scholarly journals The PCY-SAG14 phytocyanin module regulated by PIFs and miR408 promotes dark-induced leaf senescence in Arabidopsis

2022 ◽  
Vol 119 (3) ◽  
pp. e2116623119
Author(s):  
Chen Hao ◽  
Yanzhi Yang ◽  
Jianmei Du ◽  
Xing Wang Deng ◽  
Lei Li
Keyword(s):  
Leaf Senescence ◽  
Reverse Genetics ◽  
Agronomic Traits ◽  
Experimental System ◽  
Photosynthetic Electron Transport ◽  
Forward Genetics ◽  
Copper Proteins ◽  
Reciprocal Regulation ◽  
Mobile Electron ◽  
Necessary And Sufficient

Leaf senescence is a critical process in plants and has a direct impact on many important agronomic traits. Despite decades of research on senescence-altered mutants via forward genetics and functional assessment of senescence-associated genes (SAGs) via reverse genetics, the senescence signal and the molecular mechanism that perceives and transduces the signal remain elusive. Here, using dark-induced senescence (DIS) of Arabidopsis leaf as the experimental system, we show that exogenous copper induces the senescence syndrome and transcriptomic changes in light-grown plants parallel to those in DIS. By profiling the transcriptomes and tracking the subcellular copper distribution, we found that reciprocal regulation of plastocyanin, the thylakoid lumen mobile electron carrier in the Z scheme of photosynthetic electron transport, and SAG14 and plantacyanin (PCY), a pair of interacting small blue copper proteins located on the endomembrane, is a common thread in different leaf senescence scenarios, including DIS. Genetic and molecular experiments confirmed that the PCY-SAG14 module is necessary and sufficient for promoting DIS. We also found that the PCY-SAG14 module is repressed by a conserved microRNA, miR408, which in turn is repressed by phytochrome interacting factor 3/4/5 (PIF3/4/5), the key trio of transcription factors promoting DIS. Together, these findings indicate that intracellular copper redistribution mediated by PCY-SAG14 has a regulatory role in DIS. Further deciphering the copper homeostasis mechanism and its interaction with other senescence-regulating pathways should provide insights into our understanding of the fundamental question of how plants age.

scholarly journals Review of Current Methodological Approaches for Characterizing MicroRNAs in Plants

2009 ◽  
Vol 2009 ◽  
pp. 1-11 ◽  
Author(s):  
Turgay Unver ◽  
Deana M. Namuth-Covert ◽  
Hikmet Budak
Keyword(s):  
Gene Expression ◽  
Molecular Biology ◽  
Reverse Genetics ◽  
Methodological Approach ◽  
Forward Genetics ◽  
Methodological Approaches

Advances in molecular biology have led to some surprising discoveries. One of these includes the complexities of RNA and its role in gene expression. One particular class of RNA called microRNA (miRNA) is the focus of this paper. We will first briefly look at some of the characteristics and biogenesis of miRNA in plant systems. The remainder of the paper will go into details of three different approaches used to identify and study miRNA. These include two reverse genetics approaches: computation (bioinformatics) and experimental, and one rare forward genetics approach. We also will summarize how to measure and quantify miRNAs, and how to detect their possible targets in plants. Strengths and weaknesses of each methodological approach are discussed.

scholarly journals Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

2021 ◽  
Vol 12 ◽  
Author(s):  
Nur Shuhadah Mohd Saad ◽  
Anita A. Severn-Ellis ◽  
Aneeta Pradhan ◽  
David Edwards ◽  
Jacqueline Batley
Keyword(s):  
Climate Change ◽  
Reverse Genetics ◽  
Agronomic Traits ◽  
Crop Evolution ◽  
Breeding Cycle ◽  
World Population ◽  
Genome Wide ◽  
The Face ◽  
Selection Of ◽  
The Way

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

scholarly journals Creating Porcine Biomedical Models Through Recombineering

2004 ◽  
Vol 5 (3) ◽  
pp. 262-267 ◽  
Author(s):  
Margarita M. Rogatcheva ◽  
Laurie A. Rund ◽  
Kelly S. Swanson ◽  
Brandy M. Marron ◽  
Jonathan E. Beever ◽  
...  
Keyword(s):  
Genetic Information ◽  
Positional Cloning ◽  
Reverse Genetics ◽  
Genetic Model ◽  
Phenotypic Diversity ◽  
Model Organism ◽  
Artificial Chromosome ◽  
Forward Genetics ◽  
Working Definition ◽  
Definition Of

Recent advances in genomics provide genetic information from humans and other mammals (mouse, rat, dog and primates) traditionally used as models as well as new candidates (pigs and cattle). In addition, linked enabling technologies, such as transgenesis and animal cloning, provide innovative ways to design and perform experiments to dissect complex biological systems. Exploitation of genomic information overcomes the traditional need to choose naturally occurring models. Thus, investigators can utilize emerging genomic knowledge and tools to create relevant animal models. This approach is referred to as reverse genetics. In contrast to ‘forward genetics’, in which gene(s) responsible for a particular phenotype are identified by positional cloning (phenotype to genotype), the ‘reverse genetics’ approach determines the function of a gene and predicts the phenotype of a cell, tissue, or organism (genotype to phenotype). The convergence of classical and reverse genetics, along with genomics, provides a working definition of a ‘genetic model’ organism (3). The recent construction of phenotypic maps defining quantitative trait loci (QTL) in various domesticated species provides insights into how allelic variations contribute to phenotypic diversity. Targeted chromosomal regions are characterized by the construction of bacterial artificial chromosome (BAC) contigs to isolate and characterize genes contributing towards phenotypic variation. Recombineering provides a powerful methodology to harvest genetic information responsible for phenotype. Linking recombineering with gene-targeted homologous recombination, coupled with nuclear transfer (NT) technology can provide ‘clones’ of genetically modified animals.

Phenotypic Screen and Transcriptomics Approach Complement Each Other in Functional Genomics of Defensive Stink Gland Physiology

2021 ◽  
Author(s):  
Sabrina Lehmann ◽  
Bibi Atika ◽  
Daniela Grossmann ◽  
Christian Schmitt-Engel ◽  
Nadi Strohlein ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Large Scale ◽  
Reverse Genetics ◽  
Expression Profiles ◽  
Forward Genetics ◽  
Large Set ◽  
Knock Down ◽  
Genome Wide ◽  
Phenotypic Screen ◽  
A Genome

Abstract Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using a reverse genetics strategy based on RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause knock-down gland phenotypes, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. Moreover, of the 29 previously transcriptomics-identified genes causing a gland phenotype, only one gene was recognized by this phenotypic screen despite the fact that 13 of them were covered by the screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles.

scholarly journals Genome-Wide Identification of Essential and Auxiliary Gene Sets for Magnetosome Biosynthesis in Magnetospirillum gryphiswaldense

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Karen T. Silva ◽  
Margarete Schüler ◽  
Frank Mickoleit ◽  
Theresa Zwiener ◽  
Frank D. Müller ◽  
...  
Keyword(s):  
Reverse Genetics ◽  
Intracellular Localization ◽  
Anaerobic Respiration ◽  
Magnetotactic Bacteria ◽  
Transposon Mutagenesis ◽  
Forward Genetics ◽  
Genetic Determinants ◽  
Content Type ◽  
Magnetospirillum Gryphiswaldense ◽  
Genome Wide

ABSTRACT Magnetotactic bacteria (MTB) stand out by their ability to manufacture membrane-enclosed magnetic organelles, so-called magnetosomes. Previously, it has been assumed that a genomic region of approximately 100 kbp, the magnetosome island (MAI), harbors all genetic determinants required for this intricate biosynthesis process. Recent evidence, however, argues for the involvement of additional auxiliary genes that have not been identified yet. In the present study, we set out to delineate the full gene complement required for magnetosome production in the alphaproteobacterium Magnetospirillum gryphiswaldense using a systematic genome-wide transposon mutagenesis approach. By an optimized procedure, a Tn5 insertion library of 80,000 clones was generated and screened, yielding close to 200 insertants with mild to severe impairment of magnetosome biosynthesis. Approximately 50% of all Tn5 insertion sites mapped within the MAI, mostly leading to a nonmagnetic phenotype. In contrast, in the majority of weakly magnetic Tn5 insertion mutants, genes outside the MAI were affected, which typically caused lower numbers of magnetite crystals with partly aberrant morphology, occasionally combined with deviant intracellular localization. While some of the Tn5-struck genes outside the MAI belong to pathways that have been linked to magnetosome formation before (e.g., aerobic and anaerobic respiration), the majority of affected genes are involved in so far unsuspected cellular processes, such as sulfate assimilation, oxidative protein folding, and cytochrome c maturation, or are altogether of unknown function. We also found that signal transduction and redox functions are enriched in the set of Tn5 hits outside the MAI, suggesting that such processes are particularly important in support of magnetosome biosynthesis. IMPORTANCE Magnetospirillum gryphiswaldense is one of the few tractable model magnetotactic bacteria (MTB) for studying magnetosome biomineralization. So far, knowledge on the genetic determinants of this complex process has been mainly gathered using reverse genetics and candidate approaches. In contrast, nontargeted forward genetics studies are lacking, since application of such techniques in MTB has been complicated for a number of technical reasons. Here, we report on the first comprehensive transposon mutagenesis study in MTB, aiming at systematic identification of auxiliary genes necessary to support magnetosome formation in addition to key genes harbored in the magnetosome island (MAI). Our work considerably extends the candidate set of novel subsidiary determinants and shows that the full gene complement underlying magnetosome biosynthesis is larger than assumed. In particular, we were able to define certain cellular pathways as specifically important for magnetosome formation that have not been implicated in this process so far.

scholarly journals Plastocyanin is the long-range electron carrier between photosystem II and photosystem I in plants

2020 ◽  
Vol 117 (26) ◽  
pp. 15354-15362 ◽  
Author(s):  
Ricarda Höhner ◽  
Mathias Pribil ◽  
Miroslava Herbstová ◽  
Laura Susanna Lopez ◽  
Hans-Henning Kunz ◽  
...  
Keyword(s):  
Electron Transport ◽  
Photosystem Ii ◽  
Long Range ◽  
Narrow Range ◽  
Higher Plants ◽  
Regulatory Element ◽  
Photosynthetic Electron Transport ◽  
Electron Carrier ◽  
Mobile Electron ◽  
Electron Carriers

In photosynthetic electron transport, large multiprotein complexes are connected by small diffusible electron carriers, the mobility of which is challenged by macromolecular crowding. For thylakoid membranes of higher plants, a long-standing question has been which of the two mobile electron carriers, plastoquinone or plastocyanin, mediates electron transport from stacked grana thylakoids where photosystem II (PSII) is localized to distant unstacked regions of the thylakoids that harbor PSI. Here, we confirm that plastocyanin is the long-range electron carrier by employing mutants with different grana diameters. Furthermore, our results explain why higher plants have a narrow range of grana diameters since a larger diffusion distance for plastocyanin would jeopardize the efficiency of electron transport. In the light of recent findings that the lumen of thylakoids, which forms the diffusion space of plastocyanin, undergoes dynamic swelling/shrinkage, this study demonstrates that plastocyanin diffusion is a crucial regulatory element of plant photosynthetic electron transport.

A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics

2020 ◽  
Author(s):  
Erhui Xiong ◽  
Zhiyong Li ◽  
Chen Zhang ◽  
Jing Zhang ◽  
Ye Liu ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Chlorophyll Synthesis ◽  
Research Progress ◽  
Rice Leaf ◽  
Acid Pathway ◽  
Relationship Of ◽  
The Relationship ◽  
Synthesis And Degradation

Abstract Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.

Variation I: Genetics

Mate Choice ◽  
2017 ◽  
Author(s):  
Gil G. Rosenthal
Keyword(s):  
Genetic Variation ◽  
Gene Structure ◽  
Infinite Number ◽  
Reverse Genetics ◽  
Forward Genetics ◽  
Genetic Models ◽  
Genetic Studies ◽  
Quantitative Genetic ◽  
Negative Effect ◽  
Genomic Regions

This chapter reviews the main approaches for characterizing preference genetics. Approaches to understanding the genetics underlying preferences (or any other phenotype) take two broad forms. The first approach consists of attempts to identify particular genes or genomic regions associated with preference variation; for preferences, this is typically done using so-called forward genetics, whereby variation in phenotype is correlated with variation in genotype. Alternatively, the effects of candidate genes on preference can be characterized using reverse genetics, whereby gene structure or function is altered to test its effect on phenotype. The second approach encompasses quantitative genetic studies that assume that the underlying genetic variation is continuous and additive. Quantitative genetic models often assume an infinite number of loci each contributing infinitely small positive or negative effect, summing to determine trait value.

scholarly journals The PIF1-miR408-PLANTACYANIN Repression Cascade Regulates Light-Dependent Seed Germination

2021 ◽  
Author(s):  
Anlong Jiang ◽  
Zhonglong Guo ◽  
Jiawei Pan ◽  
Yanzhi Yang ◽  
Yan Zhuang ◽  
...  
Keyword(s):  
Seed Germination ◽  
Red Light ◽  
Experimental System ◽  
Seed Plants ◽  
Cellular Mechanisms ◽  
Copper Protein ◽  
Early Germination ◽  
Light Signals ◽  
Necessary And Sufficient ◽  
Mature Seeds

Abstract Light-dependent seed germination is a vital process for many seed plants. A decisive event in light-induced germination is degradation of the central repressor PHYTOCHROME INTERACTING FACTOR 1 (PIF1). The balance between gibberellic acid (GA) and abscisic acid (ABA) helps to control germination. However, the cellular mechanisms linking PIF1 turnover to hormonal balancing remain elusive. Here, employing far-red light-induced Arabidopsis thaliana seed germination as the experimental system, we identified PLANTACYANIN (PCY) as an inhibitor of germination. It is a blue copper protein associated with the vacuole that is both highly expressed in mature seeds and rapidly silenced during germination. Molecular analyses showed that PIF1 binds to the miR408 promoter and represses miR408 accumulation. This in turn posttranscriptionally modulates PCY abundance, forming the PIF1-miR408-PCY repression cascade for translating PIF1 turnover to PCY turnover during early germination. Genetic analysis, RNA-sequencing, and hormone quantification revealed that PCY is necessary and sufficient to maintain the PIF1-mediated seed transcriptome and the low-GA-high-ABA state. Furthermore, we found that PCY domain organization and regulation by miR408 are conserved features in seed plants. These results revealed a cellular mechanism whereby PIF1-relayed external light signals are converted through PCY turnover to internal hormonal profiles for controlling seed germination.

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