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The New Phytologist Jun 2024Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage...
Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.
PubMed: 38840557
DOI: 10.1111/nph.19875 -
The New Phytologist Jun 2024Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These...
Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.
PubMed: 38840553
DOI: 10.1111/nph.19860 -
The New Phytologist Jun 2024Differences in demographic and environmental niches facilitate plant species coexistence in tropical forests. However, the adaptations that enable species to achieve...
Differences in demographic and environmental niches facilitate plant species coexistence in tropical forests. However, the adaptations that enable species to achieve higher demographic rates (e.g. growth or survival) or occupy unique environmental niches (e.g. waterlogged conditions) remain poorly understood. Anatomical traits may better predict plant environmental and demographic strategies because they are direct measurements of structures involved in these adaptations. We collected 18 leaf and twig traits from 29 tree species in a tropical freshwater swamp forest in Singapore. We estimated demographic parameters of the 29 species from growth and survival models, and degree of association toward swamp habitats. We examined pairwise trait-trait, trait-demography and trait-environment links while controlling for phylogeny. Leaf and twig anatomical traits were better predictors of all demographic parameters than other commonly measured leaf and wood traits. Plants with wider vessels had faster growth rates but lower survival rates. Leaf and spongy mesophyll thickness predicted swamp association. These findings demonstrate the utility of anatomical traits as indicators of plant hydraulic strategies and their links to growth-mortality trade-offs and waterlogging stress tolerance that underlie species coexistence mechanisms in tropical forest trees.
PubMed: 38840520
DOI: 10.1111/nph.19876 -
The New Phytologist Jun 2024The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first...
The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown. Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes. Our results show that deletion of two tandemly arranged genes encoding Q-type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af-harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes. Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops.
PubMed: 38837425
DOI: 10.1111/nph.19800 -
The New Phytologist Jun 2024
PubMed: 38837421
DOI: 10.1111/nph.19881 -
The New Phytologist Jun 2024
PubMed: 38837388
DOI: 10.1111/nph.19879 -
International Journal of Systematic and... Jun 2024During a study on the diversity of culturable actinobacteria from coastal halophytes in Thailand, strain LSe6-5 was isolated from leaves of sea purslane ( L.), and a...
During a study on the diversity of culturable actinobacteria from coastal halophytes in Thailand, strain LSe6-5 was isolated from leaves of sea purslane ( L.), and a polyphasic approach was employed to determine its taxonomic position. The 16S rRNA gene sequences analysis indicated that the strain was most closely related to Tu 6233 (99.2 %), YIM M13156 (99.1 %), and PB261 (98.7 %). The genome of strain LSe6-5 was estimated to be 4.33 Mbp in size, with DNA G+C contents of 74.3%. A phylogenomic tree based on whole-genome sequences revealed that strain LSe6-5 formed a clade with DSM 45722, indicating their close relationship. However, the average nucleotide identity (ANI)-blast, ANI-MUMmer, and dDDH values between strain LSe6-5 with DSM 45722 (87.1, 88.9, and 33.0 %) were below the thresholds of 95-96 % ANI and 70 % dDDH for identifying a novel species. Furthermore, strain LSe6-5 showed morphological and chemotaxonomic characteristics of the genus . Cells were motile, rod-shaped, and Gram-stain-positive. Optimal growth of strain LSe6-5 occurred at 28 °C, pH 7.0, and 0-3 % NaCl. The whole-cell hydrolysates contained -diaminopimelic acid as the diagnostic diamino acid, with galactose, glucose, mannose, and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H) and MK-9(H). The polar lipid profile was composed of diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified phospholipid, and an unidentified lipid. Major cellular fatty acids were -C, -C, and -C. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, it is supported that strain LSe6-5 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is strain LSe6-5 (=TBRC 16417= NBRC 115929).
Topics: Phylogeny; Base Composition; RNA, Ribosomal, 16S; Fatty Acids; Plant Leaves; Thailand; Salt-Tolerant Plants; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Vitamin K 2; Phospholipids; Whole Genome Sequencing; Genome, Bacterial
PubMed: 38832855
DOI: 10.1099/ijsem.0.006410 -
The New Phytologist Jun 2024Plant secreted peptides RAPID ALKALINISATION FACTORs (RALFs), which act through the receptor FERONIA (FER), play important roles in plant growth. However, it remains...
Plant secreted peptides RAPID ALKALINISATION FACTORs (RALFs), which act through the receptor FERONIA (FER), play important roles in plant growth. However, it remains unclear whether and how RALF-FER contributes to the trade-off of plant growth-defense. Here, we used a variety of techniques such as CRISPR/Cas9, protein-protein interaction and transcriptional regulation methods to investigate the role of RALF2 and its receptor FER in regulating lignin deposition, root growth, and defense against Fusarium oxysporum f. sp. lycopersici (Fol) in tomato (Solanum lycopersicum). The ralf2 and fer mutants show reduced primary root length, elevated lignin accumulation, and enhanced resistance against Fol than the wild-type. FER interacts with and phosphorylates MYB63 to promote its degradation. MYB63 serves as an activator of lignin deposition by regulating the transcription of dirigent protein gene DIR19. Mutation of DIR19 suppresses lignin accumulation, and reverses the short root phenotype and Fol resistance in ralf2 or fer mutant. Collectively, our results demonstrate that the RALF2-FER-MYB63 module fine-tunes root growth and resistance against Fol through regulating the deposition of lignin in tomato roots. The study sheds new light on how plants maintain the growth-defense balance via RALF-FER.
PubMed: 38831656
DOI: 10.1111/nph.19865 -
The New Phytologist Jun 2024Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell...
Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell motility, exopolysaccharide biosynthesis, and lipid metabolism; however, their involvement in regulating carbon metabolism in Synechocystis sp. PCC 6803 has not been reported. We identified a novel GT protein, Slr1064, involved in carbon metabolism. The effect of slr1064 deletion on the growth of Synechocystis cells and functional mechanisms of Slr1064 on carbon metabolism were thoroughly investigated through physiological, biochemistry, proteomic, and metabolic analyses. We found that this GT, which is mainly distributed in the membrane compartment, is essential for the growth of Synechocystis under heterotrophic and mixotrophic conditions, but not under autotrophic conditions. The deletion of slr1064 hampers the turnover rate of Gap2 under mixotrophic conditions and disrupts the assembly of the PRK/GAPDH/CP12 complex under dark culture conditions. Additionally, UDP-GlcNAc, the pivotal metabolite responsible for the O-GlcNAc modification of GAPDH, is downregulated in the Δslr1064. Our work provides new insights into the role of GTs in carbon metabolism in Synechocystis and elucidate the mechanism by which carbon metabolism is regulated in this important model organism.
PubMed: 38831647
DOI: 10.1111/nph.19872 -
The New Phytologist Jul 2024In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included...
In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included Picturatum/Eluta, which restricts the accumulation of magenta anthocyanin pigments, forming bullseye markings on the flower face. We identified the gene underlying the Eluta locus by transposon-tagging, using an Antirrhinum line that spontaneously lost the nonsuppressive el phenotype. A candidate MYB repressor gene at this locus contained a CACTA transposable element. We subsequently identified plants where this element excised, reverting to a suppressive Eluta phenotype. El alleles inhibit expression of anthocyanin biosynthetic genes, confirming it to be a regulatory locus. The modes of action of Eluta were investigated by generating stable transgenic tobacco lines, biolistic transformation of Antirrhinum petals and promoter activation/repression assays. Eluta competes with MYB activators for promoter cis-elements, and also by titrating essential cofactors (bHLH proteins) to reduce transcription of target genes. Eluta restricts the pigmentation established by the R2R3-MYB factors, Rosea and Venosa, with the greatest repression on those parts of the petals where Eluta is most highly expressed. Baur questioned the origin of heredity units determining flower colour variation in cultivated A. majus. Our findings support introgression from wild species into cultivated varieties.
Topics: Antirrhinum; Flowers; Pigmentation; Plant Proteins; Gene Expression Regulation, Plant; Anthocyanins; Phenotype; Plants, Genetically Modified; Genes, Plant; Nicotiana; Promoter Regions, Genetic; DNA Transposable Elements; Alleles
PubMed: 38822654
DOI: 10.1111/nph.19866