Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans
Abstract
:1. Introduction
2. Results
2.1. kaeA19 and kaeA25 Mutations Do Not Influence the Modification of A37 in tRNA
2.2. kaeA19 and kaeA25 Mutations Affect Expression of Many Genes
2.3. In Addition to Subunits of KEOPS Complex, KaeA Also Interacts with Other Proteins
2.4. KaeA Interacts with Chromatin
3. Discussion
4. Materials and Methods
4.1. A. nidulans and S. cerevisiae Strains, Growth Conditions, and Transformation
4.2. Transcriptomics
4.3. RT-qPCR Analysis
4.4. Plasmids for Aspergillus Transformation
4.4.1. Golden Gate Cloning
4.4.2. Overlap Extension PCR Cloning
4.5. Purification of Proteins Interacting with KaeA
4.6. Primer Extension
4.7. Western Analysis
4.8. ChIP-Seq Analysis
4.9. Bioinformatics Analysis of KaeA Protein
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene AN Number | Gene Name | Yeast Homologue Gene Name 1 | Protein Function 2 |
---|---|---|---|
AN5170 | rosA | UME6 | Putative Zn(II)2Cys6 transcription factor; negative regulator of sexual development. Homologue of yeast Ume6p, encoding histone Rpd3p deacetylase subunit, general regulator of chromatin structure and transcriptional repressor. |
AN1848 | nosA | UME6 | Putative Zn(II)2Cys6 transcription factor; negative regulator of sexual development. Homologue of yeast Ume6p, encoding histone Rpd3p deacetylase subunit, general regulator of chromatin structure and transcriptional repressor. |
AN1812 | jlbA | – | bZIP transcription factor involved in amino acid biosynthesis. |
AN8168 | nmrA | – | Co-repressor of general nitrogen regulator AreA |
AN0948 | – | GCN20 | Protein with predicted ATPase activity. Homologue of yeast GCN20p, positive regulator of Gcn2p kinase; forms a complex with Gcn1p; proposed to stimulate Gcn2p activation by an uncharged tRNA. |
AN1298 | – | RTG3 | Homologue of yeast Rtg3p, bHLH/Zip transcription factor for retrograde (RTG) and TOR pathways. |
AN6076 | – | SWR1 | Protein with helicase domain of SNF2 type. Homologue of yeast Swr1p, Swi2/Snf2-related ATPase; catalytic subunit of SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A. |
AN10854 | – | SNF4 | Putative serine-threonine protein kinase. Homologue of yeast Snf4p, activating subunit of AMP-activated Snf1p kinase complex; activates glucose-repressed genes, represses glucose-induced genes. |
AN2366 | – | – | Putative trypsin-like protease involved in proteolytic cleavage of NmrA, a regulatory protein involved in repression of nitrogen metabolism. |
Gene AN Number | Gene Name | Protein Function (from FungiDB) | Yeast Homologue Gene Name | Protein Function of Yeast Homologue (from SGD) | DNAse * +/− |
---|---|---|---|---|---|
AN2845 | pccA | Putative component of EKC/KEOPS complex | PCC1 | Component of KEOPS complex | + |
AN2513 | pipA | Putative component of EKC/KEOPS complex | BUD32 | Protein kinase, component of KEOPS complex | + |
AN11910 | cgi121 | Putative component of EKC/KEOPS complex | CGI121 | Component of KEOPS complex | − |
AN11901 | gonG | Putative component of EKC/KEOPS complex | GON7 | Component of KEOPS complex | + |
AN6505 | rcoA | WD40 repeat protein | TUP1 | Chromatin-silencing transcriptional regulator; forms complex with Cyc8p, involved in establishment of repressive chromatin structure | − |
AN12054 | ssnF | Orthologue of S. cerevisiae Ssn6p | CYC8 | Chromatin-silencing transcriptional regulator; acts together with Tup1p | − |
AN2181 | – | Orthologue(s) have RNA polymerase II transcription factor activity, TBP-class protein binding | TOA2 | TFIIA small subunit; involved in transcriptional activation, acts as anti-repressor or co-activator | + |
AN2412 | cmkA | Calcium/calmodulin-dependent protein kinase A | CMK2 | Calmodulin-dependent protein kinase | − |
AN6305 | pkaA | cAMP-dependent protein kinase catalytic subunit | TPK2 | Catalytic subunit of cAMP-dependent protein kinase | + |
AN4987 | pkaR | Putative protein kinase A (PKA) regulatory subunit | BCY1 | Regulatory subunit of cyclic AMP-dependent protein kinase PKA | + |
AN5973 | pkcB | Protein with similarity to protein kinase C | YPK1 | Serine/threonine protein kinase | + |
AN1545 | – | Putative regulatory subunit of protein phosphatase 2A (PP2A) | CDC55 | Non-essential regulatory subunit B of protein phosphatase 2A (PP2A) | + |
Gene AN Number | Gene Name | Protein Function (from FungiDB) | Yeast Homologue Gene Name * | Protein Function of Yeast Homologue (from SGD) | Chromatin Region Interacting with KaeA |
---|---|---|---|---|---|
AN0733 | hhtA | Histone H3 | HHT1 | Histone H3; core histone protein required for chromatin assembly, part of heterochromatin-mediated telomeric and HM silencing | 5′ UTR |
AN0734 | H4.1 | Histone H4.1 | HHF2 | Histone H4; core histone protein required for chromatin assembly and chromosome function; contributes to telomeric silencing | 5′ UTR |
AN3468 | H2A.X | Histone H2A | HTA1 | Histone H2A; core histone protein required for chromatin assembly and chromosome function | 5′ UTR |
AN1007 | niiA | Putative nitrite reductase with predicted role in nitrogen metabolism | – | – | Promoter region |
AN2436 | aclB | Putative ATP citrate synthase with predicted role in TCA cycle | – | – | 5′ UTR |
AN2435 | aclA | Putative ATP citrate synthase with predicted role in TCA cycle | – | – | 5′ UTR |
AN3675 | cpcA | Transcription factor of c-Jun family of Gcn4p-like transcriptional activators | GCN4 | bZIP transcriptional activator of amino acid biosynthetic genes; responds to amino acid starvation | 5′ UTR |
AN4159 | glnA | Putative ammonium glutamate ligase with predicted role in glutamate and glutamine metabolism | GLN1 | Glutamine synthetase (GS); synthesizes glutamine from glutamate and ammonia; with Glt1p, forms secondary pathway for glutamate biosynthesis from ammonia | 5′ UTR |
AN4376 | gdhA | Putative glutamate dehydrogenase associated with NADP | GDH1 | NADP(+)-dependent glutamate dehydrogenase | 5′ UTR |
AN5823 | sidA | L-ornithine N5-monooxygenase | – | – | 5′ UTR |
AN7463 | meaA | Main ammonium transporter in A. nidulans | MEP3 | Ammonium permease with high capacity and low affinity | 5′ UTR |
AN8041 | gpdA | Glyceraldehyde-3-phosphate dehydrogenase with predicted role in gluconeogenesis and glycolysis | TDH3 | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isozyme 3; involved in glycolysis and gluconeogenesis | 5′UTR |
AN8251 | hapX | bZIP transcription factor | – | – | exon |
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Gawlik, J.; Koper, M.; Bogdanowicz, A.; Weglenski, P.; Dzikowska, A. Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans. Int. J. Mol. Sci. 2022, 23, 11138. https://doi.org/10.3390/ijms231911138
Gawlik J, Koper M, Bogdanowicz A, Weglenski P, Dzikowska A. Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans. International Journal of Molecular Sciences. 2022; 23(19):11138. https://doi.org/10.3390/ijms231911138
Chicago/Turabian StyleGawlik, Joanna, Michal Koper, Albert Bogdanowicz, Piotr Weglenski, and Agnieszka Dzikowska. 2022. "Nuclear Functions of KaeA, a Subunit of the KEOPS Complex in Aspergillus nidulans" International Journal of Molecular Sciences 23, no. 19: 11138. https://doi.org/10.3390/ijms231911138