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Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches.

Romanowski A, Garavaglia MJ, Goya ME, Ghiringhelli PD, Golombek DA - PLoS ONE (2014)

Bottom Line: Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive.In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda.With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Cronobiología, Dto de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.

ABSTRACT
Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.

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Core clock proteins phylogenetic analysis.A) Phylogenetic tree of the conserved proteins mmBMAL, dmCYCLE and its homolog ceAHA-1. B) Phylogenetic tree of the conserved PERIOD proteins. A zoomed in view of the branches corresponding to the Chordata (A and B) and Nematoda (A) phylum are shown in the insets.
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pone-0112871-g003: Core clock proteins phylogenetic analysis.A) Phylogenetic tree of the conserved proteins mmBMAL, dmCYCLE and its homolog ceAHA-1. B) Phylogenetic tree of the conserved PERIOD proteins. A zoomed in view of the branches corresponding to the Chordata (A and B) and Nematoda (A) phylum are shown in the insets.

Mentions: The analysis of trees based on a single core clock protein indicates the same kind of grouping (figure 3). One interesting case is that of the TIMELESS homolog. ceTIM-1 is closer to dmTIMEOUT and to mmTIMELESS, that to dmTIMELESS (figure S1). In mammals, this protein is essential for embryonic development and is associated to DNA metabolism. It is also known to associate with peroxirredoxin 2 during cell cycle check points [72]. In Drosophila, TIMEOUT is also involved in DNA metabolism, chromosomal cohesion and circadian photoreception [73]–[75]. This means that C. elegans' similarity to TIMELESS is closer to the proteins that perform developmental roles rather than to the protein involved in circadian rhythms; indeed, there is experimental evidence to support ceTIM-1's role in chromosomal cohesion and developmental timing [44], [76], [77].


Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches.

Romanowski A, Garavaglia MJ, Goya ME, Ghiringhelli PD, Golombek DA - PLoS ONE (2014)

Core clock proteins phylogenetic analysis.A) Phylogenetic tree of the conserved proteins mmBMAL, dmCYCLE and its homolog ceAHA-1. B) Phylogenetic tree of the conserved PERIOD proteins. A zoomed in view of the branches corresponding to the Chordata (A and B) and Nematoda (A) phylum are shown in the insets.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232591&req=5

pone-0112871-g003: Core clock proteins phylogenetic analysis.A) Phylogenetic tree of the conserved proteins mmBMAL, dmCYCLE and its homolog ceAHA-1. B) Phylogenetic tree of the conserved PERIOD proteins. A zoomed in view of the branches corresponding to the Chordata (A and B) and Nematoda (A) phylum are shown in the insets.
Mentions: The analysis of trees based on a single core clock protein indicates the same kind of grouping (figure 3). One interesting case is that of the TIMELESS homolog. ceTIM-1 is closer to dmTIMEOUT and to mmTIMELESS, that to dmTIMELESS (figure S1). In mammals, this protein is essential for embryonic development and is associated to DNA metabolism. It is also known to associate with peroxirredoxin 2 during cell cycle check points [72]. In Drosophila, TIMEOUT is also involved in DNA metabolism, chromosomal cohesion and circadian photoreception [73]–[75]. This means that C. elegans' similarity to TIMELESS is closer to the proteins that perform developmental roles rather than to the protein involved in circadian rhythms; indeed, there is experimental evidence to support ceTIM-1's role in chromosomal cohesion and developmental timing [44], [76], [77].

Bottom Line: Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive.In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda.With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Cronobiología, Dto de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.

ABSTRACT
Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.

Show MeSH