ABSTRACT: The title compound, C(24)H(30)N(2)O(4), was obtained by the reaction of (2R,6S)-4-(tert-but-oxy-carbon-yl)-6-methyl-morpho-line-2-carb-oxy-lic acid with diphenyl-methanamine in dimethyl-formamide solution. The morpholine ring is in a chair conformation. In the crystal, weak inter-molecular C-H?O hydrogen bonds link mol-ecules into chains along the b axis.
Project description:In the title compound, C(11)H(21)NO(5), the H atoms of the hydr-oxy groups are disordered over two positions, each in a 1:1 ratio. In the crystal, inter-molecular O-H?O hydrogen bonds link pairs of mol-ecules into centrosymmetric dimers. Weak inter-molecular O-H?O inter-actions further link these dimers into chains extended in the  direction.
Project description:The title compound, C(15)H(22)NO(4)S(+)·Cl(-), is a hydrolysis product of lesatropane [(1R,3S,5R,6S)-6-acet-oxy-3-tosyl-oxytropane] hydro-chloride, a potential anti-glaucoma agent. As in lesatropane, the piperidine and pyrrolidine rings in the title compound adopt chair and envelope conformations, respectively. There are two mol-ecules in the unit cell with similar conformations. The crystal structure is stabilized by inter-molecular O-H?Cl and N-H?Cl hydrogen bonds.
Project description:6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.
Project description:6S RNA is a small RNA regulator of RNA polymerase (RNAP) that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNAP resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity, including (i) addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; (ii) the nature of the 6S RNA-RNAP interaction through examination of variant proteins and mutant RNAs, cross-linking approaches, and ultimately a cryo-electron microscopic structure; (iii) the physiological consequences of 6S RNA function through identification of the 6S RNA regulon and promoter features that determine 6S RNA sensitivity; and (iv) the mechanism and cellular impact of 6S RNA-directed synthesis of product RNAs (i.e., pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action, and how it is regulated; yet much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.
Project description:In the ionic title compound, K(+)·C(5)H(8)NOS(2) (-)·H(2)O, the morpholine ring of the morpholine-4-carbodithio-ate anion has a chair conformation. The potassium cation is coordinated by four S and four O atoms in a bipyramidal reversed geometry. In the crystal, the three components are linked, generating infinite two-dimensional networks that lie parallel to the bc plane. These layers are linked via O-H?S hydrogen bonds, forming a three-dimensional structure.
Project description:The mol-ecular structure of the title compound, C8H11N3O, is nearly planar despite the chair conformation of the morpholine moiety. In the crystal, the mol-ecules form sheets parallel to the b axis, which are supported by non-classical hydrogen-bonding inter-actions between C-H functionalities and the O atom of morpholine and the 4-N atom of pyrazine, respectively. The title compound crystallizes in the monoclinic space group P21/c with four mol-ecules in the unit cell.
Project description:The global transcriptional regulator 6S RNA is abundant in a broad range of bacteria. The RNA competes with DNA promoters for binding to the housekeeping RNA polymerase (RNAP) holoenzyme. When bound to RNAP, 6S RNA serves as a transcription template for RNAP in an RNA-dependent RNA polymerization reaction. The resulting short RNA transcripts (so-called product RNAs = pRNAs) can induce a stable structural rearrangement of 6S RNA when reaching a certain length. This rearrangement leads to the release of RNAP and thus the recovery of transcription at DNA promoters. While most bacteria express a single 6S RNA, some harbor a second 6S RNA homolog (termed 6S-2 RNA in Bacillus subtilis). Bacillus subtilis 6S-2 RNA was recently shown to exhibit essentially all hallmark features of a bona fide 6S RNA in vitro, but evidence for the synthesis of 6S-2 RNA-derived pRNAs in vivo has been lacking so far. This raised the question of whether the block of RNAP by 6S-2 RNA might be lifted by a mechanism other than pRNA synthesis. However, here we demonstrate that 6S-2 RNA is able to serve as a template for pRNA synthesis in vivo. We verify this finding by using three independent approaches including a novel primer extension assay. Thus, we demonstrate the first example of an organism that expresses two distinct 6S RNAs that both exhibit all mechanistic features defined for this type of regulatory RNA.
Project description:In Escherichia coli, the sigma factor ?70 directs RNA polymerase to transcribe growth-related genes, while ?38 directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to ?70, and the non-coding 6S RNA which binds to the RNA polymerase-?70 holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show that Rsd and 6S RNA facilitate ?38 activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.
Project description:The title compound, C(11)H(11)NO(3), was synthesized by the reaction of maleic andydride and phenyl-methanamine. The mol-ecular conformation is stabilized by by an intra-molecular O-H?O hydrogen bond. In the crystal, mol-ecules are linked by inter-molecular N-H?O and C-H?O hydrogen bonds, forming a chain along the b axis.