General transcription factor IIIAa regulates the transcription of somatic 5S rRNA and influences embryonic organ development in zebrafish

Abstract

Transcription factor IIIA (TFIIIA) is a zinc finger protein that facilitates the assembly of a transcription complex by recruiting transcription factors TFIIIB and TFIIIC, along with RNA polymerase III, to initiate the transcription of 5S rRNA genes. However, the effects of TFIIIA knockout in vertebrates remain unclear. To address this, we investigated the function of a homologous general transcription factor IIIAa, gtf3aa, identified as a maternal factor in zebrafish. During early embryonic development, gtf3aa expression initially increased and subsequently declined. At 12 h postfertilization, gtf3aa mRNA was detected at notably low levels in the embryo, whereas by three days postfertilization, its mRNA level gradually increased in the larvae. The gtf3aa was broadly expressed in various embryonic tissues of zebrafish, with higher expression levels observed in the brain, heart, liver, and muscle. Knockout of gtf3aa significantly suppressed somatic 5S rRNA transcription in early zebrafish embryos and larvae, resulting in a reduction in the number of mature monoribosomes and polyribosomes. The gtf3aa^−/− larvae exhibited slow growth and delayed yolk absorption, along with impaired development of the eyes, heart, swim bladder, liver, and intestinal tissues. Additionally, expression of genes involved in metabolic signaling pathways, including the peroxisome proliferator-activated receptor pathway, was reduced. The gtf3aa^−/− zebrafish did not survive beyond seven days postfertilization. This study offers preliminary insights into the role of gtf3aa in regulating somatic 5S rRNA transcription and embryonic organ development in zebrafish.

Keywords

Zebrafish / gtf3aa / 5S rRNA / Ribosome / Organ development

References

[1] Allison LA, North MT, Neville LA. Differential binding of oocyte-type and somatic-type 5S rRNA to TFIIIA and ribosomal protein L5 in Xenopus oocytes: specialization for storage versus mobilization. Dev Biol, 1995, 168: 284-295.

[2] Blackburn ML, Ono-Moore KD, Hoppel CL, Ellis JM, Adams SH. Limited fatty acid oxidation (fao) in cpt2 knockout myocytes associates with insulin resistance and cell stress: possible role of acylcarnitine lipotoxicity. FASEB J, 2019, 33701.10-701.10

[3] Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30: 2114-2120.

[4] Camier S, Dechampesme AM, Sentenac A. The only essential function of TFIIIA in yeast is the transcription of 5S rRNA genes. Proc Natl Acad Sci USA, 1995, 92: 9338-9342.

[5] Cenik ES, Meng X, Tang NH, Hall RN, Arribere JA, Cenik C, Jin Y, Fire A. Maternal ribosomes are sufficient for tissue diversification during embryonic development in C. elegans. Dev Cell, 2019, 48: 811-826.e6.

[6] Chen J, Ruan H, Ng SM, Gao C, Soo HM, Wu W, Zhang Z, Wen Z, Lane DP, Peng J. Loss of function of def selectively up-regulates ∆113p53 expression to arrest expansion growth of digestive organs in zebrafish. Genes Dev, 2005, 19: 2900-2911.

[7] Choudhuri A, Maitra U, Evans T. Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis. Proc Natl Acad Sci USA, 2013, 110: 9818-9823.

[8] Ciganda M, Williams N. Eukaryotic 5S rRNA biogenesis. Wiley Interdiscip Rev RNA, 2011, 2: 523-533.

[9] Danilova N, Sakamoto KM, Lin S. Ribosomal protein L11 mutation in zebrafish leads to haematopoietic and metabolic defects. Br J Haematol, 2011, 152: 217-228.

[10] Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 2013, 29: 15-21.

[11] Donati G, Peddigari S, Mercer CA, Thomas G. 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint. Cell Rep, 2013, 4: 87-98.

[12] Fang C, Dean J, Smith JW. A novel variant of ileal bile acid binding protein is up-regulated through nuclear factor-kappaB activation in colorectal adenocarcinoma. Cancer Res, 2007, 67: 9039-9046.

[13] Haig D. Concerted evolution of ribosomal DNA: somatic peace amid germinal strife: intranuclear and cellular selection maintain the quality of rRNA. BioEssays, 2021, 43e2100179

[14] Hao JW, Wang J, Guo H, Zhao YY, Sun HH, Li YF, Lai XY, Zhao N, Wang X, Xie C, Hong L, Huang X, Wang HR, Li CB, Liang B, Chen S, Zhao TJ. CD36 facilitates fatty acid uptake by dynamic palmitoylation-regulated endocytosis. Nat Commun, 2020, 11: 4765

[15] He J, Yang Y, Zhang J, Chen J, Wei X, He J, Luo L. Ribosome biogenesis protein Urb1 acts downstream of mTOR complex 1 to modulate digestive organ development in zebrafish. J Genet Genomics, 2017, 44: 567-576.

[16] Huang W, Chen F, Ma Q, Xin J, Li J, Chen J, Zhou B, Chen M, Li J, Peng J. Ribosome biogenesis gene DEF/UTP25 is essential for liver homeostasis and regeneration. Sci China Life Sci, 2020, 63: 1651-1664.

[17] Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci, 1992, 8: 275-282. DOI:

[18] Kim SH, Wu SY, Baek JI, Choi SY, Su Y, Flynn CR, Gamse JT, Ess KC, Hardiman G, Lipschutz JH, Abumrad NN, Rockey DC. A post-developmental genetic screen for zebrafish models of inherited liver disease. PLoS ONE, 2015, 10e0125980

[19] Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 2009, 10: R25

[20] Lee J, Choi J, Scafidi S, Wolfgang MJ. Hepatic fatty acid oxidation restrains systemic catabolism during starvation. Cell Rep, 2016, 16: 201-212.

[21] Letunic I, Bork P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res, 2024, 52: W78-W82.

[22] Lezzerini M, Penzo M, O'Donohue MF, Dos Santos M, Vieira C, Saby M, Elfrink HL, Diets IJ, Hesse AM, CoutéY GM, Nin-Velez A, Nikkels PGJ, Olson AN, Zonneveld-Huijssoon E, Jongmans MCJ, Zhang G, van Weeghel M, Houtkooper RH, Wlodarski MW, Kuiper RP, et al. . Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism. Nucleic Acids Res, 2020, 48: 770-787.

[23] Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform, 2011, 12: 323

[24] Li YF, Cheng T, Zhang YJ, Fu XX, Mo J, Zhao GQ, Xue MG, Zhuo DH, Xing YY, Huang Y, Sun XZ, Wang D, Liu X, Dong Y, Zhu XS, He F, Ma J, Chen D, Jin X, Xu PF. Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1. PLoS Biol, 2022, 20e3001856

[25] Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 2001, 25: 402-408.

[26] Locati MD, Pagano JF, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Zhu K, Spaink HP, Girard G, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons. RNA, 2017, 23: 446-456.

[27] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014, 15550

[28] Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A, Tivey ARN, Lopez R, Butcher S. The EMBL-EBI job dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res, 2024, 52: W521-W525.

[29] Masuda D, Hirano K, Oku H, Sandoval JC, Kawase R, Yuasa-Kawase M, Yamashita Y, Takada M, Tsubakio-Yamamoto K, Tochino Y, Koseki M, Matsuura F, Nishida M, Kawamoto T, Ishigami M, Hori M, Shimomura I, Yamashita S. Chylomicron remnants are increased in the postprandial state in CD36 deficiency. J Lipid Res, 2009, 50: 999-1011.

[30] Naesens L, Muppala S, Acharya D, Nemegeer J, Bogaert D, Lee JH, Staes K, Debacker V, De Bleser P, De Bruyne M, De Baere E, van Gent M, Liu G, Lambrecht BN, Staal J, Kerre T, Beyaert R, Maelfait J, Tavernier SJ, Gack MU, et al. . GTF3A mutations predispose to herpes simplex encephalitis by disrupting biogenesis of the host-derived RIG-I ligand RNA5SP141. Sci Immunol, 2022, 7eabq4531

[31] Oyarbide U, Shah AN, Amaya-Mejia W, Snyderman M, Kell MJ, Allende DS, Calo E, Topczewski J, Corey SJ. Loss of Sbds in zebrafish leads to neutropenia and pancreas and liver atrophy. JCI Insight, 2020, 5e134309

[32] Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res, 2016, 44: W160-165.

[33] Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res, 2014, 42: W320-324.

[34] Romaniuk PJIuchi S, Kuldell N. TFIIIA and p43: Binding to 5S Ribosomal RNA. Zinc finger proteins, 2005, Boston. Springer56-65.

[35] Ruvinsky I, Sharon N, Lerer T, Cohen H, Stolovich-Rain M, Nir T, Dor Y, Zisman P, Meyuhas O. Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev, 2005, 19: 2199-2211.

[36] Sloan KE, Bohnsack MT, Watkins NJ. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep, 2013, 5: 237-247.

[37] Song Y, Chen J, Tao B, Luo D, Zhu Z, Hu W. Kisspeptin2 regulates hormone expression in female zebrafish (Danio rerio) pituitary. Mol Cell Endocrinol, 2020, 513110858

[38] Song Y, Peng W, Luo J, Zhu Z, Hu W. Organization of the gonadotropin-inhibitory hormone (Lpxrfa) system in the brain of zebrafish (Danio rerio). Gen Comp Endocrinol, 2021, 304113722

[39] Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res, 2019, 47: D607-D613.

[40] Szymański M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5S rRNA: structure and interactions. Biochem J, 2003, 371: 641-651.

[41] Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Mol Cell, 2023, 83(2641–2652): e2647

[42] Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol, 2021, 38: 3022-3027.

[43] Thisse C, Thisse B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc, 2008, 3: 59-69.

[44] Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform, 2013, 14: 178-192.

[45] Wang Y, Luo Y, Hong Y, Peng J, Lo L. Ribosome biogenesis factor Bms1-like is essential for liver development in zebrafish. J Genet Genomics, 2012, 39: 451-462.

[46] Wang J, Tan Y, Jia QY, Tang FQ. Transcriptional factor III A promotes colorectal cancer progression by upregulating cystatin A. World J Gastrointest Oncol, 2022, 14: 1918-1932.

[47] Westerfield M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 2000, Eugene. University of Oregon Press

[48] Wilkins BJ, Lorent K, Matthews RP, Pack M. P53-mediated biliary defects caused by knockdown of cirh1a, the zebrafish homolog of the gene responsible for North American Indian Childhood Cirrhosis. PLoS ONE, 2013, 8e77670

[49] Wu J, Jiang X, Li Y, Zhu T, Zhang J, Zhang Z, Zhang L, Zhang Y, Wang Y, Zou X, Liang B. PHA-4/FoxA senses nucleolar stress to regulate lipid accumulation in Caenorhabditis elegans. Nat Commun, 2018, 9: 1195

[50] Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G. ClusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation, 2021, 2100141

[51] Xu C, Li H, Tang CK. Sterol carrier protein 2: a promising target in the pathogenesis of atherosclerosis. Genes Dis, 2023, 10: 457-467.

[52] Zhang S, Shi M, Hui CC, Rommens JM. Loss of the mouse ortholog of the shwachman-diamond syndrome gene (Sbds) results in early embryonic lethality. Mol Cell Biol, 2006, 26: 6656-6663.

[53] Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol, 2008, 9: R137

[54] Zhang C, Huang R, Ma X, Chen J, Han X, Li L, Luo L, Ruan H, Huang H. The ribosome biogenesis factor ltv1 is essential for digestive organ development and definitive hematopoiesis in zebrafish. Front Cell Dev Biol, 2021, 9704730

[55] Zhao C, Andreeva V, Gibert Y, LaBonty M, Lattanzi V, Prabhudesai S, Zhou Y, Zon L, McCann KL, Baserga S, Yelick PC. Tissue specific roles for the ribosome biogenesis factor Wdr43 in zebrafish development. PLoS Genet, 2014, 10e1004074

[56] Zhu Q, Tao B, Chen H, Shi H, Huang L, Chen J, Hu M, Lo LJ, Peng J. Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. Nucleic Acids Res, 2021, 49: 5743-5759.

RIGHTS & PERMISSIONS

The Author(s)

Just Accepted

This article has successfully passed peer review and final editorial review, and will soon enter typesetting, proofreading and other publishing processes. The currently displayed version is the accepted final manuscript. The officially published version will be updated with format, DOI and citation information upon launch. We recommend that you pay attention to subsequent journal notifications and preferentially cite the officially published version. Thank you for your support and cooperation.