Cooperation between the chloroplast psbA 5′‐untranslated region and coding region is important for translational initiation: the chloroplast translation machinery cannot read a human viral gene coding region

Chloroplast mRNA translation is regulated by the 5′‐untranslated region (5′‐UTR). Chloroplast 5′‐UTRs also support translation of the coding regions of heterologous genes. Using an in vitro translation system from tobacco chloroplasts, we detected no translation from a human immunodeficiency virus tat coding region fused directly to the tobacco chloroplast psbA 5′‐UTR. This lack of apparent translation could have been due to rapid degradation of mRNA templates or synthesized protein products. Replacing the psbA 5′‐UTR with the E. coli phage T7 gene 10 5′‐UTR, a highly active 5′‐UTR, and substituting synonymous codons led to some translation of the tat coding region. The Tat protein thus synthesized was stable during translation reactions. No significant degradation of the added tat mRNAs was observed after translation reactions. These results excluded the above two possibilities and confirmed that the tat coding region prevented its own translation. The tat coding region was then fused to the psbA 5′‐UTR with a cognate 5′‐coding segment. Significant translation was detected from the tat coding region when fused after 10 or more codons. That is, translation could be initiated from the tat coding region once translation had started, indicating that the tat coding region inhibits translational initiation but not elongation. Hence, cooperation/compatibility between the 5′‐UTR and its coding region is important for translational initiation.     

Role of G-quadruplex located at 5ʹ end of mRNAs

BackgroundSecondary structures in 5′ UTR of mRNAs play a critical role in regulating protein synthesis. Though studies have indicated the role of secondary structure G-quadruplex in translational regulation, position-specific effect of G-quadruplex in naturally occurring mRNAs is still not understood. As a pre-initiation complex recognises 5′ cap of the mRNA and scans along the untranslated region (UTR) before initiating translation, the presence of G-quadruplex in 5′ region may have a significant contribution in regulating translation. Here, we investigate the role of G-quadruplex located at the 5′ end of an mRNA.MethodsBiophysical characterisation of putative G-quadruplexes was performed using UV and CD spectroscopy. Functional implication of G-quadruplex in the context of their location was assessed in cellulo using qRT-PCR and dual luciferase assay system.ResultsPG4 sequences in 5′ UTR of AKT interacting protein (AKTIP), cathepsin B (CTSB) and forkhead box E3 (FOXE3) mRNAs form G-quadruplex whereas it is unable to form G-quadruplex in apolipoprotein A-I binding protein (APOA1BP). Our results demonstrated diverse roles of G-quadruplex located at 5′ end of mRNAs. Though G-quadruplex in AKTIP and CTSB mRNA act as inhibitory modules, it activates translation in FOXE3 mRNA.ConclusionsOur works suggests that G-quadruplex present at the 5′ terminal of an mRNA behaves differently in a different gene context. It can activate or inhibit gene expression.General significanceThis study demonstrated that it is difficult to predict the role of G-quadruplex on the basis of its position in 5′ UTR. The neighbouring nucleotide sequence, the intracellular milieu and the interacting partners might render diverse functions to this secondary structure.     

Cap-independent translation initiation of Apaf-1 mRNA based on a scanning mechanism is determined by some features of the secondary structure of its 5′ untranslated region

We have earlier shown that the 5′-untranslated region (5′ UTR) of the mRNA coding for activation factor of apoptotic peptidase 1 (Apaf-1) can direct translation in vivo by strictly 5′ end-dependent way even in the absence of m⁷G-cap. Dependence of translational efficiency on the cap availability for this mRNA turned out to be relatively low. In this study we demonstrate that this surprising phenomenon is determined the 5′-proximal part (domains I and II) of highly structured Apaf-1 5′ UTR. Remarkably, domain II by itself was able to reduce dependence of the mRNA on the cap on its transferring to a short 5′ UTR derived from a standard vector. We suggest that the low cap-dependence inherent to some cellular mRNAs may have an important physiological significance under those stress conditions when the function of cap-binding factor eIF4E is impaired.     

Developmental regulation of an instability element from the Drosophila fushi tarazu mRNA

Summary: The Drosophila fushi tarazu (ftz) mRNA is one of the shortest‐lived metazoan mRNAs, and its instability is crucial for proper development of the embryo. Previously, we identified two cis‐acting elements that are required for ftz mRNA degradation, one within the 5′ one‐third and another in the 3′UTR of the message. Here we focus on the 3′UTR element termed FIE3 (ftz instability e lement in the 3 ′UTR). To investigate the developmental regulation of the FIE3‐dependent degrading activity we measured the abundance of an FIE3‐containing mRNA in ovaries, unfertilized eggs, and different larval and adult tissues. We found that FIE3‐degrading activity is present at all developmental stages and tissues examined, except in the ovary. Activation of the FIE3‐dependent mRNA decay is independent of fertilization because it could be triggered by egg activation. Finally, we provide evidence that mutation of conserved elements within FIE3 had no effect on mRNA instability. genesis 30:59–64, 2001. © 2001 Wiley‐Liss, Inc.     

Maternal Nanos‐Dependent RNA Stabilization in the Primordial Germ Cells of Drosophila Embryos

Nanos (Nos) is an evolutionary conserved protein expressed in the germline of various animal species. In Drosophila, maternal Nos protein is essential for germline development. In the germline progenitors, or the primordial germ cells (PGCs), Nos binds to the 3′ UTR of target mRNAs to repress their translation. In contrast to this prevailing role of Nos, here we report that the 3′ UTR of CG32425 mRNA mediates Nos‐dependent RNA stabilization in PGCs. We found that the level of mRNA expressed from a reporter gene fused to the CG32425 3′ UTR was significantly reduced in PGCs lacking maternal Nos (nos PGCs) as compared with normal PGCs. By deleting the CG32425 3′ UTR, we identified the region required for mRNA stabilization, which includes Nos‐binding sites. In normal embryos, CG32425 mRNA was maternally supplied into PGCs and remained in this cell type during embryogenesis. However, as expected from our reporter assay, the levels of CG32425 mRNA and its protein product expressed in nos PGCs were lower than in normal PGCs. Thus, we propose that Nos protein has dual functions in translational repression and stabilization of specific RNAs to ensure proper germline development.     

Translational control of activin in Xenopus laevis embryos

Activin is a potent mesoderm inducing factor present in embryos of Xenopus laevis. Recent evidence has implicated activin in the inhibition of neural development in addition to the well-established induction of mesoderm in ectodermal explants. These diverse effects are critically dependent on the concentration of activin yet little is known about the mechanisms regulating the level of activin in the embryo. We report that the 3′ untranslated region (3′ UTR) of activin βB mRNA inhibits the translation of activin in embryos. Microinjection of activin mRNA from which the 3′ UTR has been deleted is 8–10-fold more potent in inducing mesoderm than mRNA containing the 3′ UTR. Truncation of the 3′ UTR also leads to a marked enhancement of activin protein levels in embryos but has no effect when the truncated mRNA is translated in vitro. The 3′ UTR also confers translational inhibition on a heterologous mRNA. These data show that a maternal factor(s) present in X. laevis regulates the translation of injected activin βB mRNA. This factor(s) could be responsible for regulating the levels of endogenous activin βB protein during mesoderm induction and the specification of ectodermal derivatives such as neural and epidermal tissues. © 1995 Wiley-Liss, Inc.     

Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells

In prokaryotic cells, 3′–5′ exonucleases can attenuate messenger RNA (mRNA) directionally from the direction of the 3′–5′ untranslated region (UTR), and thus improving the stability of mRNAs without influencing normal cell growth and metabolism is a key challenge for protein production and metabolic engineering. Herein, we significantly improved mRNA stability by using synthetic repetitive extragenic palindromic (REP) sequences as an effective mRNA stabilizer in two typical prokaryotic microbes, namely, Escherichia coli for the production of cyclodextrin glucosyltransferase (CGTase) and Corynebacterium glutamicum for the production of N-acetylglucosamine (GlcNAc). First, we performed a high-throughput screen to select 4 out of 380 REP sequences generated by randomizing 6 nonconservative bases in the REP sequence designed as the degenerate base “N.” Secondly, the REP sequence was inserted at several different positions after the stop codon of the CGTase-encoding gene. We found that mRNA stability was improved only when the space between the REP sequence and stop codon was longer than 12 base pairs (bp). Then, by reconstructing the spacer sequence and secondary structure of the REP sequence, a REP sequence with 8 bp in a stem-loop was obtained, and the CGTase activity increased from 210.6 to 291.5 U/ml. Furthermore, when this REP sequence was added to the 3′-UTR of glucosamine-6-phosphate N-acetyltransferase 1 ( GNA1), which is a gene encoding a key enzyme GNA1 in the GlcNAc synthesis pathway, the GNA1 activity was increased from 524.8 to 890.7 U/mg, and the GlcNAc titer was increased from 4.1 to 6.0 g/L in C. glutamicum. These findings suggest that the REP sequence plays an important function as an mRNA stabilizer in prokaryotic cells to stabilize its 3′-terminus of the mRNA by blocking the processing action of the 3′–5′ exonuclease. Overall, this study provides new insight for the high-efficiency overexpression of target genes and pathway fine-tuning in bacteria.