Article
Biochemistry & Molecular Biology
Li Zhang, Jingli Chen, Liqun Zhang, Ying Wei, Yajuan Li, Xinyun Xu, Hui Wu, Zhong-Nan Yang, Jirong Huang, Fenhong Hu, Weihua Huang, Yong-Lan Cui
Summary: The plastid-localized PPR protein EMB1270 is essential for chloroplast biogenesis in Arabidopsis thaliana, playing a crucial role in the accumulation of photosynthetic proteins and splicing efficiency of specific plastid introns. EMB1270 interacts with CFM2 to facilitate the splicing of group II introns, highlighting its importance in coordinating chloroplast and nuclear gene expression.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Plant Sciences
Lisa Jung, Sarah Schleicher, Fatema Alsaied Taha, Mizuki Takenaka, Stefan Binder
Summary: The Arabidopsis thaliana genome contains over 450 nuclear genes encoding PPR proteins, many of which have unknown functions. Knockout of the At4g19440 gene, which codes for a P-type PPR protein, affects embryo development and seed maturation in Arabidopsis. Knockout of At4g19440 also leads to changes in the abundance of several mitochondria-encoded transcripts.
Article
Biochemistry & Molecular Biology
Sarah Schleicher, Stefan Binder
Summary: The study reveals the important roles of RNA processing factors 1 and 8 in Arabidopsis mitochondria, as well as the contribution of other factors to the formation of dicistronic transcripts.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Mizuki Takenaka, Sachi Takenaka, Tatjana Barthel, Brody Frink, Sascha Haag, Daniil Verbitskiy, Bastian Oldenkott, Mareike Schallenberg-Rudinger, Christian G. Feiler, Manfred S. Weiss, Gottfried J. Palm, Gert Weber
Summary: RNA editosomes selectively deaminate cytidines to uridines to restore protein functionality in plant organellar transcripts; DYW domains contain a cytidine deaminase fold and a C-terminal DYW motif, regulated by a gated zinc shutter in the deaminase fold.
Article
Plant Sciences
Shi-Kai Cao, Rui Liu, Miaodi Wang, Feng Sun, Aqib Sayyed, Hong Shi, Xiaomin Wang, Bao-Cai Tan
Summary: This study identified the role of a small P-type pentatricopeptide repeat protein, SPR2, in mediating the splicing of over half of the Group II introns in maize mitochondria. SPR2 interacts with PPR-SMR1 and other splicing factors, suggesting its involvement in the formation of a splicing complex.
Article
Biochemistry & Molecular Biology
Elena Lesch, Maximilian T. Schilling, Sarah Brenner, Yingying Yang, Oliver J. Gruss, Volker Knoop, Mareike Schallenberg-Ruedinger
Summary: RNA editing processes differ significantly between animals and plants, with plant PPR proteins playing a key role in plant organelle cytidine-to-uridine editing. It has been discovered that plant PPR editing factors can operate in the nucleo-cytosolic environment of humans and be re-engineered towards new targets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Santana Royan, Bernard Gutmann, Catherine Colas des Francs-Small, Suvi Honkanen, Jason Schmidberger, Ashley Soet, Yueming Kelly Sun, Lilian Vincis Pereira Sanglard, Charles S. Bond, Ian Small
Summary: RNA editing in plants is carried out by PPR proteins, and a synthetic editing factor using PPR motifs has been successfully designed and demonstrated high specificity. This study paves the way for the design and application of programmable RNA editing factors based on plant PPR proteins.
COMMUNICATIONS BIOLOGY
(2021)
Article
Cell Biology
Bernard Gutmann, Michael Millman, Lilian Vincis Pereira Sanglard, Ian Small, Catherine Colas des Francs-Small
Summary: In Arabidopsis thaliana, there are numerous C-to-U RNA editing events in the mitochondria and chloroplasts, with specificity provided by PPR proteins. The study identified MEF100 as essential for editing at specific sites in Arabidopsis mitochondria, affecting Complex I activity and leading to physiological consequences. Loss of the necessity for MEF100 editing results in divergence in the MEF100 binding site.
Article
Agronomy
Huadong Wang, Qing Xiao, Chao Wei, Hui Chen, Xiaohan Chen, Cheng Dai, Jing Wen, Chaozhi Ma, Jinxing Tu, Tingdong Fu, Jinxiong Shen, Bin Yi
Summary: By utilizing Brassica 60 K array, bulk segregant analysis, and map-based cloning, a mitochondria-localized pentatricopeptide repeat protein gene was identified and transferred into the hau CMS line, where it successfully restored fertility. The research showed that Rfh was highly expressed in flower buds, and the functional divergence between RFH and rfh may be attributed to 59 amino acid residue differences in the deduced protein sequences.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Xiang Wei, Yifang Zhu, Wenxiang Xie, Weiwei Ren, Yang Zhang, Hui Zhang, Shaojun Dai, Chao-Feng Huang
Summary: H2O2 plays a crucial regulatory role in aluminum resistance by affecting the stability of the key protein STOP1, which is involved in promoting aluminum resistance in plants.
Article
Plant Sciences
Ayako Maeda, Sachi Takenaka, Tenghua Wang, Brody Frink, Toshiharu Shikanai, Mizuki Takenaka
Summary: C-to-U RNA editing sites in plant organelles exhibit a strong preference for neighboring nucleotides. The PPR domain of RNA editing factors binds to the 5' sequence of target cytidines, while the DYW domain catalyzes the C-to-U deamination. The DYW domain has a distinct preference for neighboring nucleotides, contributing to target selection.
Article
Multidisciplinary Sciences
Robert D. Boyd, Michael L. Hayes
Summary: Organellar C-to-U RNA editing in plants is catalyzed by DYW-deaminases and occurs in complexes composed of various classes of nuclear-encoded proteins. Recombinant DYW-deaminases from plants have been associated with ribonuclease activity in vitro, which is not required for the editing process and lacks a clear physiological function in vivo. This study investigates the ribonuclease activity of recombinant AtDYW1 and its interaction with RNA editing factors in vitro. The results suggest that the ribonuclease activity of AtDYW1 is limited to RNAs in the absence of native editing complex partners and is specifically inhibited by RNA editing factors.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Bar-Lev Yamit, Senden Esther, Pasmanik-Chor Metsada, Sapir Yuval
Summary: The Royal Irises, characterized by large flowers and a unique pollination system, are currently undergoing speciation and are a model for evolutionary processes and pollination ecology. Although transcriptomic and genomic data are lacking, the de novo transcriptome assembly of Iris atropurpurea provides a valuable resource for gene discovery and molecular marker development in irises, facilitating further eco-evolutionary studies of this group.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Tshegofatso Dikobe, Katlego Sehlabane, Enetia Bobo, Angela Sibanda-Makuvise, Patience Chatukuta, David Kawadza, Oziniel Ruzvidzo
Summary: Downstream signalling in plants is important for cell division, growth, and stress response. A new molecule, AtPPR, was identified with both adenylyl cyclase (AC) and kinase activities, suggesting cross-talking interactions between these two domains. This discovery has implications for improving plants, particularly agricultural crops.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Article
Multidisciplinary Sciences
Thomas Hollin, Steven Abel, Alejandra Falla, Charisse Flerida A. Pasaje, Anil Bhatia, Manhoi Hur, Jay S. Kirkwood, Anita Saraf, Jacques Prudhomme, Amancio De Souza, Laurence Florens, Jacquin C. Niles, Karine G. Le Roch
Summary: Using high-throughput functional genomics, including metabolomics, Hollin et al. identified two essential RAP proteins in Plasmodium falciparum and revealed their role in controlling mitochondrial rRNAs.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Anthony Gobert, Yifat Quan, Mathilde Arrive, Florent Waltz, Nathalie Da Silva, Lucile Jomat, Mathias Cohen, Isabelle Jupin, Philippe Giege
Summary: The study demonstrates the potential of using cytosolic expressed protein-only RNase P to combat plant viruses, showing its ability for in vitro cleavage of tRNA-like structures in many plant viruses. However, varied in vivo results were observed, and further discussion is needed to understand the reasons behind these differences.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Albert Moussaron, Valerie Jouan-Hureaux, Charlotte Collet, Julien Pierson, Noemie Thomas, Laurence Choulier, Nicolas Veran, Matthieu Doyen, Philippe Arnoux, Fatiha Maskali, Dominique Dumas, Samir Acherar, Muriel Barberi-Heyob, Celine Frochot
Summary: Secondary brain tumors present a major challenge in oncology due to their poor prognosis and fatal outcome. Molecular imaging techniques, such as Positron Emission Tomography (PET), show promise in early diagnosis, but are limited by the availability of radiotracers. Tumor angiogenesis and neuropilin-1 receptor overexpression are crucial in malignant tumor progression, and a new gallium-68 radiolabeled peptide targeting NRP-1 demonstrates potential for improved detection of cerebral metastases.
Article
Cell Biology
Elisabete Cruz Da Silva, Laurence Choulier, Jessica Thevenard-Devy, Christophe Schneider, Philippe Carl, Philippe Ronde, Stephane Dedieu, Maxime Lehmann
Summary: EGFR, a therapeutic target in GBM, is closely regulated by endocytosis proteins, indicating a potential therapeutic target for improving GBM treatment.
Review
Plant Sciences
Joanna Melonek, Ian Small
Summary: Recent breakthroughs in sequencing data have revealed unexpected expansions in gene families related to restoring fertility in certain species, which will greatly benefit the development of hybrid production strategies in wheat and related species.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jeremy Cartalas, Lena Coudray, Anthony Gobert
Summary: Mitochondria are the powerhouses of eukaryote cells, playing crucial roles in energy production. Mitochondrial RNA biology is diverse, involving a wide range of factors, with a particular focus on ribonucleases. These ribonucleases are involved in various functions, including transcript maturation, RNA degradation, surveillance, as well as mitochondrial DNA maintenance and replication, and potentially mitochondrial ribosome biogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Basma Abdallah, Cendrine Seguin, Elora Aubert, Hassan Ait BenHassou, Laila Sbabou, Laurence Choulier, Catherine Vonthron, Isabelle J. Schalk, Gaetan L. A. Mislin, Sylvie Fournel, Veronique Pitchon, Pierre Fechter
Summary: This study explores the combination of metals and plants in ancient remedies and provides evidence for their potential therapeutic effects. By analyzing four medical formularies from the 9-12th century, the researchers discovered that these remedies contained a high proportion of metals and identified their specific roles in combating infections and promoting wound healing. The findings highlight the knowledge and skills of ancient physicians in manipulating metals for therapeutic purposes.
JOURNAL OF TRACE ELEMENTS IN MEDICINE AND BIOLOGY
(2022)
Article
Plant Sciences
Suvi Honkanen, Ian Small
Summary: The pentatricopeptide repeat protein GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants. It is highly conserved among land plants and plays a key role in chloroplast gene expression and retrograde signaling.
Article
Pharmacology & Pharmacy
Elisabete Cruz Da Silva, Sophie Foppolo, Benoit Lhermitte, Marina Ingremeau, Helene Justiniano, Lorraine Klein, Marie-Pierre Chenard, Romain Vauchelles, Basma Abdallah, Maxime Lehmann, Nelly Etienne-Selloum, Monique Dontenwill, Laurence Choulier
Summary: In this study, nucleic-acid aptamers were used for fluorescence imaging to detect EGFR and integrin alpha 5 beta 1 in human glioblastoma tissues. The aptafluorescence assays proved to be able to easily reveal inter-tumoral and intra-tumoral heterogeneity. The strengths and limitations of nucleic-acid aptamers for biomarker detection in histology were also discussed.
Article
Biochemical Research Methods
Rose McDowell, Ian Small, Charles S. Bond
Summary: This review presents the latest understanding of RNA site recognition by PPR proteins and the progress made towards designing synthetic PPR proteins for RNA targeting. PPR proteins are considered ideal candidates for targeting and binding RNA transcripts due to their defined RNA binding code and modular structure.
Article
Genetics & Heredity
Alejandro A. Edera, Katharine A. Howell, Paul G. Nevill, Ian Small, M. Virginia Sanchez-Puerta
Summary: In angiosperms, the distribution of cox2i373 and cox2i691 introns in the mitochondrial cox2 gene varies. Frequent intron loss events influenced by localized retroprocessing are observed in cox2i691. The elongation of cox2i691 introns, especially in domain IV, is likely due to nuclear intracelular DNA transfer followed by incorporation into mitochondrial DNA. Surprisingly, cox2i691 is erroneously annotated as absent in public databases, but studies have shown its functionality through efficient cis-splicing.
Article
Plant Sciences
Corinne Best, Ron Mizrahi, Rana Edris, Hui Tang, Hagit Zer, Catherine Colas des Francs-Small, Omri M. Finkel, Hongliang Zhu, Ian D. Small, Oren Ostersetzer-Biran
Summary: Mitochondrial biogenesis relies on nuclearly encoded factors, which regulate the expression of the organellar-encoded genes. Pentatricopeptide repeat (PPR) proteins constitute a major gene family in angiosperms that are pivotal in many aspects of mitochondrial (mt)RNA metabolism (e.g. trimming, splicing, or stability). The loss-of-function allele of the MSP1 gene leads to seed abortion.
Review
Biochemistry & Molecular Biology
Ian Small, Joanna Melonek, Alexandra-Viola Bohne, Joerg Nickelsen, Christian Schmitz-Linneweber
Summary: Plant organellar RNA metabolism is regulated by numerous nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. These post-transcriptional processes are critical for the production of essential components in chloroplasts and mitochondria, which are necessary for organellar biogenesis and plant survival. While many organellar RBPs have been identified, our understanding of their mechanisms and kinetics in fulfilling their functions remains incomplete. This review provides a comprehensive summary of plant organellar RNA metabolism, focusing on the mechanistic aspects and kinetics of RBP functions.
Article
Biochemistry & Molecular Biology
Lilian Vincis Pereira Sanglard, Ian D. Small, Catherine Colas des Francs-Small, Abir U. Igamberdiev
Summary: Researchers created a library of redesigned PPR proteins, related to restorer-of-fertility proteins, and transformed them into plants to target mitochondrial transcripts. Testing 90 different variants in vivo showed a wide range of phenotypes. One specific variant from the library induced specific cleavage of atp1 transcripts, resulting in a phenotype characterized by slow growth and downward curled leaves, validating the use of this library as a source of mitochondrial "mutants". This study is a step towards developing specific RNA targeting tools using PPR proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Sang Dang Huynh, Joanna Melonek, Catherine Colas des Francs-Small, Charles S. Bond, Ian Small
Summary: Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that target mitochondria and bind to transcripts inducing cytoplasmic male sterility. A distinct domain called RfCTD is found in most Rf proteins and is associated with cleavage of mitochondrial RNA targets. Plant genera with bisexual flowers have higher numbers of RFL genes, suggesting their role in male fertility.
Article
Biochemical Research Methods
Kalia Bernath-Levin, Jason Schmidberger, Suvi Honkanen, Bernard Gutmann, Yueming Kelly Sun, Anuradha Pullakhandam, Catherine Colas des Francs-Small, Charles S. Bond, Ian Small
Summary: In this study, synthetic PPR proteins based on the S-type PPR motif found in plant organellar RNA editing factors were investigated. The results showed that these synthetic S-type PPR proteins are easy to design, capable of binding with high affinity and specificity, and functional under a wide range of conditions. The S-type PPR proteins outperformed the P-type PPR scaffold in many situations.