4.7 Article

PSI Photoinhibition and Changing CO2 Levels Initiate Retrograde Signals to Modify Nuclear Gene Expression

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1

Namuk Kim et al.

Summary: Shade represses photosynthetic genes by increasing the expression of a small protein that disrupts the DNA binding of a key transcription factor. This protein interacts with GLK transcription factors and impairs their DNA binding activity, leading to abnormal chloroplast development and decreased expression of photosynthetic genes. This discovery reveals the molecular mechanism of RPGE-GLK regulation on photosynthetic gene expression downstream of PIFs.

PLANT PHYSIOLOGY (2023)

Review Biochemistry & Molecular Biology

Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond

Andreas S. Richter et al.

Summary: Plastids communicate with the nucleus through retrograde signaling to regulate nuclear gene expression. Plastid biogenesis and responses of mature chloroplasts to environmental changes are controlled through biogenic and operational controls, respectively. The functions of GUN proteins in retrograde signaling and the controversy surrounding GUN1 are discussed in this review, along with recent progress in understanding chloroplast-derived signals in acclimation response and flavonoid biosynthesis.

PLANT COMMUNICATIONS (2023)

Article Genetics & Heredity

The Gene Ontology knowledgebase in 2023

Suzi A. Aleksander et al.

Summary: The Gene Ontology (GO) knowledgebase is a comprehensive resource that provides information about the functions of genes and gene products. It covers a wide range of organisms and receives updates from a consortium of scientists. The knowledgebase consists of three components: GO, which describes gene functionality; GO annotations, which provide evidence-supported statements about gene products; and GO-CAMs, which are models of molecular pathways. The knowledgebase is continuously updated and reviewed, and guidance is provided to users on how to make the best use of the data.

GENETICS (2023)

Review Plant Sciences

Iron in leaves: chemical forms, signalling, and in-cell distribution

Mate Sagi-Kazar et al.

Summary: Proper control and sensing of iron incorporation is crucial for maintaining foliar iron homeostasis, especially for the synthesis of chlorophylls and stability of the photosynthetic machinery in leaves. While the signaling of iron in roots has been extensively studied, the regulation of iron status in leaves remains to be further clarified.

JOURNAL OF EXPERIMENTAL BOTANY (2022)

Review Plant Sciences

Chloroplast development in green plant tissues: the interplay between light, hormone, and transcriptional regulation

Lee Cackett et al.

Summary: Chloroplasts play a crucial role in photosynthesis and various biological processes including nitrogen and sulphur assimilation, amino acid, fatty acid, nucleotide and hormone synthesis. Light is essential for chloroplast formation and directly regulates the expression of chloroplast-related genes. Hormones such as brassinosteriods, cytokinins, auxins and gibberellins are also modulated by light and control chloroplast development during early stages of plant growth. Transcription factors, light signaling, and hormone signaling form a complex network regulating the transcription of chloroplast- and photosynthesis-related genes to control chloroplast development in green tissues.

NEW PHYTOLOGIST (2022)

Review Biochemistry & Molecular Biology

PANTHER: Making genome-scale phylogenetics accessible to all

Paul D. Thomas et al.

Summary: PANTHER is a user-focused knowledgebase that stores results of extensive phylogenetic reconstruction pipelines and provides manual review and annotation of function evolution events, aiding in protein sequence analysis tasks.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis

En-Jung Hsieh et al.

Summary: Iron is an essential micronutrient in plants, and its supply fluctuates, leading to the need for gene regulation through transcription and alternative splicing. Genes with lower splice site strengths and higher intron numbers are more likely to be regulated by alternative splicing, while transcriptionally controlled genes are not affected by gene structure. Specific genomic features are associated with particular regulatory modes, indicating functional bias in the genomic hardwiring.

RNA BIOLOGY (2022)

Review Plant Sciences

HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants

Yuntao Xiao et al.

Summary: HY5 is a master regulator in plants that controls various important physiological and biological processes. It is conserved in function among different plant species. HY5 regulates the transcription of approximately one-third of genes at the whole genome level. The transcription, protein abundance, and activity of HY5 are tightly regulated by various factors.

FRONTIERS IN PLANT SCIENCE (2022)

Article Plant Sciences

True oxygen reduction capacity during photosynthetic electron transfer in thylakoids and intact leaves

Duncan Fitzpatrick et al.

Summary: Oxygen reduction occurs at various components of the photosynthetic electron transfer chain (PETC), but only electron flow to photosystem I (PSI) leads to H2O2 accumulation. H2O2 from PETC may increase mitochondrial respiration and CO2 release. H2O2 production in PETC locations other than PSI is quickly quenched and cannot participate in H2O2 translocation and signaling.

PLANT PHYSIOLOGY (2022)

Article Plant Sciences

Pivotal roles of ELONGATED HYPOCOTYL5 in regulation of plant development and fruit metabolism in tomato

Chunli Zhang et al.

Summary: This study investigates the functions of SlHY5 in tomato plants, and reveals its critical roles in seedling growth, root development, chlorophyll biosynthesis, and fruit metabolism. The findings show that SlHY5 promotes chlorophyll accumulation in fruits, with a stronger effect on the illuminated side. Transcriptome and metabolome analyses also demonstrate that SlHY5 is involved in the regulation of phenylpropanoids and steroidal glycoalkaloids. These results highlight the importance of manipulating SlHY5 for improving seedling fitness and fruit quality in tomato.

PLANT PHYSIOLOGY (2022)

Article Plant Sciences

Plants acclimate to Photosystem I photoinhibition by readjusting the photosynthetic machinery

Tapio Lempiainen et al.

Summary: Photosynthetic light reactions require strict regulation under dynamic environmental conditions. Depending on environmental constraints, photoinhibition of either Photosystem II (PSII) or Photosystem I (PSI) occurs frequently. Repair of photodamaged PSI is very slow compared to that of PSII, leading to a functional imbalance between the two photosystems. In this study, we investigated the acclimation of photosynthesis to PSI-limited conditions, both in the short-term and long-term, after PSI-specific photoinhibition treatment. We found that short-term acclimation mechanisms were induced immediately after inhibition, while longer-term acclimation involved changes in the stromal redox system and increased abundance of ATP synthase and Cytochrome b6f. Acclimation to PSI-limited conditions restored the CO2 assimilation capacity of plants without major PSI repair. These findings demonstrate that plants efficiently acclimate to changes in the photosynthetic apparatus, which is crucial for their adaptation to adverse environmental conditions.

PLANT CELL AND ENVIRONMENT (2022)

Review Plant Sciences

ROS production and signalling in chloroplasts: cornerstones and evolving concepts

Christine H. Foyer et al.

Summary: ROS like singlet oxygen, superoxide, and hydrogen peroxide serve as markers of living cells and are produced abundantly during oxygenic photosynthesis. These ROS act as signals within chloroplasts, influencing cellular processes and redox signaling pathways. The challenge lies in understanding the organized delivery of regulated ROS from the photosynthetic electron transport chain to transmit redox signals from the environment to the nucleus, with stromal carbohydrate metabolism also playing a key role in chloroplast signaling pathways.

PLANT JOURNAL (2022)

Article Plant Sciences

The mungbean VrP locus encoding MYB90, an R2R3-type MYB protein, regulates anthocyanin biosynthesis

Yun Lin et al.

Summary: This study investigated the genetic mechanism controlling anthocyanin accumulation in mungbean and identified an R2R3-MYB gene VrMYB90 as the candidate gene for the VrP locus. The study revealed that VrMYB90 regulates anthocyanin accumulation in mungbean and its expression is light-sensitive. Furthermore, VrMYB90 may impact anthocyanin accumulation by regulating a gene encoding an enzyme involved in anthocyanin biosynthesis.

FRONTIERS IN PLANT SCIENCE (2022)

Article Plant Sciences

FE UPTAKE-INDUCING PEPTIDE1 maintains Fe translocation by controlling Fe deficiency response genes in the vascular tissue of Arabidopsis

Satoshi Okada et al.

Summary: The peptide FEP1 plays a pivotal role in iron movement and maintaining iron levels in vascular tissues in Arabidopsis. It regulates the translocation of iron and not its uptake in roots, and is involved in the iron deficiency response.

PLANT CELL AND ENVIRONMENT (2022)

Review Plant Sciences

Retrograde and anterograde signaling in the crosstalk between chloroplast and nucleus

Masood Jan et al.

Summary: This article reviews the current understanding of multiple plastid retrograde signaling pathways and potential plastid signaling molecules. It also discusses how retrograde signaling regulates nuclear gene expression within a multilayered network of transcription factors.

FRONTIERS IN PLANT SCIENCE (2022)

Article Plant Sciences

Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis

Chenyang Liu et al.

Summary: This study identified and characterized 14 VrCOL genes in mungbean, analyzed their structural features and expression patterns. The expression patterns of VrCOL genes varied significantly under long-day and short-day conditions, with VrCOL2 overexpression accelerating flowering in Arabidopsis under short-day conditions.

FRONTIERS IN PLANT SCIENCE (2021)

Review Plant Sciences

Photosystem I Inhibition, Protection and Signalling: Knowns and Unknowns

Yugo Lima-Melo et al.

Summary: Photosynthesis is a crucial process for harnessing energy, and Photosystem I (PSI) plays a key role in balancing energy harvesting and utilization. Damage to PSI can have significant impacts on plant photosynthetic efficiency. Understanding the protection mechanisms and impact of PSI photoinhibition on signaling and metabolism is essential for improving photosynthetic efficiency in crop species.

FRONTIERS IN PLANT SCIENCE (2021)

Review Biochemistry & Molecular Biology

MYB-Mediated Regulation of Anthocyanin Biosynthesis

Huiling Yan et al.

Summary: Anthocyanins play a crucial role in providing different visual effects to plants through various biosynthetic pathways, attracting pollinators and seed dispersers. MYB transcription factors are key regulators in anthocyanin biosynthesis, controlling the enrichment and sedimentation of anthocyanins. The study discusses the regulation of anthocyanin biosynthetic mechanisms by MYB-TFs and analyzes the role of the environment in controlling the anthocyanin biosynthesis network.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Plant Sciences

The Significance of Chloroplast NAD(P)H Dehydrogenase Complex and Its Dependent Cyclic Electron Transport in Photosynthesis

Mingzhu Ma et al.

Summary: The Chloroplast NAD(P)H dehydrogenase (NDH) complex, an important alternative electron transport pathway, plays a crucial role in maintaining the redox system balance in plants and providing extra ATP for biochemical reactions. Understanding NDH-mediated cyclic electron transport during photosynthesis may lead to improved crop yield by aiding plants in adapting to environmental stress.

FRONTIERS IN PLANT SCIENCE (2021)

Review Biochemistry & Molecular Biology

Regulatory Mechanisms of Anthocyanin Biosynthesis in Apple and Pear

Huimin Liu et al.

Summary: Anthocyanins play a crucial role in the quality and flavor of fruits, being produced through the phenylpropanoid pathway regulated by specific key genes. However, the molecular mechanisms of anthocyanin biosynthesis in different plants remain unclear.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Plant Sciences

Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves

Ruben Alvarez-Fernandez et al.

Summary: This study identified genes involved in the initiation and regulation of chloroplast-level acclimation to high light in mature leaves of Arabidopsis. The central role of BBX32 in this process was highlighted, along with the involvement of several other genes. The regulatory network discovered provides insights into the transcriptional control of acclimation processes distinct from other photoreceptor-regulated pathways.

PLANT JOURNAL (2021)

Review Plant Sciences

Oxygen and ROS in Photosynthesis

Sergey Khorobrykh et al.

PLANTS-BASEL (2020)

Article Biology

Photosynthetic signalling during high light stress and recovery: targets and dynamics

Peter J. Gollan et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

Review Biochemistry & Molecular Biology

The balancing act of NEET proteins: Iron, ROS, calcium and metabolism

Rachel Nechushtai et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2020)

Article Multidisciplinary Sciences

Stress response to CO2 deprivation by Arabidopsis thaliana in plant cultures

Souvik Banerjee et al.

PLOS ONE (2019)

Article Biochemistry & Molecular Biology

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Huaiyu Mi et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Plant Sciences

Switching off photoprotection of photosystem I-a novel tool for gradual PSI photoinhibition

Mikko Tikkanen et al.

PHYSIOLOGIA PLANTARUM (2018)

Article Plant Sciences

Retrograde Signals Navigate the Path to Chloroplast Development

Tamara Hernandez-Verdeja et al.

PLANT PHYSIOLOGY (2018)

Review Plant Sciences

Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation

Gregory J. MacNeill et al.

JOURNAL OF EXPERIMENTAL BOTANY (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biology

Interaction between photosynthetic electron transport and chloroplast sinks triggers protection and signalling important for plant productivity

Peter J. Gollan et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Review Biotechnology & Applied Microbiology

Jasmonate-responsive transcription factors regulating plant secondary metabolism

Meiliang Zhou et al.

BIOTECHNOLOGY ADVANCES (2016)

Review Biochemistry & Molecular Biology

The Multifaceted Roles of HY5 in Plant Growth and Development

Sreeramaiah N. Gangappa et al.

MOLECULAR PLANT (2016)

Article Biochemistry & Molecular Biology

PGR5-PGRL1-Dependent Cyclic Electron Transport Modulates Linear Electron Transport Rate in Arabidopsis thaliana

Marjaana Suorsa et al.

MOLECULAR PLANT (2016)

Review Plant Sciences

Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors

Zhenzhu Xu et al.

FRONTIERS IN PLANT SCIENCE (2016)

Review Plant Sciences

Retrograde signaling between plastid and nucleus: A review

Rachana Singh et al.

JOURNAL OF PLANT PHYSIOLOGY (2015)

Article Biochemistry & Molecular Biology

Overexpression of Plastid Transketolase in Tobacco Results in a Thiamine Auxotrophic Phenotype

Mahdi Khozaei et al.

PLANT CELL (2015)

Article Biochemistry & Molecular Biology

Photosystem II photoinhibition-repair cycle protects Photosystem I from irreversible damage

Mikko Tikkanen et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2014)

Review Biochemistry & Molecular Biology

Flavonoids as Important Molecules of Plant Interactions with the Environment

Justyna Mierziak et al.

MOLECULES (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Review Plant Sciences

ROS-Mediated Lipid Peroxidation and RES-Activated Signaling

Edward E. Farmer et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64 (2013)

Article Multidisciplinary Sciences

Cyclophilin 20-3 relays a 12-oxo-phytodienoic acid signal during stress responsive regulation of cellular redox homeostasis

Sang-Wook Park et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Arabidopsis bHLH100 and bHLH101 Control Iron Homeostasis via a FIT-Independent Pathway

Alicia B. Sivitz et al.

PLOS ONE (2012)

Article Plant Sciences

Photoinhibition of photosystem I

Kintake Sonoike

PHYSIOLOGIA PLANTARUM (2011)

Article Plant Sciences

Chalcone synthase and its functions in plant resistance

T. T. H. Dao et al.

PHYTOCHEMISTRY REVIEWS (2011)

Review Biochemistry & Molecular Biology

Ferritins and iron storage in plants

Jean-Francois Briat et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2010)

Article Plant Sciences

Molecular mechanism for jasmonate-induction of anthocyanin accumulation in Arabidopsis

Xiaoyi Shan et al.

JOURNAL OF EXPERIMENTAL BOTANY (2009)

Article Biochemistry & Molecular Biology

GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis

Mark T. Waters et al.

PLANT CELL (2009)

Article Multidisciplinary Sciences

NTRC links built-in thioredoxin to light and sucrose in regulating starch synthesis in chloroplasts and amyloplasts

Justyna Michalska et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Starch as a major integrator in the regulation of plant growth

Ronan Sulpice et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemistry & Molecular Biology

Characterization of cytosolic tetrapyrrole-binding proteins in Arabidopsis thaliana

Shigekazu Takahashi et al.

PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES (2008)

Article Multidisciplinary Sciences

Chloroplast Fe(III) chelate reductase activity is essential for seedling viability under iron limiting conditions

Jeeyon Jeong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemistry & Molecular Biology

Photoinhibition of photosystem II under environmental stress

Norio Murata et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2007)

Article Plant Sciences

FIT, the FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR in Arabidopsis

Petra Bauer et al.

PLANT PHYSIOLOGY AND BIOCHEMISTRY (2007)

Article Biotechnology & Applied Microbiology

Microarray analysis of nitric oxide responsive transcripts in Arabidopsis

M Parani et al.

PLANT BIOTECHNOLOGY JOURNAL (2004)

Article Biochemistry & Molecular Biology

The F box protein AFR is a positive regulator of phytochrome A-mediated light signaling

FG Harmon et al.

CURRENT BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Rapid induction of distinct stress responses after the release of singlet oxygen in arabidopsis

RGL op den Camp et al.

PLANT CELL (2003)

Article Biochemistry & Molecular Biology

Nitric oxide-mediated transcriptional changes in Arabidopsis thaliana

A Polverari et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2003)

Article Multidisciplinary Sciences

Plant defense in the absence of jasmonic acid: The role of cyclopentenones

A Stintzi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biochemistry & Molecular Biology

Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis

JO Borevitz et al.

PLANT CELL (2000)