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1.
Cell ; 181(5): 964-966, 2020 05 28.
Article in English | MEDLINE | ID: mdl-32470404

ABSTRACT

Approximately 500 Ma ago, freshwater algae adapted to live on Earth's surface, subsequently enabling animal life to pursue. Over the last decade, genomes of non-seed plants enabled us to infer trait evolution of early land plants. In this issue of Cell, Jiao et al. uncovered another genome, of the streptophyte algae Penium, enhancing our understanding of the water-to-land transition.


Subject(s)
Biological Evolution , Embryophyta , Embryophyta/genetics , Genome , Phylogeny , Plants/genetics
2.
Cell ; 181(5): 1097-1111.e12, 2020 05 28.
Article in English | MEDLINE | ID: mdl-32442406

ABSTRACT

The evolutionary features and molecular innovations that enabled plants to first colonize land are not well understood. Here, insights are provided through our report of the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The genome has a high proportion of repeat sequences that are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with representatives of earlier diverging algal lineages, P. margaritaceum has expanded repertoires of gene families, signaling networks, and adaptive responses that highlight the evolutionary trajectory toward terrestrialization. These encompass a broad range of physiological processes and protective cellular features, such as flavonoid compounds and large families of modifying enzymes involved in cell wall biosynthesis, assembly, and remodeling. Transcriptome profiling further elucidated adaptations, responses, and selective pressures associated with the semi-terrestrial ecosystems of P. margaritaceum, where a simple body plan would be an advantage.


Subject(s)
Desmidiales/genetics , Desmidiales/metabolism , Embryophyta/genetics , Biological Evolution , Cell Wall/genetics , Cell Wall/metabolism , Ecosystem , Evolution, Molecular , Phylogeny , Plants
3.
Cell ; 179(5): 1057-1067.e14, 2019 11 14.
Article in English | MEDLINE | ID: mdl-31730849

ABSTRACT

The transition to a terrestrial environment, termed terrestrialization, is generally regarded as a pivotal event in the evolution and diversification of the land plant flora that changed the surface of our planet. Through phylogenomic studies, a group of streptophyte algae, the Zygnematophyceae, have recently been recognized as the likely sister group to land plants (embryophytes). Here, we report genome sequences and analyses of two early diverging Zygnematophyceae (Spirogloea muscicola gen. nov. and Mesotaenium endlicherianum) that share the same subaerial/terrestrial habitat with the earliest-diverging embryophytes, the bryophytes. We provide evidence that genes (i.e., GRAS and PYR/PYL/RCAR) that increase resistance to biotic and abiotic stresses in land plants, in particular desiccation, originated or expanded in the common ancestor of Zygnematophyceae and embryophytes, and were gained by horizontal gene transfer (HGT) from soil bacteria. These two Zygnematophyceae genomes represent a cornerstone for future studies to understand the underlying molecular mechanism and process of plant terrestrialization.


Subject(s)
Biological Evolution , Embryophyta/genetics , Genome, Plant , Streptophyta/genetics , Abscisic Acid/pharmacology , Amino Acid Sequence , Multigene Family , Phylogeny , Plant Proteins/chemistry , Protein Domains , Streptophyta/classification , Symbiosis/genetics , Synteny/genetics
4.
Cell ; 174(2): 448-464.e24, 2018 07 12.
Article in English | MEDLINE | ID: mdl-30007417

ABSTRACT

Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.


Subject(s)
Chara/genetics , Genome, Plant , Biological Evolution , Cell Wall/metabolism , Chara/growth & development , Embryophyta/genetics , Gene Regulatory Networks , Pentosyltransferases/genetics , Plant Growth Regulators/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Reactive Oxygen Species/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcriptome
5.
Cell ; 171(2): 287-304.e15, 2017 Oct 05.
Article in English | MEDLINE | ID: mdl-28985561

ABSTRACT

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.


Subject(s)
Biological Evolution , Embryophyta/genetics , Genome, Plant , Marchantia/genetics , Adaptation, Biological , Embryophyta/physiology , Gene Expression Regulation, Plant , Marchantia/physiology , Molecular Sequence Annotation , Signal Transduction , Transcription, Genetic
6.
Plant Cell ; 36(7): 2709-2728, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38657101

ABSTRACT

Lignin production marked a milestone in vascular plant evolution, and the emergence of syringyl (S) lignin is lineage specific. S-lignin biosynthesis in angiosperms, mediated by ferulate 5-hydroxylase (F5H, CYP84A1), has been considered a recent evolutionary event. F5H uniquely requires the cytochrome b5 protein CB5D as an obligatory redox partner for catalysis. However, it remains unclear how CB5D functionality originated and whether it coevolved with F5H. We reveal here the ancient evolution of CB5D-type function supporting F5H-catalyzed S-lignin biosynthesis. CB5D emerged in charophyte algae, the closest relatives of land plants, and is conserved and proliferated in embryophytes, especially in angiosperms, suggesting functional diversification of the CB5 family before terrestrialization. A sequence motif containing acidic amino residues in Helix 5 of the CB5 heme-binding domain contributes to the retention of CB5D function in land plants but not in algae. Notably, CB5s in the S-lignin-producing lycophyte Selaginella lack these residues, resulting in no CB5D-type function. An independently evolved S-lignin biosynthetic F5H (CYP788A1) in Selaginella relies on NADPH-dependent cytochrome P450 reductase as sole redox partner, distinct from angiosperms. These results suggest that angiosperm F5Hs coopted the ancient CB5D, forming a modern cytochrome P450 monooxygenase system for aromatic ring meta-hydroxylation, enabling the reemergence of S-lignin biosynthesis in angiosperms.


Subject(s)
Cytochromes b5 , Lignin , Plant Proteins , Lignin/biosynthesis , Lignin/metabolism , Cytochromes b5/genetics , Cytochromes b5/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Phylogeny , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Evolution, Molecular , Magnoliopsida/genetics , Magnoliopsida/metabolism , Embryophyta/genetics , Charophyceae/genetics , Charophyceae/metabolism
7.
Proc Natl Acad Sci U S A ; 121(30): e2318982121, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39012828

ABSTRACT

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.


Subject(s)
Embryophyta , Gene Expression Regulation, Plant , Mycorrhizae , Plant Proteins , Symbiosis , Symbiosis/genetics , Mycorrhizae/physiology , Mycorrhizae/genetics , Embryophyta/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Marchantia/genetics , Marchantia/microbiology , Phylogeny
8.
Proc Natl Acad Sci U S A ; 121(10): e2310464121, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38412122

ABSTRACT

The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Embryophyta , Transcription Factors/genetics , Transcription Factors/metabolism , Arabidopsis/metabolism , Plant Proteins/metabolism , Plants/genetics , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Embryophyta/genetics , Inflorescence/metabolism , DNA/metabolism , Gene Expression Regulation, Plant , Flowers , Nuclear Proteins/metabolism
9.
Proc Natl Acad Sci U S A ; 119(15): e2100361119, 2022 04 12.
Article in English | MEDLINE | ID: mdl-35394876

ABSTRACT

As a midsized gene family conserved more by lineage than function, the typical plant terpene synthases (TPSs) could be a valuable tool to examine plant evolution. TPSs are pivotal in biosynthesis of gibberellins and related phytohormones as well as in formation of the extensive arsenal of specialized plant metabolites mediating ecological interactions whose production is often lineage specific. Yet the origin and early evolution of the TPS family is not well understood. Systematic analysis of an array of transcriptomes and sequenced genomes indicated that the TPS family originated after the divergence of land plants from charophytic algae. Phylogenetic and biochemical analyses support the hypothesis that the ancestral TPS gene encoded a bifunctional class I and II diterpene synthase producing the ent-kaurene required for phytohormone production in all extant lineages of land plants. Moreover, the ancestral TPS gene likely underwent duplication at least twice early in land plant evolution. Together these two gave rise to three TPS lineages leading to the extant TPS-c, TPS-e/f, and the remaining TPS (h/d/a/b/g) subfamilies, with the latter dedicated to secondary rather than primary metabolism while the former two contain those genes involved in ent-kaurene production. Nevertheless, parallel evolution from the ent-kaurene­producing class I and class II diterpene synthases has led to roles for TPS-e/f and -c subfamily members in secondary metabolism as well. These results clarify TPS evolutionary history and provide context for the role of these genes in producing the vast diversity of terpenoid natural products observed today in various land plant lineages.


Subject(s)
Alkyl and Aryl Transferases , Embryophyta , Evolution, Molecular , Plant Proteins , Alkyl and Aryl Transferases/classification , Alkyl and Aryl Transferases/genetics , Embryophyta/enzymology , Embryophyta/genetics , Gene Duplication , Phylogeny , Plant Growth Regulators , Plant Proteins/classification , Plant Proteins/genetics , Terpenes/metabolism
10.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Article in English | MEDLINE | ID: mdl-35042803

ABSTRACT

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.


Subject(s)
Base Sequence/genetics , Genomics/trends , Viridiplantae/genetics , Biodiversity , Biological Evolution , DNA Transposable Elements/genetics , Ecology , Ecosystem , Embryophyta/genetics , Evolution, Molecular , Genome , Genome, Plant/genetics , Genomics/methods , Information Dissemination/methods , Information Storage and Retrieval/methods , Phylogeny , Plants/genetics
11.
Mol Biol Evol ; 40(9)2023 09 01.
Article in English | MEDLINE | ID: mdl-37652031

ABSTRACT

MADS-box transcription factors (TFs), among the first TFs extensively studied, exhibit a wide distribution across eukaryotes and play diverse functional roles. Varying by domain architecture, MADS-box TFs in land plants are categorized into Type I (M-type) and Type II (MIKC-type). Type I and II genes have been considered orthologous to the SRF and MEF2 genes in animals, respectively, presumably originating from a duplication before the divergence of eukaryotes. Here, we exploited the increasing availability of eukaryotic MADS-box sequences and reassessed their evolution. While supporting the ancient duplication giving rise to SRF- and MEF2-types, we found that Type I and II genes originated from the MEF2-type genes through another duplication in the most recent common ancestor (MRCA) of land plants. Protein structures predicted by AlphaFold2 and OmegaFold support our phylogenetic analyses, with plant Type I and II TFs resembling the MEF2-type structure, rather than SRFs. We hypothesize that the ancestral SRF-type TFs were lost in the MRCA of Archaeplastida (the kingdom Plantae sensu lato). The retained MEF2-type TFs acquired a Keratin-like domain and became MIKC-type before the divergence of Streptophyta. Subsequently in the MRCA of land plants, M-type TFs evolved from a duplicated MIKC-type precursor through loss of the Keratin-like domain, leading to the Type I clade. Both Type I and II TFs expanded and functionally differentiated in concert with the increasing complexity of land plant body architecture. The recruitment of these originally stress-responsive TFs into developmental programs, including those underlying reproduction, may have facilitated the adaptation to the terrestrial environment.


Subject(s)
Embryophyta , Transcription Factors , Animals , Phylogeny , Embryophyta/genetics , Keratins , Eukaryota
12.
Plant Physiol ; 192(2): 1183-1203, 2023 05 31.
Article in English | MEDLINE | ID: mdl-36869858

ABSTRACT

Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back to the American sweet flag (Acorus americanus), the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events of AGO genes that were lost, retained, or further duplicated in subgroups, indicating that the evolution of AGOs is complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17, and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins shed light on the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.


Subject(s)
Embryophyta , MicroRNAs , Phylogeny , RNA, Small Interfering/genetics , Plants/genetics , Plants/metabolism , MicroRNAs/genetics , RNA, Double-Stranded , Embryophyta/genetics , Argonaute Proteins/genetics , Argonaute Proteins/metabolism
13.
Plant Cell ; 33(9): 2915-2934, 2021 09 24.
Article in English | MEDLINE | ID: mdl-34240188

ABSTRACT

An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question-how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in nonangiosperms. These discoveries provoke questions regarding coevolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective, we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.


Subject(s)
Embryophyta/genetics , Evolution, Molecular , Genome, Plant , Peptides/metabolism , Plant Proteins/metabolism , Signal Transduction , Embryophyta/metabolism , Peptides/genetics , Phylogeny , Plant Proteins/genetics
14.
Plant Cell ; 33(5): 1472-1491, 2021 07 02.
Article in English | MEDLINE | ID: mdl-33638637

ABSTRACT

The plant phenylpropanoid pathway generates a major class of specialized metabolites and precursors of essential extracellular polymers that initially appeared upon plant terrestrialization. Despite its evolutionary significance, little is known about the complexity and function of this major metabolic pathway in extant bryophytes, which represent the non-vascular stage of embryophyte evolution. Here, we report that the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE (HCT) gene, which plays a critical function in the phenylpropanoid pathway during seed plant development, is functionally conserved in Physcomitrium patens (Physcomitrella), in the moss lineage of bryophytes. Phylogenetic analysis indicates that bona fide HCT function emerged in the progenitor of embryophytes. In vitro enzyme assays, moss phenolic pathway reconstitution in yeast and in planta gene inactivation coupled to targeted metabolic profiling, collectively indicate that P. patens HCT (PpHCT), similar to tracheophyte HCT orthologs, uses shikimate as a native acyl acceptor to produce a p-coumaroyl-5-O-shikimate intermediate. Phenotypic and metabolic analyses of loss-of-function mutants show that PpHCT is necessary for the production of caffeate derivatives, including previously reported caffeoyl-threonate esters, and for the formation of an intact cuticle. Deep conservation of HCT function in embryophytes is further suggested by the ability of HCT genes from P. patens and the liverwort Marchantia polymorpha to complement an Arabidopsis thaliana CRISPR/Cas9 hct mutant, and by the presence of phenolic esters of shikimate in representative species of the three bryophyte lineages.


Subject(s)
Acyltransferases/genetics , Acyltransferases/metabolism , Conserved Sequence , Embryophyta/enzymology , Evolution, Molecular , Acylation , Acyltransferases/deficiency , Biocatalysis , Bryophyta/enzymology , Embryophyta/genetics , Gene Expression Regulation, Enzymologic , Genes, Plant , Kinetics , Models, Biological , Phenols/metabolism , Phylogeny , Recombinant Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Shikimic Acid/chemistry , Shikimic Acid/metabolism
15.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Article in English | MEDLINE | ID: mdl-33531363

ABSTRACT

Many enzymes involved in photosynthesis possess highly conserved cysteine residues that serve as redox switches in chloroplasts. These redox switches function to activate or deactivate enzymes during light-dark transitions and have the function of fine-tuning their activities according to the intensity of light. Accordingly, many studies on chloroplast redox regulation have been conducted under the hypothesis that "fine regulation of the activities of these enzymes is crucial for efficient photosynthesis." However, the impact of the regulatory system on plant metabolism is still unclear. To test this hypothesis, we here studied the impact of the ablation of a redox switch in chloroplast NADP-malate dehydrogenase (MDH). By genome editing, we generated a mutant plant whose MDH lacks one of its redox switches and is active even in dark conditions. Although NADPH consumption by MDH in the dark is expected to be harmful to plant growth, the mutant line did not show any phenotypic differences under standard long-day conditions. In contrast, the mutant line showed severe growth retardation under short-day or fluctuating light conditions. These results indicate that thiol-switch redox regulation of MDH activity is crucial for maintaining NADPH homeostasis in chloroplasts under these conditions.


Subject(s)
Chloroplasts/genetics , Malate Dehydrogenase (NADP+)/genetics , Photosynthesis/genetics , Thioredoxins/genetics , Arabidopsis/genetics , Arabidopsis/growth & development , Arabidopsis Proteins/genetics , Cysteine/genetics , Embryophyta/genetics , Embryophyta/growth & development , Light , Oxidation-Reduction
16.
Plant J ; 109(1): 92-111, 2022 01.
Article in English | MEDLINE | ID: mdl-34713507

ABSTRACT

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


Subject(s)
Embryophyta/enzymology , Malate Dehydrogenase/metabolism , Protein Processing, Post-Translational , Acetylation , Embryophyta/genetics , Lysine/metabolism , Malate Dehydrogenase/genetics , Mitochondria/enzymology , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism
17.
Plant Mol Biol ; 112(6): 325-340, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37380791

ABSTRACT

The contrasting genome size between homosporous and heterosporous plants is fascinating. Different from the heterosporous seed plants and mainly homosporous ferns, the lycophytes are either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). Many lycophytes are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer's disease. For the seed-free vascular plants, several high-quality genomes of heterosporous Selaginella, homosporous ferns (maidenhair fern, monkey spider tree fern), and heterosporous ferns (Azolla) have been published and provided important insights into the origin and evolution of early land plants. However, the homosporous lycophyte genome has not been decoded. Here, we assembled the first homosporous lycophyte genome and conducted comparative genomic analyses by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size of Lycopodium clavatum is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is long terminal repeat (LTR). This study disclosed a high birth rate and a low death rate of the LTR-RTs in homosporous lycophytes, but the opposite occurs in heterosporous lycophytes. we propose that the recent activity of LTR-RT is responsible for the immense genome size variation between homosporous and heterosporous lycophytes. By combing Ks analysis with a phylogenetic approach, we discovered two whole genome duplications (WGD). Morover, we identified all the five recognized key enzymes for the HupA biosynthetic pathway in the L. clavatum genome, but found this pathway incomplete in other major lineages of land plants. Overall, this study is of great importance for the medicinal utilization of lycophytes and the decoded genome data will be a key cornerstone to elucidate the evolution and biology of early vascular land plants.


Subject(s)
Embryophyta , Ferns , Phylogeny , Genome Size , Plants/genetics , Ferns/genetics , Embryophyta/genetics , Terminal Repeat Sequences , Evolution, Molecular
18.
Plant Mol Biol ; 113(4-5): 121-142, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37991688

ABSTRACT

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Embryophyta , Marchantia , MicroRNAs , Marchantia/genetics , Marchantia/metabolism , Plants/genetics , MicroRNAs/genetics , Biological Evolution , Arabidopsis/genetics , Embryophyta/genetics , Arabidopsis Proteins/genetics , Ribonuclease III/genetics , Ribonuclease III/metabolism
19.
New Phytol ; 238(3): 977-982, 2023 05.
Article in English | MEDLINE | ID: mdl-36811171

ABSTRACT

Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.


Subject(s)
Embryophyta , Protein Serine-Threonine Kinases , Protein Serine-Threonine Kinases/metabolism , Plant Proteins/metabolism , Leucine , Phylogeny , Signal Transduction/physiology , Peptides/genetics , Embryophyta/genetics , Embryophyta/metabolism
20.
Plant Physiol ; 190(1): 85-99, 2022 08 29.
Article in English | MEDLINE | ID: mdl-35904762

ABSTRACT

The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.


Subject(s)
Embryophyta , Biological Evolution , Embryophyta/genetics , Evolution, Molecular , Fossils , Phylogeny , Plants/genetics
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