scholarly journals A New Escherichia coli Entry Vector Series (pIIS18) for Seamless Gene Cloning Using Type IIS Restriction Enzymes

2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Hend Altaib ◽  
Yuka Ozaki ◽  
Tomoya Kozakai ◽  
Yassien Badr ◽  
Izumi Nomura ◽  
...  

A series of new Escherichia coli entry vectors (pIIS18-SapI, pIIS18-BsmBI, pIIS18-BsaI, pIIS18-BfuAI-1, and pIIS18-BfuAI-2) was constructed based on a modified pUC18 backbone, which carried newly designed multiple cloning sites, consisting of two facing type IIS enzyme cleavage sites and one blunt-end enzyme cleavage site. These vectors are useful for seamless gene cloning.

2010 ◽  
Vol 25 (1) ◽  
pp. 89-95 ◽  
Author(s):  
Syed Ali Raza Naqvi ◽  
Torkjel Matzow ◽  
Ciara Finucane ◽  
Saeed A. Nagra ◽  
Malik M. Ishfaq ◽  
...  

Author(s):  
Hend Altaib ◽  
Yuka Ozaki ◽  
Tomoya Kozakai ◽  
Kouta Sakaguchi ◽  
Izumi Nomura ◽  
...  

A series of Bifidobacterium - Escherichia coli shuttle vectors (pKO403- lacZ′ -Cm, pKO403- lacZ′ -Sp, pKO403- lacZ′ -p15A) were constructed based on the pKO403 backbone, which carries a temperature-sensitive replication origin. These vectors carry the lacZ′ α fragment, overhung by two facing type IIS restriction sites, for blue-white selection and seamless gene cloning.


2020 ◽  
Vol 56 (53) ◽  
pp. 7289-7292 ◽  
Author(s):  
Shin Hye Ahn ◽  
James N. Iuliano ◽  
Eszter Boros

The identity of the trivalent metal ion controls the rate of the enzymatic cleavage of a series of metal-complexed cathepsin B substrates. Increasing the distance between the metal complex and the enzyme cleavage site diminishes this effect.


mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Linfeng Huang ◽  
Padraig Deighan ◽  
Jingmin Jin ◽  
Yingxue Li ◽  
Hung-Chi Cheung ◽  
...  

ABSTRACT Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombusvirus p19 in Escherichia coli stabilizes ∼21-nucleotide (nt) dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA. RNase III-produced small dsRNA were formed at most bacterial genes in the bacterial genome and in a plasmid. We classified the types of asRNA in genomic clusters producing the most abundant p19-captured dsRNA and confirmed RNase III regulation of asRNA and sense RNA decay at three type I toxin-antitoxin loci and at a coding gene, rsd. Furthermore, we provide potential evidence for the RNase III-dependent regulation of CspD protein by asRNA. The analysis of p19-captured dsRNA revealed an RNase III sequence preference for AU-rich sequences 3 nucleotides on either side of the cleavage sites and for GC-rich sequences in the 2-nt overhangs. Unexpectedly, GC-rich sequences were enriched in the middle section of p19-captured dsRNA, suggesting some unexpected sequence bias in p19 protein binding. Nonetheless, the ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in dsRNA formed by overlapping sense and antisense transcripts in bacteria.


2020 ◽  
Vol 202 (23) ◽  
Author(s):  
Hélène Barreteau ◽  
Delphine Patin ◽  
Ahmed Bouhss ◽  
Didier Blanot ◽  
Dominique Mengin-Lecreulx ◽  
...  

ABSTRACT Colicin M is an enzymatic bacteriocin produced by some Escherichia coli strains which provokes cell lysis of competitor strains by hydrolysis of the cell wall peptidoglycan undecaprenyl-PP-MurNAc(-pentapeptide)-GlcNAc (lipid II) precursor. The overexpression of a gene, cbrA (formerly yidS), was shown to protect E. coli cells from the deleterious effects of this colicin, but the underlying resistance mechanism was not established. We report here that a major structural modification of the undecaprenyl-phosphate carrier lipid and of its derivatives occurred in membranes of CbrA-overexpressing cells, which explains the acquisition of resistance toward this bacteriocin. Indeed, a main fraction of these lipids, including the lipid II peptidoglycan precursor, now displayed a saturated isoprene unit at the α-position, i.e., the unit closest to the colicin M cleavage site. Only unsaturated forms of these lipids were normally detectable in wild-type cells. In vitro and in vivo assays showed that colicin M did not hydrolyze α-saturated lipid II, clearly identifying this substrate modification as the resistance mechanism. These saturated forms of undecaprenyl-phosphate and lipid II remained substrates of the different enzymes participating in peptidoglycan biosynthesis and carrier lipid recycling, allowing this colicin M-resistance mechanism to occur without affecting this essential pathway. IMPORTANCE Overexpression of the chromosomal cbrA gene allows E. coli to resist colicin M (ColM), a bacteriocin specifically hydrolyzing the undecaprenyl-PP-MurNAc(-pentapeptide)-GlcNAc (lipid II) peptidoglycan precursor of targeted cells. This resistance results from a CbrA-dependent modification of the precursor structure, i.e., reduction of the α-isoprenyl bond of C55-carrier lipid moiety that is proximal to ColM cleavage site. This modification, observed here for the first time in eubacteria, annihilates the ColM activity without affecting peptidoglycan biogenesis. These data, which further increase our knowledge of the substrate specificity of this colicin, highlight the capability of E. coli to generate reduced forms of C55-carrier lipid and its derivatives. Whether the function of this modification is only relevant with respect to ColM resistance is now questioned.


Sign in / Sign up

Export Citation Format

Share Document