Antimicrobial lipopeptide tridecaptin A1 selectively binds to Gram-negative lipid II

Tridecaptin A₁ (TriA₁) is a nonribosomal lipopeptide with selective antimicrobial activity against Gram-negative bacteria. Here we show that TriA₁ exerts its bactericidal effect by binding to the bacterial cell-wall precursor lipid II on the inner membrane, disrupting the proton motive force. Biochemical and biophysical assays show that binding to the Gram-negative variant of lipid II is required for membrane disruption and that only the proton gradient is dispersed. The NMR solution structure of TriA₁ in dodecylphosphocholine micelles with lipid II has been determined, and molecular modeling was used to provide a structural model of the TriA₁–lipid II complex. These results suggest that TriA₁ kills Gram-negative bacteria by a mechanism of action using a lipid-II–binding motif.Recently, a lot of media coverage has been focused on the problem of antimicrobial resistance. A report commissioned by the UK government predicts that by 2050 antimicrobial resistance will have caused 300 million premature deaths and cost the global economy over $100 trillion (1). Even more worrying is the lack of new classes of antibiotics active against Gram-negative bacteria. In the past 50 y, only a few structurally and mechanistically distinct classes of antibiotics have been clinically approved to treat systemic infections (including fidaxomicin, bedaquiline, linezolid, and daptomycin), yet none of these are active against Gram-negative bacteria (2, 3). Two new classes of Gram-negative targeting antibiotics in the clinical pipeline are POL7080 and brilacidin (4, 5). Both of these compounds are modeled on antimicrobial peptides, which are becoming increasingly important in the fight against antibiotic resistance (6). Bacteria produce a wealth of antimicrobial peptides, both ribosomally, including the lantibiotics (7, 8), and nonribosomally, including lipopeptides (9). In particular, lipopeptides are a rich source of antimicrobial compounds, and several examples with activity against Gram-positive (10, 11) and/or Gram-negative bacteria (12) have been recently characterized.Tridecaptin A₁ (TriA₁) is a member of the tridecaptin family, a group of nonribosomal lipopeptides produced by Bacillus and Paenibacillus species (Fig. 1) (13–15). This acylated tridecapeptide displays strong and selective antimicrobial activity against Gram-negative bacteria, including multidrug-resistant strains of Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli (16). TriA₁ analogs have low cytotoxicity and have been shown to treat K. pneumoniae infections in mice (16, 17). Therefore, we believe that tridecaptin A₁ could be an excellent antibiotic candidate. However, before our investigations little was known about how TriA₁ exerts its selective bactericidal effect against Gram-negative bacteria. A previous structure–activity relationship study by our group suggested that TriA₁, akin to many other lipopeptides, is a membrane-targeting agent. We found that removal of the N-terminal lipid tail abolishes antimicrobial activity; however, the chiral lipid tail could be replaced with an octanoyl chain to give Oct-TriA₁ (Fig. 1), which retains full activity (16). We therefore sought to identify the precise mode and mechanism of action by which TriA₁ kills Gram-negative bacteria.Open in a separate windowFig. 1.Structures of the tridecaptin analogs TriA₁ and Oct-TriA₁.     

UDP-glucuronosyltransferase1A1 directly binds to albumin.

UDP-glucuronosyltransferase1A1 (UGT1A1) catalyses glucuronidation of bilirubin (the final break down product of heme which is produced mainly in the spleen and liver) and is located on the lumen of the endoplasmic reticulum (ER). To identify partner UGTs that form hetero-oligomers with UGT1A1, or other proteins that bind directly to UGT1A1, yeast two-hybrid screening was performed using UGT1A1 as bait. From these studies, cDNA clones specific for human serum albumin (HSA) were unexpectedly isolated. The direct interaction between UGT1A1 and albumin was confirmed in vitro by a pull-down assay. FITC-albumin uptake into HepG2 and Huh7 cells was observed only when bilirubin are present in the culture medium. Furthermore, the endocytosis inhibitor phenylarsine oxide (PAO) prevented albumin uptake into the cells, suggesting that the albumin/bilirubin complex is internalized through receptor-mediated endocytosis. From these studies, it would appear that production of large amounts of toxic bilirubin might use different uptake pathways for entry into hepatocytes.     

A human 200-kDa protein binds selectively to DNA fragments containing G.T mismatches.

G.T mispairs, the sole mismatch type that can arise in "resting" mammalian DNA (through spontaneous hydrolytic deamination of 5-methylcytosine), are corrected in vivo with high efficiency and mostly to a G.C. We identified a protein factor, present in HeLa cell extracts, that binds selectively to DNA substrates containing this mismatch. The partially purified protein was shown by gel-filtration chromatography and UV cross-linking experiments to have an apparent molecular mass of 200 kDa. Its binding to G.T mispairs was not influenced by sequences flanking the mismatch, but methylation of guanines either within the mismatch itself or in its immediate vicinity abolished the formation of the protein-DNA complex. The protein appears to lack both endo- and exonuclease activities and requires neither magnesium nor zinc nor ATP for binding. We discuss the possible role of this protein in a repair pathway, which helps mammalian cells counter the mutagenic effect of the hydrolytic deamination of 5-methylcytosine.     

Platinum binds selectively to phosphorothioate groups in mono- and polynucleotides: a general method for heavy metal staining of specific nucleotides.

Platinum binding to nucleoside phosphorothioates has been examined to determine their suitability as heavy metal labeling sites for the potential electron microscopic sequencing of nucleic acids. The complex platinum terpyridine nitrate forms a 1:1 adduct with either adenosine or uridine monophosphorothioate. Spectroscopic evidence strongly indicates the presence of platinum-sulfur bonds. Both platinum terpyridine nitrate and chloroterpyridineplatinum(II) bind to poly(sA-U), a polymer prepared from adenosine 5'-O-(1-thiotriphosphate) and UTP. Binding to the sulfur atoms of the phosphorothioate groups is quantitative, as shown by double label experiments using [35S]poly(sA-U) and [3H]chloroterpyridine-platinum(II). Similar experiments with [14C]poly(A-U) indicated no platinum binding. No evidence of nicking or loss of sulfur from poly(sA-U) could be detected after platinum binding. The phosphorothioate group is a strong, highly selective binding site for platinum in polynucleotides. Previous studies have demonstrated quantitative enzymatic incorporation of phosphorothioate groups into a polynucleotide adjacent to a specific base [Matzura, H. & Eckstein, F. (1968) Eur. J. Biochem. 3, 448-452]. The use of heavy metal-labeled phosphorothioate groups for the sequencing of nucleic acids by electron microscopy therefore appears feasible.     

Ecto-F_1-ATPase: A moonlighting protein complex and an unexpected apoA-I receptor

Mitochondrial ATP synthase has been recently detected at the surface of different cell types, where it is a high affinity receptor for apoA-I, the major protein component in high density lipoproteins (HDL). Cell surface ATP synthase (namely ecto-F1-ATPase) expression is related to different biological effects, such as regulation of HDL uptake by hepatocytes, endothelial cell proliferation or antitumor activity of Vγ9/Vδ2 T lymphocytes. This paper reviews the recently discovered functions and regulations of ...     

Thrombopoietin induces an SH2-containing protein, CIS1, which binds to Mpl: involvement of the ubiquitin proteosome pathway.

The interaction of thrombopoietin (TPO) with its receptor, Mpl, triggers growth and differentiation of megakaryocytes and their progenitors. The Mpl cytoplasmic domain controls this process through src homology 2 (SH2)-containing target molecules and their receptor docking sites. A novel cytokine inducible SH2-containing protein, CIS1, has been isolated. CIS1 is induced by interleukin-2 (IL-2), IL-3, GM-CSF, and erythropoietin (EPO), but not by IL-6, granulocyte colony-stimulating factor (G-CSF), or stem cell factor. To investigate the functional domains of Mpl for induction of CIS1, we examined FDCP-2 cell lines expressing seven carboxyl truncations of the human Mpl cytoplasmic domain. We found that the box1 and box2 regions of Mpl were necessary for induction of CIS1 after TPO stimulation. CIS1 was degraded very quickly and was found to be involved in the ubiquitin-proteosome pathway. A 4-hour depletion of TPO almost completely eliminated CIS1 protein; within 1 hour after TPO stimulation, CIS1 protein reappeared as 37- and 32-kDa proteins in the wild type Mpl-expressing FDCP-2 cells. Further, CIS1 was stably associated with tyrosine-phosphorylated Mpl. The SH2 domains of CIS1, constructed as glutathione S-transferase fusion protein, bound to activated Mpl in vitro. These results suggest that CIS1 may be an important signaling component downstream of Mpl and may regulate the proliferation and differentiation of hematopoietic cells.     

A monoclonal anti-double-stranded DNA autoantibody binds to a 94-kDa cell-surface protein on various cell types via nucleosomes or a DNA-histone complex.

A crude supernatant of hybridoma secreting a monoclonal anti-double-stranded (ds)DNA antibody (PME77 mAb), used to stain fibroblasts (CVI cells) in immunofluorescence, gives a punctuated staining of variable intensity. We had suggested that anti-DNA antibodies bind to cell-surface protein(s) of several cells. When the mAb of this crude supernatant was purified on a dsDNA-cellulose column and a histone-Trisacryl column, the mAb no longer bound to the cell surface. Only when dsDNA plus purified histones was added to the purified antibody did the immune complex strongly and uniformly stain again the cell surface of CVI cells. No significant staining was observed if either DNA or histones were omitted. A signal 94-kDa protein from membrane fractions of CVI, Raji, and RINm cell lines was visualized in immunoblots when mAb-DNA-histone complexes were applied to the nitrocellulose strips. No polypeptide was seen if one component was omitted. This 94-kDa protein behaved like a plasma membrane protein since it required the use of detergent to be solubilized and was quantitatively recovered in the Triton X-114 detergent-rich phase. Moreover, a brief treatment of living cells with trypsin cleared off this protein. Purified nucleosomes could be substituted to DNA-histone complexes, giving rise to identical results. Finally, purified polyclonal anti-DNA antibodies from sera of systemic lupus erythematosus patients labeled a 94-kDa protein provided that DNA-histone complexes were added. Anti-DNA autoantibodies could be pathogenic when they are bound to nucleosomes.     

Quantitative determination that one of two potential RNA-binding domains of the A protein component of the U1 small nuclear ribonucleoprotein complex binds with high affinity to stem-loop II of U1 RNA.

Many RNA-associated proteins contain a ribonucleoprotein (RNP) consensus octamer encompassed by a conserved 80 amino acid sequence, which we have termed an RNA recognition motif (RRM). RRM family members contain either one (class I) or multiple (class II) copies of this motif. We report here that a class II component of the U1 small nuclear RNP (snRNP), the A protein of U1 snRNP (U1snRNP-A), contains two RRMs (RRM1 and -2), yet has only one binding domain (RRM1) that interacts specifically with stem-loop II of U1 RNA. Quantitative analysis of binding affinities of fragments of U1snRNP-A demonstrated that an 86-amino acid polypeptide was competent to bind to U1 RNA with an affinity comparable to that of the full-length protein (Kd approximately 80 nM). The carboxyl-terminal RRM2 of U1snRNP-A did not bind to U1 RNA and may recognize an unidentified heterologous RNA. We propose that class II proteins may function as bridges between RNA components of RNP complexes such as the spliceosome.     

The E1 glycoprotein of an avian coronavirus is targeted to the cis Golgi complex.

It was previously reported that the E1 protein of an avian coronavirus was targeted to the juxtanuclear region in COS cells expressing the protein from cloned cDNA, suggesting that the protein contains information for targeting to the Golgi complex. The first of three membrane-spanning domains was required for intracellular targeting, because a mutant E1 (delta m1,2) lacking this domain was delivered to the plasma membrane. We have used immunoelectron microscopy to localize the wild-type E1 protein within Golgi elements of COS cells and AtT-20 cells expressing these proteins from recombinant vaccinia vectors. By immunoperoxidase and immunogold labeling, the wild-type E1 protein was localized to one or two cisternae located on one side of the Golgi stack that could be identified as the cis side in AtT-20 cells. In contrast, the mutant E1 protein was detected in all cisternae across the stack as well as at the plasma membrane. When the E1 proteins were immunoprecipitated and subjected to digestion with endoglycosidase H, the majority of the wild-type E1 glycoprotein was endoglycosidase H sensitive, whereas the majority of the mutant E1 was processed to an endoglycosidase H-resistant, polylactosaminoglycan-containing form. The findings indicate that the wild-type E1 protein is specifically targeted to cis Golgi cisternae and are consistent with the assumption that the first membrane-spanning domain is required for targeting to the cis Golgi.     

Human plasma kallikrein and C1 inhibitor form a complex possessing an epitope that is not detectable on the parent molecules: demonstration using a monoclonal antibody.

The inactivation of human plasma kallikrein (EC 3.4.21.8) by the inhibitor of activated complement component 1 (C1 inhibitor) induces the formation of a 1:1 stoichiometric kallikrein-C1 inhibitor complex and a proteolytically modified form of C1 inhibitor. We have produced a monoclonal antibody that recognizes the kallikrein-C1 inhibitor complex as well as modified C1 inhibitor but fails to react with virgin C1 inhibitor or native plasma kallikrein. This observation constitutes an unequivocal demonstration that the reaction between plasma kallikrein and C1 inhibitor leads to the emergence of an epitope that is undetectable on the parent enzyme and inhibitor molecules.     

Selenol binds to iron in nitrogenase iron-molybdenum cofactor: an extended x-ray absorption fine structure study.

The biological N2-fixation reaction is catalyzedby the enzyme nitrogenase. The metal cluster active site of this enzyme, theiron-molybdenum cofactor (FeMoco), can be studied either while bound within theMoFe protein component of nitrogenase or after it has been extracted intoN-methylformamide. The two species are similar but not identical. For example,the addition of thiophenol or selenophenol to isolated FeMoco causes its ratherbroad S = 3/2 electron paramagnetic resonance signal to sharpen and more closelyapproach the signal exhibited by protein-bound FeMoco. The nature of thisthiol/selenol binding site has been investigated by using Se-K edge extendedx-ray absorption fine structure (EXAFS) to study selenophenol ligated to FeMoco,and the results are reported here. EXAFS data analysis at the ligand Se-K edgewas performed with a set of software, GNXAS, that provides for directcalculation of the theoretical EXAFS signals and least-squares fits to theexperimental data. Data analysis results show definitively that the selenol (andby inference thiol) binds to Fe at a distance of 2.4 A. In contrast,unacceptable fits are obtained with either Mo or S as the liganded atom (insteadof Fe). These results provide quantitative details about an exchangeablethiol/selenol binding site on FeMoco in its isolated, solution state andestablish an Fe atom as the site of this reaction. Furthermore, the utility ofligand-based EXAFS as a probe of coordination in polynuclear metal clusters isdemonstrated.     

A biologic function for an "orphan" messenger: D-myo-inositol 3,4,5,6-tetrakisphosphate selectively blocks epithelial calcium-activated chloride channels.

Inositol phosphates are a family of water-soluble intracellular signaling molecules derived from membrane inositol phospholipids. They undergo a variety of complex interconversion pathways, and their levels are dynamically regulated within the cytosol in response to a variety of agonists. Relatively little is known about the biological function of most members of this family, with the exception of inositol 1,4,5-trisphosphate. Specifically, the biological functions of inositol tetrakisphosphates are largely obscure. In this paper, we report that D-myo-inositol 3,4,5,6-tetrakisphosphate (D-Ins(3,4,5,6)P4) has a direct biphasic (activation/inhibition) effect on an epithelial Ca(2+)-activated chloride channel. The effect of D-Ins(3,4,5,6)P4 is not mimicked by other inositol tetrakisphosphate isomers, is dependent on the prevailing calcium concentration, and is influenced when channels are phosphorylated by calmodulin kinase II. The predominant effect of D-Ins(3,4,5,6)P4 on phosphorylated channels is inhibitory at levels of intracellular calcium observed in stimulated cells. Our findings indicate the biological function of a molecule hitherto considered as an "orphan" messenger. They suggest that the molecular target for D-Ins(3,4,5,6)P4 is a plasma membrane Ca(2+)-activated chloride channel. Regulation of this channel by D-Ins(3,4,5,6)P4 and Ca2+ may have therapeutic implications for the disease states of both diabetic nephropathy and cystic fibrosis.     

A heterotrimeric G protein complex couples the muscarinic m1 receptor to phospholipase C-beta.

We addressed the question as to which subtypes of G protein subunits mediate the activation of phospholipase C-beta by the muscarinic m1 receptor. We used the rat basophilic leukemia cell line RBL-2H3-hm1 stably transfected with the human muscarinic m1 receptor cDNA. We microinjected antisense oligonucleotides into the nuclei of the cells to inhibit selectively the expression of G protein subunits; 48 hr later muscarinic receptors were activated by carbachol, and the increase in free cytosolic calcium concentration ([Ca2+]i) was measured. Antisense oligonucleotides directed against the mRNA coding for alpha(q) and alpha11 subunits both suppressed the carbachol-induced increase in [Ca2+]i. In cells injected with antisense oligonucleotides directed against alpha(o1) and alpha14 subunits, the carbachol effect was unchanged. A corresponding reduction of Galpha(q), and Galpha11 proteins by 70-80% compared to uninjected cells was immunochemically detected 2 days after injection of a mixture of alpha(q) and alpha11 antisense oligonucleotides. Expression of Galpha(q) and Galpha11 completely recovered after 4 days. Cells injected with antisense oligonucleotides directed against the mRNAs encoding for beta1, beta4, and gamma4 subunits showed a suppression of the carbachol-induced increase in [Ca2+]i compared to uninjected cells measured at the same time from the same coverslip, whereas in cells injected with antisense oligonucleotides directed against the beta2, beta3, gamma1, gamma2, gamma3, gamma5, and gamma7 subunits, no suppression of carbachol effect was observed. In summary, the results from RBL-2H3-hm1 cells indicate that the m1 receptor utilizes a G protein complex composed of the subunits alpha(q), alpha11, beta1, beta4, and gamma4 to activate phospholipase C.