The evolving story of the omega subunit of bacterial RNA polymerase

Omega (omega) is the smallest subunit of bacterial RNA polymerase (RNAP). Although identified early in RNAP research, its function remained ambiguous and shrouded by controversy for a considerable period. It has subsequently been shown that the protein has a structural role in maintenance of the conformation of the largest subunit, beta', and recruitment of beta' to the enzyme assembly. Conservation of this function across all forms of life indicates the importance of its role. Several recent observations have suggested additional functional roles for this protein and have settled some long-standing controversies surrounding it. In this context, revisiting the omega subunit story is especially interesting; here, we review the progress of omega research since its discovery and highlight the importance of these recent observations.     

Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of mycobacterial glycopeptidolipids

Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C(26)-C(34) fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs.     

Paracrine effects of a uterine agglutinin are mediated via the sialic acids present in the rat uterine endometrium

A 32 kDa estrogen-induced, sialic acid-specific agglutinin (P-SAS) was isolated from rat endometrium in its proestrus stage [1]. To investigate the functional importance of P-SAS in the uterine milieu, specific binding assays were carried out with ¹²⁵I-labeled P-SAS and different cellular components of the uterus (epithelial, stromal and myometrial cells), that were isolated from different stages of the estrus cycle. The results indicate that although the protein is secreted from the epithelial cells in the estrogenic phase, it binds specifically to the stromal cells, especially to those isolated from the diestrus stage of the estrus cycle. The specific binding, however, is seen to decrease with the progression of pregnancy. Scatchard analysis performed with varying amounts of ¹²⁵I-P-SAS in the presence of excess cold P-SAS revealed that the binding occurs with a Ka = 1.69 × 10⁸ M^-1. As P-SAS binds specifically to sialic acids on the stromal cell surface, further characterization of the sialic acid molecule to which P-SAS binds was carried out by gas liquid chromatography (GLC). The studies revealed that P-SAS preferentially binds to N-glycolylneuraminic acid, which is attached to the penultimate sugar of the stromal cell surface glycoprotein chain via 2,6 linkage. As P-SAS is further known to be mitogenic [2], the effect of P-SAS on cultured stromal cells was studied in vitro. The growth regulatory assays revealed that P-SAS induced ³H-thymidine uptake by stromal cells in culture. Thus, from the above observations, paracrine effects of P-SAS on the stromal cells and on the subsequent growth and development of the uterus can be assumed.     

A highly conserved arginine in gp120 governs HIV-1 binding to both syndecans and CCR5 via sulfated motifs

HIV-1 has maximized its utilization of syndecans. It uses them as in cis receptors to infect macrophages and as in trans receptors to infect T-lymphocytes. In this study, we investigated at a molecular level the mechanisms that control HIV-1-syndecan interactions. We found that a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans. We found that an amine group on the side chain of this residue is necessary for syndecan utilization by HIV-1. Furthermore, we showed that HIV-1 binds syndecans via a 6-O sulfation, demonstrating that this binding is not the result of random interactions between basic residues and negative charges, but the result of specific contacts between gp120 and a well defined sulfation in syndecans. Surprisingly, we found that Arg-298, which mediates HIV-1 binding to syndecans, also mediates HIV-1 binding to CCR5. We postulated that HIV-1 recognizes similar motifs on syndecans and CCR5. Supporting this hypothesis, we obtained several lines of evidence that suggest that the 6-O sulfation recognized by HIV-1 on syndecans mimics the sulfated tyrosines recognized by HIV-1 in the N terminus of CCR5. Our finding that CCR5 and syndecans are exploited by HIV-1 via a single determinant echoes the mechanisms by which chemokines utilize these two disparate receptors and suggests that the gp120/chemokine mimicry may represent a common strategy in microbial pathogenesis.     

Spectroscopic studies on the denaturation of papain solubilized and Triton X-100-solubilized glucoamylase from rabbit small intestine

Intestinal brush border proteins consist of an enzymatically active hydrophilic moiety attached to a hydrophobic tail. Papain dissociates the hydrophilic part by cleaving off the hydrophobic tail, whereas the detergentTriton X-100 solubilizes the whole molecule. Denaturation by 8 M urea or 4 M guanidinium chloride does not alter the structure of the papain-solubilized enzyme. An appreciable alteration of the structure of detergent-solubilized enzyme was observed on denaturation. The difference spectra of Triton X-100 (1%)—solubilized enzyme and its urea denatured form shifts and intensifies, with increase in the concentration of the denaturant with an isobestic point at 252 nm. A new band at 280 nm also appears at 4 M urea concentration. Papain-solubilized glucoamylase has an ∞ -helical conformation in solution unlike the detergentsolubilized fraction. An elongated structure for the papain solubilized enzyme is inferred from the urea denaturation studies and from molecular weight determinations.     

Nuclear magnetic resonance studies on the role of intrinsic metals in Escherichia coli RNA polymerase. Effect of DNA template on the nucleotide-enzyme interaction

Nuclear magnetic resonance studies were performed to investigate the effect of DNA template on the interaction of initiating nucleotide ATP with Escherichia coli RNA polymerase (RPase) in which one of the two intrinsic Zn ions was substituted with a Co(II) (Co-Zn RPase) or Mn(II) (Mn-Zn RPase) ion. This intrinsic metal ion is located at the initiation site in the beta subunit of RPase. The paramagnetic effects of Co-Zn and Mn-Zn RPases on the relaxation rates of 1H- and 31P-nuclei of ATP were used to determine the distances from the intrinsic metal to various atoms of ATP bound at the initiation sites in the presence of DNA. The distances from the metal to H2, H8, H1', alpha-P, beta-P, and gamma-P atoms were estimated to be 6.7 +/- 0.9, 4.1 +/- 0.6, 6.0 +/- 1.2, 7.5 +/- 0.8, 9.4 +/- 1.0, and 9.8 +/- 1.0 A, respectively. These distances were compared with those measured in the absence of DNA (Chatterji, D., and Wu, F. Y.-H. (1982) Biochemistry 21, 4657). In both the presence and absence of DNA, the close proximity between the intrinsic metal and the H8 atom strongly indicates that the metal is coordinated directly to the base moiety of ATP. Such a coordination may provide a structural basis for the selection of a purine nucleotide during the initiation process. The presence of DNA causes the H2 atom to move away (greater than 2 A) from the intrinsic metal, whereas all three phosphorus atoms shift closer (greater than 3 A) toward the metal. The possible mechanistic implications of the conformational alteration of ATP at the initiation site induced by the DNA template is discussed.