Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution

Fattash, Isam; Voß, Björn; Reski, Ralf; Hess, Wolfgang R.; Frank, Wolfgang

doi:10.1186/1471-2229-7-13

Cited by 112 publications

(99 citation statements)

References 76 publications

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“…At least 88 annotated miRNA families have been identified in the moss P. patens and 44 in the lycopod Selaginella moellendorffii (Axtell et al, 2007;Fattash et al, 2007). The target analysis indicates that in P. patens several miRNAs regulate overall development and are involved in signal transduction, cell wall biosynthesis and defense pathways.…”

Section: Bryophytes As An Ancient Lineage May Have Retained Many Novementioning

confidence: 99%

Hormonal regulation in green plant lineage families

Johri

2008

Physiol Mol Biol Plants

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The patterns of phytohormones distribution, their native function and possible origin of hormonal regulation across the green plant lineages (chlorophytes, charophytes, bryophytes and tracheophytes) are discussed. The five classical phytohormonesauxins, cytokinins, gibberellins (GA), abscisic acid (ABA) and ethylene occur ubiquitously in green plants. They are produced as secondary metabolites by microorganisms. Some of the bacterial species use phytohormones to interact with the plant as a part of their colonization strategy. Phytohormone biosynthetic pathways in plants seem to be of microbial origin and furthermore, the origin of high affinity perception mechanism could have preceded the recruitment of a metabolite as a hormone. The bryophytes represent the earliest land plants which respond to the phytohormones with the exception of gibberellins. The regulation by auxin and ABA may have evolved before the separation of green algal lineage. Auxin enhances rhizoid and caulonemal differentiation while cytokinins enhance shoot bud formation in mosses. Ethylene retards cell division but seems to promote cell elongation. The presence of responses specific to cytokinins and ethylene strongly suggest the origin of their regulation in bryophytes. The hormonal role of GAs could have evolved in some of the ferns where antheridiogens (compounds related to GAs) and GAs themselves regulate the formation of antheridia.During migration of life forms to land, the tolerance to desiccation may have evolved and is now observed in some of the microorganisms, animals and plants. Besides plants, sequences coding for late embryogenesis abundant-like proteins occur in the genomes of other anhydrobiotic species of microorganisms and nematodes. ABA acts as a stress signal and increases rapidly upon desiccation or in response to some of the abiotic stresses in green plants. As the salt stress also increases ABA release in the culture medium of cyanobacterium Trichormus variabilis, the recruitment of ABA in the regulation of stress responses could have been derived from prokaryotes and present at the level of common ancestor of green plants. The overall hormonal action mechanisms in mosses are remarkably similar to that of the higher plants. As plants are thought to be monophyletic in origin, the existence of remarkably similar hormonal mechanisms in the mosses and higher plants, suggests that some of the basic elements of regulation cascade could have also evolved at the level of common ancestor of plants. The networking of various steps in a cascade or the crosstalk between different cascades is variable and reflects the dynamic interaction between a species and its specific environment.

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Section: Bryophytes As An Ancient Lineage May Have Retained Many Novementioning

confidence: 99%

Hormonal regulation in green plant lineage families

Johri

2008

Physiol Mol Biol Plants

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“…Direct sequencing of small RNAs and computational predictions have resulted in the annotation of 44 distinct P. patens miRNA families (Arazi et al, 2005;Talmor-Neiman et al, 2006a;Fattash et al, 2007). We have recently reported a data set of 127,135 unique P. patens small RNAs from three libraries, represented by a total of 561,102 reads, which provided insights into siRNA biogenesis in plants .…”

Section: Identification Of Mirnas From P Patens and S Moellendorffiimentioning

confidence: 99%

“…To date, >40 distinct miRNA families have been annotated from P. patens based upon analysis of sequenced small RNAs or bioinformatic predictions (Arazi et al, 2005;Talmor-Neiman et al, 2006a;Fattash et al, 2007). In lycopods, the expression of miR166 has been confirmed in S. moellendorffii (Floyd and Bowman, 2004), and the expression of two additional families proposed based upon microarray experiments using RNA from Selaginella uncinata (Axtell and Bartel, 2005).…”

Section: Introductionmentioning

confidence: 99%

Common Functions for Diverse Small RNAs of Land Plants

2007

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Endogenous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are critical components of plant gene regulation. Some abundant miRNAs involved in developmental control are conserved between anciently diverged plants, while many other less-abundant miRNAs appear to have recently emerged in the Arabidopsis thaliana lineage. Using largescale sequencing of small RNAs, we extended the known diversity of miRNAs in basal plants to include 88 confidently annotated miRNA families in the moss Physcomitrella patens and 44 in the lycopod Selaginella moellendorffii. Cleavage of 29 targets directed by 14 distinct P. patens miRNA families and a trans-acting siRNA (ta-siRNA) was experimentally confirmed. Despite a core set of 12 miRNA families also expressed in angiosperms, weakly expressed and apparently lineage-specific miRNAs accounted for the majority of miRNA diversity in both species. Nevertheless, the molecular functions of several of these lineage-specific small RNAs matched those of angiosperms, despite dissimilarities in the small RNA sequences themselves, including small RNAs that mediated negative feedback regulation of the miRNA pathway and miR390-dependent ta-siRNAs that guided the cleavage of AUXIN RESPONSE FACTOR mRNAs. Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants.

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“…7,[9][10][11][12] The evolution of such nonconserved miRNAs could have reshaped gene networks during the history of the diversification of plants to promote the development of novel, derived characteristics. Mechanistically, it has been shown that miRNAs can evolve de novo from tandem gene duplicates that are inverted relative to each other and that such miRNAs can subsequently target their progenitors by sequence similarity.…”

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confidence: 99%