Explanipedia

GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins Open

Michael Dennis, Amy Viljoen, Catherine Colas des Francs‐Small, Leni Campbell‐Clause, Ian Small , et al. · 2025

Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins with multiple roles in mitochondrial and chloroplast transcript processing. PPR proteins are naturally modular and hold great potential for development into tools …

A genus-wide pangenome of Hordeum Open

Martin Mascher, Jia‐Wu Feng, Axel Himmelbach, Andreas Houben, Nils Stein , et al. · 2025

The genus Hordeum, which includes cultivated barley and its wild relatives, represents a diverse group of grasses with agricultural, ecological, and evolutionary importance. Here, we present a genus-wide pangenome based on 25 chromosome-sc…

High Conservation of Translation-Enabling RNA Editing Sites in Hyper-editing Ferns Implies They Are Not Selectively Neutral Open

Farley M. Kwok van der Giezen, Rose McDowell, Owen Duncan, Simon Zumkeller, Catherine Colas des Francs‐Small , et al. · 2025

RNA editing is essential for processing transcripts in plant chloroplasts and mitochondria. Levels of RNA editing vary between lineages, but some hornworts, lycophytes, and ferns have an extraordinary abundance of RNA editing. A feature of…

The genetic architecture of temperature-induced partial fertility restoration in A1 cytoplasm in sorghum (Sorghum bicolor (L.) Moench) Open

David Jordan, Robert R. Klein, Joanna Melonek, Ian Small, Alan Cruickshank , et al. · 2025

GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins Open

Michael Dennis, S.Y. Low, Amy Viljoen, Anuradha Pullakhandam, Catherine Colas des Francs‐Small , et al. · 2025

Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA binding proteins with multiple roles in mitochondrial and chloroplast transcript processing. PPR proteins are naturally modular and hold great potential for development into tools …

The chloroplast RNA–binding protein CP29A supports rbcL expression during cold acclimation Open

Benjamin Lenzen, Florian Rösch, Julia Legen, Hannes Ruwe, Nitin Kachariya , et al. · 2025

The chloroplast genome encodes key components of the photosynthetic light reaction machinery as well as the large subunit of the enzyme central for carbon fixation, Ribulose-1,5-bisphosphat-carboxylase/-oxygenase (RuBisCo). Its expression …

Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein Open

Nicholas R. Marzano, Brady Johnston, Bishnu P. Paudel, Jason W. Schmidberger, Slobodan Jergic , et al. · 2024

Pentatricopeptide repeat proteins (PPR) are a large family of modular RNA-binding proteins, whereby each module can be modified to bind to a specific ssRNA nucleobase. As such, there is interest in developing ‘designer’ PPRs (dPPRs) for a …

The genetic architecture of temperature-induced partial fertility restoration in A1 cytoplasm in sorghum (Sorghum bicolor (L.) Moench) Open

David Jordan, Robert R. Klein, Joanna Melonek, Ian Small, Alan Cruickshank , et al. · 2024

Cytoplasmic male sterility (CMS) is used for commercial production of hybrid seed in sorghum. CMS-based hybrid breeding systems require female parental lines (CMS lines) to remain male sterile to prevent self-pollination and enable cross-p…

CRISPRi-based circuits to control gene expression in plants Open

Muhammad Adil Khan, Gabrielle Herring, Jia Yuan Zhu, Marina Oliva, Elliott Fourie , et al. · 2024

CRISPRi-based circuits to control gene expression in plants Open

Muhammad Adil Khan, Gabrielle Herring, Jia Yuan Zhu, Marina Oliva, Elliott Fourie , et al. · 2024

The plasmid data supporting the publication: CRISPRi-based circuits to control gene expression in plants

Insights into U‐to‐C RNA editing from the lycophyte Phylloglossum drummondii Open

Farley M. Kwok van der Giezen, Amy Viljoen, Leni Campbell‐Clause, Nhan Trong Dao, Catherine Colas des Francs‐Small , et al. · 2024

SUMMARY The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast a…

Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein Open

Nicholas R. Marzano, Brady Johnston, Bishnu P. Paudel, Jason W. Schmidberger, Slobodan Jergic , et al. · 2024

Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins that recognize specific ssRNA target sequences. There is significant interest in developing ‘designer’ PPRs for use in diagnostics or as tools to de…

CRISPRi-based circuits for genetic computation in plants Open

Muhammad Adil Khan, Gabrielle Herring, Jia Yuan Zhu, Marina Oliva, Elliott Fourie , et al. · 2024

The plasmid data supporting the publication: CRISPRi-based circuits for genetic computation in plants

Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase Open

Fei Yang, Lilian Vincis Pereira Sanglard, Chun Pong Lee, Elke Ströher, S.P. Singh , et al. · 2024

Spontaneous mutations are rare in mitochondria and the lack of mitochondrial transformation methods has hindered genetic analyses. We show that a custom-designed RNA-binding pentatricopeptide repeat (PPR) protein binds and specifically ind…

Global mitochondrial and chloroplast genome diversity in the threatened aquatic carnivorous plant Aldrovanda vesiculosa Open

Helena Štorchová, Manuela Krüger, Ian Small, Lubomı́r Adamec, Paul Nevill , et al. · 2023

Applications of Synthetic Pentatricopeptide Repeat Proteins Open

Farley M. Kwok van der Giezen, Suvi Honkanen, Catherine Colas des Francs‐Small, Charles S. Bond, Ian Small · 2023

RNA-binding proteins play integral roles in the regulation of essential processes in cells and as such are attractive targets for engineering to manipulate gene expression at the RNA level. Expression of transcripts in chloroplasts and mit…

The Chloroplast RNA Binding Protein CP29A supportsrbcLexpression during cold acclimation Open

Benjamin Lenzen, Florian Rösch, Hannes Ruwe, Nitin Kachariya, Julia Legen , et al. · 2023

The chloroplast genome encodes key components of the photosynthetic light reaction machinery as well as the large subunit of the enzyme central for carbon fixation, RuBisCo. Its expression is predominantly regulated post-transcriptionally,…

Alteration of Mitochondrial Transcript Expression in Arabidopsis thaliana Using a Custom-Made Library of Pentatricopeptide Repeat Proteins Open

Lilian Vincis Pereira Sanglard, Ian Small, Catherine Colas des Francs‐Small · 2023

Pentatricopeptide repeat (PPR) proteins are considered a potential tool for manipulating organelle gene expression in plants because they can recognise a wide range of different RNA sequences, and the molecular basis for this sequence reco…

A unique C‐terminal domain contributes to the molecular function of Restorer‐of‐fertility proteins in plant mitochondria Open

H Sang, Joanna Melonek, Catherine Colas des Francs‐Small, Charles S. Bond, Ian Small · 2023

Summary Restorer‐of‐fertility ( Rf ) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In…

A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria Open

H Sang, Joanna Melonek, Catherine Colas des Francs‐Small, Charles S. Bond, Ian Small · 2023

Summary Restorer-of-fertility ( Rf ) genes have practical applications in hybrid seed production as a means to control self-pollination. They encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they speci…

Plant organellar RNA maturation Open

Ian Small, Joanna Melonek, Alexandra‐Viola Bohne, Jörg Nickelsen, Christian Schmitz‐Linneweber · 2023

Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital …

RNA splicing of a long cox2i691 and the evolution of cox2 introns in angiosperm mitochondria Open

Alejandro Edera, Anna V. Williams, Katharine A. Howell, Paul G. Nevill, Ian Small , et al. · 2022

In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. Although each of these introns is ~1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae)…

MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria Open

Corinne Best, Ron Mizrahi, Rana Edris, Hui Tang, Hagit Zer , et al. · 2022

Summary Mitochondria are semi-autonomous organelles that serve as hubs for aerobic energy metabolism. The biogenesis of the respiratory (OXPHOS) system relies on nuclear-encoded factors, which regulate the transcription, processing and tra…

Knockdown of mitochondrialatp1mRNA by a custom-designed pentatricopeptide repeat protein alters F1FoATP synthase Open

Fei Yang, Lilian Vincis Pereira Sanglard, Chun Pong Lee, Elke Ströher, Swati Singh , et al. · 2022

We show that a custom-designed RNA-binding protein binds and specifically induces cleavage of atp1 RNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F 1 F o ATP synthase in Arabidopsis thalia…

Field Corn Production Guide Open

David Wright, Ian Small, Cheryl Mackowiak, Zane J. Grabau, Pratap Devkota , et al. · 2022

This publication discusses several aspects of field corn production in Florida, such as economics, land preparation, hybrid selection, fertilization, irrigation, and disease management. Written by David Wright, Ian Small, Cheryl Mackowiak,…

Camelina Production in Florida Open

Ramdeo Seepaul, David Wright, Sheeja George, Ian Small · 2022

This publication discusses camelina adaptability, stand establishment, pest and disease management, and nutrient management. Written by Ramdeo Seepaul, David Wright, Sheeja George, and Ian Small, and published by the UF/IFAS Agronomy Depar…

CRISPRi-based circuits for genetic computation in plants Open

Muhammad Adil Khan, Gabrielle Herring, Marina Oliva, Elliott Fourie, Jia Yuan Zhu , et al. · 2022

Synthetic gene circuits can enable new cellular behaviours by integrating multiple input signals into customisable genetic programs. However, gene circuit development in plants has been limited by a lack of orthogonal and modular parts req…

Reversible CRISPRi-based circuits for genetic computation in plants Open

Muhammad Adil Khan, Gabrielle Herring, Marina Oliva, Elliott Fourie, Jia Yuan Zhu , et al. · 2022

The plasmid data supporting the publication: Reversible CRISPRi-based circuits for genetic computation in plants

CRISPRi-based circuits for genetic computation in plants Open

Muhammad Adil Khan, Gabrielle Herring, Marina Oliva, Elliott Fourie, Jia Yuan Zhu , et al. · 2022

The plasmid data supporting the publication: CRISPRi-based circuits for genetic computation in plants

The GENOMES UNCOUPLED1 protein has an ancient, highly conserved role but not in retrograde signalling Open

Suvi Honkanen, Ian Small · 2022

Summary The pentatricopeptide repeat protein GENOMES UNCOUPLED1 (GUN1) is required for chloroplast‐to‐nucleus signalling when plastid translation becomes inhibited during chloroplast development in Arabidopsis thaliana , but its exact mole…

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