WormBase Tree Display for Variation: WBVar00249869
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WBVar00249869 | Name | Public_name | tm843 | ||||||
---|---|---|---|---|---|---|---|---|---|
Other_name | C30H6.6.1:c.487+12_1146del | ||||||||
HGVSg | CHROMOSOME_IV:g.17377430_17378268del | ||||||||
Sequence_details | SMap | S_parent | Sequence | C30H6 | |||||
Flanking_sequences | tactgcttgcaaattgcaggcaagttgtga | ggagcttcatctaggcttctcgagctgaaa | |||||||
Mapping_target | C30H6 | ||||||||
Source_location | 7 | CHROMOSOME_IV | 17377429 | 17378269 | Inferred_automatically | National_Bioresource_Project | |||
Type_of_mutation | Deletion | ||||||||
PCR_product | tm843_external | ||||||||
tm843_internal | |||||||||
SeqStatus | Sequenced | ||||||||
Variation_type | Allele | ||||||||
Origin | Species | Caenorhabditis elegans | |||||||
Laboratory | FX | ||||||||
Author | Mitani S | ||||||||
DB_info | Database | National_Bioresource_Project | seq | 843 | |||||
NBP_allele | |||||||||
Status | Live | ||||||||
Affects | Gene | WBGene00001811 | |||||||
Transcript | C30H6.6.1 | VEP_consequence | splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant | ||||||
VEP_impact | HIGH | ||||||||
HGVSc | C30H6.6.1:c.487+12_1146del | ||||||||
cDNA_position | ?-1155 | ||||||||
CDS_position | ?-1146 | ||||||||
Protein_position | ?-382 | ||||||||
Intron_number | 4-7/10 | ||||||||
Exon_number | 5-8/11 | ||||||||
Interactor (16) | |||||||||
Isolation | Mutagen | TMP/UV | |||||||
Genetics | Map | IV | |||||||
Description | Phenotype | WBPhenotype:0000031 | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "Apart from a slightly impaired growth rate, haf-1 mutants are indistinguishable from WT worms under normal laboratory conditions. However, development of haf-1 mutants was delayed when mitochondrial protein folding was perturbed either by spg-7(RNAi) or by hsp-60(RNAi), whereas conditions that perturb ER protein folding had no deleterious effects on development of haf-1 mutants (Figure 2A)." | Paper_evidence | WBPaper00035985 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0034514 | PATO:0000460 | Paper_evidence | WBPaper00035985 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | spg-7(RNAi) or hsp-60(RNAi) | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000137 | Paper_evidence | WBPaper00035985 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "In two models of mitochondrial stress, feeding of spg-7(RNAi) as well as a previously characterized temperature-sensitive allele (zc32) (Benedetti et al., 2006), GFP fluorescence increased over the course of postembryonic development. The increase in fluorescence and GFP levels was attenuated in haf-1(ok705) deletion animals (Figures 1A and 1B). Inhibition of the UPRmt reporter was mirrored by the effects of haf-1(ok705) and haf-1(tm843) deletions on the expression of the endogenous mitochondrial chaperone gene hsp-60, as determined by quantitative RT-PCR (Figure 1C)." | Paper_evidence | WBPaper00035985 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
"In two models of mitochondrial stress, feeding of spg-7(RNAi) as well as a previously characterized temperature-sensitive allele (zc32) (Benedetti et al., 2006), GFP fluorescence increased over the course of postembryonic development. The increase in fluorescence and GFP levels was attenuated in haf-1(ok705) deletion animals (Figures 1A and 1B). Inhibition of the UPRmt reporter was mirrored by the effects of haf-1(ok705) and haf-1(tm843) deletions on the expression of the endogenous mitochondrial chaperone gene hsp-60, as determined by quantitative RT-PCR (Figure 1C). Similar results were obtained for the mitochondrial HSP70 gene, hsp-6 (Figures S1C and S1D)." | Paper_evidence | WBPaper00035985 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0034514 | PATO:0000460 | Paper_evidence | WBPaper00035985 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | hsp-6(RNAi) or spg-7(RNAi) | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000145 | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "Both haf-1 mutants strongly suppressed the infertility phenotype of ub-m-nonN-Nmnat1 (Figure 3e and Supplementary Table S2)." | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | gcIs40 [ub-m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0001090 | Paper_evidence | WBPaper00035985 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "Compared with WT, haf-1-deleted worms displayed markedly impaired survival at the elevated temperature of 30°C (Figure S2A)." | Paper_evidence | WBPaper00035985 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0010286 | PATO:0000460 | Paper_evidence | WBPaper00035985 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Temperature | 30 | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0001278 | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "Consistent with this hypothesis, basal mitoUPR induction by m-nonN-Nmnat1 was significantly suppressed by haf-1(lf) (Figure 4e)." | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | zcIs13 [Phsp-6::GFP]; gcIs41 [Neuro-m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0001918 | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "However, taxol was lethally toxic to elderly haf-1 but not atfs-1 loss-of-function animals (Figure 5d)." | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Affected_by | Molecule | WBMol:00003010 | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | zdIs5 [Pmec-4::GFP; lin-15AB(+)]; gcIs35 [Prab3::mCherry::m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0002423 | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "However, we found that loss-of-function mutations in the gene haf-1, which encodes a mitochondrial outer membrane ABC transporter previously shown to function as an activator of the mitochondrial unfolded protein response (mitoUPR), significantly suppressed the hypoxia resistance of both ub-m-nonN-Nmnat1 and neuro-m-nonN-Nmnat1 transgenes (Figures 3a and b)." | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0001666 | PATO:0000460 | Paper_evidence | WBPaper00049307 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | gcIs40 [ub-m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
gcIs30 [Neuro-m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_not_observed | WBPhenotype:0000039 | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "However, surprisingly, haf-1(tm843) did not suppress lifespan extension (Figure 3f)." of ub-m-nonN-Nmnat1 (also Supplementary Table S2) | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
haf-1(tm843) did not significantly affect lifespan extension (Figure 3f, Supplementary Table S2) | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | gcIs40 [ub-m-nonN-Nmnat1] | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000062 | Person_evidence | WBPerson7743 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Classified as homozygous viable by the National Bioresource Project of Japan. | Person_evidence | WBPerson7743 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Laboratory_evidence | FX | ||||||||
WBPhenotype:0000523 | Paper_evidence | WBPaper00035985 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "By contrast, haf-1-deleted worms were indistinguishable from WT in their survival under reductive stress imposed by dithiothreitol (DTT), which promotes ER stress and activates the UPRER (Figure S2B)." | Paper_evidence | WBPaper00035985 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Affected_by | Molecule | WBMol:00004908 | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0042221 | PATO:0000460 | Paper_evidence | WBPaper00035985 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Treatment | Animals were exposed to 5 millimolar dithiothreitol (DTT) and assayed for survival over several days | Paper_evidence | WBPaper00035985 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000743 | Person_evidence | WBPerson7743 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Comments to the National Bioresource Project of Japan: Dr. L. Timmons: negative for RNAi defects using various feeding strains to deliver dsRNA. | Person_evidence | WBPerson7743 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Comment to the National Bioresource Project of Japan from Dr. L. Timmons: negative for RNAi defects using various feeding strains to deliver dsRNA. | Person_evidence | WBPerson7743 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Laboratory_evidence | FX | ||||||||
WBPhenotype:0000886 | Person_evidence | WBPerson7001 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001258 | Paper_evidence | WBPaper00035985 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | "Whereas the positive control, eri-1(mg366), markedly sensitized worms to dpy-13(RNAi), haf-1 deletion had no effect on the sensitivity of worms to the RNAi feeding procedure (Figure S1E)." | Paper_evidence | WBPaper00035985 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0002423 | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | Figure 3a, 3b | Paper_evidence | WBPaper00049307 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
"Additionally, the suppression by the haf-1 is specific to Nmnat1 hypoxia resistance in that haf-1(lf) did not suppress the hypoxic protection produced by a previously identified hypoxia-resistant allele of the arginyl tRNA synthetase gene - rars-1(gc47) (Figure 3d)." | Paper_evidence | WBPaper00049307 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | GO_term | GO:0001666 | PATO:0000460 | Paper_evidence | WBPaper00049307 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | rars-1(gc47) | Paper_evidence | WBPaper00049307 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
Reference | WBPaper00035985 | ||||||||
WBPaper00049307 | |||||||||
Remark | 25783/25784-26622/26623 (839 bp deletion) | ||||||||
This knockout was generated by the National Bioresource Project, Tokyo, Japan, which is part of the International C. elegans Gene Knockout Consortium, which should be acknowledged in any publications resulting from its use. | Paper_evidence | WBPaper00041807 | |||||||
Method | NBP_knockout_allele |