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Maureen R Hanson - One of the best experts on this subject based on the ideXlab platform.
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arabidopsis ranbp2 type zinc finger proteins related to Chloroplast RNA editing factor oz1
Plants (Basel Switzerland), 2020Co-Authors: Andrew B Gipson, Maureen R Hanson, Ludovic Giloteaux, Stephane BentolilaAbstract:OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis Chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of Chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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a zinc finger motif containing protein is essential for Chloroplast RNA editing
PLOS Genetics, 2015Co-Authors: Giulia Friso, Stephane Bentolila, Klaas J Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or Chloroplasts. By co-immunoprecipitation of the Chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in Chloroplasts and affects editing efficiency of another 16 Chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the Chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the Chloroplast RNA editosome. The RNA editosomes that act upon most Chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to Chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.
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A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing
PLoS genetics, 2015Co-Authors: Tao Sun, Stephane Bentolila, Giulia Friso, Xiaowen Shi, Klaas J. Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (
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Chloroplast RNA metabolism.
Annual review of plant biology, 2010Co-Authors: David B Stern, Michel Goldschmidt-clermont, Maureen R HansonAbstract:The Chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the Chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers four major Chloroplast posttranscriptional processes: RNA processing, editing, splicing, and turnover. RNA processing includes the generation of transcript 5' and 3' termini, as well as the cleavage of polycistronic transcripts. Editing converts specific C residues to U and often changes the amino acid that is specified by the edited codon. Chloroplasts feature introns of groups I and II, which undergo protein-facilitated cis- or trans-splicing in vivo. Each of these RNA-based processes involves proteins of the pentatricopeptide motif-containing family, which does not occur in prokaryotes. Plant-specific RNA-binding proteins may underpin the adaptation of the Chloroplast to the eukaryotic context.
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Substrate and cofactor requirements for RNA editing of Chloroplast transcripts in Arabidopsis in vitro
The Plant journal : for cell and molecular biology, 2005Co-Authors: Carla E. Hegeman, Michael L. Hayes, Maureen R HansonAbstract:None of the macromolecular components of the Chloroplast RNA editing apparatus has yet been identified. In order to facilitate biochemical purification and characterization of the Chloroplast RNA editing apparatus, we have identified conditions suitable for production of Chloroplast extracts from the model plant Arabidopsis that are capable of editing exogenous substrates produced by in vitro transcription. A simple poisoned primer extension assay readily quantified editing extent of mutated and wild-type substrates. Maximum editing efficiency typically varied from 10 to 40% with different Chloroplast preparations. Substrates carrying as little as 47 nt surrounding the psbE editing site were as efficiently edited as longer substrates. Editing activity was stimulated when either ATP, CTP, or dCTP was provided to the extract, an unusual observation also recently seen with plant mitochondrial editing extracts. Editing was sensitive to a zinc chelator, also a characteristic of the mammalian APOBEC editing enzyme, which is a zinc-dependent cytidine deaminase.
Robert F. Troxler - One of the best experts on this subject based on the ideXlab platform.
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CHARACTERIZATION OF A NUCLEAR‐ENCODED PHOTOGENE FOR A Chloroplast RNA POLYMERASE SIGMA FACTOR IN THE UNICELLULAR ALGA CYANIDIUM CALDARIUM (RHODOPHYTA)
Journal of Phycology, 1999Co-Authors: Bin Liu, Shi Tan, Robert F. TroxlerAbstract:Previously we identified the gene (rpoD1) for a σ factor of Chloroplast RNA polymerase from the unicellular rhodophyte Cyanidium caldarium Geitler and presented evidence for a multigene family of σ factors in this organism. In the present investigation, a new member of this gene family, rpoD2, was isolated and characterized. This gene was identified in a subgenomic library screened with the “rpoD box” probe, a highly conserved 28-base sequence found in the −10 promoter recognition motif of σ factors from eubacteria and cyanobacteria. Alignment of the deduced amino acid sequence of RpoD2 (the gene product of rpoD2) with other σ factors from C. caldarium showed that this protein contained all four conserved regions found in eubacterial and cyanobacterial σ factors in addition to a newly identified conserved domain. Northern analyses showed that rpoD2 transcripts were not detectable in dark-grown cells but were enriched in polyA+ RNA from illuminated cells, which suggests that rpoD2 is a positively regulated, nuclear-encoded photogene. The patterns of rpoD2 and rpoD1 transcript accumulation after transfer of cells from dark to light were distinct, which suggests that σ-factor genes are differentially expressed. Collectively, the results obtained support the hypothesis that differentially expressed, nuclear-encoded σ factors may transcribe subsets of plastid genes for photosynthesis during Chloroplast development.
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Molecular characterization of a positively photoregulated nuclear gene for a Chloroplast RNA polymerase sigma factor in Cyanidium caldarium
Proceedings of the National Academy of Sciences of the United States of America, 1996Co-Authors: Bin Liu, Robert F. TroxlerAbstract:Abstract We have cloned the gene for a putative Chloroplast RNA polymerase sigma factor from the unicellular rhodophyte Cyanidium caldarium. This gene contains an open reading frame encoding a protein of 609 amino acids with domains highly homologous to all four conserved regions found in bacterial and cyanobacterial sigma 70-type subunits. When Southern blots of genomic DNA were hybridized to the "rpoD box" oligonucleotide probe, up to six hybridizing hands were observed. Transcripts of the sigma factor gene were undetectable in RNA from dark-grown cells but were abundant in the poly(A)+ fraction of RNA from illuminated cells. The sigma factor gene was expressed in Escherichia coli, and antibodies against the expressed sigma factor fusion protein cross-reacted with a 55-kDa protein in partially purified Chloroplast RNA polymerase. Antibodies directed against a cyanobacterial RNA polymerase sigma factor also cross-reacted with a 55-kDa protein in the same enzyme preparation. Immunoprecipitation experiments showed that this enzyme preparation contains proteins with the same molecular weights as the alpha, beta, beta', and beta" subunits of Chloroplast RNA polymerase in higher plants. This study identifies a gene for a plastid RNA polymerase sigma factor and indicates that there may be a family of nuclear-encoded sigma factors that recognize promoters in subsets of plastid genes and regulate differential gene expression at the transcriptional level.
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Evidence That [sigma] Factors Are Components of Chloroplast RNA Polymerase
Plant Physiology, 1994Co-Authors: Robert F. Troxler, F. Zhang, Lawrence BogoradAbstract:Plastid genes are transcribed by DNA-dependent RNA polymerase(s), which have been incompletely characterized and have been examined in a limited number of species. Plastid genomes contain rpoA, rpoB, rpoC1, and rpoC2 coding for [alpha], [beta], [beta]9, and [beta]” RNA polymerase subunits that are homologous to the [alpha], [beta], and [beta]9subunits that constitute the core moiety of RNA polymerase in bacteria. However, genes with homology to [sigma] subunits in bacteria have not been found in plastid genomes. An antibody directed against the principal [sigma] subunit of RNA polymerase from the cyanobacterium Anabaena sp. PCC 7120 was used to probe western blots of purified Chloroplast RNA polymerase from maize, rice, Chlamydomonas reinhardtii, and Cyanidium caldarium. Chloroplast RNA polymerase from maize and rice contained an immunoreactive 64-kD protein. Chloroplast RNA polymerase from C. reinhardtii contained immunoreactive 100- and 82-kD proteins, and Chloroplast RNA polymerase from C. caldarium contained an immunoreactive 32-kD protein. The elution profile of enzyme activity of both algal Chloroplast RNA polymerases coeluted from DEAE with the respective immunoreactive proteins, indicating that they are components of the enzyme. These results provide immunological evidence for [sigma]-like factors in Chloroplast RNA polymerase in higher plants and algae.
Giulia Friso - One of the best experts on this subject based on the ideXlab platform.
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a zinc finger motif containing protein is essential for Chloroplast RNA editing
PLOS Genetics, 2015Co-Authors: Giulia Friso, Stephane Bentolila, Klaas J Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or Chloroplasts. By co-immunoprecipitation of the Chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in Chloroplasts and affects editing efficiency of another 16 Chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the Chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the Chloroplast RNA editosome. The RNA editosomes that act upon most Chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to Chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.
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A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing
PLoS genetics, 2015Co-Authors: Tao Sun, Stephane Bentolila, Giulia Friso, Xiaowen Shi, Klaas J. Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (
Gerhard Link - One of the best experts on this subject based on the ideXlab platform.
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The multisubunit Chloroplast RNA polymerase A from mustard (Sinapis alba L.)
European journal of biochemistry, 2000Co-Authors: Thomas Pfannschmidt, Sacha Baginsky, Karsten Ogrzewalla, Albert Sickmann, Helmut E. Meyer, Gerhard LinkAbstract:We previously identified two multisubunit plastid RNA polymerases termed A and B. The B enzyme has a bacterial-type polypeptide composition and is sensitive to the prokaryotic transcription inhibitor rifampicin (Rif); the A enzyme has a more complex subunit structure and is Rif-resistant. Here we report results of N-terminal sequencing and MS carried out with the A enzyme, which establish that the latter contains rpo gene products and is structurally related to the B enzyme. Furthermore, evidence is provided that the A enzyme can be converted into a Rif-sensitive enzyme form in a phosphorylation-dependent manner in vitro by a treatment that results in depletion of a β-like subunit. Database searches using sequence information derived from additional polypeptides that are present in purified A preparations revealed sequence similarity with Chloroplast proteins involved in RNA processing and redox control. This proteomics approach thus points to the complexity of the Chloroplast transcription apparatus and its interconnections with post-transcriptional and signalling mechanisms.
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Transcription factor phosphorylation by a protein kinase associated with Chloroplast RNA polymerase from mustard (Sinapis alba)
Plant Molecular Biology, 1997Co-Authors: Sacha Baginsky, Kai Tiller, Gerhard LinkAbstract:The Chloroplast transcription machinery involves multiple components with both catalytic and regulatory functions. Here we describe a serine-specific protein kinase activity that is associated with the major Chloroplast RNA polymerase and phosphorylates sigma-like transcription factors in vitro. The kinase activity can be assigned to a 54 kDa polypeptide of partially purified RNA polymerase (KPC, kinase polymerase complex). This polypeptide is also present in a smaller complex that contains several putative polymerase subunits and reveals kinase activity but lacks transcription activity (KC, kinase complex). Although the 54 kDa component could not be chromatographically separated from the rest of this complex without loss of activity, it retained residual kinase activity in an electrophoretic blot assay. The polymerase-associated kinase is itself affected by in vitro phosphorylation and dephosphorylation, which raises the possibility that it is part of a signalling cascade that controls Chloroplast transcription in vivo by factor phosphorylation.
Stephane Bentolila - One of the best experts on this subject based on the ideXlab platform.
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arabidopsis ranbp2 type zinc finger proteins related to Chloroplast RNA editing factor oz1
Plants (Basel Switzerland), 2020Co-Authors: Andrew B Gipson, Maureen R Hanson, Ludovic Giloteaux, Stephane BentolilaAbstract:OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis Chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of Chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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a zinc finger motif containing protein is essential for Chloroplast RNA editing
PLOS Genetics, 2015Co-Authors: Giulia Friso, Stephane Bentolila, Klaas J Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (<400 kD) protein complexes called editosomes. Recognition of the proper C target for editing is mediated by pentatricopeptide repeat (PPR) containing proteins that recognize cis-elements. Members of two additional gene families, the RIP/MORF and ORRM families, have each been found to be required for editing of particular sets of Cs in mitochondria and/or Chloroplasts. By co-immunoprecipitation of the Chloroplast editing factor ORRM1, followed by mass spectrometry, we have now identified a member of the RanBP2 type zinc fingers (pFAM00641) protein family that is required for editing of 14 sites in Chloroplasts and affects editing efficiency of another 16 Chloroplast C targets. In yeast two-hybrid assays, OZ1 (Organelle Zinc finger 1) interacts with PPR site recognition factors whose cognate sites are affected when OZ1 is mutated. No interaction of OZ1 with the Chloroplast editing factors RIP2 and RIP9 was detected; however, OZ1 interacts with ORRM1, which binds to RIP proteins, allowing us to build a model for the Chloroplast RNA editosome. The RNA editosomes that act upon most Chloroplast C targets are likely to contain a PPR protein recognition factor, either RIP2 or RIP9, ORRM1, and OZ1. The organelle zinc finger editing factor family (OZ) contains 4 members in Arabidopsis, three that are predicted to be targeted to Chloroplasts and one to mitochondria. With the identification of OZ1, there are now 4 nuclear-encoded protein families known to be essential for plant organelle RNA editing.
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A Zinc Finger Motif-Containing Protein Is Essential for Chloroplast RNA Editing
PLoS genetics, 2015Co-Authors: Tao Sun, Stephane Bentolila, Giulia Friso, Xiaowen Shi, Klaas J. Van Wijk, Maureen R HansonAbstract:C-to-U editing of transcripts in plant organelles is carried out by small (