Molecular determinants for interfacial binding and conformational change in a soluble diacylglycerol kinase

Staphylococcus aureus uses a GGDEF protein to recruit diacylglycerol kinase to the membrane for lipid recycling

Staphylococcus aureus is a Gram-positive pathogen responsible for numerous antibiotic-resistant infections. Identifying vulnerabilities in S. aureus is crucial for developing new antibiotics to treat these infections. With this in mind, we probed the function of GdpS, a conserved Staphylococcal membrane protein containing a cytoplasmic GGDEF domain. These domains are canonically involved in cyclic-di-GMP signaling processes, but S. aureus is not known to make cyclic-di-GMP. Using a transposon screen, we found that loss of GdpS is lethal when combined with disruption in synthesis of the glycolipid anchor of a cell surface polymer called lipoteichoic acid (LTA) or with deletion of genes important in cell division. Taking advantage of a small molecule that inhibits LTA glycolipid anchor synthesis, we selected for suppressors of ΔgdpS lethality. The most prevalent suppressors were hypermorphic alleles of dgkB, which encodes a soluble diacylglycerol (DAG) kinase required to recycle DAG to phosphatidylglycerol. By following up on these suppressors, we found that the GGDEF domain of GdpS interacts directly with DgkB, orienting its active site at the membrane to promote DAG recycling. DAG kinase hypermorphs also suppressed the lethality caused by combined loss of gdpS and cell division factors, highlighting the importance of lipid homeostasis for cell division. GdpS' positive regulation of DAG kinase function was dependent on the GGDEF domain but not its catalytic residues. As the sole conserved GGDEF-domain protein in Staphylococci, GdpS promotes an enzymatic process independent of cyclic-di-GMP signaling, revealing a new function for the ubiquitously conserved GGDEF domain.

The membrane: transertion as an organizing principle in membrane heterogeneity

The bacterial membrane exhibits a significantly heterogeneous distribution of lipids and proteins. This heterogeneity results mainly from lipid-lipid, protein-protein, and lipid-protein associations which are orchestrated by the coupled transcription, translation and insertion of nascent proteins into and through membrane (transertion). Transertion is central not only to the individual assembly and disassembly of large physically linked groups of macromolecules (alias hyperstructures) but also to the interactions between these hyperstructures. We review here these interactions in the context of the processes in Bacillus subtilis and Escherichia coli of nutrient sensing, membrane synthesis, cytoskeletal dynamics, DNA replication, chromosome segregation, and cell division.

Bacterial lipids: metabolism and membrane homeostasis

Membrane lipid homeostasis is a vital facet of bacterial cell physiology. For decades, research in bacterial lipid synthesis was largely confined to the Escherichia coli model system. This basic research provided a blueprint for the biochemistry of lipid metabolism that has largely defined the individual steps in bacterial fatty acid and phospholipids synthesis. The advent of genomic sequencing has revealed a surprising amount of diversity in the genes, enzymes and genetic organization of the components responsible for bacterial lipid synthesis. Although the chemical steps in fatty acid synthesis are largely conserved in bacteria, there are surprising differences in the structure and cofactor requirements for the enzymes that perform these reactions in Gram-positive and Gram-negative bacteria. This review summarizes how the explosion of new information on the diversity of biochemical and genetic regulatory mechanisms has impacted our understanding of bacterial lipid homeostasis. The potential and problems of developing therapeutics that block pathogen phospholipid synthesis are explored and evaluated. The study of bacterial lipid metabolism continues to be a rich source for new biochemistry that underlies the variety and adaptability of bacterial life styles.

Development of a Novel β-Secretase Binding Assay Using the AlphaScreen Platform

Alzheimer’s disease (AD) is a devastating neurodegenerative disease affecting millions of people. β-secretase-1 (BACE1), an enzyme involved in the processing of the amyloid precursor protein (APP) to form Aβ is a validated target for AD. Herein, the authors develop and validate a novel binding assay for BACE1 using the AlphaScreen platform that is amenable for high-throughput screening (HTS). Small-molecule BACE1 inhibitors of the hydroxyethylamine, hydantoin, and sulfamide classes were functionalized by biotin PEG linkers of varying lengths forming probes that were bound to streptavidin donor beads. BACE1 was coupled to nickel-chelate acceptor beads. Upon mixing, probes designed from all three classes registered high signal-to-background values in the AlphaScreen binding assay, where the interaction between probe and BACE1 was completely blocked by free parent compound. A probe from the hydantoin class was chosen for further optimization, where the final assay conditions of 50 nM BACE and 250 nM probe were used and Z′ values >0.75 were commonly observed. IC50 values determined by the AlphaScreen assay format exhibited ~10-fold greater sensitivity when compared with a fluorescence polarization–based activity assay. The assay was miniaturized to a 1536-well format for HTS, in which 525 000 compounds were screened.

The basis of the substrate specificity of the epsilon isoform of human diacylglycerol kinase is not a consequence of competing hydrolysis of ATP

The diacylglycerol kinase from E. coli transfers some of the γ-phosphate of ATP to water as well as to diacylglycerol. We also demonstrate that glycerol can act as an acceptor for the phosphate of ATP. We have compared this behavior with that of the only mammalian isoform of diacylglycerol kinase that exhibits acyl chain specificity, i.e. DGKɛ. The purpose of the study was to determine if differences in the competition between ATPase activity and lipid phosphorylation could contribute to the observed acyl chain specificity with different diacylglycerols. Neither with the highly specific substrate of DGKɛ, 1-stearoyl-2-arachidonoyl glycerol, nor with a less specific substrate, 1-stearoyl-2-linoleoyl glycerol, is there any evidence for ATP hydrolysis accompanying substrate phosphorylation. Thus, at least for this isoform of diacylglycerol kinase, water does not compete with diacylglycerol as an acceptor of the γ-phosphate of ATP. The results demonstrate that the substrate specificity of mammalian DGKɛ is not a consequence of different degrees of ATP hydrolysis in the presence of different species of diacylglycerol.

Phosphatidic acid synthesis in bacteria

Membrane phospholipid synthesis is a vital facet of bacterial physiology. Although the spectrum of phospholipid headgroup structures produced by bacteria is large, the key precursor to all of these molecules is phosphatidic acid (PtdOH). Glycerol-3-phosphate derived from the glycolysis via glycerol-phosphate synthase is the universal source for the glycerol backbone of PtdOH. There are two distinct families of enzymes responsible for the acylation of the 1-position of glycerol-3-phosphate. The PlsB acyltransferase was discovered in Escherichia coli, and homologs are present in many eukaryotes. This protein family primarily uses acyl-acyl carrier protein (ACP) endproducts of fatty acid synthesis as acyl donors, but may also use acyl-CoA derived from exogenous fatty acids. The second protein family, PlsY, is more widely distributed in bacteria and utilizes the unique acyl donor, acyl-phosphate, which is produced from acyl-ACP by the enzyme PlsX. The acylation of the 2-position is carried out by members of the PlsC protein family. All PlsCs use acyl-ACP as the acyl donor, although the PlsCs of the γ-proteobacteria also may use acyl-CoA. Phospholipid headgroups are precursors in the biosynthesis of other membrane-associated molecules and the diacylglycerol product of these reactions is converted to PtdOH by one of two distinct families of lipid kinases. The central importance of the de novo and recycling pathways to PtdOH in cell physiology suggest that these enzymes are suitable targets for the development of antibacterial therapeutics in Gram-positive pathogens. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.

Acyl-Acyl carrier protein regulates transcription of fatty acid biosynthetic genes via the FabT repressor in Streptococcus pneumoniae

Long-chain acyl-acyl carrier proteins (acyl-ACP) are established biochemical regulators of bacterial type II fatty acid synthases due to their ability to feedback-inhibit the early steps in the biosynthetic pathway. In Streptococcus pneumoniae, the expression of the fatty acid synthase (fab) genes is controlled by a helix-turn-helix transcriptional repressor called FabT. A screen of pathway intermediates identified acyl-ACP as a ligand that increased the affinity of FabT for DNA. FabT bound to a wide range of acyl-ACP chain lengths in the absence of DNA, but only the long-chain acyl-ACPs increase the affinity of FabT for DNA. FabT affinity for DNA increased with increasing acyl-ACP chain length with cis-vaccenoyl-ACP being the most effective ligand. Thus, FabT is a new ACP-interacting partner that acts as a transcriptional rheostat to fine tune the expression of the fab genes based on the demand for fatty acids.