An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels—The Global View
Abstract
:1. Introduction
2. Results and Discussion
2.1. Data Extraction, Juxtaposition, and Global Clustering—Clusters Overview
2.2. Statistical Overrepresentation Test Delimited Two Major Categories amongst TFs
2.3. Usefulness of Specific Deregulation Patterns as Selectors of TFs Involved in Specific Biological Processes
2.4. Direct Comparison of Phenotypes Elicited by Y. lipolytica Strains Bearing OE or KO of Selected TFs
3. Summary and Conclusions
4. Materials and Methods
4.1. Microbial Strains Used for Transcriptomics and Functional OE Screens Data Acquisition
4.2. Microbial Strains Used for Functional Studies—KO in a Specific TF loci
Construction of the KO Strains—Deletion Cassette and CRISPR-Cas9 Targeting
4.3. Functional Studies—Direct Comparative Study of OE and KO Strains
4.3.1. Cultivation Conditions
4.3.2. Samples Analysis
4.4. Omics and Functional Data Acquisition
4.5. Data Processing and Mathematical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Yali Signature | Assigned Name | Putative/Known Function | Reference |
---|---|---|---|
B12716 | HAC1 | Transcriptional activator of genes involved in ER-based Unfolded Protein Response (UPR). | [16,19] |
E31757 | BRG1 | Biofilm regulator 1. | [20] |
D14520 | SKN7 | TF involved in the activation of osmotic and oxidative stress. | [22,40] |
D07744 | YAP-like | TF involved in pH-dependent dimorphic transition and maintaining redox balance. | [22,41] |
D20482 | GZF1 | Inducer of the nitrogen catabolite repression (NCR) genes. | [23,42] |
E13948 | HSF1 | Heat shock transcription factor. | [22,23] |
D05041 | KLF1 | Krueppel-like factor 15, regulates the expression of genes for gluconeogenic and amino acid-degrading enzymes. | [23] |
A16841 | AZF1 | Asparagine-rich Zinc Finger protein, regulates carbon metabolism in yeast and cell wall organization. | [20,23] |
F05896 | DEP1 | Part of the Rpd3C(L) histone deacetylase complex (HDAC). Transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes. | [20,23] |
C19151 | CAT8 | CATabolite repression TF 8. Inducer of gluconeogesis, maintains energy homeostasis, presumed to regulate formate dehydrogenases expression. | [39] |
F21923 | ADR1 | Alcohol Dehydrogenase II synthesis Regulator, inducer of genes involved in alternative carbon utilization upon glucose starvation. | [11,39] |
D20460 | LAC9 | LACtose regulatory protein, controls induction of the lactose-galactose regulation. | [23] |
B14443 | JMC2 | JmjC domain family histone demethylase, promotes global demethylation of H3K4. | [23,43] |
D02783 | DAL81 | Positive regulator of genes in multiple nitrogen degradation pathways, involved in nitrogen catabolite activation of transcription from RNA polymerase II promoter. | [23] |
B19602 | MGF2 | Mycelial growth factor 2. TF of known roles in the dimorphic transition. | [16,41] |
B21582 | MHY1 | Mns2/Mns4-like protein, a key regulator of yeast-to hypha dimorphic transition but not stress resistance, regulates both alkaline-pH and glucose-induced filamentation. | [44,45,46] |
D01573 | MGF1 | Mycelial growth factor. Potential driver of the transition between morphological phases. | [16] |
B05038 | ZNC1 | Zinc finger transcriptional factor, regulates the yeast-to-hypha transition in the dimorphic yeast. | [47] |
F17886 | GZF2 | GATA—binding zinc finger transcription factor 2, inducer of NCR, essential for growth on simple nitrogen sources. | [42] |
C22682 | GZF3 | GATA-zinc finger transcription factor 3, repressor of NCR. | [20,42] |
E05555 | GZF4 | GATA-zinc finger transcription factor 4. Putative: inducer of NCR. | [42] |
E16577 | GZF5 | Non-genuine GATA-zinc finger transcription factor. | [20,42] |
E03410 | ERT1-2 | Positive regulator of gluconeogenesis. | [20] |
E27742 | GCN4 | General Control Non-derepressible 4 TF. Key transcriptional activator of amino acid biosynthesis genes. | [48] |
F17424 | HAP1 | TF responsible for oxygen sensing and signaling. | [49] |
D04785 | SFL1 | Repressor of filamentous growth and flocculation. | |
F01562 | EUF1 | Transcription factor mediating expression of erythritol synthesis genes. | [11,50,51] |
C16863 | SKO1 | ATF/CREB family transcription factor, repressor that mediates HOG pathway-dependent regulation of osmotic stress response, involved in protection from oxidative damage. | [40] |
C14784 | YAS3 | Transcriptional repressor of ALK genes, de-repressed on alkanes. | [52] |
C13750 | MSN4 | General stress response, regulates tolerance to acid-induced stress. Regulates genes involved in the antioxidant cellular response. | [53] |
B13640 | RIM101 | pH-response transcription factor, regulator of alkaline-induced filamentation | [46] |
C12364 | NRG1 | NRG1 repressor of erythritol utilization genes, plays a minor role in repression of filamentation. | [50,54] |
D23749 | ZAP1 | ZAP1 involved in zinc ion homeostasis by zinc-responsive transcriptional regulation. | [20] |
E30789 | Putativea: transcriptional regulator of form adherence 5. | ||
C07821 | Putativea: glucose transport transcription regulator RGT1-related. | ||
C18645 | ARO80 | Transcription activator required for the expression of genes involved in the catabolism of aromatic amino acids. | [55] |
B08206 | CRF1 | Copper resistance protein transcriptional regulator. | [56] |
D14872 | Putative a: transcriptional regulatory protein STB4 | ||
E18304 | ERT1-1 | Transcription activator of gluconeogenesis. | [20] |
E07942 | MIG1 | Controls genes involved in beta-oxidation, involved in carbon catabolite repression. | [57] |
A18469 | HOY1 | Homeobox protein, a positive regulator of hyphae formation. | [20,58] |
B06853 | PUT3 | PUT3 proline utilization trans-activator. | |
B09713 | PPR1 | PPR1 pyrimidine pathway regulatory protein, de novo biosynthesis. | [54,59] |
D13904 | LEU3 | Leucine-responsive transcription regulator, regulates genes involved in branched-chain amino acid biosynthesis and ammonia assimilation. | |
D23045 | AHR1 | AHR1 adhesion and hyphal regulator 1. | |
E10681 | WAR1 | Weak Acid Resistance transcription factor. | |
E20449 | YOX1 | Homeobox protein YOX1. Transcriptional repressor of ECB-dependent genes (early cell box) to the G1/M phase. | |
F03157 | MET32 | MET32 auxiliary transcriptional regulator of sulfonate and sulfur amino acid metabolism, methionine biosynthesis, and sulfate assimilation. | |
F05104 | TFIIIA | PZF1 general transcription factor IIIA. | |
F09361 | U4/U6.U5 component | U4/U6.U5 tri-snRNP, spliceosomal complex—may play a role in mRNA splicing. | |
F09493 | SAP61 | Pre-mRNA-splicing factor sap61, involved in mRNA splicing, associates with cdc5 and the other cwf proteins as part of the spliceosome. | |
F16599 | STB4 | Putative transcription factor STB4—Sin Three Binding protein, involved in the transcription of transmembrane transporters. | [60] |
F18788 | RLM1 | May function as a TF downstream of MPK1, at least some RML1 target genes are involved in cell wall biosynthesis. | |
E31845 | PRZ1 | Involved in the regulation of calcium ion homeostasis. | |
B15818 | SterTF | Sterol transcription factor, regulating sterol biogenesis. | [61] |
D05005 | SEF1 | Zn2-Cys6 transcription factor; regulates iron uptake. | |
D12628 | POR1 | Primary oleate regulator 1—transcriptional activator regulating genes involved in fatty acid utilization. | [62] |
C02387 | YAS1 | Transcription factor essential for cytochrome p450 induction in response to alcanes, heteromeric Yas1p/Yas2p complex transcription factor. | [63] |
B08734 | REI1 | Cytoplasmic pre-60S factor REI1 involved in maturation of the ribosomal 60S subunit. | |
E01606 | OAF3 | Oleate activated transcription factor 3, transcriptional inhibitor with a significantly increased number of target genes in response to oleate. | |
C06842 | MCM1 | MCM1 transcription factor involved in biofilm formation, cell adhesion, and hyphal growth. | |
A19778 | MBP1 | MluI-box Binding Protein, involved in regulation of cell cycle progression from G1 to S phase. | [39,53] |
D15334 | CPH2 | Transcription factor that positively controls filamentous growth. | |
D01463 | CRZ1 | CRZ1 transcription regulator involved in the regulation of calcium ion homeostasis. | |
D13068 | BUD20 | BUD20 bud site selection protein 20—positioning the proximal bud pole signal; protein required for ribosome assembly. | |
B13354 | AP-4 | Transcription factor that activates viral and cellular genes. | |
F25861 | RPN4 | RPN4 transcription factor regulating proteasomal genes. | |
D24167 | CBF1 | CBF1 centromere binding factor 1, required for chromosome stability and chromosomal segregation. | |
C12639 | SWI6 | SWI6 part of a complex involved in cell-cycle-dependent transcription. SWI4 and SWI6 are required for formation of the cell-cycle box factor-DNA complex | |
E25960 | SWI1 | SWI/SNF chromatin-remodeling complex subunit SWI1. | |
F13321 | OAF1 | Oleate activated transcription factor 1, activates transcription of genes involved in fatty acid beta-oxidation. | |
F11487 | STP1 | Nutrient- and stress-responsive activator of ribosome biogenesis genes. | |
B05478 | STP3 | Possibly involved in pre-tRNA splicing and in uptake of branched-chain amino acids. | [59] |
E15510 | Putative a: Homeobox protein YOX1. | ||
C22990 | Putative a: ASG1 general activator of stress genes. | ||
D04466 | Putative a: Regulatory protein cys-3. Turns on the expression of structural genes which encode sulfur-catabolic enzymes. | ||
D09647 | Putative a: Arginine metabolism regulation protein II. With ARG80, ARG82 and MCM1, coordinates the expression of arginine anabolic and catabolic genes in response to arginine. | ||
D10681 | Putative a: Adhesion and hyphal regulator 1. | ||
D18678 | Putative a: Respiration factor 2. Transcription factor that regulates expression genes required for glycerol-based growth and respiration. | ||
E17721 | Putative a: Phosphatidylinositol N-acetylglucosaminyltransferase subunit P. | ||
E31669 | Putative a: Metal-binding activator 1. Copper ion-sensing transcription factor, promotes filamentous and invasive growth. | ||
F05126 | Putative a: Phosphorus acquisition-controlling protein. | ||
F17468 | Putative a: Multidrug resistance regulator 1. Acts as the central regulator of the MDR1 efflux pump. | ||
E11693 | Putative a: TF required for repression of genes during iron starvation. Represses iron-dependent and mitochondrial-localized activities including respiration, TCA cycle, amino acid metabolism, iron-sulfur-cluster and heme biosynthesis. | ||
E10131 | Putative a: Transcription elongation factor 1. Implicated in the maintenance of proper chromatin structure in actively transcribed regions. | ||
D09757 | Putative a: AP-1-like transcription factor. | ||
F05346 | Putative a: Binds a palindromic promoter element essential for induction of fungal cutinase gene. | ||
C11858 | Putative a: DNA-binding transcription factor Moc3. | ||
B15312 | Putative a: May act as a co-chaperone for HSP70. | ||
C18667 | Putative a: Transcriptional activator of the arabinanolytic system. | ||
E16973 | Putative a: Metallothionein expression activator. | ||
F11979 | Putative a: Retrograde regulation protein 1. | ||
C19063 | Putative a: Transcription factor that mediates stress and developmental response. | ||
F18326, E05577, B08360, C20977, C13794 | Putative a: sterol uptake control. |
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Gorczyca, M.; Korpys-Woźniak, P.; Celińska, E. An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels—The Global View. Int. J. Mol. Sci. 2024, 25, 9450. https://doi.org/10.3390/ijms25179450
Gorczyca M, Korpys-Woźniak P, Celińska E. An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels—The Global View. International Journal of Molecular Sciences. 2024; 25(17):9450. https://doi.org/10.3390/ijms25179450
Chicago/Turabian StyleGorczyca, Maria, Paulina Korpys-Woźniak, and Ewelina Celińska. 2024. "An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels—The Global View" International Journal of Molecular Sciences 25, no. 17: 9450. https://doi.org/10.3390/ijms25179450