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WormBase Tree Display for Variation: WBVar00241238

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Name Class

WBVar00241238EvidencePaper_evidenceWBPaper00006240
NamePublic_nameqm30
Other_nameqm30tsmat
HGVSgCHROMOSOME_III:g.5278938_5279527del
Sequence_detailsSMapS_parentSequenceZC395
Flanking_sequencesacaagattacgtgatgaggagcttcatcataacttctgatgatgaccagaactttttttc
Mapping_targetZC395
Type_of_mutationDeletion
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00026639
WBStrain00026647
LaboratoryMQ
StatusLive
AffectsGeneWBGene00000536
TranscriptZC395.2.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant
VEP_impactHIGH
cDNA_position454-?
CDS_position454-?
Protein_position152-?
Intron_number4/5
Exon_number4-6/6
InteractorWBInteraction000500522
WBInteraction000500523
WBInteraction000500524
WBInteraction000500525
WBInteraction000500526
WBInteraction000500527
WBInteraction000500528
WBInteraction000500529
WBInteraction000500530
WBInteraction000517492
WBInteraction000518773
WBInteraction000520261
WBInteraction000520262
WBInteraction000520263
WBInteraction000520264
WBInteraction000520265
WBInteraction000520266
WBInteraction000520267
WBInteraction000520268
WBInteraction000520269
WBInteraction000520270
WBInteraction000520271
WBInteraction000520272
WBInteraction000520273
WBInteraction000520274
WBInteraction000520275
WBInteraction000520276
WBInteraction000520277
WBInteraction000520278
WBInteraction000520279
WBInteraction000520280
WBInteraction000520281
WBInteraction000520282
WBInteraction000520283
WBInteraction000520284
WBInteraction000520285
WBInteraction000520707
WBInteraction000520708
WBInteraction000520727
WBInteraction000525028
WBInteraction000534733
WBInteraction000534734
WBInteraction000534735
WBInteraction000534736
WBInteraction000534737
WBInteraction000534738
WBInteraction000534739
WBInteraction000534740
WBInteraction000534741
WBInteraction000534742
WBInteraction000534743
WBInteraction000534744
WBInteraction000534745
WBInteraction000535966
WBInteraction000535968
WBInteraction000535970
WBInteraction000535972
WBInteraction000535975
WBInteraction000535979
WBInteraction000535980
WBInteraction000535982
WBInteraction000537384
WBInteraction000537430
WBInteraction000537431
WBInteraction000537432
WBInteraction000537433
WBInteraction000537434
WBInteraction000537435
WBInteraction000541823
GeneticsInterpolated_map_positionIII-1.84661
DescriptionPhenotypeWBPhenotype:0000031Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
Remark"As previously demonstrated, both clk-1(qm30) and isp-1(qm150) worms developed considerably slower than wild-type animals [22,28]."Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
WBPhenotype:0000042Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000003PATO:0000460Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000061Paper_evidenceWBPaper00036073
WBPaper00038379
WBPaper00027157
WBPaper00006515
WBPaper00046786
WBPaper00051094
Curator_confirmedWBPerson712
WBPerson2987
WBPerson6852
RemarkAnimals are long-lived.Paper_evidenceWBPaper00038379
Curator_confirmedWBPerson712
Mutants are long-lived.Paper_evidenceWBPaper00027157
Curator_confirmedWBPerson712
"Interestingly, the expression of CLK-1-nuc(+) in clk-1 null worms caused a decrease in their enhanced longevity phenotype (Fig. 5a,b and Supplementary Table 1). This infers that nuclear CLK-1 can regulate longevity and that this is unrelated to the mitochondrial role of CLK-1 in ubiquinone biosynthesis."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
EQ_annotationsGO_termGO:0007568PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Phenotype_assayControl_strainWBStrain00000001Paper_evidenceWBPaper00051094
Curator_confirmedWBPerson6852
WBPhenotype:0000119Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
RemarkAlthough SOD-1 levels were unchanged from wild-type levels, SOD-2 levels appeared to be increased.Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000136Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remark"We found that expression of CLK-1-nuc(+) could rescue the increased expression of the closest WWOX homologue, dhs-7, in clk-1 null worms, and that human WWOX expression was increased on loss of nuclear COQ7 (Fig. 4f,g,i and Supplementary Fig. 3a,d)... We found that transcripts of sod-2, encoding a ROS detoxification enzyme, were increased in clk-1 null worms as previously reported. Furthermore, transcripts of skn-1, encoding a transcription factor that is a central regulator of ROS homeostatic gene expression, were also increased (Supplementary Fig. 3b). The expression of nuclear CLK-1 in clk-1 null worms abrogated the increased transcript levels of these genes (Supplementary Fig. 3b)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
"We subsequently monitored transcript levels for a range of UPRmt genes and identified a subset (hsp-6, hsp-60, spg-7) where increased expression in clk-1 null worms was abrogated by expression of CLK-1-nuc(+) (Fig. 6b and Supplementary Fig. 4a)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
clk-1(qm30) resulted in increased mRNA levels of ymel-1 and tim-17 (Figure 6b, S4a); "Furthermore, we noted that some of the UPRmt-associated genes that were not regulated by nuclear COQ7 (DNAJA3, ENDOG, PMPCB, tim-17, ymel-1/YME1L1) are downstream targets of a distinct UPRmt instigated in the mitochondrial matrix (Fig. 6b,c and Supplementary Fig. 4a,b)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
WBPhenotype:0000137Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remark"In clk-1 null worms, glna-1 transcript levels were decreased compared with wild-type animals, an effect that was rescued in the presence of CLK-1-nuc(+) (Fig. 4e and Supplementary Fig. 3a)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
WBPhenotype:0000154Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000207Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
Remarkslow defecationPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000208Paper_evidenceWBPaper00031896
WBPaper00051094
Curator_confirmedWBPerson712
WBPerson6852
RemarkThe defecation mean cycle time was increased about 40% above the defecation cycle of wild-type animals.Paper_evidenceWBPaper00031896
Curator_confirmedWBPerson712
Phenotype_assayControl_strainWBStrain00000001Paper_evidenceWBPaper00051094
Curator_confirmedWBPerson6852
WBPhenotype:0000442Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remark"The expression of CLK-1-nuc(+) did not rescue the delayed larval development observed in clk-1 null worms (Fig. 5c), which is consistent with this phenotype being due to the loss of mitochondrial CLK-1."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0000462Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remark"CLK-1-nuc(+) was also able to significantly rescue the ROS-sensitivity phenotype of clk-1 null worms when exposed to the mitochondrial respiratory chain inhibitor Paraquat (Fig. 4b)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
Affected_byMoleculeWBMol:00002747Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
EQ_annotationsGO_termGO:0000302PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0000463Paper_evidenceWBPaper00041750
Curator_confirmedWBPerson2987
Remarkclk-1(qm30) mutants were found to produce several metabolite compounds in significantly altered amounts relative to wild-type worms (Figure 1B, S5).Paper_evidenceWBPaper00041750
Curator_confirmedWBPerson2987
WBPhenotype:0000641Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
RemarkClk mutants had a longer period of mobility than wild-type worms.Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000674Paper_evidenceWBPaper00036073
WBPaper00045829
Curator_confirmedWBPerson712
WBPerson2987
Remark"Exposure to P. aeruginosa also caused striking developmental delays in combination with mild mitochondrial stresses such as ethidium bromide, paraquat or the clk-1(qm30) allele (Fig. 2b), consistent with the pathogen causingmodest mitochondrial stress."Paper_evidenceWBPaper00045829
Curator_confirmedWBPerson2987
EQ_annotationsLife_stageWBls:0000022PATO:0000460Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
GO_termGO:0034514PATO:0000460Paper_evidenceWBPaper00045829
Curator_confirmedWBPerson2987
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0000688Person_evidenceWBPerson261
Curator_confirmedWBPerson712
RemarkWorms are viable at 20C but become sterile at 25C.Person_evidenceWBPerson261
Curator_confirmedWBPerson712
Temperature_sensitiveHeat_sensitive25Person_evidenceWBPerson261
Curator_confirmedWBPerson712
WBPhenotype:0000722Paper_evidenceWBPaper00055188
Curator_confirmedWBPerson21876
RemarkReduced nucleolar sizePaper_evidenceWBPaper00055188
Curator_confirmedWBPerson21876
WBPhenotype:0001236Paper_evidenceWBPaper00041370
WBPaper00041212
WBPaper00046786
Curator_confirmedWBPerson2987
Remarkclk-1(qm30) mutation induced the mitochondrial unfolded protein response, as indicated by increased expression of hsp-60p::GFP (Figure 3B)Paper_evidenceWBPaper00041370
Curator_confirmedWBPerson2987
"We next investigated ATFS-1-dependent hsp-60pr::gfp activation in strains harboring the well-characterized clk-1(qm30) or isp- 1(qm150) mutations [26,27]... As both mutations affect respiration and display impaired development [22,23], we hypothesized that they would cause activation of the UPRmt. Indeed, hsp-60pr::gfp expression was consistently elevated in both strains consistent with the presence of mitochondrial stress. The isp-1(qm150) mutation caused considerably stronger hsp-60pr::gfp induction suggestive of a larger impact on mitochondrial function [29] (Figure 1B)."Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
"Thus, it is plausible that there could be crosstalk between CLK-1 nuclear signalling and the UPRmt. Indeed, we found that the expression of an UPRmt-responsive fluorescent reporter, which is activated in clk-1 null worms, was significantly reduced in the presence of CLK-1-nuc(+) (Fig. 6a)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
Phenotype_assayGenotypehsp-60p::gfpPaper_evidenceWBPaper00041370
Curator_confirmedWBPerson2987
hsp-60pr::gfpPaper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
zcIs13 [hsp-6::GFP]Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0001282Paper_evidenceWBPaper00039867
Curator_confirmedWBPerson431
RemarkBiochemical measurements. Not behavioral.Paper_evidenceWBPaper00039867
Curator_confirmedWBPerson431
WBPhenotype:0001350Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
Remark"... phospho-eIF2a levels were increased relative to total eIF2a protein levels in the clk-1(qm30) mutant... (Figure 4A)."Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
WBPhenotype:0001621Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
RemarkWorms are more sensitive to oxidative stress than wild-type worms. | At 0.2 mM paraquat, worms showed early developmental arrest in response to oxidative stress. | Worms all showed developmental deficits compared to N2 worms.Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00004938Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBMol:00002747Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0001696Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remarkclk-1(qm30) worms exhibit reduced biosynthesis of ubiquinone (Figure 3c); "We next crossed transgenic worms expressing either full-length CLK-1 (clk-1-wt) or this truncated nuclear-only form of CLK-1 (clk-1-nuc(+)) with the clk-1 null worm qm30 (clk-1(-)). As expected, full-length CLK-1 was able to rescue ubiquinone biosynthesis in these worms; however, CLK-1-nuc(+) could not (Fig. 3c). This infers that, similar to nuclear COQ7 in human cells, nuclear CLK-1 does not contribute to the mitochondrial biosynthetic role of CLK-1 in worms."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020964
Variation_effectNullPaper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
EQ_annotationsGO_termGO:0006744PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Molecule_affectedWBMol:00001550PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Phenotype_assayTreatmentUbiquinone levels detected by reverse-phase HPLC chromatograms of quinones extracted from worm strainsPaper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0002163Paper_evidenceWBPaper00036073
WBPaper00041212
Curator_confirmedWBPerson712
WBPerson2987
RemarkMeasurement of whole-worm oxygen consumption in day 1 adult worms revealed that Clk mutants showed decreased oxygen consumption compared to wild-type worms. | Unlike control animals, the Clk mutants do not show any decrease in oxygen consumption from day 1 to day 7.Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
"clk-1(qm30) worms displayed a slight reduction in oxygen consumption when compared to wild-type worms consistent with mild mitochondrial dysfunction (Figure 5E) [40]."Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0002238Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remark"Expression of CLK-1-nuc(+) in clk-1 null worms partially rescued the increased ROS levels observed in these animals (Fig. 4a)."Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Rescued_by_transgeneWBTransgene00020965
EQ_annotationsGO_termGO:1903409PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Molecule_affectedWBMol:00001911PATO:0000460Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Phenotype_assayTreatmentAnimals were stained with the reactive oxygen species (ROS)-sensitive dye DHEPaper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0002359Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
Remark"In order to examine levels of oxidative damage in mitochondrial stressed worms, we visualized the accumulation of carbonylated proteins using the Oxyblot system [44]. Consistent with the clk-1(qm30) mutation causing mitochondrial dysfunction, significantly more carbonylated material was detected in lysates from clk-1(qm30) worms than lysates from wild-type worms (Figure 5F)."Paper_evidenceWBPaper00041212
Curator_confirmedWBPerson2987
WBPhenotype:0002468Paper_evidenceWBPaper00055188
Curator_confirmedWBPerson21876
RemarkReduced polysome numberPaper_evidenceWBPaper00055188
Curator_confirmedWBPerson21876
Phenotype_not_observedWBPhenotype:0000114Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
Remarkclk-1(qm30) does not affect mRNA levels of the gene hsp-4Paper_evidenceWBPaper00046786
Curator_confirmedWBPerson2987
WBPhenotype:0000246Paper_evidenceWBPaper00031896
Curator_confirmedWBPerson712
RemarkAlthough animals exhibited an extended mean time between execution of the defecation motor program, the variance between DMP activation was not significantly different from wild-type.Paper_evidenceWBPaper00031896
Curator_confirmedWBPerson712
WBPhenotype:0001574Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
RemarkATP levels are normal, with a trend towards and increase, despite decreased mitochondrial function.Paper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
MaternalWith_maternal_effectPaper_evidenceWBPaper00036073
Curator_confirmedWBPerson712
WBPhenotype:0002087Paper_evidenceWBPaper00031326
Curator_confirmedWBPerson2857
Remarkgrowth in hydrogen sulfide enhances thermotolerance relative to untreated animalsPaper_evidenceWBPaper00031326
Curator_confirmedWBPerson2857
ReferenceWBPaper00038379
WBPaper00039867
WBPaper00041212
WBPaper00041370
WBPaper00041750
WBPaper00017902
WBPaper00015392
WBPaper00011038
WBPaper00021890
WBPaper00017025
WBPaper00036073
WBPaper00031896
WBPaper00027157
WBPaper00006515
WBPaper00031326
WBPaper00006155
WBPaper00027130
WBPaper00010277
WBPaper00025727
WBPaper00016841
WBPaper00018757
WBPaper00005534
WBPaper00006261
WBPaper00015771
WBPaper00006240
WBPaper00045829
WBPaper00046786
WBPaper00051094
WBPaper00055188
WBPaper00065803
MethodDeletion_allele