The chloroplast psbK operon from mustard (Sinapis alba L.): multiple transcripts during seedling development and evidence for divergent overlapping transcription

Neuhaus, H.; Link, Gerhard

doi:10.1007/bf00318220

Cited by 29 publications

(17 citation statements)

References 45 publications

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“…Thus, the intergenic transcript contains an antisense tRNA (or an antisense tRNA precursor). It is not clear how inhibitory effects that one might expect for the function (or maturation) ofthe serine tRNA are avoided, but similar situations have been reported for other polycistronic chloroplast transcripts containing antisense tRNA sequences (31,32). Our observation of the rps4-IRF170 linkage supports the supposition that the entire gene cluster constitutes a single transcriptional unit (18), although it still remains to be determined whether the flanking tRNA genes (trnT and trnR) have to be included in this unit.…”

Section: Atagaaggg T T S Gsupporting

confidence: 75%

Complete RNA editing of unspliced and dicistronic transcripts of the intron-containing reading frame IRF170 from maize chloroplasts.

Ruf

Zeltz

Kössel

1994

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

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The maize plastome harbors within the rps4-rpsl4 gene cluster the reading frame IRF170, which is interrupted by two introns. Although the function of the encoded peptide of 170 amino acids is not known, the conservation of IRF170 homologs in other plastomes is a strong indication that IRF170 is a functional gene. Amplification and sequence analyses ofIRF170 specific cDNAs reveals two C-to-U editing events occurring within each of the first two exons. This situation allows an analysis of the temporal order between editing and splicing of a chloroplast transcript. By using intron-specific primer combinations, cDNAs derived from partially or even uuspliced IRF170 transcripts could be amplfied which in all cases showed complete editing. Complete editing was also observed with a cDNA derived from a transcript in which the proximal rps4 and the 5' half of IRF170-encoded sequences were still linked. This demonstrates that editing of the IRF170 transcript is an early processing step preceding both splicing and cleavage to monocistronic mRNA.The primary transcripts encoded by chloroplast protein genes are known to undergo a series of processing steps such as splicing, cleavage to monocistronic mRNAs, and trimming of terminal sequences (1, 2). More recently, editing has been detected as an additional step of chloroplast mRNA maturation (3-7). This process was originally observed in mitochondrial transcripts of trypanosomes (8, 9) but was subsequently also found in nuclear-encoded transcripts of mammals (10) and in mitochondrial transcripts of plants (11-13) and of the acellular slime mold Physarum (14). Depending on the different types of editing processes, the genetic information transmitted to the primary transcripts of the respective genes can be altered by nucleotide insertions and deletions (8,9,14) or by base substitutions (10-13). The editing events observed in chloroplast transcripts so far all result in C-to-U transitions, thereby restoring codons for conserved amino acid residues of the respective peptides (3-7).The reading frame designated IRF170 is subdivided by two introns and is well conserved within the rps4-rpsl4 gene cluster of the plastomes of higher plants (ref. 15; see Fig. 1), whereas a homologous reading frame without introns could be identified in the cyanobacterium Synechocystis (16). Although the function of the encoded peptide, consisting in maize of 170 amino acids, is not known, the absence of an IRF170 homolog in the plastome of the nonphotosynthetic parasitic plant Epifagus (17) as well as differences in the processing of IRF170 transcripts between amyloplasts and chloroplasts from maize (18) appears to suggest a function as a component of the photosynthetic apparatus. This supposition is further supported by the codon usage of IRF170-encoded mRNAs (15) and by the existence of a cyanobacterial IRF170 homolog (16).The existence of a large primary transcript which includes sequences of the flanking genes of the rps4-rpsl4 gene cluster and the presence of two introns in the IRF170-enco...

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Section: Atagaaggg T T S Gsupporting

confidence: 75%

Complete RNA editing of unspliced and dicistronic transcripts of the intron-containing reading frame IRF170 from maize chloroplasts.

Ruf

Zeltz

Kössel

1994

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

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“…Similar to most protein-encoding genes/operons and the rRNA gene cluster, the majority of tRNA genes are transcribed by PEP from typical σ 70 -like promoters upstream of the transcription start site [155]. In addition, some reports suggest that several tRNAs are transcribed from gene-internal promoters; these include the spinach trnS, trnR and trnT [53, 86,323], the mustard trnS, trnH and trnR [156,195,196], and the Chlamydomonas trnE [119]. However, the exact tRNA-related internal promoter elements and the polymerase(s) capable of recognizing them have not yet been elucidated.…”

Section: Pep Promotersmentioning

confidence: 99%

Chloroplast Gene Expression—RNA Synthesis and Processing

Börner¹,

Zhelyazkova²,

Legen³

et al. 2014

Plastid Biology

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Both transcription and transcript processing are more complex in chloroplasts than in bacteria. Plastid genes are transcribed by a plastid-encoded RNA polymerase (PEP) and one (monocots) or two (dicots) nuclear-encoded RNA polymerase(s) (NEP). PEP is a bacterial-type multisubunit enzyme composed of core subunits (coded for by the plastid rpoA, B, C1 and C2 genes) and additional protein factors encoded in the nuclear genome. The nuclear genome of Arabidopsis contains six genes for sigma factors required by PEP for promoter recognition. NEP activity is represented by phage-type RNA polymerases. Factors supporting NEP activity have not been identified yet. NEP and PEP use different promoters. Both types of RNA polymerase are active in proplastids and all stages of chloroplast development. PEP is the dominating transcriptase in chloroplasts.Chloroplast RNA processing consists of hundreds of mostly independent events. In recent years, much progress has been made in identifying factors behind RNA splicing and RNA editing. Namely, pentatricopeptide repeat (PPR) proteins have come into focus as RNA binding proteins conferring specificity to individual processing events. Also, studies on chloroplast RNases have helped considerably to understand chloroplast RNA turnover. Such mechanistic insights are set in contrast to how little we know about the regulatory role of RNA processing in chloroplasts.Keywords Chloroplast transcription · Chloroplast RNA polymerase · Chloroplast promoter · Chloroplast RNA processing · Chloroplast RNA-binding proteins · PPR proteins · Chloroplast splicing · Chloroplast editing · Chloroplast RNA degradation · Chloroplast nucleases Abbreviations CRS2 Chloroplast RNA splicing 2 protein IR Inverted repeat NEP Nuclear-encoded plastid RNA polymerase

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“…Five of them were identical between green and white libraries (see Supplemental Data Set 2 and Supplemental Table 3 online). These TSSs could either result from upstream promoters or indicate transcription from internal promoters as proposed for several chloroplast tRNA genes in spinach (Gruissem et al, 1986;Cheng et al, 1997) and mustard (Sinapis alba; Neuhaus and Link, 1990;Nickelsen and Link, 1990;Liere and Link, 1994). They might be false-positive TSS candidates due to the particular structure of tRNAs in which the amino acid acceptor stem might protect some mature 59 ends of tRNAs from the attack of TEX.…”

Section: The Primary Transcriptome Of Annotated Genesmentioning

confidence: 99%

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

et al. 2012

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Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.

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The chloroplast psbK operon from mustard (Sinapis alba L.): multiple transcripts during seedling development and evidence for divergent overlapping transcription

Cited by 29 publications

References 45 publications

Complete RNA editing of unspliced and dicistronic transcripts of the intron-containing reading frame IRF170 from maize chloroplasts.

Complete RNA editing of unspliced and dicistronic transcripts of the intron-containing reading frame IRF170 from maize chloroplasts.

Chloroplast Gene Expression—RNA Synthesis and Processing

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

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