scholarly journals Genetic Interaction Screens with Ordered Overexpression and Deletion Clone Sets Implicate the Escherichia coli GTPase YjeQ in Late Ribosome Biogenesis

2008 ◽  
Vol 190 (7) ◽  
pp. 2537-2545 ◽  
Author(s):  
Tracey L. Campbell ◽  
Eric D. Brown
Keyword(s):  
Escherichia Coli ◽  
Ribosome Biogenesis ◽  
Slow Growth ◽  
Genetic Interaction ◽  
Initiation Factor ◽  
Genetic Screens ◽  
Genomic Libraries ◽  
Initiation Factor 2 ◽  
Bona Fide

ABSTRACT The Escherichia coli protein YjeQ is a circularly permuted GTPase that is broadly conserved in bacteria. An emerging body of evidence, including cofractionation and in vitro binding to the ribosome, altered polysome profiles after YjeQ depletion, and stimulation of GTPase activity by ribosomes, suggests that YjeQ is involved in ribosome function. The growth of strains lacking YjeQ in culture is severely compromised. Here, we probed the cellular function of YjeQ with genetic screens of ordered E. coli genomic libraries for suppressors and enhancers of the slow-growth phenotype of a ΔyjeQ strain. Screening for suppressors using an ordered library of 374 clones overexpressing essential genes and genes associated with ribosome function revealed that two GTPases, Era and initiation factor 2, ameliorated the growth and polysome defects of the ΔyjeQ strain. In addition, seven bona fide enhancers of slow growth were identified (Δtgt, ΔksgA, ΔssrA, ΔrimM, ΔrluD, ΔtrmE/mnmE, and ΔtrmU/mnmA) among 39 deletions (in genes associated with ribosome function) that we constructed in the ΔyjeQ genetic background. Taken in context, our work is most consistent with the hypothesis that YjeQ has a role in late 30S subunit biogenesis.

scholarly journals Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly

2015 ◽  
Vol 112 (34) ◽  
pp. E4707-E4716 ◽  
Author(s):  
Taiga Arai ◽  
Kensuke Ishiguro ◽  
Satoshi Kimura ◽  
Yuriko Sakaguchi ◽  
Takeo Suzuki ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosome Biogenesis ◽  
Slow Growth ◽  
Genetic Interaction ◽  
Ribosomal Subunit ◽  
23S Rrna ◽  
Subunit Assembly ◽  
Interdomain Interactions ◽  
Multiple Assembly

Ribosome biogenesis requires multiple assembly factors. In Escherichia coli, deletion of RlmE, the methyltransferase responsible for the 2′-O-methyluridine modification at position 2552 (Um2552) in helix 92 of the 23S rRNA, results in slow growth and accumulation of the 45S particle. We demonstrate that the 45S particle that accumulates in ΔrlmE is a genuine precursor that can be assembled into the 50S subunit. Indeed, 50S formation from the 45S precursor could be promoted by RlmE-mediated Um2552 formation in vitro. Ribosomal protein L36 (encoded by rpmJ) was completely absent from the 45S precursor in ΔrlmE, and we observed a strong genetic interaction between rlmE and rpmJ. Structural probing of 23S rRNA and high-salt stripping of 45S components revealed that RlmE-mediated methylation promotes interdomain interactions via the association between helices 92 and 71, stabilized by the single 2′-O-methylation of Um2552, in concert with the incorporation of L36, triggering late steps of 50S subunit assembly.

scholarly journals σE Regulates and Is Regulated by a Small RNA in Escherichia coli

2007 ◽  
Vol 189 (11) ◽  
pp. 4243-4256 ◽  
Author(s):  
Karl M. Thompson ◽  
Virgil A. Rhodius ◽  
Susan Gottesman
Keyword(s):  
Escherichia Coli ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Response Regulator ◽  
Heterologous Promoter ◽  
Genomic Libraries ◽  
Multicopy Suppressors ◽  
Intergenic Regions ◽  
Transposon Mutants

ABSTRACT RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in Escherichia coli. Fusions of the rybB promoter to lacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of rybB expression. A number of plasmids, including some carrying rybB, negatively regulated the fusion. An insertion in the rep helicase and one upstream of dnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained mipA, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the rybB promoter might be dependent on σE. The sequence upstream of the +1 of rybB contains a consensus σE promoter. The activity of rybB-lacZ was increased in cells lacking the RseA anti-sigma factor and when σE was overproduced from a heterologous promoter. The activity of rybB-lacZ and the detection of RybB were totally abolished in an rpoE-null strain. In vitro, σE efficiently transcribes from this promoter. Both a rybB mutation and an hfq mutation significantly increased expression of both rybB-lacZ and rpoE-lacZ fusions, consistent with negative regulation of the σE response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate σE-dependent promoters in an RseA-independent fashion.

scholarly journals MazG, a Nucleoside Triphosphate Pyrophosphohydrolase, Interacts with Era, an Essential GTPase in Escherichia coli

2002 ◽  
Vol 184 (19) ◽  
pp. 5323-5329 ◽  
Author(s):  
Junjie Zhang ◽  
Masayori Inouye
Keyword(s):  
Escherichia Coli ◽  
Direct Interaction ◽  
Kanamycin Resistance ◽  
Nucleoside Triphosphate ◽  
Cellular Functions ◽  
Genomic Libraries ◽  
E Coli ◽  
Yeast Two Hybrid System ◽  
Nucleoside Triphosphate Pyrophosphohydrolase

ABSTRACT Era is an essential GTPase in Escherichia coli, and Era has been implicated in a number of cellular functions. Homologues of Era have been identified in various bacteria and some eukaryotes. Using the era gene as bait in the yeast two-hybrid system to screen E. coli genomic libraries, we discovered that Era interacts with MazG, a protein of unknown function which is highly conserved among bacteria. The direct interaction between Era and MazG was also confirmed in vitro, being stronger in the presence of GDP than in the presence of GTPγS. MazG was characterized as a nucleoside triphosphate pyrophosphohydrolase which can hydrolyze all eight of the canonical ribo- and deoxynucleoside triphosphates to their respective monophosphates and PPi, with a preference for deoxynucleotides. A mazG deletion strain of E. coli was constructed by replacing the mazG gene with a kanamycin resistance gene. Unlike mutT, a gene for another conserved nucleotide triphosphate pyrophosphohydrolase that functions as a mutator gene, the mazG deletion did not result in a mutator phenotype in E. coli.

scholarly journals Phosphorylation of Eukaryotic Initiation Factor 2 by Heme-Regulated Inhibitor Kinase-Related Protein Kinases in Schizosaccharomyces pombe Is Important for Resistance to Environmental Stresses

2002 ◽  
Vol 22 (20) ◽  
pp. 7134-7146 ◽  
Author(s):  
Ke Zhan ◽  
Krishna M. Vattem ◽  
Bettina N. Bauer ◽  
Thomas E. Dever ◽  
Jane-Jane Chen ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Schizosaccharomyces Pombe ◽  
Environmental Stresses ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Α Subunit ◽  
Eukaryotic Initiation Factor 2 ◽  
Initiation Factor 2 ◽  
Eif2α Kinase

ABSTRACT Protein synthesis is regulated by the phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α) in response to different environmental stresses. One member of the eIF2α kinase family, heme-regulated inhibitor kinase (HRI), is activated under heme-deficient conditions and blocks protein synthesis, principally globin, in mammalian erythroid cells. We identified two HRI-related kinases from Schizosaccharomyces pombe which have full-length homology with mammalian HRI. The two HRI-related kinases, named Hri1p and Hri2p, exhibit autokinase and kinase activity specific for Ser-51 of eIF2α, and both activities were inhibited in vitro by hemin, as previously described for mammalian HRI. Overexpression of Hri1p, Hri2p, or the human eIF2α kinase, double-stranded-RNA-dependent protein kinase (PKR), impeded growth of S. pombe due to elevated phosphorylation of eIF2α. Cells from strains with deletions of the hri1+ and hri2+ genes, individually or in combination, exhibited a reduced growth rate when exposed to heat shock or to arsenic compounds. Measurements of in vivo phosphorylation of eIF2α suggest that Hri1p and Hri2p differentially phosphorylate eIF2α in response to these stress conditions. These results demonstrate that HRI-related enzymes are not unique to vertebrates and suggest that these eIF2α kinases are important participants in diverse stress response pathways in some lower eukaryotes.

scholarly journals Alpha Interferon and Not Gamma Interferon Inhibits Salmonid Alphavirus Subtype 3 Replication In Vitro

2010 ◽  
Vol 84 (17) ◽  
pp. 8903-8912 ◽  
Author(s):  
Cheng Xu ◽  
Tz-Chun Guo ◽  
Stephen Mutoloki ◽  
Øyvind Haugland ◽  
Inderjit S. Marjara ◽  
...  
Keyword(s):  
Inhibitory Effect ◽  
Cellular Protein ◽  
Alpha Interferon ◽  
Initiation Factor ◽  
Antiviral State ◽  
Antiviral Responses ◽  
Initiation Factor 2 ◽  
A Minor

ABSTRACT Salmonid alphavirus (SAV) is an emerging virus in salmonid aquaculture, with SAV-3 being the only subtype found in Norway. Until now, there has been little focus on the alpha interferon (IFN-α)-induced antiviral responses during virus infection in vivo or in vitro in fish. The possible involvement of IFN-γ in the response to SAV-3 is also not known. In this study, the two IFNs were cloned and expressed as recombinant proteins (recombinant IFN-α [rIFN-α] and rIFN-γ) and used for in vitro studies. SAV-3 infection in a permissive salmon cell line (TO cells) results in IFN-α and IFN-stimulated gene (ISG) mRNA upregulation. Preinfection treatment (4 to 24 h prior to infection) with salmon rIFN-α induces an antiviral state that inhibits the replication of SAV-3 and protects the cells against virus-induced cytopathic effects (CPE). The antiviral state coincides with a strong expression of Mx and ISG15 mRNA and Mx protein expression. When rIFN-α is administered at the time of infection and up to 24 h postinfection, virus replication is not inhibited, and cells are not protected against virus-induced CPE. By 40 h postinfection, the alpha subunit of eukaryotic initiation factor 2 (eIF2α) is phosphorylated concomitant with the expression of the E2 protein as assessed by Western blotting. Postinfection treatment with rIFN-α results in a moderate reduction in E2 expression levels in accordance with a moderate downregulation of cellular protein synthesis, an approximately 65% reduction by 60 h postinfection. rIFN-γ has only a minor inhibitory effect on SAV-3 replication in vitro. SAV-3 is sensitive to the preinfection antiviral state induced by rIFN-α, while postinfection antiviral responses or postinfection treatment with rIFN-α is not able to limit viral replication.

Binding of initiation factor 2 and initiator tRNA to the Escherichia coli 30S ribosomal subunit induces allosteric transitions in 16S rRNA

Biochemistry ◽  
1990 ◽  
Vol 29 (35) ◽  
pp. 8144-8151 ◽  
Author(s):  
Hiroshi Wakao ◽  
Pascale Romby ◽  
Soumaya Laalami ◽  
Jean Pierre Ebel ◽  
Chantal Ehresmann ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Ribosomal Subunit ◽  
Initiation Factor ◽  
Initiator Trna ◽  
Initiation Factor 2 ◽  
Allosteric Transitions

scholarly journals Expression of the Gene for Escherichia coli Initiation Factor IF-3 in vivo and in vitro

2005 ◽  
Vol 123 (3) ◽  
pp. 483-488 ◽  
Author(s):  
Patrick LESTIENNE ◽  
Jean-FranCois MAYAUX ◽  
Sylvain BLANQUET ◽  
Jacques DONDON ◽  
Jacqueline A. PLUMBRIDGE ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Initiation Factor
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