The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Liere, Karsten; Weihe, Andreas; Börner, Thomas

doi:10.1016/j.jplph.2011.01.005

Cited by 204 publications

(184 citation statements)

References 346 publications

(420 reference statements)

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“…However, we detected the YRTa motif typical for NEP type Ia and Ib promoters (Liere et al, 2011) upstream of only 73% of the TSSs in white leaves. Similarly, upstream of many TSSs in higher plant mitochondria, where transcription is performed by NEPrelated phage-type RNA polymerases, no conserved promoter motifs could be detected.…”

Section: Promoter Motifs In Green and White Plastidsmentioning

confidence: 75%

“…During evolution, the majority of the cyanobacterial genes were lost or transferred to the nucleus of the host cell, while several genes mainly required for photosynthesis and gene expression were retained in the organellar genome (Kleine et al, 2009). The plastid genome (plastome) contains functional rpo genes coding for homologs of the cyanobacterial RNA polymerase subunits a, b, b', and b'', which form the core of the plastid-encoded plastid RNA polymerase (PEP; Ohyama et al, 1986;Shinozaki et al, 1986;Sijben-Mü ller et al, 1986;Hajdukiewicz et al, 1997;Liere et al, 2011). Nuclear-encoded sigma factors interact with PEP to confer promoter recognition (Liu and Troxler, 1996;Tanaka et al, 1996Tanaka et al, , 1997Schweer et al, 2010;Lerbs-Mache, 2011).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Promoter Motifs In Green and White Plastidsmentioning

confidence: 75%

Section: Introductionmentioning

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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“…Besides PEP, a nuclear-encoded plastid RNA polymerase, NEP, has been postulated to be involved in plastid gene transcription (for a recent review see Liere et al 2011). So far, this NEP has neither been identified in the TAC fraction nor in the soluble protein fraction (Pfannschmidt and Link 1994;Krause and Krupinska 2000) that has recently been subjected to proteomic analysis (Schröter et al 2010) nor in any of the nucleoid or TAC proteomes.…”

Section: Transcriptionmentioning

confidence: 99%

New insights into plastid nucleoid structure and functionality

Krupinska¹,

Melonek²,

Krause

2012

Planta

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Investigations over many decades have revealed that nucleoids of higher plant plastids are highly dynamic with regard to their number, their structural organization and protein composition. Membrane attachment and environmental cues seem to determine the activity and functionality of the nucleoids and point to a highly regulated structure-function relationship. The heterogeneous composition and the many functions that are seemingly associated with the plastid nucleoids could be related to the high number of chromosomes per plastid. Recent proteomic studies have brought novel nucleoidassociated proteins into the spotlight and indicated that plastid nucleoids are an evolutionary hybrid possessing prokaryotic nucleoid features and eukaryotic (nuclear) chromatin components, several of which are dually targeted to the nucleus and chloroplasts. Future studies need to unravel if and how plastid-nucleus communication depends on nucleoid structure and plastid gene expression.

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“…The plastome in land plants carries over 120 genes encoding key components of the plastidial transcriptional, translational, and photosynthetic apparatuses (Sugiura, 1992;Wakasugi et al, 2001). Plastomic genes are transcribed by two types of plastid RNA polymerases: a phage-type nuclear-encoded plastid RNA polymerase (NEP) and a eubacterial-type plastid-encoded plastid RNA polymerase (PEP; LerbsMache, 1993;Allison et al, 1996;Hricová et al, 2006;Liere et al, 2011). Although most plastid genes are transcribed by both the NEP and PEP (Legen et al, 2002;Demarsy et al, 2006Demarsy et al, , 2012, housekeeping genes are preferentially transcribed by the NEP, whereas photosynthetic genes are transcribed mainly by the PEP (Allison et al, 1996;Hajdukiewicz et al, 1997;Hübschmann and Börner, 1998).…”

mentioning

confidence: 99%

Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus

et al. 2017

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HEMERA (HMR) is a nuclear and plastidial dual-targeted protein. While it functions in the nucleus as a transcriptional coactivator in phytochrome signaling to regulate a distinct set of light-responsive, growth-relevant genes, in plastids it is known as pTAC12, which associates with the plastid-encoded RNA polymerase, and is essential for inducing the plastomic photosynthetic genes and initiating chloroplast biogenesis. However, the mechanism of targeting HMR to the nucleus and plastids is still poorly understood. Here, we show that HMR can be directly imported into chloroplasts through a transit peptide residing in the N-terminal 50 amino acids. Upon cleavage of the transit peptide and additional proteolytic processing, mature HMR, which begins from Lys-58, retains its biochemical properties in phytochrome signaling. Unexpectedly, expression of mature HMR failed to rescue not only the plastidial but also the nuclear defects of the hmr mutant. This is because the predicted nuclear localization signals of HMR are nonfunctional, and therefore mature HMR is unable to accumulate in either plastids or the nucleus. Surprisingly, fusing the transit peptide of the small subunit of Rubisco with mature HMR rescues both its plastidial and nuclear localization and functions. These results, combined with the observation that the nuclear form of HMR has the same reduced molecular mass as plastidial HMR, support a retrograde protein translocation mechanism in which HMR is targeted first to plastids, processed to the mature form, and then relocated to the nucleus.

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The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Cited by 204 publications

References 346 publications

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

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

New insights into plastid nucleoid structure and functionality

Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus

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