced sampling technique called parallel cascade selection MD simulation to explore different conformational states of the Escherichia coli adenylate kinase. Based on the simulation results, we propose a possible entrance/release order of substrates during the catalytic cycle. The substrate-free protein prefers an open conformation, but changes to a closed state once ATP·Mg enters into its binding pocket first and then AMP does. After the reaction of ATP transferring the terminal phosphate group to AMP, ADP·Mg and ADP are released sequentially, and finally the whole catalyze cycle is completed. Detailed contact and distance analysis reveals that the entrance/release order of substrates may be largely controlled by electrostatic interactions between the protein and the substrates.

Adenylate kinase potentiates the capsular polysaccharide by modulating Cps2D in Streptococcus pneumoniae D39

Streptococcus pneumoniae is a polysaccharide-encapsulated bacterium. The capsule thickens during blood invasion compared with the thinner capsules observed in asymptomatic nasopharyngeal colonization. However, the underlying mechanism regulating differential CPS expression remains unclear. CPS synthesis requires energy that is supplied by ATP. Previously, we demonstrated a correlation between ATP levels and adenylate kinase in S. pneumoniae (SpAdK). A dose-dependent induction of SpAdK in serum was also reported. To meet medical needs, this study aimed to elucidate the role of SpAdK in the regulation of CPS production. CPS levels in S. pneumoniae type 2 (D39) increased proportionally with SpAdK levels, but they were not related to pneumococcal autolysis. Moreover, increased SpAdK levels resulted in increased total tyrosine kinase Cps2D levels and phosphorylated Cps2D, which is a regulator of CPS synthesis in the D39 strain. Our results also indicated that the SpAdK and Cps2D proteins interact in the presence of Mg-ATP. In addition, in silico analysis uncovered the mechanism behind this protein–protein interaction, suggesting that SpAdK binds with the Cps2D dimer. This established the importance of the ATP-binding domain of Cps2D. Taken together, the biophysical interaction between SpAdK and Cps2D plays an important role in enhancing Cps2D phosphorylation, which results in increased CPS synthesis.

A physical interaction between two key enzymes explains how the bacterium responsible for causing pneumococcal disease thickens its external capsule during infection of the bloodstream. A team led by Dong-Kwon Rhee from Sungkyunkwan University in Suwon, South Korea, studied strains of Streptococcus pneumoniae expressing varying levels of an enzyme that helps maintain the proper balance of cellular energy. They found that this enzyme stimulated the production of sugar chains that coat the outside of the bacterial capsule by binding and activating an intermediary enzyme involved in the synthesis of these sugar chains. Since the capsule is critical in warding off the human immune response, the findings suggest that drugs designed to disrupt the enzyme-mediated induction of capsule formation could help prevent or treat pneumococcal disease.

Molecular Docking Evaluation of (E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors

Multi-drug resistant microorganism infections with emerging problems that require not only a prevention strategy, but also the development of new inhibitory compounds. Six previously synthesized 5-arylidene-2-thioxothiazolidin-4-one derivatives 1a–f, were screened for inhibitory activity on adenylate kinases of different origins by molecular docking. The compounds 1c and 1d were the most efficient inhibitors of bacterial and some archean adenylate kinases. Hydrogen bond interactions were observed with the residues belonging to the ATP binding site. Moreover human adenylate kinases are poor targets, suggesting that this selectivity offers promising prospectives for refining the structure of our compounds.

Impact of cellular health conditions on the protein folding state in mammalian cells

By using in-cell NMR experiments, we have demonstrated that the protein folding state in cells is significantly influenced by the cellular health conditions. hAK1 was denatured in cells under stressful culture conditions, while it remained functional and properly folded in cells continuously supplied with a fresh medium.

Aggregatibacter actinomycetemcomitans Growth in Biofilm versus Planktonic State: Differential Expression of Proteins

Aggregatibacter actinomycetemcomitans (Aa) is a pathogenic bacterium residing in the subgingival plaque biofilm strongly associated with the pathogenesis of periodontitis. The aim of this investigation was to study the protein differential expression of Aa when growing on biofilm compared with planktonic state using proteomic analysis by the 2D-DIGE system. Eighty-seven proteins were differentially expressed during biofilm growth (1.5-fold, p < 0.05), with 13 overexpressed and 37 down-expressed. Those repressed were mainly proteins involved in metabolism, biosynthesis, and transport. The overexpressed proteins were outer membrane proteins (OMPs) and highly immunogenic proteins such as YaeT (OMP), FtsZ, OMP39, OMP18/16, the chaperone GroEL, OMPA, adenylate kinase (Adk), and dihydrolipoamide acetyltransferase. The enrichment fractions of the OMPs from biofilm and planktonic states were obtained, and these proteins were analyzed by Western blotting with human serum from a periodontitis patient and one healthy control. These immunogenic proteins overexpressed in the biofilm may represent candidate virulence factors.

Lysyl-tRNA synthetase from Myxococcus xanthus catalyzes the formation of diadenosine penta- and hexaphosphates from adenosine tetraphosphate

Myxococcus xanthus lysyl-tRNA synthetase (LysS) produces diadenosine tetraphosphate (Ap4A) from ATP in the presence of Mn(2+); in the present study, it also generated Ap4 from ATP and triphosphate. When ATP and Ap4 were incubated with LysS and pyrophosphatase, first Ap4A, Ap5A, and ADP, and then Ap5, Ap6A, and Ap3A were generated. The results suggest that in the first step, LysS can form lysyl-AMP and lysyl-ADP intermediates from Ap4 and release triphosphate and diphosphate, respectively, whereas in the second step, it can produce Ap5 from lysyl-ADP with triphosphate, and Ap6A from lysyl-ADP with Ap4. In addition, in the presence of Ap4 and pyrophosphatase, but absence of ATP, LysS also generates diadenosine oligophosphates (ApnAs: n = 3-6). These results indicate that LysS has the ability to catalyze the formation of various ApnAs from Ap4 in the presence of pyrophosphatase. Furthermore, the formation of Ap4A by LysS was inhibited by tRNA(Lys) in the presence of 1 mM ATP. To the best of our knowledge, this is the first report of Ap5A and Ap6A synthesis by lysyl-tRNA synthetase.

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation

Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.

Co-Transcriptomes of Initial Interactions In Vitro between Streptococcus Pneumoniae and Human Pleural Mesothelial Cells

Streptococcus pneumoniae (Spn) is a major causative organism of empyema, an inflammatory condition occurring in the pleural sac. In this study, we used human and Spn cDNA microarrays to characterize the transcriptional responses occurring during initial contact between Spn and a human pleural mesothelial cell line (PMC) in vitro. Using stringent filtering criteria, 42 and 23 Spn genes were up-and down-regulated respectively. In particular, genes encoding factors potentially involved in metabolic processes and Spn adherence to eukaryotic cells were up-regulated e.g. glnQ, glnA, aliA, psaB, lytB and nox. After Spn initial contact, 870 human genes were differentially regulated and the largest numbers of significant gene expression changes were found in canonical pathways for eukaryotic initiation factor 2 signaling (60 genes out of 171), oxidative phosphorylation (32/103), mitochondrial dysfunction (37/164), eIF4 and p70S6K signaling (28/142), mTOR signaling (27/182), NRF2-mediated oxidative stress response (20/177), epithelial adherens junction remodeling (11/66) and ubiquitination (22/254). The cellular response appeared to be directed towards host cell survival and defense. Spn did not activate NF-kB or phosphorylate p38 MAPK or induce cytokine production from PMC. Moreover, Spn infection of TNF-α pre-stimulated PMC inhibited production of IL-6 and IL-8 secretion by >50% (p<0.01). In summary, this descriptive study provides datasets and a platform for examining further the molecular mechanisms underlying the pathogenesis of empyema.

New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a=73.5, b=54.3, c=62.7 Å, β=118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cα atoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate (Ap5A) belonged to space group P1, with unit-cell parameters a=53.9, b=62.3, c=63.0 Å, α=101.9, β=112.6, γ=89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.