Genome-Wide Characterization of Wholly Disordered Proteins in Arabidopsis DOI Open Access
William J. Long, Liang Zhao, Huimin Yang

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(3), P. 1117 - 1117

Published: Jan. 28, 2025

Intrinsically disordered proteins (IDPs) include two types of proteins: partial regions (IDRs) and wholly (WDPs). Extensive studies focused on the with IDRs, but less is known about WDPs because their difficult-to-form folded tertiary structure. In this study, we developed a bioinformatics method for screening more than 50 amino acids in genome level found total 27 categories, including 56 WDPs, Arabidopsis. After comparing randomly selected structural proteins, that possessed wide range theoretical isoelectric point (PI), negative Grand Average Hydropathicity (GRAVY), higher value Instability Index (II), lower values Aliphatic (AI). addition, by calculating FCR (fraction charged residue) NCPR (net charge per each WDP, 20 R1 (FCR < 0.25 0.25) group, 15 R2 (0.25 ≤ 0.35 0.35), 19 R3 > R4 0.35). Moreover, gene expression protein-protein interaction (PPI) network analysis showed perform different biological functions. We also SIS (Salt Induced Serine rich) RAB18 (a dehydrin family protein), undergo vitro liquid-liquid phase separation (LLPS). Therefore, our results provide insight into understanding biochemical characters functions plants.

Language: Английский

A deep dive into bryophyte genome space reveals opposing evolutionary trends in the sister lineages, mosses and liverworts DOI Open Access
Tao Fujiwara, Liu HongMei, Lei Shu

et al.

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Abstract Among the lineages of tree life, land plants exhibit a remarkably high genomic disparity because their distinct evolutionary trajectories in phylogenetic history major lineages. The macroevolutionary pattern evolution has been mainly investigated to obtain insights into well‐studied such as angiosperms, but little attention given many important bryophytes. This study was designed resolve this gap by comparing mosses and liverworts. Thus, data set comprising chromosome number genome size compiled, including previously published newly generated that were used trace these two parameters among liverworts via ancestral state reconstruction comparative analyses. Contrasting patterns evolutions detected between sister Mosses accumulated repeated whole‐genome duplications descending dysploidy maintained small size. By contrast, highly conserved, heterogeneous trends identified These contrasting may be partly explained difference dynamics: Active dynamics enables downsizing reorganization mosses, whereas stability leads accumulation large genomes results confirmed

Language: Английский

Citations

1
The plant response to highCO2levels is heritable and orchestrated byDNAmethylation DOI Creative Commons
Kaushik Panda, Boominathan Mohanasundaram,

Jorge Gutierrez

et al.

New Phytologist, Journal Year: 2023, Volume and Issue: 238(6), P. 2427 - 2439

Published: March 15, 2023

Summary Plant responses to abiotic environmental challenges are known have lasting effects on the plant beyond initial stress exposure. Some of these transgenerational, affecting next generation. The response elevated carbon dioxide (CO 2 ) levels has been well studied. However, investigations typically limited plants grown for a single generation in high CO environment while transgenerational studies rare. We aimed determine growth after exposure by investigating direct progeny when returned baseline levels. found that both flowering Arabidopsis thaliana and seedless nonvascular Physcomitrium patens continue display accelerated rates exposed . used model species dissect molecular mechanism DNA methylation pathways necessary heritability this response. More specifically, pathway RNA‐directed is required initiate proteins CMT2 CMT3 needed propagation plants. Together, two establish then maintain cellular memory

Language: Английский

Citations

22
Evolution of phenotypic disparity in the plant kingdom DOI Creative Commons
James Clark, Alexander J. Hetherington, Jennifer L. Morris

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(10), P. 1618 - 1626

Published: Sept. 4, 2023

The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with ploidy history, reflecting role genome duplication in macroevolution. Overall, a pattern episodically increasing throughout its history mirrors floras reflects ecological expansion facilitated innovations. This also parallels seen animal fungal kingdoms, suggesting general for evolution bodyplans.

Language: Английский

Citations

18
Evolutionary origins and functional diversification of Auxin Response Factors DOI Creative Commons
Jorge Hernández‐García, Vanessa Polet Carrillo‐Carrasco, Juriaan Rienstra

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Dec. 30, 2024

The Auxin Response Factors (ARFs) family of transcription factors are the central mediators auxin-triggered transcriptional regulation. Functionally different classes extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part evolutionary trajectory to present auxin response functions has been reconstructed, it is unclear how emerged, early diversification led functionally proteins. Here, we use in silico vivo analyses revisit molecular events that origin subsequent evolution ARFs. We reveal shared from preexisting domains, uncovering a protein fold homologous ARF DNA-binding conserved eukaryotic chromatin regulator. Building on this, reconstruct complete history ARFs, including divergence leading appearance defining main targets for their functional diversification. derive emergence nuclear signalling pathway.

Language: Английский

Citations

6
An optimized transformation protocol for Anthoceros agrestis and three more hornwort species DOI Creative Commons
Manuel Waller, Eftychios Frangedakis, Alan O. Marron

et al.

The Plant Journal, Journal Year: 2023, Volume and Issue: 114(3), P. 699 - 718

Published: Feb. 22, 2023

SUMMARY Land plants comprise two large monophyletic lineages, the vascular and bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of three lineages of only mosses liverworts are systematically investigated, while hornworts understudied. Despite importance for understanding fundamental questions land plant evolution, they recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability high‐quality genome assembly genetic transformation technique makes A. an attractive species hornworts. Here we describe updated optimized protocol , can be successfully used genetically modify one more strain species, punctatus Leiosporoceros dussii Phaeoceros carolinianus. The new method is less laborious, faster, results in generation greatly increased numbers transformants compared previous method. We have also selection marker transformation. Finally, report development set different cellular localization signal peptides providing tools better understand cell biology.

Language: Английский

Citations

16
Convergent evolution of water-conducting cells in Marchantia recruited the ZHOUPI gene promoting cell wall reinforcement and programmed cell death DOI Creative Commons
Yen‐Ting Lu,

Jeanne Loue-Manifel,

Norbert Bollier

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(4), P. 793 - 807.e7

Published: Jan. 30, 2024

A key adaptation of plants to life on land is the formation water-conducting cells (WCCs) for efficient long-distance water transport. Based morphological analyses it thought that WCCs have evolved independently multiple occasions. For example, been lost in all but a few lineages bryophytes but, strikingly, within liverworts derived group, complex thalloids, has novel externalized tissue composed reinforced, hollow termed pegged rhizoids. Here, we show rhizoid differentiation Marchantia polymorpha controlled by orthologs ZHOUPI and ICE bHLH transcription factors required endosperm cell death Arabidopsis seeds. By contrast, development was not affected disruption MpNAC5, ortholog VND genes control WCC flowering plants. We characterize rapid, genetically programmed process rhizoids undergo terminate cellular identify corresponding upregulation conserved putative plant effector genes. Lastly, ectopic expression MpZOU1 increases production enhances drought tolerance. Our results support other WCCs. suggest elements genetic developmental are throughout ZHOUPI/ICE regulatory module recruited promote wall modification liverwort seed.

Language: Английский

Citations

5
Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land DOI Creative Commons
Philip C. J. Donoghue, James Clark

Current Biology, Journal Year: 2024, Volume and Issue: 34(3), P. R86 - R89

Published: Feb. 1, 2024

Language: Английский

Citations

5
Unveiling the molecular mechanisms of arsenic tolerance and resilience in the primitive bryophyte Marchantia polymorpha L. DOI
Prasanna Dutta, Priti Prasad,

Yuvraj Indoilya

et al.

Environmental Pollution, Journal Year: 2024, Volume and Issue: 346, P. 123506 - 123506

Published: Feb. 13, 2024

Language: Английский

Citations

5
Metagenome‐assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land DOI Creative Commons
Alexander M. C. Bowles, Tom A. Williams, Philip C. J. Donoghue

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: June 6, 2024

Summary Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation UV radiation. These same environmental challenges have been hypothesised as the driving force behind evolution land plants from algal ancestors in Cryogenian (720–635 million years ago). We sequenced, assembled analysed metagenome‐assembled genome glacier alga Ancylonema nordenskiöldii to investigate its adaptations life ice, whether this represents a vestige exaptations. Phylogenetic analysis confirms placement within sister lineage plants, Zygnematophyceae. The is characterised an expansion genes involved high irradiance light, while lineage‐specific diversification linked novel screening pigmentation algae. found no support for hypothesis common genomic basis ice streptophytes. Comparative genomics revealed reductive morphological ancestor Zygnematophyceae was accompanied evolution. This first genome‐scale data suggests ‐specific adaptation cryosphere, sheds light on

Language: Английский

Citations

5
Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha DOI Creative Commons
Nataliya E. Yelina, Eftychios Frangedakis,

Zhemin Wang

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(9), P. 114696 - 114696

Published: Sept. 1, 2024

Language: Английский

Citations

5