Determination of the optimal aligned spacing between the Shine – Dalgarno sequence and the translation initiation codon of Escherichia coli m RNAs

Chen, Hongyun; Bjerknes, Matthew; Kumar, Ravindra; Jay, Ernest

doi:10.1093/nar/22.23.4953

Cited by 316 publications

(267 citation statements)

References 32 publications

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“…5). These results confirmed the importance of the SD sequence in protein synthesis (32)(33)(34). The SD sequence of the OppA mRNA was relatively distant (12 nucleotides) from the AUG compared with other mRNAs, in which the typical position of SD sequence was 7 nucleotides upstream from the AUG.…”

Section: Polyamine Stimulation Of Oppa Synthesis Is Dependent Onsupporting

confidence: 76%

Molecular Mechanism of Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein

Igarashi

Saisho

Yuguchi

et al. 1997

Journal of Biological Chemistry

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Section: Polyamine Stimulation Of Oppa Synthesis Is Dependent Onsupporting

confidence: 76%

Molecular Mechanism of Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein

Igarashi

Saisho

Yuguchi

et al. 1997

Journal of Biological Chemistry

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“…novicida IglI. A possible explanation for these differences may, however, be subtle differences in the cloning strategies that led to slightly different spacing between the Shine-Dalgarno sequence and the initiation codon (15) and possibly also iglI expression. Inflammasomes are multiprotein molecular platforms that recruit and activate inflammatory caspase, such as caspase-1, upon stimulation.…”

Section: Discussionmentioning

confidence: 99%

IglG and IglI of the Francisella Pathogenicity Island Are Important Virulence Determinants of Francisella tularensis LVS

et al. 2011

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The Gram-negative bacterium Francisella tularensis is the causative agent of tularemia, a disease intimately associated with the multiplication of the bacterium within host macrophages. This in turn requires the expression of Francisella pathogenicity island (FPI) genes, believed to encode a type VI secretion system. While the exact functions of many of the components have yet to be revealed, some have been found to contribute to the ability of Francisella to cause systemic infection in mice as well as to prevent phagolysosomal fusion and facilitate escape into the host cytosol. Upon reaching this compartment, the bacterium rapidly multiplies, inhibits activation of the inflammasome, and ultimately causes apoptosis of the host cell. In this study, we analyzed the contribution of the FPI-encoded proteins IglG, IglI, and PdpE to the aforementioned processes in F. tularensis LVS. The ⌬pdpE mutant behaved similarly to the parental strain in all investigated assays. In contrast, ⌬iglG and ⌬iglI mutants, although they were efficiently replicating in J774A.1 cells, both exhibited delayed phagosomal escape, conferred a delayed activation of the inflammasome, and exhibited reduced cytopathogenicity as well as marked attenuation in the mouse model. Thus, IglG and IglI play key roles for modulation of the intracellular host response and also for the virulence of F. tularensis.

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“…The alternate start codon, GUG, is used in the third ORF, while the remaining ORFs all have the predicted AUG start codons. All but the second and fourth ORFs are preceded by sites similar to the E. coli ribosome-binding site consensus sequence (6). Putative 70 promoter sequences (13) are present upstream of the first and sixth ORFs.…”

Section: Analysis Of Mutantsmentioning

confidence: 99%

Novel Genes Affecting Urease Activity inActinobacillus pleuropneumoniae

2001

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Characterization of a series of urease-negative transposon mutations of Actinobacillus pleuropneumoniae revealed that many of the mutants had insertions 2 to 4 kbp upstream of the urease gene cluster. A 5-kbp upstream region of DNA was sequenced and found to contain six open reading frames (ORFs) transcribed in the same orientation as the urease genes. As well, a partial ORF, apuR, 202 bp upstream of these six ORFs, is transcribed in the opposite orientation. The predicted product of this partial ORF shows homology with many members of the LysR family of transcriptional regulators. Five of the ORFs (cbiKLMQO) appear to form an operon encoding a putative nickel and cobalt periplasmic permease system. The cbiM and cbiQ genes encode proteins that have sequence similarity with known cobalt transport membrane proteins, and the cbiO gene encodes a cobalt transport ATP-binding protein homologue. The product of the cbiK gene is predicted to be the periplasmic-binding-protein component of the system, though it does not show any sequence similarity with CbiN, the cobalt-binding periplasmic protein. Escherichia coli clones containing this putative transport operon together with the urease genes of A. pleuropneumoniae were urease positive when grown in unsupplemented Luria-Bertani broth, whereas a clone containing only the minimal urease gene cluster required the addition of high concentrations of NiCl 2 for full urease activity. This result supports the hypothesis that nickel is a substrate for this permease system. The sixth ORF, utp, appears to encode an integral membrane protein which has significant sequence identity with mammalian urea transport proteins, though its function in A. pleuropneumoniae remains to be determined.The genes required for urease activity in various bacterial species typically include those encoding the structural subunits and those encoding the accessory proteins involved in insertion of two nickel ions within the catalytic site (24). In bacteria with urea-inducible gene clusters, the regulatory gene, ureR, is also present (24). Because of the requirement for nickel as a cofactor, genes such as Helicobacter pylori nixA and Alcaligenes eutrophus hoxN that encode nickel uptake systems have also been shown to affect urease activity (23,41).We recently identified the urease gene cluster of the gramnegative swine pathogen Actinobacillus pleuropneumoniae (4). The organization of the A. pleuropneumoniae gene cluster was found to be similar to that of other bacterial ureases, with the first three genes encoding the structural subunits (UreABC), and the accessory proteins (UreEFGD) encoded by four contiguous genes downstream. There was no evidence of a regulatory gene (ureR) upstream of the cluster.In order to further characterize the urease activity of A. pleuropneumoniae, a bank of transposon mutants of strain CM5 Nal r was generated and screened for urease-negative isolates. A large number of insertions in the urease-negative mutants mapped upstream of the urease gene cluster. Therefore, the 5-kbp reg...

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Determination of the optimal aligned spacing between the Shine – Dalgarno sequence and the translation initiation codon of Escherichia coli m RNAs

Cited by 316 publications

References 32 publications

Molecular Mechanism of Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein

Molecular Mechanism of Polyamine Stimulation of the Synthesis of Oligopeptide-binding Protein

IglG and IglI of the Francisella Pathogenicity Island Are Important Virulence Determinants of Francisella tularensis LVS

Novel Genes Affecting Urease Activity inActinobacillus pleuropneumoniae

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