Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

Pires, Nuno D.; Dolan, Liam

doi:10.1093/molbev/msp288

Cited by 507 publications

(631 citation statements)

References 105 publications

(111 reference statements)

Supporting

Mentioning

564

Contrasting

Order By: Relevance

“…2C), but we did not find RSL sequences in chlorophyte algae. This result indicates that, like most other plant bHLH subfamilies (27), RSL class I and class II proteins evolved sometime after the divergence of the chlorophyte and streptophyte lineages 700-1,000 million y ago (28,29), but before the evolution of vascular plants over 443 million y ago (30). This finding means that RSL proteins evolved in multicellular streptophytes either before or shortly after their colonization of terrestrial environments.…”

Section: Rsl Network Controls Rootmentioning

confidence: 67%

“…S2) [subfamilies VIIIc (1) and VIIIc(2) in ref. 27]. We found both RSL classes in all species of land plants for which a complete genomic sequence is available, including mosses, lycophytes, eudicots, and monocots ( Fig.…”

Section: Rsl Network Controls Rootmentioning

confidence: 92%

“…(B) Maximum-likelihood tree of A. thaliana (red) and P. patens (green) RSL proteins. The tree was based on the bHLH and RSL domains of the alignment shown in A, together with the bHLH sequence of the outgroups AtbHLH040 and PpbHLH069 (27); approximate likelihood ratio test support values are indicated in the nodes. See also Fig.…”

Section: Rsl Network Controls Rootmentioning

confidence: 99%

See 2 more Smart Citations

Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

Pires

Breuninger

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

123

105

View full text Add to dashboard Cite

The evolution of multicellular organisms was made possible by the evolution of underlying gene regulatory networks. In animals, the core of gene regulatory networks consists of kernels, stable subnetworks of transcription factors that are highly conserved in distantly related species. However, in plants it is not clear when and how kernels evolved. We show here that RSL (ROOT HAIR DEFECTIVE SIX-LIKE) transcription factors form an ancient land plant kernel controlling caulonema differentiation in the moss Physcomitrella patens and root hair development in the flowering plant Arabidopsis thaliana. Phylogenetic analyses suggest that RSL proteins evolved in aquatic charophyte algae or in early land plants, and have been conserved throughout land plant radiation. Genetic and transcriptional analyses in loss of function A. thaliana and P. patens mutants suggest that the transcriptional interactions in the RSL kernel were remodeled and became more hierarchical during the evolution of vascular plants. We predict that other gene regulatory networks that control development in derived groups of plants may have originated in the earliest land plants or in their ancestors, the Charophycean algae.T he development of multicellular organisms is controlled by gene regulatory networks (GRNs) and the reorganization of GRN architecture is thought to be a major factor underlying morphological evolution (1-5). GRNs are hierarchic and modular structures where four major component classes can be identified (3): at the periphery of GRNs are differentiation gene batteries encoding proteins that execute cell type-specific functions (such as building a pigmented cell); upstream of these batteries are switches that allow or prevent subcircuits to function in specific developmental contexts, and "plug-ins," small subcircuits that are flexibly and repeatedly used during development (such as signal transduction pathways); at the core of GRNs are kernels, small conserved subcircuits that execute specific developmental functions (such as defining spatial patterns in an embryo). Kernels are comprised of transcription factors that are highly conserved in distantly related species and are unusually stable components of GRNs.Ancient kernels that regulate body plan and organ development are highly conserved among diverse groups of metazoans (animals) (6-10). In contrast, the core components of plant GRNs are difficult to identify because of the dynamic nature of plant genome evolution and the plastic character of plant development. Floral homeotic genes form a relatively recent kernel controlling flower development (11). Homologs of KNOX and LEAFY transcription factors control shoot development in vascular plants and sporophyte development in mosses (12-15). KNOX/BEL genes also control the development of the diploid phase in unicellular chlorophytes (16) and the haploid-to-diploid transition in mosses (15), suggesting that KNOX and LEAFY genes may be core members of ancient GRNs that control diploid development in plants. Auxin signaling (17,18), et...

show abstract

Section: Rsl Network Controls Rootmentioning

confidence: 67%

Section: Rsl Network Controls Rootmentioning

confidence: 92%

Section: Rsl Network Controls Rootmentioning

confidence: 99%

See 1 more Smart Citation

Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

Pires

Breuninger

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

123

105

View full text Add to dashboard Cite

show abstract

“…Therefore, it is likely that RSL genes regulate the development of filamentous cells at the plant-soil interface in all groups of land plants. This hypothesis is supported by the observation that RSL genes have been found in all land plants for which genome sequence is available (Pires and Dolan, 2010).…”

Section: Discussionmentioning

confidence: 80%

RSL genes are sufficient for rhizoid system development in early diverging land plants

Jang

Pires

et al. 2011

Development

View full text Add to dashboard Cite

Land plants are anchored to their substratum from which essential inorganic nutrients are taken up. These functions are carried out by a system of rhizoids in early diverging groups of land plants, such as mosses, liverworts and hornworts. Physcomitrella patens RHD SIX-LIKE1 (PpRSL1) and PpRSL2 transcription factors are necessary for rhizoid development in mosses. Similar proteins, AtRHD6 and AtRSL1, control the development of root hairs in Arabidopsis thaliana. Auxin positively regulates root hair development independently of AtRHD6 and AtRSL1 in A. thaliana but the regulatory interactions between auxin and PpRSL1 and PpRSL2 are unknown. We show here that co-expression of PpRSL1 and PpRSL2 is sufficient for the development of the rhizoid system in the moss P. patens; constitutive expression of PpRSL1 and PpRSL2 converts developing leafy shoot axes (gametophores) into rhizoids. During wild-type development, PpRSL1 and PpRSL2 are expressed in the specialized cells that develop rhizoids, indicating that cell-specific expression of PpRSL1 and PpRSL2 is sufficient to promote rhizoid differentiation during wild-type P. patens development. In contrast to A. thaliana, auxin promotes rhizoid development by positively regulating PpRSL1 and PpRSL2 activity in P. patens. This indicates that even though the same genes control the development of root hairs and rhizoids, the regulation of this transcriptional network by auxin is different in these two species. This suggests that auxin might have controlled the development of the first land plant soil anchoring systems that evolved 465 million years ago by regulating the expression of RSL genes and that this regulatory network has changed since mosses and angiosperms last shared a common ancestor.

show abstract

“…Recently, more and more bHLH genes has been identified and bHLH TF families have been analyzed in many organisms whose genome drafts have been available (Ledent et al, 2002;Toledo-Ortiz et al, 2003;Buck and Atchley, 2003;Heim et al, 2003;Li et al, 2006a, b;Simionato et al, 2007;Stevens et al, 2008;Wang et al, 2007Wang et al, , 2008Wang et al, , 2009Pires and Dolan, 2010;Carretero-Paulet et al, 2010;Liu andZhao, 2010, 2011;Liu et al, 2012Liu and Chen, 2013). However, the family of bHLH TFs has not yet been studied and characterized in Xenopus laevis.…”

Section: Introductionmentioning

confidence: 99%

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Liu¹,

Li²

2015

Pakistan J. of Biological Sciences

View full text Add to dashboard Cite

A B S T R A C TXenopus laevis is a long established model organism for developmental, behavioral and neurological studies. Herein, an updated genome-wide survey was conducted using the ongoing genome project of Xenopus laevis and 106 non-redundant Basic Helix-Loop-Helix (bHLH) genes were identified in the Xenopus laevis genome databases. Gene Ontology (GO) enrichment statistics showed 51 significant GO annotations of biological processes and molecular functions and 5 significant KEGG pathways and a number of Xenopus laevis bHLH genes play significant role in specific development or special physiology processes like the development processes of muscle and eye and other organs. Furthermore, each sub-group of the bHLH family has its special gene functions except for the common GO term categories. Molecular phylogenetic analyses revealed that among these identified bHLH proteins, 105 sequences could classified into 39 families with 46, 25, 10, 5, 16 and 3 members in the corresponding high-order groups A, B, C, D, E and F, respectively with an addition bHLH member categorized as an orphan. The present study provides much useful information for further researches on Xenopus laevis.

show abstract

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

Cited by 507 publications

References 105 publications

Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

RSL genes are sufficient for rhizoid system development in early diverging land plants

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Contact Info

Product

Resources

About