Post-transcriptional control of bacteriophage T4 gene 25 expression: mRNA secondary structure that enhances translational initiation

Nivinskas, Rimas; Malys, Naglis; Klausa, Vytautas; Vaiškunaite, Rita; Gineikiene, Egle

doi:10.1006/jmbi.1999.2695

Cited by 31 publications

(28 citation statements)

References 46 publications

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“…However, secondary structures within the RBS do not invariably depress translation; in some cases, their effect is neutral, presumably because they do not compromise the interaction between the mRNA and the 30S subunit. Such noninhibitory structures have been found upstream of the SD (36), between the SD and the initiation codon (16,30,33), or downstream of the start codon (33). That secondary structures can be accommodated by the ribosome illustrates the fact that the mRNA does not necessarily bind continuously to the ribosomal mRNA track, a feature recently documented by structural studies (21).…”

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confidence: 87%

The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element

et al. 2006

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The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position ؊91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the "specialized ribosome" approach. Depending upon the constructs used, translation initiation was decreased three-to sevenfold upon changing the conserved GGA to CCU. However, although chemical probing showed that the mutated trinucleotides were accessible, no restoration was observed when the ribosome anti-SD was symmetrically changed from CCUCC to GGAGG. When the same change was introduced in the SD from a conventional TIR as a control, activity was stimulated. This result suggests that the GGA trinucleotides do not form a discontinuous SD. Others hypotheses that may account for their role are discussed. Curiously, we also find that, when expressed at moderate level (30 to 40% of total ribosomes), specialized ribosomes are only twofold disadvantaged over normal ribosomes for the translation of bulk cellular mRNAs. These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.

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confidence: 87%

The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element

et al. 2006

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“…The following translation initiation mechanisms are shown: a SDdependent, b SD-independent; both (a, b) are common to Archaea and Bacteria; c a leaderless mechanism, which occurs in Archaea, Bacteria, Eukarya, and mitochondria and may be initiated by small ribosomal subunits or 70S and 80S ribosomes; d 5 0 enddependent, which is represented as a 'canonical' cap-dependent mechanism; e 5 0 end-dependent mechanism found in Hantavirus, which uses a viral multifunctional translation factor that substitutes cap binding complex; f internal initiation, which is represented as an IRES-driven mechanism. Initiation factors aIF1, aIF1A, and eIF2 of Archaea are labeled as 1, 1A, and 2; IF1, IF2, and IF3 of Bacteria are 1, 2, and 3; eIF1, eIF1A, eIF2, eIF3, eIF4A, eIF4B, eIF4E, eIF4G, and eIF5 of Eukarya are 1, 1A, 2, 3, 4A, 4B, 4E, 4G, and 5, respectively the transcript has to be stabilized through the capping of the 5 0 end and mRNA secondary structure [16,18,19]; and (4) translation initiation in prokaryotes is tightly regulated through the polycistronic gene arrangement (occasionally with overlapped ORFs) causing coupled translation and translation driven by reinitiation [2,20,21], and through the primary mRNA sequence, e.g., the 5 0 -UTR region, which, in addition to the SD sequence, may include a pyrimidinerich region for interaction with the ribosomal protein S1, a mRNA sequence that forms a secondary structure, a repressor protein binding site, and/or a riboswitch that binds low molecular weight effectors [10,[22][23][24][25][26][27]. Although eukaryotes occasionally use strategies that depend on the mRNA sequence, e.g., reinitiation or secondary structure, translation initiation is significantly more dependent on other elements, e.g., initiation factors [2,12,19].…”

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confidence: 99%

Translation initiation: variations in the mechanism can be anticipated

Malys

McCarthy

2010

Cell. Mol. Life Sci.

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Translation initiation is a critical step in protein synthesis. Previously, two major mechanisms of initiation were considered as essential: prokaryotic, based on SD interaction; and eukaryotic, requiring cap structure and ribosomal scanning. Although discovered decades ago, cap-independent translation has recently been acknowledged as a widely spread mechanism in viruses, which may take place in some cellular mRNA translations. Moreover, it has become evident that translation can be initiated on the leaderless mRNA in all three domains of life. New findings demonstrate that other distinguishable types of initiation exist, including SD-independent in Bacteria and Archaea, and various modifications of 5' end-dependent and internal initiation mechanisms in Eukarya. Since translation initiation has developed through the loss, acquisition, and modification of functional elements, all of which have been elevated by competition with viral translation in a large number of organisms of different complexity, more variation in initiation mechanisms can be anticipated.

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“…Furthermore, the SD sequence and AUG, are located at the optimum spacing of 8 nt, therefore, in the absence of RNA secondary structure it can be used for effcient translational initiation (Ringquist et al 1992). These results clearly demonstrate that the spacing between the Shine-Dalgarno sequence and AUG, and stability of mRNA secondary structures are important determinants of translation efficiency (Hartz et al 1991, Nivinskas et al 1999.…”

Section: Resultsmentioning

confidence: 87%

“…The a-L-arabinofuranosidase gene (hereafter referred to as araA), however, was poorly expressed in E. coli by using pET 20b (Xue et al 2004), and therefore it is worthwhile to raise gene expression level to meet industrial requirements by sequence modification on the gene or vectors. Low-level expression can be caused by the foreign genes through forming secondary structures of mRNA, spacing between the Shine-Dalgarno sequence and start codon, or using rare codons of E. coli in numerous reports (Spanjiaard et al 1990, Nivinskas et al 1999, Watson et al 1995. In this report, we describe the site directed mutagenesis of araA, overexpression of the a-L-arabinofuranosidase gene in E. coli BL21-CodonPlus (DE3)-RIL, and application of the recombinant enzyme in the production of xylobiose.…”

Section: Introductionmentioning

confidence: 98%

High-level Expression of an α-l-arabinofuranosidase from Thermotoga maritima in Escherichia coli for the Production of Xylobiose from Xylan

Xue

Zeng

et al. 2006

Biotechnol Lett

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To efficiently produce xylobiose from xylan, high-level expression of an alpha-L-arabinofuranosidase gene from Thermotoga maritima was carried out in Escherichia coli. A 1.5-kb DNA fragment, coding for an alpha-L-arabinofuranosidase of T. maritima, was inserted into plasmid pET-20b without the pelB signal sequence leader, and produced pET-20b-araA1 with 8 nt spacing between ATG and Shine-Dalgarno sequence. A maximum activity of 12 U mg(-1) was obtained from cellular extract of E. coli BL21-CodonPlus (DE3)-RIL harboring pET-20b-araA1. The over-expressed alpha-L-arabinofuranosidase was purified 13-fold with a 94% yield from the cellular extract of E. coli by a simple heat treatment. Production of xylooligosaccharides from corncob xylan by endoxylanase and alpha-L-arabinofuranosidase was examined by TLC and HPLC: xylobiose was the major product from xylan at 90 degrees C and its proportion in the xylan hydrolyzates increased with the reaction time. Hydrolysis with in the xylanase absence of alpha-L-arabinofuranosidase gave only half this yield.

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Post-transcriptional control of bacteriophage T4 gene 25 expression: mRNA secondary structure that enhances translational initiation

Cited by 31 publications

References 46 publications

The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element

The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element

Translation initiation: variations in the mechanism can be anticipated

High-level Expression of an α-l-arabinofuranosidase from Thermotoga maritima in Escherichia coli for the Production of Xylobiose from Xylan

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