Potential Conservation of Circadian Clock Proteins in the phylum Nematoda as Revealed by Bioinformatic Searches

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.

• Publication year

  2014

• Venue

  PLoS ONE

• Publication date

  2014-11-14

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0112871PMID 25396739PMCID 4232591
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Adaptive evolution of the circadian gene timeout in insects

  2014cited by this paper
• Extensive oscillatory gene expression during C. elegans larval development.

  2014cited by this paper
• Molecular components of the Mammalian circadian clock.

  2013cited by this paper
• Mammalian TIMELESS Is Involved in Period Determination and DNA Damage-Dependent Phase Advancing of the Circadian Clock

  2013cited by this paper
• Peroxiredoxins are conserved markers of circadian rhythms

  2012cited by this paper
• The circadian clock of Neurospora crassa.

  2012cited by this paper
• (Re)inventing the circadian feedback loop.

  2012cited by this paper
• PDF receptor signaling in Caenorhabditis elegans modulates locomotion and egg-laying.

  2012cited by this paper
• University of Groningen Circadian regulation of olfaction and an evolutionarily conserved , nontranscriptional marker in Caenorhabditis elegans

  2012cited by this paper
• Daily variation in melatonin synthesis and arylalkylamine N‐acetyltransferase activity in the nematode Caenorhabditis elegans

  2012cited by this paper
• MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

  2011cited by this paper
• Circadian rhythms in metabolic variables in Caenorhabditis elegans.

  2011cited by this paper
• Alternative splicing adds a new loop to the circadian clock

  2011cited by this paper
• Molecular Evolution of Phosphoprotein Phosphatases in Drosophila

  2011cited by this paper
• Accelerated Profile HMM Searches

  2011cited by this paper
• Shared developmental roles and transcriptional control of autophagy and apoptosis in Caenorhabditis elegans

  2011cited by this paper
• Circadian variation in Pseudomonas fluorescens (CHA0)-mediated paralysis of Caenorhabditis elegans.

  2011cited by this paper
• The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex.

  2011cited by this paper
• HMMER web server: interactive sequence similarity searching

  2011cited by this paper
• Genetics of circadian rhythms in Mammalian model organisms.

  2011cited by this paper
• LIN-42/PERIOD controls cyclical and developmental progression of C. elegans molts.

  2011influential reference
• HIF-1 Regulates Iron Homeostasis in Caenorhabditis elegans by Activation and Inhibition of Genes Involved in Iron Uptake and Storage

  2011cited by this paper
• Timing in plants – A rhythmic arrangement

  2011cited by this paper
• C. elegans homologs of insect clock proteins: a tale of many stories

  2011cited by this paper
• The effects of transient starvation persist through direct interactions between CaMKII and ether-a-go-go K+ channels in C. elegans males.

  2011cited by this paper
• Peroxiredoxin Functions as a Peroxidase and a Regulator and Sensor of Local Peroxides*

  2011cited by this paper
• A methyl transferase links the circadian clock to the regulation of alternative splicing

  2010cited by this paper
• Genome-Wide Analysis of Light- and Temperature-Entrained Circadian Transcripts in Caenorhabditis elegans

  2010cited by this paper
• Simplicity and complexity in the cyanobacterial circadian clock mechanism.

  2010cited by this paper
• IPRStats: visualization of the functional potential of an InterProScan run

  2010cited by this paper
• Circadian rhythms persist without transcription in a eukaryote

  2010cited by this paper
• C. elegans phototransduction requires a G protein-dependent cGMP pathway and a taste receptor homolog

  2010cited by this paper
• The many facets of the Tim-Tipin protein families’ roles in chromosome biology

  2010cited by this paper
• Circadian Clocks in Human Red Blood Cells

  2010cited by this paper
• A comparative view of insect circadian clock systems

  2010cited by this paper
• Hidden Markov model speed heuristic and iterative HMM search procedure

  2010cited by this paper
• Drosophila timeless2 is required for chromosome stability and circadian photoreception.

  2010cited by this paper
• Multiple ERK substrates execute single biological processes in Caenorhabditis elegans germ-line development

  2009cited by this paper
• Timing of Locomotor Activity Circadian Rhythms in Caenorhabditis elegans

  2009cited by this paper
• Discovery and characterization of a conserved pigment dispersing factor‐like neuropeptide pathway in Caenorhabditis elegans

  2009cited by this paper
• Mammalian TIMELESS Is Required for ATM-dependent CHK2 Activation and G2/M Checkpoint Control*

  2009cited by this paper
• A Novel Molecular Solution for Ultraviolet Light Detection in Caenorhabditis elegans

  2008cited by this paper
• Comparative analysis of circadian clock genes in insects

  2008cited by this paper
• Circadian stress tolerance in adult Caenorhabditis elegans

  2008cited by this paper
• Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

  2008cited by this paper
• Light-sensitive neurons and channels mediate phototaxis in C. elegans

  2008cited by this paper
• Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks

  2008cited by this paper
• Control of Apoptosis by Asymmetric Cell Division

  2008cited by this paper
• Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock

  2008cited by this paper
• An automated tracking system for Caenorhabditis elegans locomotor behavior and circadian studies application.

  2007cited by this paper
• Natural plasticity in circadian rhythms is mediated by reorganization in the molecular clockwork in honeybees

  2007cited by this paper
• Insect cryptochromes: gene duplication and loss define diverse ways to construct insect circadian clocks.

  2007influential reference
• Mammalian TIMELESS and Tipin are evolutionarily conserved replication fork-associated factors.

  2007cited by this paper
• The Human Tim/Tipin Complex Coordinates an Intra-S Checkpoint Response to UV That Slows Replication Fork Displacement

  2007cited by this paper
• Characterization of Drosophila and Caenorhabditis elegans NXF-like-factors, putative homologs of mammalian NXF.

  2007cited by this paper
• Novel heterochronic functions of the Caenorhabditis elegans period-related protein LIN-42.

  2006cited by this paper
• Molecular components of the mammalian circadian clock.

  2006cited by this paper
• Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro.

  2006cited by this paper
• The Caenorhabditis elegans AHR-1 transcription complex controls expression of soluble guanylate cyclase genes in the URX neurons and regulates aggregation behavior.

  2006cited by this paper
• The bZip proteins CES-2 and ATF-2 alter the timing of transcription for a cell-specific target gene in C. elegans.

  2006cited by this paper
• A Timeless debate: resolving TIM's noncircadian roles with possible clock function

  2006cited by this paper
• jPREdictor: a versatile tool for the prediction of cis-regulatory elements

  2006cited by this paper
• System-level identification of transcriptional circuits underlying mammalian circadian clocks

  2005influential reference
• Introduction to nematode evolution and ecology.

  2005cited by this paper
• InterProScan: protein domains identifier

  2005cited by this paper
• WormBase: better software, richer content

  2005cited by this paper
• LIN-23-Mediated Degradation of β-Catenin Regulates the Abundance of GLR-1 Glutamate Receptors in the Ventral Nerve Cord of C. elegans

  2005cited by this paper
• Developmental timing in C. elegans is regulated by kin-20 and tim-1, homologs of core circadian clock genes.

  2005cited by this paper
• Coupling of Human Circadian and Cell Cycles by the Timeless Protein

  2005cited by this paper
• Caenorhabditis elegans Opens Up New Insights into Circadian Clock Mechanisms

  2005influential reference
• Pulses of prolactin promoter activity depend on a noncanonical E-box that can bind the circadian proteins CLOCK and BMAL1.

  2005cited by this paper
• Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans.

  2004cited by this paper
• A Genetic Screen for Neurite Outgrowth Mutants in Caenorhabditis elegans Reveals a New Function for the F-box Ubiquitin Ligase Component LIN-23

  2004cited by this paper
• The Caenorhabditis elegans aryl hydrocarbon receptor, AHR-1, regulates neuronal development.

  2004cited by this paper
• The Circadian E-Box: When Perfect Is Not Good Enough

  2003cited by this paper
• Chromosome cohesion is regulated by a clock gene paralogue TIM-1

  2003cited by this paper
• Requirement of Mammalian Timeless for Circadian Rhythmicity

  2003cited by this paper
• PAS Proteins: Regulators and Sensors of Development and Physiology

  2003cited by this paper
• Getting (chromosomes) loaded--a new role for timeless.

  2003cited by this paper
• fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen.

  2002cited by this paper
• Comparative studies on the phylogeny and systematics of the rhabditidae (nematoda).

  2001cited by this paper
• Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis elegans

  2001cited by this paper
• C. elegans odour discrimination requires asymmetric diversity in olfactory neurons

  2001cited by this paper
• Structural and Evolutionary Relationships among Protein Tyrosine Phosphatase Domains

  2001cited by this paper
• Circadian regulation of gene expression systems in the Drosophila head.

  2001cited by this paper
• The Caenorhabditis elegans hif-1 gene encodes a bHLH-PAS protein that is required for adaptation to hypoxia

  2001cited by this paper
• Cryptochrome: the second photoactive pigment in the eye and its role in circadian photoreception.

  2000cited by this paper
• The C. elegans F-box/WD-repeat protein LIN-23 functions to limit cell division during development.

  2000cited by this paper
• The period E-box Is Sufficient to Drive Circadian Oscillation of Transcription In Vivo

  2000cited by this paper
• Light-dependent sequestration of TIMELESS by CRYPTOCHROME.

  1999cited by this paper
• Block of an ether-a-go-go-Like K+ Channel by Imipramine Rescues egl-2 Excitation Defects inCaenorhabditis elegans

  1999cited by this paper
• Similarity of the C. elegans developmental timing protein LIN-42 to circadian rhythm proteins.

  1999cited by this paper
• A mammalian ortholog of Drosophila timeless, highly expressed in SCN and retina, forms a complex with mPER1

  1999cited by this paper
• Caenorhabditis elegans orthologs of the aryl hydrocarbon receptor and its heterodimerization partner the aryl hydrocarbon receptor nuclear translocator.

  1998cited by this paper
• Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria.

  1998cited by this paper
• Independent photoreceptive circadian clocks throughout Drosophila.

  1997cited by this paper
• A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster

  1997cited by this paper
• Evidence for a clade of nematodes, arthropods and other moulting animals

  1997cited by this paper
• Protein serine/threonine phosphatases.

  1996cited by this paper
• The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1

  1995cited by this paper

• Phylogeny of Core Molecular Components of Metazoan Circadian Clocks

  2025cites this paper
• Caenorhabditis elegans as an emerging high throughput chronotherapeutic drug screening platform for human neurodegenerative disorders.

  2025cites this paper
• Role of the clock gene homolog aha-1 in the circadian system of Caenorhabditis elegans

  2025influential citation
• Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans

  2024cites this paper
• The rhythmic transcriptional landscape in Caenorhabditis elegans: daily, circadian and novel 16-hour cycling gene expression revealed by RNA-sequencing

  2024cites this paper
• Caenorhabditis elegans as a Promising Model Organism in Chronobiology

  2023cites this paper
• Regulation of the circadian clock in C. elegans by clock gene homologs kin-20 and lin-42

  2023cites this paper
• Contribution of cryptochromes and photolyases for insect life under sunlight

  2023cites this paper
• Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

  2021cites this paper
• Unveiling “Musica Universalis” of the Cell: A Brief History of Biological 12-Hour Rhythms

  2018cites this paper
• The Doubletime Homolog KIN-20 Mainly Regulates let-7 Independently of Its Effects on the Period Homolog LIN-42 in Caenorhabditis elegans

  2018cites this paper
• Sleeping Beauty? Developmental Timing, Sleep, and the Circadian Clock in Caenorhabditis elegans.

  2017cites this paper
• A Cell-Autonomous Mammalian 12 hr Clock Coordinates Metabolic and Stress Rhythms.

  2017cites this paper
• Genetic control of circadian rhythms and aging

  2016cites this paper
• Circadian rhythms identified in Caenorhabditis elegans by in vivo long-term monitoring of a bioluminescent reporter

  2016cites this paper
• Circadian rhythms and post-transcriptional regulation in higher plants

  2015cites this paper
• Edinburgh Research Explorer Guidelines for Genome-Scale Analysis of Biological Rhythms

  year unknowncites this paper