Chloroplast RNA-binding proteins

Nickelsen, Jörg

doi:10.1007/s00294-003-0425-0

Cited by 73 publications

(57 citation statements)

References 74 publications

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“…It has been estimated that up to 5000 unique nuclear genes encode proteins that are targeted to plastids (Martin and Herrmann,participate in stable or transient interactions with plastidencoded proteins or nucleic acids (Barkan and GoldschmidtClermont, 2000;Nickelsen, 2003). Intertaxonomic variability between such partners could trigger nuclear-organellar incompatibility.…”

Section: Introductionmentioning

confidence: 99%

Pigment Deficiency in Nightshade/Tobacco Cybrids Is Caused by the Failure to Edit the Plastid ATPase α-Subunit mRNA

et al. 2005

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The subgenomes of the plant cell, the nuclear genome, the plastome, and the chondriome are known to interact through various types of coevolving macromolecules. The combination of the organellar genome from one species with the nuclear genome of another species often leads to plants with deleterious phenotypes, demonstrating that plant subgenomes coevolve. The molecular mechanisms behind this nuclear-organellar incompatibility have been elusive, even though the phenomenon is widespread and has been known for >70 years. Here, we show by direct and reverse genetic approaches that the albino phenotype of a flowering plant with the nuclear genome of Atropa belladonna (deadly nightshade) and the plastome of Nicotiana tabacum (tobacco) develops as a result of a defect in RNA editing of a tobacco-specific editing site in the plastid ATPase a-subunit transcript. A plastome-wide analysis of RNA editing in these cytoplasmic hybrids and in plants with a tobacco nucleus and nightshade chloroplasts revealed additional defects in the editing of species-specific editing sites, suggesting that differences in RNA editing patterns in general contribute to the pigment deficiencies observed in interspecific nuclear-plastidial incompatibilities.

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Section: Introductionmentioning

confidence: 99%

Pigment Deficiency in Nightshade/Tobacco Cybrids Is Caused by the Failure to Edit the Plastid ATPase α-Subunit mRNA

et al. 2005

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“…This complexity is reflected by the existence of hundreds of nuclear genes encoding predicted organellar RNA binding proteins, many of which are specific to plants (Aubourg et al, 1999;Fedoroff, 2002;Landsberger et al, 2002;Lorkovic and Barta, 2002;Vermel et al, 2002;Belostotsky, 2003;Nickelsen, 2003;Ostheimer et al, 2003;Lurin et al, 2004;Nakamura et al, 2004). Some organellar RNA binding proteins have been detected through their ability to bind RNA in vitro and others have surfaced through genetic screens, but most are unstudied.…”

Section: Introductionmentioning

confidence: 99%

RNA Immunoprecipitation and Microarray Analysis Show a Chloroplast Pentatricopeptide Repeat Protein to Be Associated with the 5′ Region of mRNAs Whose Translation It Activates

2005

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Plant nuclear genomes encode hundreds of predicted organellar RNA binding proteins, few of which have been connected with their physiological RNA substrates and functions. In fact, among the largest family of putative RNA binding proteins in plants, the pentatricopeptide repeat (PPR) family, no physiologically relevant RNA ligands have been firmly established. We used the chloroplast-splicing factor CAF1 to demonstrate the fidelity of a microarray-based method for identifying RNAs associated with specific proteins in chloroplast extract. We then used the same method to identify RNAs associated with the maize (Zea mays) PPR protein CRP1. Two mRNAs whose translation is CRP1-dependent were strongly and specifically enriched in CRP1 coimmunoprecipitations. These interactions establish CRP1 as a translational regulator by showing that the translation defects in crp1 mutants are a direct consequence of the absence of CRP1. Additional experiments localized these interactions to the 59 untranslated regions and suggested a possible CRP1 interaction motif. These results enhance understanding of the PPR protein family by showing that a PPR protein influences gene expression through association with specific mRNAs in vivo, suggesting an unusual mode of RNA binding for PPR proteins, and highlighting the possibility that translational regulation may be a particularly common function of PPR proteins. Analogous methods should have broad application for the study of native RNA-protein interactions in both mitochondria and chloroplasts.

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“…Detailed analyses have demonstrated that within these UTRs lie cis-elements, often forming secondary structures, which facilitate the interaction with nucleus-encoded RBPs (Yang et al, 1995;Hirose and Sugiura, 1996;Klaff et al, 1997;Alexander et al, 1998;Zou et al, 2003;Merhige et al, 2005). RBPs display an array of functions, including processing of polycistronic transcription units, RNA maturation and editing, transcript stability and turnover, and the recruitment of additional protein factors involved in the initiation of translation in response to the requirements of the cell (Nickelsen, 2003;Schmitz-Linneweber and Barkan, 2007). In contrast to the high level of conservation found within protein-coding regions and ribosomal RNAs, intergenic and UTRs are highly variable in chloroplast genomes (Daniell et al, 2006;Saski et al, 2007;Timme et al, 2007).…”

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confidence: 99%

The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression

et al. 2010

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Heterologous regulatory elements and flanking sequences have been used in chloroplast transformation of several crop species, but their roles and mechanisms have not yet been investigated. Nucleotide sequence identity in the photosystem II protein D1 (psbA) upstream region is 59% across all taxa; similar variation was consistent across all genes and taxa examined. Secondary structure and predicted Gibbs free energy values of the psbA 5# untranslated region (UTR) among different families reflected this variation. Therefore, chloroplast transformation vectors were made for tobacco (Nicotiana tabacum) and lettuce (Lactuca sativa), with endogenous (Nt-Nt, Ls-Ls) or heterologous (Nt-Ls, Ls-Nt) psbA promoter, 5# UTR and 3# UTR, regulating expression of the anthrax protective antigen (PA) or human proinsulin (Pins) fused with the cholera toxin B-subunit (CTB). Unique lettuce flanking sequences were completely eliminated during homologous recombination in the transplastomic tobacco genomes but not unique tobacco sequences. Nt-Ls or Ls-Nt transplastomic lines showed reduction of 80% PA and 97% CTB-Pins expression when compared with endogenous psbA regulatory elements, which accumulated up to 29.6% total soluble protein PA and 72.0% total leaf protein CTB-Pins, 2-fold higher than Rubisco. Transgene transcripts were reduced by 84% in Ls-Nt-CTB-Pins and by 72% in Nt-Ls-PA lines. Transcripts containing endogenous 5# UTR were stabilized in nonpolysomal fractions. Stromal RNA-binding proteins were preferentially associated with endogenous psbA 5# UTR. A rapid and reproducible regeneration system was developed for lettuce commercial cultivars by optimizing plant growth regulators. These findings underscore the need for sequencing complete crop chloroplast genomes, utilization of endogenous regulatory elements and flanking sequences, as well as optimization of plant growth regulators for efficient chloroplast transformation.Over the expanse of time since the endosymbiotic events that led to the establishment of plant organelles, plant cells have evolved elaborate mechanisms to coordinate the expression of plastid genes with the changing developmental and functional requirements of the cell. In addition to the nucleus-encoded, plastidlocalized RNA polymerase, the nucleus controls the expression of a suite of s-factors required for the active transcription of photosynthetic genes by the plastidencoded RNA polymerase (PEP), with PEP itself being transcribed by nucleus-encoded, plastid-localized RNA polymerase (Allison et al., 1996;Hess and Borner, 1999). Nuclear control over translation of plastid mRNA is exerted through the activities of numerous plastid-localized RNA-binding proteins (RBPs). RBPs appear to have a tight affinity for their cognate sequences in plastid mRNAs, and studies have demonstrated that their interactions are specific for particular genes (Nakamura et al., 1999(Nakamura et al., , 2001Shen et al., 2001;Meierhoff et al., 2003;Schmitz-Linneweber et al., 2005.Plastid mRNAs, expressed as monocistrons or polycistro...

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Chloroplast RNA-binding proteins

Cited by 73 publications

References 74 publications

Pigment Deficiency in Nightshade/Tobacco Cybrids Is Caused by the Failure to Edit the Plastid ATPase α-Subunit mRNA

Pigment Deficiency in Nightshade/Tobacco Cybrids Is Caused by the Failure to Edit the Plastid ATPase α-Subunit mRNA

RNA Immunoprecipitation and Microarray Analysis Show a Chloroplast Pentatricopeptide Repeat Protein to Be Associated with the 5′ Region of mRNAs Whose Translation It Activates

The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression

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