scholarly journals Origin and evolution of the nuclear auxin response system

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sumanth K Mutte ◽  
Hirotaka Kato ◽  
Carl Rothfels ◽  
Michael Melkonian ◽  
Gane Ka-Shu Wong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Land Plant ◽  
Land Plants ◽  
Response Mechanism ◽  
Auxin Response ◽  
Evolutionary Trajectory ◽  
Origin And Evolution ◽  
Response System ◽  
Large Families ◽  
System Properties

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

scholarly journals Origin and evolution of the nuclear auxin response system

2017 ◽  
Author(s):  
Sumanth K. Mutte ◽  
Hirotaka Kato ◽  
Carl Rothfels ◽  
Michael Melkonian ◽  
Gane Ka-Shu Wong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Land Plant ◽  
Land Plants ◽  
Response Mechanism ◽  
Auxin Response ◽  
Evolutionary Trajectory ◽  
Origin And Evolution ◽  
Response System ◽  
Large Families ◽  
System Properties

AbstractThe small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

scholarly journals Design principles of a minimal auxin response system

2019 ◽  
Author(s):  
Hirotaka Kato ◽  
Sumanth K. Mutte ◽  
Hidemasa Suzuki ◽  
Isidro Crespo ◽  
Shubhajit Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression System ◽  
Expression Patterns ◽  
Land Plants ◽  
Marchantia Polymorpha ◽  
Gene Duplications ◽  
Auxin Response ◽  
Response System ◽  
Genes Expression

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1–3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development2–4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.

scholarly journals Author response: Origin and evolution of the nuclear auxin response system

2018 ◽  
Author(s):  
Sumanth K Mutte ◽  
Hirotaka Kato ◽  
Carl Rothfels ◽  
Michael Melkonian ◽  
Gane Ka-Shu Wong ◽  
...  
Keyword(s):  
Author Response ◽  
Auxin Response ◽  
Origin And Evolution ◽  
Response System

scholarly journals The Genome of the Charophyte Alga Penium margaritaceum Bears Footprints of the Evolutionary Origins of Land Plants

2019 ◽  
Author(s):  
Chen Jiao ◽  
Iben Sørensen ◽  
Xuepeng Sun ◽  
Honghe Sun ◽  
Hila Behar ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Gene Families ◽  
Land Plant ◽  
Land Plants ◽  
Adaptive Responses ◽  
Evolutionary Trajectory ◽  
Cell Wall Assembly ◽  
Evolutionary Origins ◽  
Life Styles ◽  
Evolutionary Features

ABSTRACTThe colonization of land by plants was a pivotal event in the history of the biosphere, and yet the underlying evolutionary features and innovations of the first land plant ancestors are not well understood. Here we present the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The P. margaritaceum genome has a high proportion of repeat sequences, which are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with earlier diverging plant lineages, P. margaritaceum has uniquely expanded repertoires of gene families, signaling networks and adaptive responses, supporting its phylogenetic placement and highlighting the evolutionary trajectory towards terrestrialization. These encompass a broad range of physiological processes and cellular structures, such as large families of extracellular polymer biosynthetic and modifying enzymes involved in cell wall assembly and remodeling. Transcriptome profiling of cells exposed to conditions that are common in terrestrial habitats, namely high light and desiccation, further elucidated key adaptations to the semi-aquatic ecosystems that are home to the Zygnematophyceae. Such habitats, in which a simpler body plan would be advantageous, likely provided the evolutionary crucible in which selective pressures shaped the transition to land. Earlier diverging charophyte lineages that are characterized by more complex land plant-like anatomies have either remained exclusively aquatic, or developed alternative life styles that allow periods of desiccation.

scholarly journals Joint profiling of gene expression and chromatin accessibility of amphioxus development at single cell resolution

2021 ◽  
Author(s):  
Pengcheng Ma ◽  
Xingyan Liu ◽  
Huimin Liu ◽  
Zaoxu Xu ◽  
Xiangning Ding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Genetic Regulatory Networks ◽  
Public Access ◽  
Origin And Evolution ◽  
Key Species

Abstract Vertebrate evolution was accompanied with two rounds of whole genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single cell sequencing has been widely employed to construct the developmental cell atlas of several key species of vertebrates (human, mouse, zebrafish and frog) and tunicate (sea squirts). Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated we constructed the developmental tree for amphioxus cell fate commitment and lineage specification, and revealed the underlying key regulators and genetic regulatory networks. The generated data were integrated into an online platform, AmphioxusAtlas, for public access at http://120.79.46.200:81/AmphioxusAtlas.

scholarly journals Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microRNA repertoire in land plants

2016 ◽  
Author(s):  
Florencia Berruezo ◽  
Flavio S. J. de Souza ◽  
Pablo I. Picca ◽  
Sergio I. Nemirovsky ◽  
Leandro Martinez-Tosar ◽  
...  
Keyword(s):  
Small Rna ◽  
Land Plant ◽  
Land Plants ◽  
Phylogenetic Position ◽  
Seed Plants ◽  
Messenger Rnas ◽  
Rna Molecules ◽  
Functional Studies ◽  
Mirna Genes ◽  
Ecological Importance

AbstractMicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, and functional studies indicate that ancient miRNAs play key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plant miRNAs. Land plants are divided into bryophytes (liverworts, mosses), lycopods (clubmosses and spikemosses), monilophytes (ferns and horsetails), gymnosperms (cycads, conifers and allies) and angiosperms (flowering plants). Among these, the fern group occupies a key phylogenetic position, since it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.

Unusual Features of the Light Response System Regulating Ferredoxin Gene Expression

1991 ◽  
pp. 201-216
Author(s):  
W. F. Thompson ◽  
R. C. Elliott ◽  
L. F. Dickey ◽  
M. Gallo ◽  
T. J. Pedersen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Light Response ◽  
Response System
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