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Plant Physiology and Biochemistry : PPB Jun 2024In land plants plastid type differentiation occurs concomitantly with cellular differentiation and the transition from one type to another is under developmental and...
In land plants plastid type differentiation occurs concomitantly with cellular differentiation and the transition from one type to another is under developmental and environmental control. Plastid dynamism is based on a bilateral communication between plastids and nucleus through anterograde and retrograde signaling. Signaling occurs through the interaction with specific phytohormones (abscisic acid, strigolactones, jasmonates, gibberellins, brassinosteroids, ethylene, salicylic acid, cytokinin and auxin). The review is focused on the modulation of plastid capabilities at both transcriptional and post-translational levels at the crossroad between development and stress, with a particular attention to the chloroplast, because the most studied plastid type. The role of plastid-encoded and nuclear-encoded proteins for plastid development and stress responses, and the changes of plastid fate through the activity of stromules and plastoglobules, are discussed. Examples of plastid dynamism in response to soil stress agents (salinity, lead, cadmium, arsenic, and chromium) are described. Albinism and root greening are described based on the modulation activities of auxin and cytokinin. The physiological and functional responses of the sensory epidermal and vascular plastids to abiotic and biotic stresses along with their specific roles in stress sensing are described together with their potential modulation of retrograde signaling pathways. Future research perspectives include an in-depth study of sensory plastids to explore their potential for establishing a transgenerational memory to stress. Suggestions about anterograde and retrograde pathways acting at interspecific level and on the lipids of plastoglobules as a novel class of plastid morphogenic agents are provided.
PubMed: 38861821
DOI: 10.1016/j.plaphy.2024.108813 -
Methods in Molecular Biology (Clifton,... 2024Glutamate:glyoxylate aminotransferase (GGAT; EC 2.6.1.4) and serine:glyoxylate aminotransferase activities (SGAT; EC 2.6.1.45) are central photorespiratory reactions...
Glutamate:glyoxylate aminotransferase (GGAT; EC 2.6.1.4) and serine:glyoxylate aminotransferase activities (SGAT; EC 2.6.1.45) are central photorespiratory reactions within plant peroxisomes. Both enzymatic reactions convert glyoxylate, a product of glycolate oxidase, to glycine, a substrate of the mitochondrial glycine decarboxylase complex. The GGAT reaction uses glutamate as an amino group donor and also produces α-ketoglutarate, which is recycled to glutamate in plastids by ferredoxin-dependent glutamate synthase. Using serine, a product of mitochondrial serine hydroxymethyltransferase, as an amino group donor, the SGAT reaction also produces hydroxypyruvate, a substrate of hydroxypyruvate reductase. The activities of these photorespiratory aminotransferases can be measured using indirect, coupled, spectrophotometric assays, detailed herein.
Topics: Transaminases; Spectrophotometry; Glyoxylates; Glutamic Acid; Enzyme Assays; Cell Respiration
PubMed: 38861077
DOI: 10.1007/978-1-0716-3802-6_4 -
Plant Molecular Biology Jun 2024Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited...
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
Topics: Oryza; Plant Proteins; Exonucleases; Gene Editing; Gene Expression Regulation, Plant; DNA, Plant; Pollen; Plant Leaves; Genome, Plant; Mutation
PubMed: 38856917
DOI: 10.1007/s11103-024-01452-x -
Wellcome Open Research 2023We present a genome assembly from a specimen of (the silverweed cinquefoil; Streptophyta; eudicotyledons; Rosales; Potentilleae). The haploid genome sequence is 237...
We present a genome assembly from a specimen of (the silverweed cinquefoil; Streptophyta; eudicotyledons; Rosales; Potentilleae). The haploid genome sequence is 237 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 294.6 and 155.6 kilobases in length respectively.
PubMed: 38855725
DOI: 10.12688/wellcomeopenres.19908.1 -
Frontiers in Plant Science 2024The orchid genus comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to...
The orchid genus comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, , occurs in a single location in northern Vietnam within a lowland limestone karstic area. and , in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of ( and ) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, is sister to the photosynthetic genus . is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for . Flower morphology is concordant with the molecular data in placing into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, shows no close structural similarity with any of its genera; in particular, the proximity between and has never been proposed. Finally, we assembled the plastid genome of , which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected.
PubMed: 38855461
DOI: 10.3389/fpls.2024.1393225 -
Frontiers in Plant Science 2023The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The...
The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only section with a center of diversity in Australasia is sect. . However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within , and interspecific relationships within sect. , a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (K and 1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in , including phylogenetic evidence for the non-monophyly of sections , , , , , , , , , and . Section and sect. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of in the Early Oligocene (ca. 33.2 Ma) and sect. in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. facilitating allopatric speciation.
PubMed: 38854888
DOI: 10.3389/fpls.2023.1219354 -
Wellcome Open Research 2024We present a genome assembly from a diploid female (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2...
We present a genome assembly from a diploid female (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.
PubMed: 38854694
DOI: 10.12688/wellcomeopenres.21004.1 -
PhytoKeys 2024This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker...
Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of and its allies in the Old World.
This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for , , sensu lato, and . In addition, we present a comprehensive taxonomic synopsis of and its morphological allies in the Old World, recognizing 27 species and ten varieties within , three species and two varieties within , and two species and three varieties within . Furthermore, we also lectotypified 12 names and made two new combinations, (J.E.Vidal) B.B.Liu and (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.
PubMed: 38854497
DOI: 10.3897/phytokeys.242.117481 -
BioRxiv : the Preprint Server For... May 2024The heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional...
The heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional regulation. The ACC represents almost all ACCs from pathogenic bacteria making it a key antibiotic development target to fight growing antibiotic resistance. Furthermore, it is a model for cyanobacterial and plant plastid ACCs as biofuel engineering targets. Here we report the catalytic ACC complex surprisingly forms tubes rather than dispersed particles. The cryo-EM structure reveals key protein-protein interactions underpinning efficient catalysis and how transcriptional regulatory roles are masked during catalysis. Discovering the protein-protein interaction interfaces that facilitate catalysis, allosteric and transcriptional regulation provides new routes to engineering catalytic activity and new targets for drug discovery.
PubMed: 38854064
DOI: 10.1101/2024.05.28.596234 -
American Journal of Botany Jun 2024Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a...
PREMISE
Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa.
METHODS
We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method (ASTRAL-III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time-calibrated in BEAST. Introgression between species was explored using Phylonet.
RESULTS
The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene-Pleistocene.
CONCLUSIONS
These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations.
PubMed: 38853465
DOI: 10.1002/ajb2.16352