New Phytologist最新文献

• Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. Chlamydomonas reinhardtii is a valuable model organism with profound potential to study the impact of ploidy increase on the longer term in a laboratory environment. This is partly due to the ability to increase the ploidy level.
• We developed a strategy to engineer ploidy in C. reinhardtii using noninterfering, antibiotic, selectable markers. This approach allows us to induce higher ploidy levels in C. reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy.
• We demonstrate the creation of diploids, triploids, and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in C. reinhardtii. However, our newly formed triploids and tetraploids show signs of rapid aneuploidization.
• Our study greatly facilitates the application of C. reinhardtii to study polyploidy, in both fundamental and applied settings.

• U2AF65B is one of the splicing factors that are involved in the recognition of the 3′ splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner.
• Through mutant screening and map-based cloning, protein–protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in Arabidopsis thaliana.
• We found in the u2af65b mutant that the exogenous transgene 35S::HYG is activated in expression with decreased DNA methylation on the 35S core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in u2af65b, nearly half of them are also hypomethylated in the dms3 mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the 35S::HYG transgene and endogenous RdDM loci.
• Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.

What inspired your interest in plant science?

My early years were spent in Kokoda in Papua New Guinea (where my dad was a teacher) – a place where one lived surrounded by forests and grasslands. From family albums, it is clear that we spent a lot of time playing barefoot outdoors, surrounded by, and immersed in lush tropical vegetation. On returning to Australia as a 6-year-old, I had to adjust to wearing shoes in an ordered, suburban landscape that lacked Kokoda's greenness. A yearning for green-dominated environments played a role in my interest in plants, along with: talking to my grandfather about what he was growing in his vegetable garden (and debating whether he really needed to chop down a tree that was shading his vegetables !); and, an uncle introducing me to the landscape wonders of bushwalking and back country cross-country skiing in Australia's high country. These experiences gave me a deep emotional appreciation for the role plants play in regulating ecosystem services and in defining the ‘human condition’. Then, in time, I became fascinated with the question of how plants survive where they do and what factors regulate their ability to grow and reproduce.

• Stomatal immunity and apoplastic immunity are critical for preventing microbial phytopathogenesis. However, the specific regulatory mechanisms of these resistances remain unclear.
• In this study, a BBX11 transcription factor (TF) was identified in Arabidopsis and was found to participate in stomatal and apoplast immunity. Phenotypic, biochemical, and genetic analyses revealed that NAC053 contributed to Arabidopsis resistance against Pseudomonas syringae pv tomato DC3000 (Pst DC3000) by positively regulating BBX11.
• BBX11 TF that was expressed constitutively in guard cells acts as a positive regulator of plant defense against Pst DC3000 through the suppression of coronatine (COR)-induced stomatal reopening, mitigating the virulence of COR and alleviating COR-triggered systemic susceptibility in the apoplast. BBX11 was found to be involved in PTI responses induced by flg22, such as stomatal closure, reactive oxygen species accumulation, MAPK activation, and callose deposition, thereby enhancing disease resistance. Yeast one-hybrid screening identified NAC053 as a potential TF that interacted with the promoter of BBX11. NAC053 also positively regulated resistance to Pst DC3000.
• These findings underscore the significance of transcriptional activation of BBX11 by NAC053 in stomatal and apoplastic immunity against Pst DC3000, enhancing understanding of plant regulatory mechanisms in response to bacterial pathogens.

Response to Bowles et al. (2024) ‘Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land’

As plants began to colonize the land c. 470–450 million years ago, they had to overcome many abiotic stresses not experienced by their marine ancestors (Rensing, 2018). One such stress was freezing and thawing, which can damage plant cell walls. Bacteria, which had established their presence on land well before the arrival of plants, greatly aided the transition of plants to land by the horizontal transfer of key genes (Yue et al., 2012; Ma et al., 2020). Bacteria are likely donors of genes that can mitigate freeze–thaw injury, as proteins with ice-binding activity have been found in several bacteria (Raymond et al., 2007, 2008; Vance et al., 2018). Each of the proteins in those studies contains a c. 200-aa domain called DUF3494 that has a beta solenoid structure with one side that binds to ice crystals (Vance et al., 2019). At very low concentrations, these proteins can drastically prevent the recrystallization of ice that occurs during thawing, which is thought to damage cell walls. Similar proteins have been identified in hundreds of species of bacteria, although not all of them have been examined for ice-binding activity. Horizontally acquired genes of this type appear to be the source of freeze–thaw tolerance in a number of algae and fungi that live in icy habitats (Raymond & Kim, 2012).

Zygnematophyceae, being the closest known relatives of all land plants (Cheng et al., 2019), are of interest because of their remarkable ability to find solutions for the stresses encountered by early land plants (Kunz et al., 2024). In this vein, Bowles et al. (2024) recently obtained the metagenome of algae inhabiting the Morteratsch Glacier in Switzerland to investigate the adaptation of the early streptophyte alga Ancylonema nordenskioeldii to life in ice. Among the survival mechanisms investigated, the authors looked for genes encoding ice-binding proteins (IBPs). They found several candidates in the protein kinase superfamily, ATP-binding cassette protein family and heat shock protein family, although none were confirmed to have ice-binding activity. Apparently, they did not see our earlier paper in which we identified an IBP in A. nordenskioeldii (AnIBP) from the Morteratsch Glacier (Procházková et al., 2024). Here, we summarize the main findings of this paper, in which we showed that AnIBP has ice-binding activity and that this activity could be attributed to a protein of the DUF3494 family.

• Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures.
• Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago.
• Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions.
• Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.

• The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient.
• To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components.
• Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation.
• Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.