scholarly journals Bioinformatic Prediction of an tRNASec Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria

2021 ◽  
Vol 22 (9) ◽  
pp. 4605
Author(s):  
Takahito Mukai
Keyword(s):  
Insertion Sequence ◽  
Trna Gene ◽  
Stop Codon ◽  
Elongation Factor ◽  
Selenium Deficiency ◽  
Open Reading Frame ◽  
Start Codon ◽  
Sequence Element ◽  
Reading Frame ◽  
Insertion Sequence Element

In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNASec is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following the codon on the mRNA. Since the excess of SelB may lead to sequestration of Sec-tRNASec under selenium deficiency or oxidative stress, the expression levels of SelB and tRNASec should be regulated. In this bioinformatic study, I analyzed the Rhizobiales SelB species because they were annotated to have a non-canonical C-terminal extension. I found that the open reading frame (ORF) of diverse Alphaproteobacteria selB genes includes an entire tRNASec sequence (selC) and overlaps with the start codon of the downstream ORF. A remnant tRNASec sequence was found in the Sinorhizobium melilotiselB genes whose products have a shorter C-terminal extension. Similar overlapping traits were found in Gammaproteobacteria and Nitrospirae. I hypothesized that once the tRNASec moiety is folded and processed, the expression of the full-length SelB may be repressed. This is the first report on a nested tRNA gene inside a protein ORF in bacteria.

scholarly journals The Cytochrome c Maturation Locus of Legionella pneumophila Promotes Iron Assimilation and Intracellular Infection and Contains a Strain-Specific Insertion Sequence Element

2002 ◽  
Vol 70 (4) ◽  
pp. 1842-1852 ◽  
Author(s):  
V. K. Viswanathan ◽  
Sherry Kurtz ◽  
Lisa L. Pedersen ◽  
Yousef Abu Kwaik ◽  
Kevin Krcmarik ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Legionella Pneumophila ◽  
Insertion Sequence ◽  
Open Reading Frame ◽  
Growth Defect ◽  
Sequence Element ◽  
Reading Frame ◽  
Intracellular Infection ◽  
Iron Assimilation ◽  
Insertion Sequence Element

ABSTRACT Previously, we obtained a Legionella pneumophila mutant, NU208, that is hypersensitive to iron chelators when grown on standard Legionella media. Here, we demonstrate that NU208 is also impaired for growth in media that simply lack their iron supplement. The mutant was not, however, impaired for the production of legiobactin, the only known L. pneumophila siderophore. Importantly, NU208 was also highly defective for intracellular growth in human U937 cell macrophages and Hartmannella and Acanthamoeba amoebae. The growth defect within macrophages was exacerbated by treatment of the host cells with an iron chelator. Sequence analysis demonstrated that the transposon disruption in NU208 lies within an open reading frame that is highly similar to the cytochrome c maturation gene, ccmC. CcmC is generally recognized for its role in the heme export step of cytochrome biogenesis. Indeed, NU208 lacked cytochrome c. Phenotypic analysis of two additional, independently derived ccmC mutants confirmed that the growth defect in low-iron medium and impaired infectivity were associated with the transposon insertion and not an entirely spontaneous second-site mutation. trans-complementation analysis of NU208 confirmed that L. pneumophila ccmC is required for cytochrome c production, growth under low-iron growth conditions, and at least some forms of intracellular infection. Although ccm genes have recently been implicated in iron assimilation, our data indicate, for the first time, that a ccm gene can be required for bacterial growth in an intracellular niche. Complete sequence analysis of the ccm locus from strain 130b identified the genes ccmA-H. Interestingly, however, we also observed that a 1.8-kb insertion sequence element was positioned between ccmB and ccmC. Southern hybridizations indicated that the open reading frame within this element (ISLp 1) was present in multiple copies in some strains of L. pneumophila but was absent from others. These findings represent the first evidence for a transposable element in Legionella and the first identification of an L. pneumophila strain-specific gene.

scholarly journals Translation of a minigene in the 5′ leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene

2011 ◽  
Vol 441 (1) ◽  
pp. 247-253 ◽  
Author(s):  
Md. Shahidul Islam ◽  
Robert K. Shaw ◽  
Gad Frankel ◽  
Mark J. Pallen ◽  
Stephen J. W. Busby
Keyword(s):  
Escherichia Coli ◽  
Translation Initiation ◽  
Stop Codon ◽  
Leader Sequence ◽  
Open Reading Frame ◽  
Start Codon ◽  
Target Cells ◽  
Reading Frame ◽  
Enterohaemorrhagic Escherichia Coli ◽  
Translation Start

The 5′ end of the major RNA transcript of the LEE1 operon of enterohaemorrhagic Escherichia coli contains ~170 bases before the AUG translation start codon of the first recognized gene, ler. This unusually long leader sequence carries three potential alternative AUG start codons. Using a lac fusion expression vector, we confirmed that the ler gene AUG is functional for translation initiation, and we checked for translation initiation at the three alternative AUG codons. Whereas two of the alternative AUG codons appear incompetent for translation initiation, we detected strong initiation at the third AUG, which is followed by one AAA codon and a UAG stop codon. The location of this very short two-codon open reading frame with respect to the ler translation start appears to be critical. Hence mutations that destroy the UAG stop codon, or short deletions between the UAG stop codon and the ler translation initiation region, result in big effects on ler expression. In the context of the full-length LEE1 operon leader sequence, translation of this very short two-codon open reading frame is necessary for optimal expression of the ler gene and for the subsequent interactions of enterohaemorrhagic Escherichia coli with host target cells.

scholarly journals Distribution of the ermG Gene among Bacterial Isolates from Porcine Intestinal Contents

2005 ◽  
Vol 71 (8) ◽  
pp. 4930-4934 ◽  
Author(s):  
Yanping Wang ◽  
Gui-Rong Wang ◽  
Nadja B. Shoemaker ◽  
Terence R. Whitehead ◽  
Abigail A. Salyers
Keyword(s):  
Insertion Sequence ◽  
Bacillus Sphaericus ◽  
Gram Positive ◽  
Sequence Element ◽  
Conjugative Transposon ◽  
Gram Positive Bacteria ◽  
First Finding ◽  
Intestinal Contents ◽  
Porcine Feces ◽  
Insertion Sequence Element

ABSTRACT The ermG gene was first found in the soil bacterium Bacillus sphaericus. More recently, it was found in several human intestinal Bacteroides species. We report here the first finding of ermG genes in gram-positive bacteria isolated from porcine feces and from under-barn manure pits used to store porcine wastes. The porcine ermG sequences were identical to the sequence of the B. sphaericus ermG gene except that six of the seven ermG-containing strains contained an insertion sequence element insertion in the C-terminal end of the gene. The porcine ermG genes were found in three different gram-positive genera, an indication that it is possible that the gene is being spread by horizontal gene transfer. A segment of a Bacteroides conjugative transposon that carries an ermG gene cross-hybridized with DNA from six of the seven porcine isolates, but the restriction patterns in the porcine strains were different from that of the Bacteroides conjugative transposon.

scholarly journals Characterization and Functional Complementation of a Nonlethal Deletion in the Chromosome of a β-Glycosidase Mutant of Sulfolobus solfataricus

2003 ◽  
Vol 185 (13) ◽  
pp. 3948-3957 ◽  
Author(s):  
Simonetta Bartolucci ◽  
Mosè Rossi ◽  
Raffaele Cannio
Keyword(s):  
Insertion Sequence ◽  
Genomic Sequence ◽  
Sulfolobus Solfataricus ◽  
Major Facilitator Superfamily ◽  
Gene Encoding ◽  
Sequence Element ◽  
Plasmid Construct ◽  
Major Facilitator ◽  
Flanking Regions ◽  
Insertion Sequence Element

ABSTRACT LacS− mutants of Sulfolobus solfataricus defective in β-glycosidase activity were isolated in order to explore genomic instability and exploit novel strategies for transformation and complementation. One of the mutants showed a stable phenotype with no reversion; analysis of its chromosome revealed the total absence of the β-glycosidase gene (lacS). Fine mapping performed in comparison to the genomic sequence of S. solfataricus P2 indicated an extended deletion of ∼13 kb. The sequence analysis also revealed that this chromosomal rearrangement was a nonconservative transposition event driven by the mobile insertion sequence element ISC1058. In order to complement the LacS− phenotype, an expression vector was constructed by inserting the lacS coding sequence with its 5′ and 3′ flanking regions into the pEXSs plasmid. Since no transformant could be recovered by selection on lactose as the sole nutrient, another plasmid construct containing a larger genomic fragment was tested for complementation; this region also comprised the lacTr (lactose transporter) gene encoding a putative membrane protein homologous to the major facilitator superfamily. Cells transformed with both genes were able to form colonies on lactose plates and to be stained with the β-glycosidase chromogenic substrate X-Gal (5-bromo-4-chloro-3-indoyl-β-d-galactopyranoside).

scholarly journals Characterization of IS18, an Element Capable of Activating the Silent aac(6′)-Ij Gene ofAcinetobacter sp. 13 Strain BM2716 by Transposition

1998 ◽  
Vol 42 (10) ◽  
pp. 2759-2761 ◽  
Author(s):  
Eric Rudant ◽  
Patrice Courvalin ◽  
Thierry Lambert
Keyword(s):  
Resistance Gene ◽  
Insertion Sequence ◽  
Resistant Mutant ◽  
Open Reading Frame ◽  
Inverted Repeats ◽  
Aminoglycoside Resistance ◽  
Reading Frame ◽  
Terminal Inverted Repeats ◽  
Hybrid Promoter

ABSTRACT Insertion sequence IS18 was detected by analysis of the spontaneous aminoglycoside resistant mutant Acinetobactersp. 13 strain BM2716-1. Insertion of the element upstream from the silent acetyltransferase gene aac(6′)-Ij created a hybrid promoter that putatively accounts for the expression of the aminoglycoside resistance gene. The 1,074-bp IS18 element contained partially matched (20 out of 26 bases) terminal inverted repeats, one of which overlapped the 3′ end of a 935-bp open reading frame potentially encoding a protein related to the transposases of the IS30 family. IS18 was found in 6 out of 29 strains of Acinetobacter sp. 13 but not in 10 strains each of A. baumannii and A. haemolyticus.

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