During development of yeast colonies, various cell subpopulations form, which differ in their properties and specifically localize within the structure. Three branches of mitochondrial retrograde (RTG) signaling play a role in colony development and differentiation, each of them activating the production of specific markers in different cell types. Here, aiming to identify proteins and processes controlled by the RTG pathway, we analyzed proteomes of individual cell subpopulations from colonies of strains, mutated in genes of the RTG pathway. Resulting data, along with microscopic analyses revealed that the RTG pathway predominantly regulates processes in U cells, long-lived cells with unique properties, which are localized in upper colony regions. Rtg proteins therein activate processes leading to amino acid biosynthesis, including transport of metabolic intermediates between compartments, but also repress expression of mitochondrial ribosome components, thus possibly contributing to reduced mitochondrial translation in U cells. The results reveal the RTG pathway's role in activating metabolic processes, important in U cell adaptation to altered nutritional conditions. They also point to the important role of Rtg regulators in repressing mitochondrial activity in U cells.

Department of Genetics and Microbiology Faculty of Science Charles University BIOCEV 12800 Prague Czech Republic

Institute of Microbiology of the Czech Academy of Sciences BIOCEV 14220 Prague Czech Republic

Zobrazit více v PubMed

Guha M., Avadhani N.G. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion. 2013;13:577–591. doi: 10.1016/j.mito.2013.08.007. PubMed DOI PMC

Jazwinski S.M. The retrograde response: A conserved compensatory reaction to damage from within and from without. Prog. Mol. Biol. Transl. Sci. 2014;127:133–154. PubMed PMC

Liu Z., Butow R.A. Mitochondrial retrograde signaling. Annu. Rev. Genet. 2006;40:159–185. doi: 10.1146/annurev.genet.40.110405.090613. PubMed DOI

Ferreira Junior J.R., Spirek M., Liu Z., Butow R.A. Interaction between Rtg2p and Mks1p in the regulation of the RTG pathway of Saccharomyces cerevisiae. Gene. 2005;354:2–8. doi: 10.1016/j.gene.2005.03.048. PubMed DOI

Liu Z., Sekito T., Spirek M., Thornton J., Butow R.A. Retrograde signaling is regulated by the dynamic interaction between Rtg2p and Mks1p. Mol. Cell. 2003;12:401–411. doi: 10.1016/S1097-2765(03)00285-5. PubMed DOI

Dilova I., Aronova S., Chen J.C., Powers T. Tor signaling and nutrient-based signals converge on Mks1p phosphorylation to regulate expression of Rtg1.Rtg3p-dependent target genes. J. Biol. Chem. 2004;279:46527–46535. doi: 10.1074/jbc.M409012200. PubMed DOI

Dilova I., Chen C.Y., Powers T. Mks1 in concert with TOR signaling negatively regulates RTG target gene expression in S. cerevisiae. Curr. Biol. 2002;12:389–395. doi: 10.1016/S0960-9822(02)00677-2. PubMed DOI

Chelstowska A., Butow R.A. RTG genes in yeast that function in communication between mitochondria and the nucleus are also required for expression of genes encoding peroxisomal proteins. J. Biol. Chem. 1995;270:18141–18146. doi: 10.1074/jbc.270.30.18141. PubMed DOI

Epstein C.B., Waddle J.A., Hale IV W., Dave V., Thornton J., Macatee T.L., Garner H.R., Butow R.A. Genome-wide responses to mitochondrial dysfunction. Mol. Biol. Cell. 2001;12:297–308. doi: 10.1091/mbc.12.2.297. PubMed DOI PMC

Guaragnella N., Coyne L.P., Chen X.J., Giannattasio S. Mitochondria-cytosol-nucleus crosstalk: Learning from Saccharomyces cerevisiae. FEMS Yeast Res. 2018;18:foy088. doi: 10.1093/femsyr/foy088. PubMed DOI PMC

Palkova Z., Vachova L. Yeast cell differentiation: Lessons from pathogenic and non-pathogenic yeasts. Semin. Cell Dev. Biol. 2016;57:110–119. doi: 10.1016/j.semcdb.2016.04.006. PubMed DOI

Vachova L., Palkova Z. How structured yeast multicellular communities live, age and die? FEMS Yeast Res. 2018;18:foy033. doi: 10.1093/femsyr/foy033. PubMed DOI

Podholová K., Plocek V., Rešetárová S., Kučerová H., Hlaváček O., Váchová L., Palková Z. Divergent branches of mitochondrial signaling regulate specific genes and the viability of specialized cell types of differentiated yeast colonies. Oncotarget. 2016;7:15299–15314. doi: 10.18632/oncotarget.8084. PubMed DOI PMC

Cap M., Stepanek L., Harant K., Vachova L., Palkova Z. Cell differentiation within a yeast colony: Metabolic and regulatory parallels with a tumor-affected organism. Mol. Cell. 2012;46:436–448. doi: 10.1016/j.molcel.2012.04.001. PubMed DOI

Palkova Z., Devaux F., Ricicova M., Minarikova L., Le Crom S., Jacq C. Ammonia pulses and metabolic oscillations guide yeast colony development. Mol. Biol. Cell. 2002;13:3901–3914. doi: 10.1091/mbc.e01-12-0149. PubMed DOI PMC

Palkova Z., Janderova B., Gabriel J., Zikanova B., Pospisek M., Forstova J. Ammonia mediates communication between yeast colonies. Nature. 1997;390:532–536. doi: 10.1038/37398. PubMed DOI

Vachova L., Hatakova L., Cap M., Pokorna M., Palkova Z. Rapidly developing yeast microcolonies differentiate in a similar way to aging giant colonies. Oxid. Med. Cell Longev. 2013;2013:102485. doi: 10.1155/2013/102485. PubMed DOI PMC

Cap M., Vachova L., Palkova Z. Longevity of U cells of differentiated yeast colonies grown on respiratory medium depends on active glycolysis. Cell Cycle. 2015;14:3488–3497. doi: 10.1080/15384101.2015.1093706. PubMed DOI PMC

Franken J., Kroppenstedt S., Swiegers J.H., Bauer F.F. Carnitine and carnitine acetyltransferases in the yeast Saccharomyces cerevisiae: A role for carnitine in stress protection. Curr. Genet. 2008;53:347–360. doi: 10.1007/s00294-008-0191-0. PubMed DOI

Van Rossum H.M., Kozak B.U., Niemeijer M.S., Duine H.J., Luttik M.A., Boer V.M., Kotter P., Daran J.M., van Maris A.J., Pronk J.T. Alternative reactions at the interface of glycolysis and citric acid cycle in Saccharomyces cerevisiae. FEMS Yeast Res. 2016;16:fow017. doi: 10.1093/femsyr/fow017. PubMed DOI PMC

Xiberras J., Klein M., Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses—Knowledge gaps regarding the central carbon catabolism of this ‘non-fermentable’ carbon source. Biotechnol. Adv. 2019;37:107378. doi: 10.1016/j.biotechadv.2019.03.017. PubMed DOI

Xiberras J., Klein M., Prosch C., Malubhoy Z., Nevoigt E. Anaplerotic reactions active during growth of Saccharomyces cerevisiae on glycerol. FEMS Yeast Res. 2020;20:foz086. doi: 10.1093/femsyr/foz086. PubMed DOI

Graybill E.R., Rouhier M.F., Kirby C.E., Hawes J.W. Functional comparison of citrate synthase isoforms from S. cerevisiae. Arch. Biochem. Biophys. 2007;465:26–37. doi: 10.1016/j.abb.2007.04.039. PubMed DOI

Nakatsukasa K., Nishimura T., Byrne S.D., Okamoto M., Takahashi-Nakaguchi A., Chibana H., Okumura F., Kamura T. The ubiquitin ligase SCF(Ucc1) acts as a metabolic switch for the glyoxylate cycle. Mol. Cell. 2015;59:22–34. doi: 10.1016/j.molcel.2015.04.013. PubMed DOI

Liu Z., Butow R.A. A transcriptional switch in the expression of yeast tricarboxylic acid cycle genes in response to a reduction or loss of respiratory function. Mol. Cell Biol. 1999;19:6720–6728. doi: 10.1128/MCB.19.10.6720. PubMed DOI PMC

Schuller H.J. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr. Genet. 2003;43:139–160. doi: 10.1007/s00294-003-0381-8. PubMed DOI

Becker-Kettern J., Paczia N., Conrotte J.F., Kay D.P., Guignard C., Jung P.P., Linster C.L. Saccharomyces cerevisiae forms D-2-Hydroxyglutarate and couples its degradation to D-lactate formation via a cytosolic transhydrogenase. J. Biol. Chem. 2016;291:6036–6058. doi: 10.1074/jbc.M115.704494. PubMed DOI PMC

Pallotta M.L. Mitochondrial involvement to methylglyoxal detoxification: D-Lactate/Malate antiporter in Saccharomyces cerevisiae. Antonie Van Leeuwenhoek. 2012;102:163–175. doi: 10.1007/s10482-012-9724-0. PubMed DOI

De Bari L., Atlante A., Armeni T., Kalapos M.P. Synthesis and metabolism of methylglyoxal, S-D-lactoylglutathione and D-lactate in cancer and Alzheimer’s disease. Exploring the crossroad of eternal youth and premature aging. Ageing Res. Rev. 2019;53:100915. doi: 10.1016/j.arr.2019.100915. PubMed DOI

Stewart B.J., Navid A., Kulp K.S., Knaack J.L., Bench G. D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae. Yeast. 2013;30:81–91. doi: 10.1002/yea.2942. PubMed DOI PMC

Passarella S., Schurr A. l-Lactate transport and metabolism in mitochondria of Hep G2 cells-The Cori cycle revisited. Front. Oncol. 2018;8:120. doi: 10.3389/fonc.2018.00120. PubMed DOI PMC

Dilova I., Powers T. Accounting for strain-specific differences during RTG target gene regulation in Saccharomyces cerevisiae. FEMS Yeast Res. 2006;6:112–119. doi: 10.1111/j.1567-1364.2005.00008.x. PubMed DOI

Tate J.J., Cox K.H., Rai R., Cooper T.G. Mks1p is required for negative regulation of retrograde gene expression in Saccharomyces cerevisiae but does not affect nitrogen catabolite repression-sensitive gene expression. J. Biol. Chem. 2002;277:20477–20482. doi: 10.1074/jbc.M200962200. PubMed DOI PMC

Giannattasio S., Liu Z., Thornton J., Butow R.A. Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression. J. Biol. Chem. 2005;280:42528–42535. doi: 10.1074/jbc.M509187200. PubMed DOI

Sekito T., Thornton J., Butow R.A. Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Mol. Biol. Cell. 2000;11:2103–2115. doi: 10.1091/mbc.11.6.2103. PubMed DOI PMC

Palkova Z., Wilkinson D., Vachova L. Aging and differentiation in yeast populations: Elders with different properties and functions. FEMS Yeast Res. 2014;14:96–108. doi: 10.1111/1567-1364.12103. PubMed DOI

Wilkinson D., Marsikova J., Hlavacek O., Gilfillan G.D., Jezkova E., Aaløkken R., Vachova L., Palkova Z. Transcriptome remodeling of differentiated cells during chronological ageing of yeast colonies: New insights into metabolic differentiation. Oxid. Med. Cell Longev. 2018;2018:4932905. doi: 10.1155/2018/4932905. PubMed DOI PMC

Ihmels J., Friedlander G., Bergmann S., Sarig O., Ziv Y., Barkai N. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 2002;31:370–377. doi: 10.1038/ng941. PubMed DOI

Graack H.R., Wittmann-Liebold B. Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem. J. 1998;329:433–448. doi: 10.1042/bj3290433. PubMed DOI PMC

Lai L.C., Kosorukoff A.L., Burke P.V., Kwast K.E. Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell. 2006;5:1468–1489. doi: 10.1128/EC.00107-06. PubMed DOI PMC

Kim H.J., Maiti P., Barrientos A. Mitochondrial ribosomes in cancer. Semin. Cancer Biol. 2017;47:67–81. doi: 10.1016/j.semcancer.2017.04.004. PubMed DOI PMC

Sheff M.A., Thorn K.S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast. 2004;21:661–670. doi: 10.1002/yea.1130. PubMed DOI

Guldener U., Heck S., Fielder T., Beinhauer J., Hegemann J.H. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 1996;24:2519–2524. doi: 10.1093/nar/24.13.2519. PubMed DOI PMC

Gietz R.D., Woods R.A. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 2002;350:87–96. PubMed

Vachova L., Chernyavskiy O., Strachotova D., Bianchini P., Burdikova Z., Fercikova I., Kubinova L., Palkova Z. Architecture of developing multicellular yeast colony: Spatio-temporal expression of Ato1p ammonium exporter. Environ. Microbiol. 2009;11:1866–1877. doi: 10.1111/j.1462-2920.2009.01911.x. PubMed DOI

Vachova L., Stovicek V., Hlavacek O., Chernyavskiy O., Stepanek L., Kubinova L., Palkova Z. Flo11p, drug efflux pumps, and the extracellular matrix cooperate to form biofilm yeast colonies. J. Cell Biol. 2011;194:679–687. doi: 10.1083/jcb.201103129. PubMed DOI PMC

Marsikova J., Pavlickova M., Wilkinson D., Vachova L., Hlavacek O., Hatakova L., Palkova Z. The Whi2p-Psr1p/Psr2p complex regulates interference competition and expansion of cells with competitive advantage in yeast colonies. Proc. Natl. Acad. Sci. USA. 2020;117:15123–15131. doi: 10.1073/pnas.1922076117. PubMed DOI PMC

Hughes C.S., Moggridge S., Muller T., Sorensen P.H., Morin G.B., Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat. Protoc. 2019;14:68–85. doi: 10.1038/s41596-018-0082-x. PubMed DOI

Vachova L., Kucerova H., Devaux F., Ulehlova M., Palkova Z. Metabolic diversification of cells during the development of yeast colonies. Environ. Microbiol. 2009;11:494–504. doi: 10.1111/j.1462-2920.2008.01789.x. PubMed DOI

Differential stability of Gcn4p controls its cell-specific activity in differentiated yeast colonies

Spatially structured yeast communities: Understanding structure formation and regulation with omics tools