Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1

Boni, Irina V.; Isaeva, D M; Musychenko, M L; Tzareva, N.V.

doi:10.1093/nar/19.1.155

Cited by 256 publications

(252 citation statements)

References 52 publications

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“…Eight additional proteins contain DNA/RNA binding domains, such as the PPR, SMR, SAP, OB fold, S1, KOW, NGN, mTERF, or single-stranded DNA (ssDNA) binding motifs (Table 2). These motifs are found in proteins involved in chromatin organization, DNA repair, transcription, RNA processing, or translation (Boni et al, 1991;Kyrpides et al, 1996;Fernandez-Silva et al, 1997;Draper and Reynaldo, 1999;Moreira and Philippe, 1999;Aravind and Koonin, 2000;Lurin et al, 2004). Furthermore, pTAC1 and pTAC11 exhibit striking similarities to p24 proteins, which are members of the Whirly proteins of nuclear transcription factors (Desveaux et al, 2002(Desveaux et al, , 2004.…”

Section: Discussionmentioning

confidence: 99%

pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression

et al. 2005

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Transcription in plastids is mediated by a plastid-encoded multimeric (PEP) and a nuclear-encoded single-subunit RNA polymerase (NEP) and a still unknown number of nuclear-encoded factors. By combining gel filtration and affinity chromatography purification steps, we isolated transcriptionally active chromosomes from Arabidopsis thaliana and mustard (Sinapis alba) chloroplasts and identified 35 components by electrospray ionization ion trap tandem mass spectrometry. Eighteen components, called plastid transcriptionally active chromosome proteins (pTACs), have not yet been described. T-DNA insertions in three corresponding genes, ptac2, -6, and -12, are lethal without exogenous carbon sources. Expression patterns of the plastid-encoded genes in the corresponding knockout lines resemble those of Drpo mutants. For instance, expression of plastid genes with PEP promoters is downregulated, while expression of genes with NEP promoters is either not affected or upregulated in the mutants. All three components might also be involved in posttranscriptional processes, such as RNA processing and/or mRNA stability. Thus, pTAC2, -6, and -12 are clearly involved in plastid gene expression.

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Section: Discussionmentioning

confidence: 99%

pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression

et al. 2005

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“…Although the 16S rRNA sequence of Prochlorococcus carries the same anti-SD sequence as described for E. coli, the absence of a Shine-Dalgarno sequence and the high number of protein-coding genes with relatively short 5 0 UTRs suggest alternative modes of translation initiation preferentially used in Prochlorococcus. Other mechanisms for translation initiation in E. coli such as the binding of ribosomal protein S1 to the 5 0 UTR in mRNAs are also known (Boni et al, 1991) and could be the preferred mechanism for translation initiation used in Prochlorococcus. In many cyanobacteria, two homologous ribosomal S1 proteins Rps1a and Rps1b exist (Figure 2).…”

Section: Utrs In Prochlorococcusmentioning

confidence: 99%

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

et al. 2014

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Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high-and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5 0 untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genomewide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.

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“…One is translation initiation mediated by a ribosomal protein S1 (RPS1), which is a component of the 30S ribosomal subunit. In Escherichia coli, RPS1 interacts with a 5′ UTR of an mRNA, initiating translation efficiently, regardless of the presence of the SD sequence (14,15). RPS1 of E. coli contains six S1 domains that are essential for RNA binding, although the number of domains is different among species (16).…”

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confidence: 99%

Dynamic evolution of translation initiation mechanisms in prokaryotes

Nakagawa

Niimura²,

Miura³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

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It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5′ UTR of an mRNA and the anti-SD sequence in the 3′ end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5′ UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution. dynamic evolution | Shine-Dalgarno sequence | ribosomal protein S1T ranslation initiation is fundamentally important for all protein-coding genes in the genome of every organism. Initiation, rather than elongation, is usually the rate-limiting step in translation, and proceeds at very different efficiencies depending on the sequences in the 5′ UTRs of mRNAs (1). In prokaryotes (for both eubacteria and archaebacteria), the Shine-Dalgarno (SD) sequence in an mRNA is well known as the initiator element of translation (2, 3). The SD sequence, typically GGAGG, is located approximately 10 nucleotides upstream of the initiator codon. The SD sequence pairs with a complementary sequence (CCUCC) in the 3′ end of a 16S rRNA. In the 16S rRNA, the sequence is called the anti-SD sequence in the 3′ tail of which region is single-stranded. The interaction between the SD and the anti-SD sequences (called the SD interaction) augments initiation by anchoring the small (30S) ribosomal subunit around the initiation codon to form a preinitiation complex (4). The importance of the SD interaction for efficient initiation of translation has been experimentally verified for both eubacteria and archaebacteria. Alterations of the SD sequence or the anti-SD sequence strongly inhibit protein synthesis, both in eubacteria including Escherichia coli (5) and Bacillus subtilis (6, 7) and in archaebacteria such as Methanocaldococcus jannaschii (8). For this reason, the SD interaction is thought to be the universal m...

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Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1

Cited by 256 publications

References 52 publications

pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression

pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

Dynamic evolution of translation initiation mechanisms in prokaryotes

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