Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli

Kirby, Janine; Trempy, Janine E.; Gottesman, Susan

doi:10.1128/jb.176.7.2068-2081.1994

Cited by 116 publications

(131 citation statements)

References 49 publications

Supporting

Mentioning

124

Contrasting

Order By: Relevance

“…Phage integration target sequences also could be scanned for nearby sRNA genes. Many phage att sites overlap tRNAs (for review, see Campbell 1992), and ssrA, encoding the tmRNA, has a 3Ј structure like a tRNA and overlaps the att site of a cryptic prophage (Kirby et al 1994). In this work, we found that the 3Ј end and terminator of #14 overlaps the previously mapped phage P2 att site (Barreiro and Haggard-Ljungquist 1992).…”

Section: Evaluation Of Selection Criteriasupporting

confidence: 50%

Identification of novel small RNAs using comparative genomics and microarrays

Wassarman¹,

Repoila²,

Rosenow³

et al. 2001

Genes Dev.

650

614

View full text Add to dashboard Cite

A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.

show abstract

Section: Evaluation Of Selection Criteriasupporting

confidence: 50%

Identification of novel small RNAs using comparative genomics and microarrays

Wassarman¹,

Repoila²,

Rosenow³

et al. 2001

Genes Dev.

650

614

View full text Add to dashboard Cite

show abstract

“…In E. coli, for instance, the growth defects of strains lacking SsrA are magnified at high temperatures or under carbon starvation (2,13), suggesting that quality assurance becomes more important when the incidence of translational errors is elevated. Other phenotypes of SsrA-defective E. coli include reduced motility (2), increased protease activity (14), defects in plating of phage immP22 and induction of temperature-sensitive lysogens of phage Mu (6,15), and increased levels of LacI, cI, and LexA repression (16).…”

mentioning

confidence: 99%

Identification of Endogenous SsrA-tagged Proteins Reveals Tagging at Positions Corresponding to Stop Codons

Roche

Sauer

2001

Journal of Biological Chemistry

112

145

View full text Add to dashboard Cite

The SsrA⅐SmpB quality control system adds a C-terminal degradation peptide (AANDENYALAA) to nascent chains on stalled ribosomes, thereby freeing the ribosome and ensuring proteolysis of the tagged protein. An SsrA mutant with the tag sequence AANDEHHHHHH was used to slow degradation and facilitate Ni 2؉ -nitrilotriacetic acid affinity purification. Display of affinitypurified Escherichia coli proteins on two-dimensional gels revealed small quantities of a diverse set of SsrA-H 6 -tagged proteins, and mass spectroscopy identified LacI repressor, cI repressor, YbeL, GalE, RbsK, and a SlyD-kan R fusion protein as members of this set. For repressor and YbeL, the SsrA-H 6 tag was added after the natural C terminus of the protein, suggesting that tagging occurred while the ribosome idled at the termination codon of these genes. Potential causes of tagging for the other proteins include interference from translation of downstream reading frames, rare codons, and gene disruption. These and previous results support a broad role for the SsrA⅐SmpB system in freeing stalled ribosomes and in directing degradation of the products of these frustrated protein synthesis reactions.

show abstract

“…coli has also a rich repertoire of elements using the tmRNA gene for their integration site (Casjens, 2003). One of such elements is a P4-related cryptic prophage CP4-57, which locates at 60 min on the K-12 chromosome (Kirby et al, 1994;Retallack et al, 1994). In strain 781-55, the fllA 44 locus was found to be flanked by the yfjJ and yfjU genes, both of which locate within CP4-57 ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli

Tominaga

Kutsukake

2007

Genes Genet. Syst.

View full text Add to dashboard Cite

Bacterial H antigens are specified by flagellin molecules, which constitute the flagellar filament. Escherichia coli 781-55 and E2987-73 are the type strains for H44 and H55 antigens, respectively. Unlike E. coli K-12, they possess two flagellin genes, fliC and fllA, on their chromosomes. However, they are monophasic, expressing exclusively the fllA genes, which specify the type antigens. In this study, the flagellin genes were cloned from these strains and their structure and expression were analyzed. It was found that the fliC genes encode apparently intact flagellin subunits but possess inefficient σ 28 -dependent promoters, which may result in these genes being silent. The chromosomal locations of the fllA genes are approximately, but not exactly, identical with that of the phase-2 flagellin gene, fljB, of diphasic Salmonella strains. However, unlike the Salmonella fljB gene, the invertible H segment and the fljA gene responsible for the control of flagellar phase variation are both absent from the fllA loci. The fllA genes are highly homologous to the E. coli fliC gene but distantly related to the Salmonella fljB gene. These results suggest a hypothesis that the fllA genes may have emerged by an intra-species lateral transfer of the fliC gene. This hypothesis is further supported by the observation that the fllA genes are flanked by several IS elements and located within cryptic prophage elements.

show abstract

Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli

Abstract: The Escherichia coli K-12 alpA gene product, when overproduced from a multicopy plasmid, leads to suppression of the capsule overproduction and UV sensitivity phenotypes of cells mutant

Cited by 116 publications

References 49 publications

Identification of novel small RNAs using comparative genomics and microarrays

Identification of novel small RNAs using comparative genomics and microarrays

Identification of Endogenous SsrA-tagged Proteins Reveals Tagging at Positions Corresponding to Stop Codons

Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli

Contact Info

Product

Resources

About