Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence by Karel Estrada, Alejandro Garciarrubio, Enrique Merino

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Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence. by Karel Estrada, Alejandro Garciarrubio, Enrique Merino

“…Translation initiation in prokaryotes is mainly defined, although not exclusively, by the interaction between the anti-Shine-Dalgarno sequence (antiSD), located at the 3'-terminus of the 16S ribosomal RNA, and a complementary sequence, the ribosome binding site, or Shine-Dalgarno (SD), located upstream of the start codon in prokaryotic mRNAs. …”
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A Proposal of the Ur-RNAome by Miryam Palacios-Pérez, Marco V. José

“…Nevertheless, at this stage of evolution there was no genetic code (as seen in the absence of the peptidyl transferase centre and any vestiges of the anti-Shine–Dalgarno sequence). Interestingly, we detected the anticodons of both glycine (GCC) and threonine (GGU) in the hairpins of proto-tRNA.…”
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Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch by Guodong Hu, Huan-Xiang Zhou

“…One Mg2+ ion unique to the apo form maintains the Shine–Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. …”
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Regulation of Leaderless mRNA Translation in Bacteria by Lorenzo Eugenio Leiva, Assaf Katz

“…Given that lmRNAs are devoid of a 5′ untranslated region and the Shine-Dalgarno sequence located within it, the mechanism of translation regulation must depend on molecular strategies that are different from what has been observed in the Shine-Dalgarno-led translation. …”
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Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH by Niraj Kumar, Shivani Sharma, Prem S. Kaushal

“…The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPFlong structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.…”
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Translation Enhancement by a Short Nucleotide Insertion at 5′UTR: Application to an In Vitro Cell-Free System and a Photosynthetic Bacterium by Tomo Kondo, Takayuki Shimizu

“…We previously showed that insertion of <i>Dictyostelium</i> gene sequences, such as <i>mlcR</i>, upstream of the Shine–Dalgarno sequence, positively impacts downstream gene expression in <i>Escherichia coli</i>. …”
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Role of ribosome recycling factor in natural termination and translational coupling as a ribosome releasing factor. by Yoshio Inokuchi, Fabio Quaglia, Akikazu Hirashima, Yoshihiro Yamamoto, Hideko Kaji, Akira Kaji

“…We used the translational coupling without the Shine-Dalgarno sequence of downstream ORF (d-ORF) as a model system of the RRF action in natural termination of protein synthesis. …”
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Cloning and expression of recombinant xylanase enzyme (xynA) in E. coli. by Amin Sadeghi Alikelayeh, Neda Mirakhorli, Mohammad Reza Akbari, Behzad Shareghi Brojeni

“…Materials and methods In present study, the thermostable xylanase (xynA) gene in a bacterial secretory expression system along with: Shine-Dalgarno sequence, Usp45 signal peptide and T7 promoter was cloned in plasmid pET-22b (+) from E. coli strain BL21 (DE3) using The heat shock method. …”
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Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in <i>Bacillus subtilis</i> DB104 through Transcriptome Analysis by Ji-Su Jun, Hyang-Eun Jeong, Kwang-Won Hong

“…We enhanced these promoters by optimizing spacer length, promoter sequence, Shine–Dalgarno sequence, regulator binding sites, and terminator sequences. …”
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Molecular cloning of Cyclodextrin glucanotransferase gene from Bacillus sp. G1 by Ong, Rui Min

“…The mature CGTase corresponds to a calculated molecular weight of 75389 Da which is very close to the molecular weight of the wild type Bacillus sp G1 (75kDa) estimated through SDS-Page. A putative Shine-Dalgarno sequence AAGG was located 5 bp upstream of the TTG codon. …”
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One-step biotransformation of ferulic acid into biovanillin using recombinant Escherichia coli BL21 (DE3) by Zamzuri, Nur Ain

“…The recognition of GTG (Guanine-Thymine-Guanine) for both genes ech and fcs as start codon was assisted by the presence of Shine-Dalgarno sequence, which located at 8 bp for ech and 7 bp for fcs upstream the initiation codon. …”
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Development of a local bacterial isolate expressing cyclodextrin glycosyltransferase through molecular cloning approaches by Ramli, Norhayati

“…The recognition of TTG as a start codon was assisted by the presence of Shine-Dalgarno sequence, which located at 6 bp upstream from the initiation codon. …”
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On the nature of picobirnaviruses by A. Yu. Kashnikov, N. V. Epifanova, N. A. Novikova

“…The genome saturation with the Shine–Dalgarno sequences, as well as the preservation of this saturation in the progeny, according to scientists, allows us to attribute PBVs to prokaryotic viruses. …”
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Flow-Seq Evaluation of Translation Driven by a Set of Natural <i>Escherichia coli</i> 5′-UTR of Variable Length by Ekaterina S. Komarova, Anna N. Slesarchuk, Maria P. Rubtsova, Ilya A. Osterman, Alexey E. Tupikin, Dmitry V. Pyshnyi, Olga A. Dontsova, Marsel R. Kabilov, Petr V. Sergiev

“…In line with previous Flow-seq experiments with randomized 5′-UTRs, we observed the influence of an RNA secondary structure and Shine–Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5′-UTRs in our library was smaller in comparison with randomized libraries. …”
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Light-Dependent Translation Change of Arabidopsis <em>psbA</em> Correlates with RNA Structure Alterations at the Translation Initiation Region by Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff

“…Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit <i>psbA</i>-like regulation, while those with strong SDs do not. …”
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Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci by Dan-Tong Zhu, Chi Zou, Fei-Xue Ban, Hua-Ling Wang, Xiao-Wei Wang, Yin-Quan Liu

“…Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs.…”
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Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene by Priyanka Bajaj, Munmun Bhasin, Raghavan Varadarajan

“…We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, predicted transcript secondary structure, and evolutionary conservation in determining phenotypic effects of ccdB synonymous mutations. …”
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Development of CRISPR Interference (CRISPRi) Platform for Metabolic Engineering of <i>Leuconostoc citreum</i> and Its Application for Engineering Riboflavin Biosynthesis by Jaewoo Son, Seung Hoon Jang, Ji Won Cha, Ki Jun Jeong

“…The expression of SpdCas9 and sgRNA was optimized by examining the combination of two synthetic promoters and Shine–Dalgarno sequences; the strong expression of sgRNA and the weak expression of SpdCas9 exhibited the most significant downregulation (20-fold decrease) of the target gene (sfGFP), without cell growth retardation caused by SpdCas9 overexpression. …”
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