High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans

Abstract This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.

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Review of Biological Effects of Acute and Chronic Radiation Exposure on Caenorhabditis elegans

Cells ◽

10.3390/cells10081966 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1966

Author(s):

Rabin Dhakal ◽

Mohammad Yosofvand ◽

Mahsa Yavari ◽

Ramzi Abdulrahman ◽

Ryan Schurr ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Ionizing Radiation ◽

Biological Effects ◽

Model Organism ◽

Model Organisms ◽

C Elegans ◽

Chronic Radiation ◽

Biological Responses ◽

Chronic Radiation Exposure ◽

Acute And Chronic Exposure

Knowledge regarding complex radiation responses in biological systems can be enhanced using genetically amenable model organisms. In this manuscript, we reviewed the use of the nematode, Caenorhabditis elegans (C. elegans), as a model organism to investigate radiation’s biological effects. Diverse types of experiments were conducted on C. elegans, using acute and chronic exposure to different ionizing radiation types, and to assess various biological responses. These responses differed based on the type and dose of radiation and the chemical substances in which the worms were grown or maintained. A few studies compared responses to various radiation types and doses as well as other environmental exposures. Therefore, this paper focused on the effect of irradiation on C. elegans, based on the intensity of the radiation dose and the length of exposure and ways to decrease the effects of ionizing radiation. Moreover, we discussed several studies showing that dietary components such as vitamin A, polyunsaturated fatty acids, and polyphenol-rich food source may promote the resistance of C. elegans to ionizing radiation and increase their life span after irradiation.

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nos-1 and nos-2, two genes related to Drosophila nanos, regulate primordial germ cell development and survival in Caenorhabditis elegans

Development ◽

10.1242/dev.126.21.4861 ◽

1999 ◽

Vol 126 (21) ◽

pp. 4861-4871 ◽

Cited By ~ 17

Author(s):

K. Subramaniam ◽

G. Seydoux

Keyword(s):

Caenorhabditis Elegans ◽

Germ Cell ◽

Rna Binding ◽

Rna Binding Proteins ◽

Primordial Germ Cell ◽

Gene Families ◽

Cell Development ◽

Embryonic Patterning ◽

Germ Cell Development ◽

C Elegans

In Drosophila, the posterior determinant nanos is required for embryonic patterning and for primordial germ cell (PGC) development. We have identified three genes in Caenorhabditis elegans that contain a putative zinc-binding domain similar to the one found in nanos, and show that two of these genes function during PGC development. Like Drosophila nanos, C. elegans nos-1 and nos-2 are not generally required for PGC fate specification, but instead regulate specific aspects of PGC development. nos-2 is expressed in PGCs around the time of gastrulation from a maternal RNA associated with P granules, and is required for the efficient incorporation of PGCs into the somatic gonad. nos-1 is expressed in PGCs after gastrulation, and is required redundantly with nos-2 to prevent PGCs from dividing in starved animals and to maintain germ cell viability during larval development. In the absence of nos-1 and nos-2, germ cells cease proliferation at the end of the second larval stage, and die in a manner that is partially dependent on the apoptosis gene ced-4. Our results also indicate that putative RNA-binding proteins related to Drosophila Pumilio are required for the same PGC processes as nos-1 and nos-2. These studies demonstrate that evolutionarily distant organisms utilize conserved factors to regulate early germ cell development and survival, and that these factors include members of the nanos and pumilio gene families.

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Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans

Genome Biology and Evolution ◽

10.1093/gbe/evab048 ◽

2021 ◽

Author(s):

Fuqiang Ma ◽

Chun Yin Lau ◽

Chaogu Zheng

Keyword(s):

Population Structure ◽

Caenorhabditis Elegans ◽

Positive Selection ◽

Model Organism ◽

Gene Families ◽

Extended Haplotype ◽

Strong Positive Selection ◽

C Elegans ◽

Population Structure Analysis ◽

Wild Strains

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Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans

10.1101/2020.07.09.194670 ◽

2020 ◽

Author(s):

Fuqiang Ma ◽

Chun Yin Lau ◽

Chaogu Zheng

Keyword(s):

Population Structure ◽

Gene Flow ◽

Caenorhabditis Elegans ◽

Positive Selection ◽

Recombination Rate ◽

Selective Sweep ◽

Gene Families ◽

Strong Positive Selection ◽

High Recombination Rate ◽

C Elegans

AbstractThe F-box and chemosensory GPCR (csGPCR) gene families are greatly expanded in nematodes, including the model organism Caenorhabditis elegans, compared to insects and vertebrates. However, the intraspecific evolution of these two gene families in nematodes remain unexamined. In this study, we analyzed the genomic sequences of 330 recently sequenced wild isolates of C. elegans using a range of population genetics approaches. We found that F-box and csGPCR genes, especially the Srw family csGPCRs, showed much more diversity than other gene families. Population structure analysis and phylogenetic analysis divided the wild strains into eight non-Hawaiian and three Hawaiian subpopulations. Some Hawaiian strains appeared to be more ancestral than all other strains. F-box and csGPCR genes maintained a great amount of the ancestral variants in the Hawaiian subpopulation and their divergence among the non-Hawaiian subpopulations contributed significantly to population structure. These genes are mostly located at the chromosomal arms and high recombination rate correlates with their large polymorphism. Gene flow might also contribute to their diversity. Moreover, we identified signatures of strong positive selection in the F-box and csGPCR genes in the non-Hawaiian population using both neutrality tests and Extended Haplotype Homozygosity analysis. Accumulation of high frequency derived alleles in these genes were found in non-Hawaiian population, leading to divergence from the ancestral genotype found in Hawaiian strains. In summary, we found that F-box and csGPCR genes harbour a large pool of natural variants, which may be subjected to positive selection during the recent selective sweep in non-Hawaiian population. These variants are mostly mapped to the substrate-recognition domains of F-box proteins and the extracellular regions of csGPCRs, possibly resulting in advantages during adaptation by affecting protein degradation and the sensing of environmental cues, respectively.Significance statementThe small nematode Caenorhabditis elegans has emerged as an important organism in studying the genetic mechanisms of evolution. F-box and chemosensory GPCR are two of the largest gene families in C. elegans, but their intraspecific evolution within C. elegans was not studied before. In this work, using the nonsynonymous SNV data of 330 C. elegans wild isolates, we found that F-box and chemosensory GPCR genes showed larger polymorphisms and stronger positive selection than other genes. The large diversity is likely the result of rapid gene family expansion, high recombination rate, and gene flow. Analysis of subpopulation suggests that positive selection of these genes occurred most strongly in the non-Hawaiian population, which underwent a selective sweep possibly linked to human activities.

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Differential expression profiles between α-dystroglycan and integrin β1 in ameloblastoma: two possible perlecan signalling pathways for cellular growth and differentiation

Histopathology ◽

10.1111/j.1365-2559.2010.03732.x ◽

2011 ◽

Vol 58 (2) ◽

pp. 234-245 ◽

Cited By ~ 16

Author(s):

Hiroko Ida-Yonemochi ◽

Md Shahidul Ahsan ◽

Takashi Saku

Keyword(s):

Differential Expression ◽

Expression Profiles ◽

Cellular Growth ◽

Signalling Pathways ◽

Integrin Β1

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Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress response, and aging

10.1101/2021.05.19.444814 ◽

2021 ◽

Author(s):

Avijit Mallick ◽

Nikita Jhaveri ◽

Jihae Jeon ◽

Yvonne Chang ◽

Krupali Shah ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Stress Response ◽

Genetic Interaction ◽

Gene Families ◽

Genetic Network ◽

Reproductive Structure ◽

Structure Development ◽

C Elegans ◽

Disease States ◽

Genetic Epistasis

The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode, Caenorhabditis elegans, have shown that the Axin homolog, PRY-1, plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Eight of the genes (ard-1, rpn-7, cpz-1, his-7, cdk-1, rnr-1, clsp-1, and spp-1), when knocked down by RNA interference, efficiently suppressed the plate-level multivulva phenotype of pry-1 mutants. In every case, other than clsp-1 and spp-1, the ectopic vulval precursor cell (VPC) induction was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that except for clsp-1, the genes participate in one or more pry-1-mediated biological events. While four of them (cpz-1, his-7, cdk-1, and rnr-1) function in VPC induction, stress response, and aging, the other three (spp-1, ard-1, and rpn-7) are specific to one or more of these processes. Further analysis of the genes involved in aging showed that his-7, cdk-1, and rnr-1 also interacted with daf-16/FOXO. The results of genetic epistasis experiments suggested that his-7 functions upstream of daf-16, whereas cdk-1and rnr-1 act downstream of the pry-1-daf-16 pathway. Altogether, these findings demonstrate the important role of pry-1 suppressors in C. elegans. Given that all of the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin under normal and disease states.

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Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress responses, and aging

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab430 ◽

2021 ◽

Author(s):

Avijit Mallick ◽

Nikita Jhaveri ◽

Jihae Jeon ◽

Yvonne Chang ◽

Krupali Shah ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Stress Response ◽

Stress Responses ◽

Genetic Interaction ◽

Gene Families ◽

Genetic Network ◽

Reproductive Structure ◽

Structure Development ◽

Developmental Processes ◽

C Elegans

Abstract The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode Caenorhabditis elegans have shown that the Axin homolog PRY-1 plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Knocking down eight of the genes (spp-1, clsp-1, ard-1, rpn-7, cpz-1, his-7, cdk-1, and rnr-1) via RNA interference efficiently suppressed the multivulva phenotype of pry-1 mutants. In all cases, the ectopic induction of P3.p vulval precursor cell was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that in addition to their role in vulval development, these genes participate in one or more pry-1-mediated biological events. Whereas four of them (cpz-1, his-7, cdk-1, and rnr-1) function in both stress response and aging, two (spp-1 and ard-1) are specific to stress response. Altogether, these findings demonstrate the important role of pry-1 suppressors in regulating developmental and post-developmental processes in C. elegans. Given that the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin in metazoans.

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Enhancers of glp-1, a gene required for cell-signaling in Caenorhabditis elegans, define a set of genes required for germline development.

Genetics ◽

10.1093/genetics/141.2.551 ◽

1995 ◽

Vol 141 (2) ◽

pp. 551-569 ◽

Cited By ~ 9

Author(s):

L Qiao ◽

J L Lissemore ◽

P Shu ◽

A Smardon ◽

M B Gelber ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Cell Signaling ◽

Cell Fate ◽

Gene Families ◽

Loss Of Function ◽

Germline Development ◽

Somatic Development ◽

C Elegans ◽

Functional Relationships ◽

New Genes

Abstract The distal tip cell (DTC) regulates the proliferation or differentiation choice in the Caenorhabditis elegans germline by an inductive mechanism. Cell signaling requires a putative receptor in the germline, encoded b y the glp-1 gene, and a putative signal from the DTC, encoded by the lag-2 gene. Both glp-1 and lag-2 belong to multigene gene families whose members are essential for cell signaling during development of various tissues in insects and vertebrates as well as C. elegans. Relatively little is known about how these pathways regulate cell fate choice. To identify additional genes involved in the glp-1 signaling pathway, we carried out screens for genetic enhancers of glp-1. We recovered mutations in five new genes, named ego (enhancer of glp-1), and two previously identified genes, lag-1 and glp-4, that strongly enhance a weak glp-1 loss-of-function phenotype in the germline. Ego mutations cause multiple phenotypes consistent with the idea that gene activity is required for more than one aspect of germline and, in some cases, somatic development. Based on genetic experiments, glp-1 appears to act upstream of ego-1 and ego-3. We discuss the possible functional relationships among these genes in light of their phenotypes and interactions with glp-1.

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Chromosome-wide evolution and sex determination in a nematode with three sexes

10.1101/466961 ◽

2018 ◽

Cited By ~ 2

Author(s):

Sophie Tandonnet ◽

Georgios D. Koutsovoulos ◽

Sally Adams ◽

Delphine Cloarec ◽

Manish Parihar ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Environmental Factors ◽

Sex Determination ◽

Differential Expression ◽

Candidate Genes ◽

X Chromosome ◽

Linkage Groups ◽

Free Living ◽

C Elegans ◽

Free Living Nematode

AbstractThe free-living nematode Auanema rhodensis is a rare example of a species with three sexes, in which males, females and hermaphrodites coexist. A. rhodensis males have only one X chromosome (XO), whereas females and hermaphrodites have two (XX). The A. rhodensis X chromosome is unusual: it does not recombine in hermaphrodites and is transmitted from father to son. The mechanism that controls the production of females versus hermaphrodites is unknown but is dependent on maternal and larval environmental factors. Here we report the genome sequence and genetic map of A. rhodensis, placing over 95% of the sequence in seven linkage groups. Comparison of the seven A. rhodensis chromosomes to chromosomal assemblies of Caenorhabditis elegans and three other rhabditine nematodes identified deeply conserved linkage groups we call Nigon units, some of which have been maintained in all species analysed. Others have undergone breakage and fusion, and the A. rhodensis karyotype is the product of a unique set of rearrangements involving three Nigon units. The A. rhodensis X chromosome is much smaller than the autosomes, is less gene dense and is 3 to 4 times more polymorphic, reflecting its unique transmission history. Differential expression analyses comparing females and hermaphrodites, identified several candidate genes, including orthologues of C. elegans gld-1, tra-1 and dmd-10/11, that are potentially involved in the female-hermaphrodite sexual decision.

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The glycomes of Caenorhabditis elegans and other model organisms

Biochemical Society Symposium ◽

10.1042/bss0690117 ◽

2002 ◽

Vol 69 ◽

pp. 117-134 ◽

Cited By ~ 47

Author(s):

Stuart M. Haslam ◽

David Gems ◽

Howard R. Morris ◽

Anne Dell

Keyword(s):

Caenorhabditis Elegans ◽

Current Knowledge ◽

Structural Data ◽

Model Organisms ◽

Entire Genome ◽

C Elegans ◽

The Face ◽

Area Of Concern ◽

Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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