The Moss Physcomitrium (Physcomitrella) patens: A Model Organism for Non-Seed Plants

The Plant Cell, Journal Year: 2020, Volume and Issue: 32(5), P. 1361 - 1376

Published: March 9, 2020

Since the discovery two decades ago that transgenes are efficiently integrated into genome of Physcomitrella patens by homologous recombination, this moss has been a premier model system to study evolutionary developmental biology questions, stem cell reprogramming, and nonvascular plants. P. was first non-seed plant have its sequenced. With level genomic information, together with increasing molecular genetic tools, large number reverse studies propelled use system. A technological advances recently opened door forward genetics as well extremely efficient precise editing in patens. Additionally, careful phylogenetic increased resolution suggested emerged from within Physcomitrium. Thus, rather than patens, species should be named Physcomitrium Here we review these describe areas where had most impact on biology.

Language: Английский

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JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(16), P. 8383 - 8401

Published: Aug. 1, 2023

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources decipher gene function and subsequently provide molecular targets improvement through editing. However, biological roles large proportions across the phylogeny are poorly annotated. Here we describe Joint Genome Institute (JGI) Plant Atlas, an updateable data resource consisting transcript abundance assays spanning 18 diverse species. To integrate these genotypes, analyzed expression profiles, built clusters that exhibited tissue/condition specific expression, tested transcriptional response queues. We discovered extensive phylogenetically constrained condition-specific profiles without any previously documented annotation. Such conserved patterns tightly co-expressed let us assign derived additional information 64 495 with otherwise unknown functions. The ever-expanding Atlas is available at JGI (https://plantgeneatlas.jgi.doe.gov) Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access user-specified queries sets. Combined, web interfaces users differentially expressed genes, track orthologs plants, graphically visualize ontology pathway enrichments.

Language: Английский

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Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

The Plant Journal, Journal Year: 2020, Volume and Issue: 103(2), P. 889 - 902

Published: April 21, 2020

The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding how oscillations mRNA levels are connected co/post-transcriptional such as splicing, has remained challenge. Here we applied combined approach using deep transcriptome sequencing bioinformatics tools identify novel circadian-regulated genes splicing events. Using stringent approach, identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 5' 350 multiple (more than one event type) annotated events under regulation. We also found seven 721 exonic intronic Depletion the factor AtSPF30 homologue resulted disruption subset clock-controlled Altogether, our global RNA-seq coupled with an silico, event-centred, analysis tool offers new for studying interplay between machinery at scale. identification broadens current level control that over this regulatory layer.

Language: Английский

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Ties between Stress and Lipid Droplets Pre-date Seeds

Trends in Plant Science, Journal Year: 2020, Volume and Issue: 25(12), P. 1203 - 1214

Published: Sept. 10, 2020

Seeds were a key evolutionary innovation. These durable structures provide concerted solution to two challenges on land: dispersal and stress. Lipid droplets (LDs) that act as nutrient storage reservoirs are one of the main cell-biological reasons for seed endurance. Although LDs in spermatophytes especially abundant seeds, they found across plants algae, increase during Further, proteins underpin their form function often have deep homologs. We propose an scenario which (i) generation arose mechanism mediate general drought desiccation resilience, (ii) required protein framework was co-opted by seed-specific program.

Language: Английский

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Exploiting plant transcriptomic databases: Resources, tools, and approaches

Plant Communications, Journal Year: 2022, Volume and Issue: 3(4), P. 100323 - 100323

Published: April 9, 2022

There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds plant species. The data have great value, as they can be re-analyzed by others to ask answer questions that go beyond the aims study generated data. Because provides essential clues where when a is active, provide powerful tools predicting function, comparative analyses allow us evolution new perspective. This review describes how we gain knowledge profiles, specificities, co-expression networks, differential expression, experiment correlation. We also introduce demonstrate databases user-friendly access these tools.

Language: Английский

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Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(2)

Published: Jan. 21, 2024

Abstract Key message Characterization of Physcomitrella 3′UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming. The production recombinant proteins health applications accounts a large share the biopharmaceutical market. While many drugs are produced microbial mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular, good manufacturing practice (GMP)-compliant moss ( Physcomitrium patens ) has outstanding features, such excellent genetic amenability, reproducible bioreactor cultivation, humanized protein glycosylation patterns. this study, we selected characterized novel their effects on heterologous gene expression. genome contains 53,346 unique (untranslated regions) which 7964 transcripts contain at least one intron. Over 91% exhibit than polyadenylation site, indicating prevalence alternative Physcomitrella. Out all 3′UTRs, 14 terminator candidates were via transient Dual-Luciferase assays, yielding collection performing equally high established CaMV35S, AtHSP90, NOS. High testing impact reporter levels, dependent identity positioning. Testing among NOS, PpActin5 showed an increase 1000-fold between whereas increased levels by less tenfold, demonstrating stronger effect play compared terminators. Among attributes, number sites well signals found influence performance most. Our results improve biotechnology platform further our understanding how general.

Language: Английский

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Moss transcription factors regulating development and defense responses to stress

Journal of Experimental Botany, Journal Year: 2022, Volume and Issue: 73(13), P. 4546 - 4561

Published: Feb. 11, 2022

Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation the environment. Land colonization by plants occurred 450-470 million years ago was accompanied an increase in complexity transcriptional associated transcription factor expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, WRKY families increased land compared with algae. In angiosperms, they play crucial roles regulating growth responses environmental stressors. However, less information is available bryophytes only a few cases functional role moss stress mechanisms known. this review, we discuss current knowledge involved defense mosses other bryophytes. By exploring analysing Physcomitrium patens public database published profiles, show high number genes are differentially expressed response abiotic stresses during biotic interactions. Expression profiles together comprehensive analysis provide insights into relevant defenses, hint at distinct conserved between angiosperms.

Language: Английский

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Comparative phyloproteomics identifies conserved plasmodesmal proteins

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 74(6), P. 1821 - 1835

Published: Jan. 11, 2023

Abstract Plasmodesmata are cytosolic bridges, lined by the plasma membrane and traversed endoplasmic reticulum; plasmodesmata connect cells tissues, critical for many aspects of plant biology. While notoriously difficult to extract, tissue fractionation proteomic analyses can yield valuable knowledge their composition. Here we have generated two novel proteomes expand taxonomic representation plasmodesmata: one from mature Arabidopsis leaves moss Physcomitrium patens, leveraged these existing data perform a comparative analysis identify evolutionarily conserved protein families that associated with plasmodesmata. Thus, identified β-1,3-glucanases, C2 lipid-binding proteins, tetraspanins as core plasmodesmal components probably serve essential structural or functional components. Our approach has not only elements proteome, but also demonstrated added power offered recalcitrant samples. Conserved proteins establish basis upon which ancient function be further investigated determine roles structures play in multicellular organism physiology green lineages.

Language: Английский

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Characterisation of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model

New Phytologist, Journal Year: 2020, Volume and Issue: 227(2), P. 440 - 454

Published: Feb. 17, 2020

Summary Defects in flagella/cilia are often associated with infertility and disease. Motile male gametes (sperm cells) an ancestral eukaryotic trait that has been lost several lineages like flowering plants. Here, we made use of a phenotypic fertility difference between two moss ( Physcomitrella patens ) ecotypes to explore spermatozoid function. We compare genetic epigenetic variation as well expression profiles the Gransden Reute ecotype identify set candidate genes infertility. generated loss‐of‐function mutant coiled‐coil domain containing 39 (ccdc39) gene is part flagellar hydin network. mammal algal homologues this coincide loss fertility, demonstrating evolutionary conservation function related across kingdoms. The Ppccdc39 resembles phenotype terms fertility. Potentially, somatic (epi‐)mutations occurred during prolonged vegetative propagation Gransden, causing regulatory differences for example homeodomain transcription factor BELL1. Probably these changes causative observed defect. propose spermatozoids might be employed easily accessible system study humans animals structure movement.

Language: Английский

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Acetylation of conserved lysines fine‐tunes mitochondrial malate dehydrogenase activity in land plants

The Plant Journal, Journal Year: 2021, Volume and Issue: 109(1), P. 92 - 111

Published: Oct. 29, 2021

SUMMARY Plants need to rapidly and flexibly adjust their metabolism changes of immediate environment. Since this necessity results from the sessile lifestyle land plants, key mechanisms for orchestrating central metabolic acclimation are likely have evolved early. Here, we explore role lysine acetylation as a post‐translational modification directly modulate function. We generated acetylome moss Physcomitrium patens identified 638 sites, mostly found in mitochondrial plastidial proteins. A comparison with available angiosperm data pinpointed conserved regulatory strategy plants. Focusing on metabolism, functionally analyzed malate dehydrogenase (mMDH), which acts hub plant flexibility. In P. mMDH1, detected single acetylated located next one four sites Arabidopsis thaliana mMDH1. assessed kinetic behavior recombinant A. mMDH1 site‐specifically incorporated acetyl‐lysines. Acetylation at K169, K170, K334 decreases its oxaloacetate reduction activity, while K172 increases activity. modulation oxidation activity only where strongly activated it. Comparative homology modeling MDH proteins revealed that evolutionarily lysines serve hotspots acetylation. Our combined analyses indicate common fine‐tune enzymes impact capacity.

Language: Английский

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