WormMine: Gene WBGene00002183

• WormBase Gene ID: WBGene00002183
• Gene Name: kat-1
• Sequence Name: T02G5.8
• Brief Description: kat-1 encodes a predicted 3-ketoacyl-coA thiolase, a conserved enzyme in the mitochondrial fatty acid beta-oxidation pathway; kat-1 acts synergistically with tub-1 and together with the Bardet-Biedl syndrome protein BBS1 ortholog, bbs-1, to regulate lipid accumulation; genetic interaction studies of kat-1 with che-2, osm-5 and daf-6, genes that are required for ciliary structure and intraflagellar transport, indicate that lipid accumulation in C. elegans is dependent on the function of ciliated sensory neurons and their interaction with the environment; kat-1 also acts to delay aging and acts independently of most known longevity pathways but is required for the lifespan extension caused by the overexpression of the protein deacetylase sir-2.1; kat-1 is localized to the mitochondria of intestine and body wall muscle.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable acetyl-CoA C-acetyltransferase activity. Predicted to be involved in fatty acid beta-oxidation. Located in mitochondrion. Expressed in body wall musculature. Used to study obesity. Human ortholog(s) of this gene implicated in arteriosclerosis; beta-ketothiolase deficiency; and carbohydrate metabolic disorder. Is an ortholog of human ACAT1 (acetyl-CoA acetyltransferase 1).
• Biotype: SO:0001217
• Genetic Position: II :0.492543 ±0.001914
• Length (nt): 1698

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002183

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T02G5.8.1	T02G5.8.1	1327	II: 7073814-7075511

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T02G5.8	T02G5.8	1224	II: 7073815-7074024

11 RNAi Result

• WBRNAi00102854
• WBRNAi00052231
• WBRNAi00018038
• WBRNAi00102779
• WBRNAi00035071
• WBRNAi00102584
• WBRNAi00102675
• WBRNAi00102684
• WBRNAi00102693
• WBRNAi00110644
• WBRNAi00090579

37 Allele

• gk963801
• gk963053
• h3553
• gk828292
• gk325592
• gk497027
• gk612279
• gk722066
• gk522749
• gk428987
• gk505923
• gk362663
• gk499335
• gk632571
• gk533235
• gk574875
• gk680860
• gk662613
• gk964012
• mg399
• mg401
• mg449
• mg400
• mg454
• mg402
• mg453
• mg448
• mg447
• tm1037
• mg446

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002183
• Start: 7073814
• End: 7075511
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

209 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:AVE-neuron_L1-larva_expressed
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:bodywall-muscle_L1-larva_expressed
	Genes that were downregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_downregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M

14 Expression Patterns

• Primary Identifier: Expr1031278
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3922
• Pattern: A transcriptional GFP fusion gene kat-1p::GFP, which included 1.5 kb of the kat-1 5' regulatory region, was expressed in the intestine from late embryogenesis throughout the life cycle and in the body wall muscle and pharynx from larval stage 2 (L2) to adulthood.

• Primary Identifier: Expr1219
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: The expression of P-44 was detected mainly in intestinal cells and hardly in the muscular cells in the pharynx, the gonad (immature) or the tail.

• Primary Identifier: Expr1220
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: The expression of P-44 was detected mainly in intestinal cells and hardly in the muscular cells in the pharynx, the gonad (immature) or the tail.

• Primary Identifier: Expr1155863
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2012902
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1012011
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031136
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr2816
• Remark: No detailed description on expression in other life stages. P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: Total RNAs obtained from specific stages (egg, L2, L4, and adult) were prepared and analyzed by Northern blot analysis. This demonstrated that mRNA encoding P-44 is transcribed in every developmental stage of the animal.

• Primary Identifier: Expr2817
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: By means of in situ hybridization, the P-44 mRNA was detected in nearly all regions of L4 larvae except the pharynx region. No signal was found in the control experiment using sense RNA as probe.

• Primary Identifier: Expr1217
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: Type-II thiolase was detectable with anti-(P-44) throughout the life cycle of C. elegans; although the amount relative to the proteins of the whole nematode was larger at the larval stages (L1, L2, L3 and L4) than at the embryo (E), young adult (YA) or egg-lying adult (EA) stages.

• Primary Identifier: Expr1218
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8.
• Pattern: The signal of 1.4-kb P-44 mRNA decreased after the L4 molt. The low level of the P-44 mRNA at the L1 stage may result from a combination of the decrease of the maternal message and the delayed zygotic expression. The tissue distribution of P-44 was then studied with L4 larvae because they express P-44 at a higher level than in adult animals and are comparable with young adults in size.

• Primary Identifier: Expr3923
• Subcellular Localization: The subcellular localization of full-length KAT-1 was examined by inserting a FLAG epitope tag within its internal loop domain. This epitope-tagged KAT-1 (KAT-1_FLAG) was functional, as it rescued the lipid accumulation phenotype of kat-1 tub-1 mutant animals when expressed under the endogenous kat-1 promoter. KAT-1_FLAG localized to the mitochondria of intestine and body wall muscle. In addition, KAT-1 possesses a functional peroxisomal targeting signal (PTS1), although full-length KAT-1 have not been detected in peroxisomes.

• Primary Identifier: Expr1221
• Remark: P-44 is referred as Type-II 3-oxoacyl-CoA thiolase, corresponding to T02G5.8. Thin sections of clofibrate-treated L4 larvae of C. elegans were examined by the double-labeling immunoelectron microscopic technique to clarify whether P-44 was located in the peroxisomes.
• Subcellular Localization: P-44 was located in the peroxisomes.

9 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002183
• Start: 7073814
• End: 7075511
• Strand: 1

9 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1698

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00040200

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_7072416..7073813
• Length (nt): 1398
• Chromosome Location: II: 7072416-7073813
• Organism: Caenorhabditis elegans