Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis

Abstract

Expression of the Arabidopsis CGS1 gene that codes for cystathionine ␥-synthase is feedback regulated at the step of mRNA stability in response to S-adenosyl-L-methionine (AdoMet). A short stretch of amino acid sequence, called the MTO1 region, encoded by the first exon of CGS1 itself is involved in this regulation. Here, we demonstrate, using a cell-free system, that AdoMet induces temporal translation elongation arrest at the Ser-94 codon located immediately downstream of the MTO1 region, by analyzing a translation intermediate and performing primer extension inhibition (toeprint) analysis. This translation arrest precedes the formation of a degradation intermediate of CGS1 mRNA, which has its 5 end points near the 5 edge of the stalled ribosome. The position of ribosome stalling also suggests that the MTO1 region in nascent peptide resides in the ribosomal exit tunnel when translation elongation is temporarily arrested. In addition to the MTO1 region amino acid sequence, downstream Trp-93 is also important for the AdoMet-induced translation arrest. This is the first example of nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in eukaryotes. Furthermore, our data suggest that the ribosome stalls at the step of translocation rather than at the step of peptidyl transfer.[Keywords: S-adenosyl-L-methionine; translation arrest; mRNA stability; MTO1 region; cystathionine ␥-synthase; feedback regulation] Supplemental material is available at http://www.genesdev.org. Cystathionine ␥-synthase (CGS; EC 2.5.1.48) catalyzes the first committed step of methionine biosynthesis in higher plants (Matthews 1999) and is encoded by the CGS1 gene in Arabidopsis thaliana (gene ID At3g01120; Kim and Leustek 1996). Expression of the CGS1 gene is regulated by negative feedback at the step of mRNA stability in response to methionine application in Arabidopsis. When wild-type calli were treated with methionine, the amount of full-length CGS1 mRNA was decreased, and a short CGS1 RNA species formed that is truncated at its 5Ј region. This 5Ј-truncated RNA species is likely an intermediate of CGS1 mRNA degradation. The mto1 mutants of Arabidopsis, which carry single amino acid sequence alterations within the first exon of CGS1, are deficient in this regulation and overaccumulate soluble methionine (Chiba et al. 1999). A short stretch of amino acid sequence, termed the MTO1 region, which is encoded within CGS1 exon 1 and covers the mto1 mutation sites, is involved in this process (Ominato et al. 2002). Since CGS1 exon 1 acts in cis, we proposed that this regulation occurs during translation, when the nascent polypeptide and its mRNA are in close proximity (Chiba et al. 1999;Suzuki et al. 2001). In support of this idea, the regulation is abolished by application of a translation inhibitor (Lambein et al. 2003).CGS1 exon 1-mediated post-transcriptional regulation was reproduced in an in vitro translation system using wheat germ extract, and S-adenosyl-L-methionine (AdoMet), a direct metabolite of methionine...

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants

“…Some regions likely encode nascent peptides which can stall ribosomes during translation elongation as the MTO1 region in CGS1 or are upstream of structured regions that can block the movement of ribosomes (Onouchi et al, 2005). The one with the last peak of 59-truncated RNA ends located 16 nucleotides upstream of main ORF stop codons as in the degradation pattern observed in CPuORFs may cause ribosome pausing during translation termination.…”

“…Besides CPuORFs, the nascent peptide encoded by a CDS region in the first exon of Arabidopsis CGS1, known as the MTO1 region, has been reported to block ribosome elongation and induce RNA decay in response to S-adenosyl-L-methionine (AdoMet) (Onouchi et al, 2005). Similar to the degradation fragments we observed in bZIP CPuORFs (Figure 2), Haraguchi et al (2008) detected a ladder of truncated 59 termini separated in length by ;30-nucleotide increments in the MTO1 region together with the 59 upstream region after treatment with AdoMet.…”

Dynamics of methionine biosynthesis

“…Significant advances in our understanding on the regulation of the methionine biosynthetic pathway in plants were provided through the isolation and characterisation of genetic mutants in which methionine accumulation is altered Chiba et al 1999;Bartlem et al 2000;Goto et al 2002;Shen et al 2002;Onouchi et al 2005), as described in further detail below.…”

Methionine catabolism in Arabidopsis cells is initiated by a γ-cleavage process and leads to S -methylcysteine and isoleucine syntheses

“…De novo Met synthesis consists of three consecutive reactions localized in plastids (4) and catalyzed by cystathionine ␥-synthase, cystathionine ␤-lyase, and methionine synthase. Several recent studies have indicated that Met synthesis and accumulation are subject to complex regulatory controls in which cystathionine ␥-synthase plays a crucial role (5)(6)(7).…”