Family Search for PF10350 (DUF2428)
PaperBLAST, GapMind, SitesBLAST, and Sites on a Tree will be down for server maintenance on Friday March 29.
Running HMMer for PF10350
PF10350 hits 11 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
G1SEM4 tRNA (32-2'-O)-methyltransferase regulator THADA from Oryctolagus cuniculus
Aligns to 1149:1450 / 2153 (14.0%), covers 99.6% of PF10350, 287.6 bits
THADA_HUMAN / Q6YHU6 tRNA (32-2'-O)-methyltransferase regulator THADA; Gene inducing thyroid adenomas protein; Thyroid adenoma-associated protein from Homo sapiens (Human) (see 2 papers)
NP_071348 tRNA (32-2'-O)-methyltransferase regulator THADA isoform a from Homo sapiens
Aligns to 947:1248 / 1953 (15.5%), covers 99.6% of PF10350, 286.4 bits
- function: Together with methyltransferase FTSJ1, methylates the 2'-O- ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs.
- Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs
Li, EMBO reports 2020 - “...crucial substrate and may serve as the main functional executor of Trm7. Human THADA (UniProt: Q6YHU6) and WDR6 (UniProt: Q9NNW5) are proposed to be the homologs of Trm732 and Trm734, respectively (Guy & Phizicky, 2015 ). THADA contains 1,953 AA residues, but only its 9881,470 peptide...”
- Increased C-X-C Motif Chemokine Ligand 12 Levels in Cerebrospinal Fluid as a Candidate Biomarker in Sporadic Amyotrophic Lateral Sclerosis.
Andrés-Benito, International journal of molecular sciences 2020 - “...kinase C delta type i Q05655 1 41.25 0.46 0.03 THADA THADA armadillo repeat containing Q6YHU6 1 46.64 0.48 0.01 NHLC2 NHL repeat-containing protein 2 Q8NBF2 1 73.60 0.49 0.03 PLSI plastin 1 Q14651 1 25.89 0.54 0.03 RFA2 replication protein A2 P15927 1 93.57 0.54...”
- MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape.
Pymm, Nature structural & molecular biology 2017 - “...epitopes from the self-repertoire of HLA-B*57:01. We selected the peptides TSTTSVASSW (UniProt Q14679), TSTFEDVKILAF (UniProt Q6YHU6) and SSTRGISQLW (UniProt Q96HA1), each of which formed part of a nested set (set 233, set 926 and set 736, respectively; Supplementary Table 2 ). Crystals of the refolded HLA-B*57:01peptide...”
- THADA, SDHAF4, and MACF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes.
Ustianowski, Genes 2022 - GeneRIF: THADA, SDHAF4, and MACF1 Gene Polymorphisms and Placental Expression in Women with Gestational Diabetes.
- Clinicopathologic Characteristics of Thyroid Nodules Positive for the THADA-IGF2BP3 Fusion on Preoperative Molecular Analysis.
Morariu, Thyroid : official journal of the American Thyroid Association 2021 (PubMed)- GeneRIF: Clinicopathologic Characteristics of Thyroid Nodules Positive for the THADA-IGF2BP3 Fusion on Preoperative Molecular Analysis.
- Replication study of THADA rs13429458 variant with PCOS susceptibility and its related traits in Indian women.
Dadachanji, Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology 2021 (PubMed)- GeneRIF: Replication study of THADA rs13429458 variant with PCOS susceptibility and its related traits in Indian women.
- Pooled genetic analysis identifies variants that confer enhanced susceptibility to PCOS in Indian ethnicity.
Vishnubotla, Gene 2020 (PubMed)- GeneRIF: Of the 15 variants, 3 variants (rs13405728 in LHCGR; rs13429458 in THADA and rs2209972 IDE genes) were found to be associated with PCOS. The association was successfully replicated in an independent cohort. Insilico analysis categorized two variants (rs13429458-THADA and rs2209972-IDE genes) as deleterious.
- Association study between variants in LHCGR DENND1A and THADA with preeclampsia risk in Han Chinese populations.
Zhang, The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 2019 (PubMed)- GeneRIF: Genetic variants of PCOS (rs13405728 in LHCGR gene; rs13429458 in THADA gene and rs2479106 in DENND1A gene) may not be involved in the development of preeclampsia in Han Chinese women.
- THADA_rs13429458 Minor Allele Increases the Risk of Polycystic Ovary Syndrome in Asian, but Not in Caucasian Women: A Systematic Review and Meta-Analysis.
Park, Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et metabolisme 2019 (PubMed)- GeneRIF: THADA_rs13429458 Minor Allele is associated with Polycystic Ovary Syndrome in Asian, but Not in Caucasian Women.
- THADA fusion is a mechanism of IGF2BP3 activation and IGF1R signaling in thyroid cancer.
Panebianco, Proceedings of the National Academy of Sciences of the United States of America 2017 - GeneRIF: THADA fusion is a mechanism of IGF2BP3 activation and IGF1R signaling in thyroid cancer.
- THADA Regulates the Organismal Balance between Energy Storage and Heat Production.
Moraru, Developmental cell 2017 - GeneRIF: this identifies THADA as a regulator of the balance between energy consumption and energy storage, which was selected during human evolution.
- More
NP_898842 thyroid adenoma-associated protein homolog from Mus musculus
A8C756 tRNA (32-2'-O)-methyltransferase regulator THADA from Mus musculus
Aligns to 938:1239 / 1938 (15.6%), covers 99.6% of PF10350, 279.8 bits
AFUA_2G14180 HEAT repeat protein from Aspergillus fumigatus Af293
Aligns to 703:940 / 1643 (14.5%), covers 99.6% of PF10350, 268.4 bits
- Receptor-mediated signaling in Aspergillus fumigatus
Grice, Frontiers in microbiology 2013 - “...ion transporter AFUA_2G12050 XP_755537.1 Midasin AFUA_2G12150 XP_755547.1 Integral membrane protein AFUA_2G12640 XP_755596.1 HEAT repeat protein AFUA_2G14180 XP_755751.2 Conserved hypothetical protein AFUA_2G15100 XP_755844.2 Integral membrane protein AFUA_2G15440 XP_755879.2 DUF92 domain protein AFUA_2G15640 XP_755899.1 Rhomboid family membrane protein AFUA_2G16490 XP_755986.1 Integral membrane protein AFUA_2G16985 XP_001481687.1 Sulfatase domain protein...”
THADA_DROME / Q9VWB9 tRNA (32-2'-O)-methyltransferase regulator THADA; Thyroid adenoma-associated protein homolog from Drosophila melanogaster (Fruit fly) (see 2 papers)
NP_608361 THADA, isoform B from Drosophila melanogaster
Aligns to 838:1113 / 1746 (15.8%), covers 97.3% of PF10350, 259.5 bits
- function: Together with methyltransferase Trm7-32, methylates the 2'-O- ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs (By similarity). Plays a key role in energy homeostasis by regulating the balance between energy storage and heat production. Functions by negatively regulating Ca(2+) signaling pathways that are involved in heat production and maintaining correct lipid storage in the fat body. Regulates Ca(2+) signaling pathways by reducing the activity of the calcium-transporting ATPase SERCA possibly by promoting uncoupling of SERCA ATP hydrolysis from calcium pumping. May also function in the nervous system to control feeding behavior (PubMed:28399403).
subunit: Interacts with SERCA.
disruption phenotype: Flies are hypersensitive to the cold, hyperphagic and display elevated triglyceride stores resulting in an increased resistance to starvation (PubMed:28399403). Heat production is impaired and flies are slow to recover after cold treatment (PubMed:28399403). The size of the lipid droplets in larval fat bodies are significantly increased and flies display increased feeding (PubMed:28399403). Total body glycogen is also significantly increased in adult females but not in males (PubMed:28399403). Mutants also display an increase in calcium-dependent SERCA activity (PubMed:28399403). No effect on levels of circulating sugars, glucose and trehalose (PubMed:28399403). RNAi- mediated knockdown impairs small interfering RNA-mediated silencing (PubMed:31943105). - THADA Regulates the Organismal Balance between Energy Storage and Heat Production.
Moraru, Developmental cell 2017 - GeneRIF: this identifies THADA as a regulator of the balance between energy consumption and energy storage, which was selected during human evolution.
THADA_SCHPO / O60081 tRNA (32-2'-O)-methyltransferase regulator trm732 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
SPCC1494.07 conserved eukaryotic protein from Schizosaccharomyces pombe
Aligns to 624:868 / 1502 (16.3%), covers 99.2% of PF10350, 244.6 bits
- function: Together with methyltransferase trm7, methylates the 2'-O- ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs.
disruption phenotype: Loss of methylation of the 2'-O-ribose of cytidine at position 32 of tRNA(Phe) (PubMed:25404562). Increases occurrence of 1-methylguanosine residue at position 37 in the tRNA anticodon loop of tRNA(Phe) and decreases occurrence of wybutosine at this position (PubMed:25404562). - Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes
Guy, RNA (New York, N.Y.) 2015 - “...between S. cerevisiae and S. pombe , we analyzed the putative S. pombe trm732 ( SPCC1494.07 ) and trm734 ( SPBC1306.02 ) strains. An Sp trm732 haploid mutant obtained by sporulation of the heterozygous diploid lacked detectable Cm in its tRNA Phe and had normal levels...”
- DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase
Sabouri, Genes & development 2012 - “...two-tailed Student's t-test. thada is the name for SPCC1494.07. (B) TCA-precipitated protein samples from nmtpfh1-GFP collected after 12, 24, 32, and 48 h...”
trm732 tRNA (cytosine 32-2'-O)-methyltransferase regulator Trm732 from Schizosaccharomyces osmophilus
Aligns to 625:869 / 1503 (16.3%), covers 99.2% of PF10350, 242.2 bits
- The life and times of a tRNA
Phizicky, RNA (New York, N.Y.) 2023 - “...et al. 2002 ). It is now known that S. cerevisiae Trm7 requires interaction partners Trm732 and Trm734 for formation of Nm 32 and Nm 34 , respectively, on each Trm7 substrate tRNA, and that the critical tRNA substrate is tRNA Phe , as overproduction of...”
- “...mutants has m 1 G 37 instead of yW 37 , and tRNA Phe from trm732 and trm734 mutants each has only partial yW 37 modification. Thus, in a trm7 mutant the entire ACL of tRNA Phe is undermodified at C 32 , G 32 ,...”
- Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis
Garg, Nucleic acids research 2023 - “...(Trm12, Tyw1), ac 4 C (Nat10), s 2 U34 (Nfs1); ribose 2- O -methylation (Trm13, Trm732); 5 processing (Pop7, Pop100)and 3 processing (Rex1, Trz2). Upregulation of Maf1, a repressor of RNA polymerase III transcription Maf1 protein is an endogenous negative regulator of Pol3 transcription that is...”
- “...to 3-fold ( Supplementary Table S4 ). The levels of six tRNA modifying proteins (Trl1, Trm732, Trm12, Pus2, Tyw1, Tad3) were diminished by 2- to 5-fold at 24 h. Ribosomal proteins The most striking proteome changes during phosphate starvation that cohered with transcriptional reprogramming entailed a...”
- The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance
Brazane, Life science alliance 2023 - “...Guy et al, 2012 ). To achieve 2-O-methylation, Trm7 teams up with two other proteins: Trm732 for the methylation of cytosine at position 32, and Trm734 for the methylation of cytosine or guanine at position 34 ( Guy et al, 2012 ; Li et al, 2020...”
- Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7
Funk, ACS omega 2022 - “...Omega ao acsodf ACS Omega 2470-1343 American Chemical Society 9088939 10.1021/acsomega.1c07231 Article Identification of a Trm732 Motif Required for 2- O -methylation of the tRNA Anticodon Loop by Trm7 Funk Holly M. DiVita Daisy J. Sizemore Hannah E. Wehrle Kendal Miller Catherine L. W. # Fraley...”
- “...results in non-syndromic X-linked intellectual disability. In yeast, the methyltransferase Trm7 forms a complex with Trm732 to 2- O -methylate tRNA residue 32 and with Trm734 to 2- O -methylate tRNA residue 34. Trm732 and Trm734 are required for the methylation activity of Trm7, but the...”
- Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs
Li, EMBO reports 2020 - “...are available online for this figure. In S.cerevisiae and S.pombe , Trm7 interacts separately with Trm732 and Trm734 to 2Omethylate C32 and N34 of tRNA Trp (CCA), tRNA Phe (GAA), and tRNA Leu (UAA) ( Guy etal , 2012 ; Guy & Phizicky, 2015 ). In...”
- “...Human THADA (UniProt: Q6YHU6) and WDR6 (UniProt: Q9NNW5) are proposed to be the homologs of Trm732 and Trm734, respectively (Guy & Phizicky, 2015 ). THADA contains 1,953 AA residues, but only its 9881,470 peptide shares 28% identity and 46% sequence similarity with the 5961,028 peptide of...”
- tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila
Angelova, Nucleic acids research 2020 - “...46 ). Deposition of Nm at C 32 by TRM7 is supported by binding to TRM732 while the interaction with TRM734 is necessary for addition of Nm at position 34. THADA and WDR6 are the orthologs of TRM732 and TRM734 in humans, respectively, and their interactions...”
- “...Drosophila , CG15618, also known as DmTHADA ( 92 ), is the potential ortholog of TRM732 and THADA, while CG33172 is the putative ortholog of TRM734 and WDR6 (Figure 6A ). Importantly, CG33172, TRM734 and WDR6 are members of the WD40-repeat-containing domain superfamily that contains also...”
- Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition
Hirata, Nucleic acids research 2019 - “...site targeted by Trm7 switches dependent on its partner subunit: a complex of Trm7 and Trm732 (Trm7Trm732) catalyzes 2- O -methylation at position 32 in tRNA ( 14 , 16 ). Furthermore, it has been reported that the formation of wyosine at position 37 requires Gm34...”
- “...Japan). All the primers used for the construction of cloning and expression vectors of trm7, trm732 and trm734 genes are listed in Supplementary Table S1 . The details of construction of Trm7Trm734 and Trm7Trm732 co-expression vectors are described in Supplementary File. Expression of Trm7Trm734 and Trm7Trm732...”
- RNA 2'-O-Methylation (Nm) Modification in Human Diseases
Dimitrova, Genes 2019 - “...circuitry required for anticodon loop modification of target tRNAs. More concretely, TRM7 separately interacts with TRM732 and TRM734 partners to form Cm 32 and Nm 34 respectively, both of which are required on tRNA Phe for efficient formation of a third modification, the wybutosine (yW) at...”
- “...growth defect of S. cerevisiae TRM7 mutants by human FTSJ1 expression requires the function of TRM732 or its human homolog THADA to form Cm 32 on tRNA Phe [ 49 ], and the formation of peroxywybutosine (o2yW 37 ) at m 1 G 37 is also...”
- More
NP_001326116 thyroid adenoma-associated-like protein from Arabidopsis thaliana
Aligns to 990:1311 / 2130 (15.1%), covers 99.2% of PF10350, 239.3 bits
AT3G55160 hypothetical protein from Arabidopsis thaliana
Aligns to 959:1280 / 2149 (15.0%), covers 99.2% of PF10350, 239.3 bits
- The Arabidopsis THADA homologue modulates TOR activity and cold acclimation
Dong, Plant biology (Stuttgart, Germany) 2019 (PubMed)- “...and homology modeling to identify the AtTHADA (AT3G55160) in Arabidopsis thaliana as the highly probable orthologue protein. Reverse genetics approaches were...”
- “...modulates TOR activity (Figure S1B). Homology modelling of AT3G55160 and human THADA revealed a similar tertiary structure of the two proteins. A search for...”
THADA_YEAST / Q03496 tRNA (32-2'-O)-methyltransferase regulator TRM732 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
NP_013986 tRNA methylation protein TRM732 from Saccharomyces cerevisiae S288C
YMR259C Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR259C is not an essential gene from Saccharomyces cerevisiae
Aligns to 614:839 / 1420 (15.9%), covers 99.6% of PF10350, 177.2 bits
- function: Together with methyltransferase TRM7, methylates the 2'-O- ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs.
subunit: Interacts with TRM7; for 2'-O-methylation of position 32 in substrate tRNAs.
disruption phenotype: Loss of methylation of the 2'-O-ribose of cytidine at position 32 of tRNA(Phe) (PubMed:35559166). Increases occurrence of 1-methylguanosine residue at position 37 tRNA anticodon loop of tRNA(Phe), indicative of a loss of wybutosine at this position (PubMed:35559166). Simultaneous knockout of RTT10/TRM734 leads to activation of the general control amino acid (GAAC) response and severely decreases cell population growth (PubMed:35559166, PubMed:29596413). - Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop.
Guy, RNA (New York, N.Y.) 2012 - GeneRIF: Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop.
- Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation
Marchand, Biomolecules 2017 - “...unique MTase Trm7 (encoded by YBR061C) [ 35 ], which also tightly interacts with ORF YMR259c (now named Trm732) for 2- O -methylation of C32 and with Rtt10 (named Trm734) for 2- O -methylation of N34 in substrate tRNAs [ 36 ]. Moreover, the presence of...”
- Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop
Guy, RNA (New York, N.Y.) 2012 - “...and in vitro evidence that Trm7 interacts with ORF YMR259c (now named Trm732) for 29-O-methylation of C32, and with Rtt10 (named Trm734) for 29-O-methylation of...”
- “...Keywords: RTT10 ; TRM7; tRNAPhe; wyebustosine; YMR259c INTRODUCTION Post-transcriptional modifications of tRNA are numerous, widely conserved in nature,...”
- Proteome-wide overexpression of host proteins for identification of factors affecting tombusvirus RNA replication: an inhibitory role of protein kinase C
Shah, Journal of virology 2012 - “...YCK1 YCT1 YDJ1 YGL262W YGR026Wb YGR130C YLR126C YMR1 YMR259C YOS1 YPT1 YPT52 YSY6 a Gene names are based on the Saccharomyces genome database. Downregulators...”
- Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data
Bryan, BMC genomics 2008 - “...MIPS ribosomal biogenesis. YDL167C (NRP1) Transcription: rRNA (11.04.01) Role in ribosome biogenesis and assembly (RCA). YMR259C Transcription: rRNA (11.04.01)/ Transport Routes (20.09) Putative protein, unknown function; GFP-fusion protein localizes to the cytoplasm. YNL022C Transcription: rRNA (11.04.01) Putative protein of unknown function. GFP-fusion protein localizes to a...”
- Detecting patterns of protein distribution and gene expression in silico
Geraghty, Proceedings of the National Academy of Sciences of the United States of America 1999 - “...YNL009W YGR154C YBR204C YLR109W YEL029C YIL094C YDR449C YGL067W YMR259C YBL071C YBR012C YJR019C YLR284C YOR180C YPR128C YOL044W PTS1 ORE SKL SKL SKF SKL AKL SKL...”
CG3368 uncharacterized protein from Drosophila melanogaster
Aligns to 636:899 / 1120 (23.6%), covers 99.2% of PF10350, 155.3 bits
- Mondo/ChREBP-Mlx-regulated transcriptional network is essential for dietary sugar tolerance in Drosophila
Havula, PLoS genetics 2013 - “...coding region of mlx as well as 17 C-terminal amino acids of the neighbouring gene CG3368 ( Figure 1A ). As controls, we recovered lines from which the P-element had been excised precisely, leaving mlx intact. If not differently stated, the precise excision line is used...”
- “...out the possibility that sugar intolerance was due to disturbed function of the neighbouring gene CG3368, we used RNAi for ubiquitous knockdown. CG3368 was efficiently silenced, but no sugar intolerance was observed ( Figure S1DS1F ). Thus, mlx gene function is essential for tolerance to dietary...”
- Drosophila sosie functions with β(H)-Spectrin and actin organizers in cell migration, epithelial morphogenesis and cortical stability
Urwyler, Biology open 2012 - “...primers used for the RT-PCR shown in D are also indicated (ad). The neighbor gene CG3368 is encoded on the opposite strand. ( B ) Compound egg chamber in a sie 1 /Df(3R)Exel6200 ovary. Two focal planes of the same egg chamber are shown and the...”
- A misexpression screen to identify regulators of Drosophila larval hemocyte development
Stofanko, Genetics 2008 - “...CG32556 CG32813 CG32813 CG33182 CG3363 CG3368 CG3624 Gene P{EPgy2}EY09041 P{EPgy2}EY09604 P{EP}EP1515 P{EPgy2}EY08487 P{EP}EP1613 P{EPgy2}EY10303...”
Or search for genetic data about PF10350 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory