Spontaneous mutations that confer resistance to 2-deoxyglucose act through Hxk2 and Snf1 pathways to regulate gene expression and HXT endocytosis

English version

Autoři: Samantha R. Soncini ^aff001; Dakshayini G. Chandrashekarappa ^aff001; David A. Augustine ^aff002; Kenny P. Callahan ^aff002; Allyson F. O’Donnell ^aff002; Martin C. Schmidt ^aff001
Působiště autorů: Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America ^aff001; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America ^aff002; Marlboro College, Marlboro Vermont, United States of America ^aff003
Vyšlo v časopise: Spontaneous mutations that confer resistance to 2-deoxyglucose act through Hxk2 and Snf1 pathways to regulate gene expression and HXT endocytosis. PLoS Genet 16(7): e32767. doi:10.1371/journal.pgen.1008484
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008484

Souhrn

Yeast and fast-growing human tumor cells share metabolic similarities in that both cells use fermentation of glucose for energy and both are highly sensitive to the glucose analog 2-deoxyglucose. Spontaneous mutations in S. cerevisiae that conferred resistance to 2-deoxyglucose were identified by whole genome sequencing. Missense alleles of the HXK2, REG1, GLC7 and SNF1 genes were shown to confer significant resistance to 2-deoxyglucose and all had the potential to alter the activity and or target selection of the Snf1 kinase signaling pathway. All three missense alleles in HXK2 resulted in significantly reduced catalytic activity. Addition of 2DG promotes endocytosis of the glucose transporter Hxt3. All but one of the 2DG-resistant strains reduced the 2DG-mediated hexose transporter endocytosis by increasing plasma membrane occupancy of the Hxt3 protein. Increased expression of the DOG (deoxyglucose) phosphatases has been associated with resistance to 2-deoxyglucose. Expression of both the DOG1 and DOG2 mRNA was elevated after treatment with 2-deoxyglucose but induction of these genes is not associated with 2DG-resistance. RNAseq analysis of the transcriptional response to 2DG showed large scale, genome-wide changes in mRNA abundance that were greatly reduced in the 2DG resistant strains. These findings suggest the common adaptive response to 2DG is to limit the magnitude of the response. Genetic studies of 2DG resistance using the dominant SNF1-G53R allele in cells that are genetically compromised in both the endocytosis and DOG pathways suggest that at least one more mechanism for conferring resistance to this glucose analog remains to be discovered.

Klíčová slova:

Alleles – Dogs – Glucose – Hexokinases – Messenger RNA – Phosphatases – Phosphorylation – Yeast

Zdroje

1. Lunt SY, Vander Heiden MG. Aerobic glycolysis: meeting the metabolic requirements of cell proliferation. Annu Rev Cell Dev Biol. 2011;27:441–64. doi: 10.1146/annurev-cellbio-092910-154237 21985671

2. Kuntz S, Mazerbourg S, Boisbrun M, Cerella C, Diederich M, Grillier-Vuissoz I, et al. Energy restriction mimetic agents to target cancer cells: comparison between 2-deoxyglucose and thiazolidinediones. Biochem Pharmacol. 2014;92(1):102–11. doi: 10.1016/j.bcp.2014.07.021 Epub Jul 30. 25083915

3. Stein M, Lin H, Jeyamohan C, Dvorzhinski D, Gounder M, Bray K, et al. Targeting tumor metabolism with 2-deoxyglucose in patients with castrate-resistant prostate cancer and advanced malignancies. Prostate. 2010;70(13):1388–94. doi: 10.1002/pros.21172 20687211

4. Zimmermann FK, Scheel I. Mutants of Saccharomyces cerevisiae resistant to carbon catabolite repression. Mol Gen Genet. 1977;154(1):75–82. Epub 1977/07/07. doi: 10.1007/BF00265579 197390.

5. Entian KD, Zimmermann FK. Glycolytic enzymes and intermediates in carbon catabolite repression mutants of Saccharomyces cerevisiae. Mol Gen Genet. 1980;177(2):345–50. Epub 1980/01/01. doi: 10.1007/BF00267449 6988675.

6. Neigeborn L, Carlson M. Mutations causing constitutive invertase synthesis in yeast: genetic interactions with snf mutations. Genetics. 1987;115(2):247–53. 3549450.

7. Zimmermann FK, Kaufmann I, Rasenberger H, Haussmann P. Genetics of carbon catabolite repression in Saccharomycess cerevisiae: genes involved in the derepression process. Molecular & General Genetics. 1977;151(1):95–103.

8. McCartney RR, Chandrashekarappa DG, Zhang BB, Schmidt MC. Genetic analysis of resistance and sensitivity to 2-deoxyglucose in Saccharomyces cerevisiae. Genetics. 2014;198:635–46. doi: 10.1534/genetics.114.169060 25116136

9. Ralser M, Wamelink MM, Struys EA, Joppich C, Krobitsch S, Jakobs C, et al. A catabolic block does not sufficiently explain how 2-deoxy-D-glucose inhibits cell growth. Proc Natl Acad Sci U S A. 2008;105(46):17807–11. Epub 2008/11/14. doi: 10.1073/pnas.0803090105 19004802; PubMed Central PMCID: PMC2584745.

10. O'Donnell AF, McCartney RR, Chandrashekarappa DG, Zhang BB, Thorner J, Schmidt MC. 2-Deoxyglucose impairs Saccharomyces cerevisiae growth by stimulating Snf1-regulated and alpha-arrestin-mediated trafficking of hexose transporters 1 and 3. Molecular and cellular biology. 2015;35(6):939–55. Epub 2014/12/31. doi: 10.1128/MCB.01183-14 25547292; PubMed Central PMCID: PMC4333089.

11. Shinoda J, Kikuchi Y. Rod1, an arrestin-related protein, is phosphorylated by Snf1-kinase in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2007;364(2):258–63. Epub 2007/10/24. doi: 10.1016/j.bbrc.2007.09.134 17949685.

12. Wu N, Zheng B, Shaywitz A, Dagon Y, Tower C, Bellinger G, et al. AMPK-dependent degradation of TXNIP upon energy stress leads to enhanced glucose uptake via GLUT1. Mol Cell. 2013;49(6):1167–75. Epub 2013/03/05. doi: 10.1016/j.molcel.2013.01.035 23453806; PubMed Central PMCID: PMC3615143.

13. Randez-Gil F, Blasco A, Prieto JA, Sanz P. DOGR1 and DOGR2: two genes from Saccharomyces cerevisiae that confer 2-deoxyglucose resistance when overexpressed. Yeast. 1995;11(13):1233–40. Epub 1995/10/01. doi: 10.1002/yea.320111303 8553694.

14. Offley SR, Schmidt MC. Protein phosphatases of Saccharomyces cerevisiae. Current genetics. 2018. Epub 2018/09/19. doi: 10.1007/s00294-018-0884-y 30225534.

15. Defenouillere Q, Verraes A, Laussel C, Friedrich A, Schacherer J, Leon S. The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose. Science signaling. 2019;12(597). Epub 2019/09/05. doi: 10.1126/scisignal.aaw8000 31481524.

16. Estruch F, Treitel MA, Yang X, Carlson M. N-terminal mutations modulate yeast SNF1 protein kinase function. Genetics. 1992;132(3):639–50. 1468623

17. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PloS one. 2015;10(5):e0128036. Epub 2015/05/23. doi: 10.1371/journal.pone.0128036 26000737; PubMed Central PMCID: PMC4441430.

18. Pelaez R, Herrero P, Moreno F. Functional domains of yeast hexokinase 2. Biochem J. 2010;432(1):181–90. Epub 2010/09/08. doi: 10.1042/BJ20100663 20815814; PubMed Central PMCID: PMC2995421.

19. Kraakman LS, Winderickx J, Thevelein JM, De Winde JH. Structure-function analysis of yeast hexokinase: structural requirements for triggering cAMP signalling and catabolite repression. Biochem J. 1999;343 Pt 1:159–68. Epub 1999/09/24. 10493925; PubMed Central PMCID: PMC1220537.

20. Hohmann S, Winderickx J, de Winde JH, Valckx D, Cobbaert P, Luyten K, et al. Novel alleles of yeast hexokinase PII with distinct effects on catalytic activity and catabolite repression of SUC2. Microbiology. 1999;145(Pt 3):703–14. doi: 10.1099/13500872-145-3-703 10217505

21. Ma H, Bloom LM, Dakin SE, Walsh CT, Botstein D. The 15 N-terminal amino acids of hexokinase II are not required for in vivo function: analysis of a truncated form of hexokinase II in Saccharomyces cerevisiae. Proteins. 1989;5(3):218–23. Epub 1989/01/01. doi: 10.1002/prot.340050305 2674934.

22. Ma H, Bloom LM, Zhu ZM, Walsh CT, Botstein D. Isolation and characterization of mutations in the HXK2 gene of Saccharomyces cerevisiae. Molecular and cellular biology. 1989;9(12):5630–42. Epub 1989/12/01. doi: 10.1128/mcb.9.12.5630 2685571; PubMed Central PMCID: PMC363734.

23. Ma H, Botstein D. Effects of null mutations in the hexokinase genes of Saccharomyces cerevisiae on catabolite repression. Molecular and cellular biology. 1986;6(11):4046–52. Epub 1986/11/01. doi: 10.1128/mcb.6.11.4046 3540605; PubMed Central PMCID: PMC367170.

24. McCartney RR, Schmidt MC. Regulation of Snf1 kinase. Activation requires phosphorylation of threonine 210 by an upstream kinase as well as a distinct step mediated by the Snf4 subunit. Journal of Biological Chemistry. 2001;276(39):36460–6. doi: 10.1074/jbc.M104418200 11486005

25. Rubenstein EM, McCartney RR, Zhang C, Shokat KM, Shirra MK, Arndt KM, et al. Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. The Journal of biological chemistry. 2008;283(1):222–30. Epub 2007/11/10. doi: 10.1074/jbc.M707957200 17991748; PubMed Central PMCID: PMC3244878.

26. Tu J, Carlson M. The GLC7 type 1 protein phosphatase is required for glucose repression in Saccharomyces cerevisiae. Molecular and cellular biology. 1994;14(10):6789–96. Epub 1994/10/01. doi: 10.1128/mcb.14.10.6789 7935396; PubMed Central PMCID: PMC359209.

27. Shashkova S, Wollman AJM, Leake MC, Hohmann S. The yeast Mig1 transcriptional repressor is dephosphorylated by glucose-dependent and -independent mechanisms. FEMS microbiology letters. 2017;364(14). Epub 2017/09/01. doi: 10.1093/femsle/fnx133 28854669.

28. Dombek KM, Voronkova V, Raney A, Young ET. Functional analysis of the yeast Glc7-binding protein Reg1 identifies a protein phosphatase type 1-binding motif as essential for repression of ADH2 expression. Molecular and cellular biology. 1999;19(9):6029–40. Epub 1999/08/24. doi: 10.1128/mcb.19.9.6029 10454550; PubMed Central PMCID: PMC84497.

29. Tabba S, Mangat S, McCartney R, Schmidt MC. PP1 phosphatase-binding motif in Reg1 protein of Saccharomyces cerevisiae is required for interaction with both the PP1 phosphatase Glc7 and the Snf1 protein kinase. Cell Signal. 2010;22(7):1013–21. Epub 2010/02/23. S0898-6568(10)00056-2 [pii] doi: 10.1016/j.cellsig.2010.02.003 20170726.

30. Tu J, Carlson M. REG1 binds to protein phosphatase type 1 and regulates glucose repression in Saccharomyces cerevisiae. EMBO J. 1995;14(23):5939–46. 8846786

31. Ludin K, Jiang R, Carlson M. Glucose-regulated interaction of a regulatory subunit of protein phosphatase 1 with the Snf1 protein kinase in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1998;95(11):6245–50. Epub 1998/05/30. doi: 10.1073/pnas.95.11.6245 9600950; PubMed Central PMCID: PMC27646.

32. Wiser MJ, Lenski RE. A Comparison of Methods to Measure Fitness in Escherichia coli. PloS one. 2015;10(5):e0126210. Epub 2015/05/12. doi: 10.1371/journal.pone.0126210 25961572; PubMed Central PMCID: PMC4427439.

33. Barrett L, Orlova M, Maziarz M, Kuchin S. Protein kinase A contributes to the negative control of Snf1 protein kinase in Saccharomyces cerevisiae. Eukaryot Cell. 2012;11(2):119–28. Epub 2011/12/06. doi: 10.1128/EC.05061-11 22140226; PubMed Central PMCID: PMC3272905.

34. Feng ZH, Wilson SE, Peng ZY, Schlender KK, Reimann EM, Trumbly RJ. The yeast GLC7 gene required for glycogen accumulation encodes a type 1 protein phosphatase. The Journal of biological chemistry. 1991;266(35):23796–801. Epub 1991/12/15. 1660885.

35. Treitel MA, Carlson M. Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proceedings of the National Academy of Sciences of the United States of America. 1995;92(8):3132–6. doi: 10.1073/pnas.92.8.3132 7724528

36. Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology. 2016;34(5):525–7. Epub 2016/04/05. doi: 10.1038/nbt.3519 27043002.

37. Ozcan S, Johnston M. Three different regulatory mechanisms enable yeast hexose transporter (HXT) genes to be induced by different levels of glucose. Molecular & Cellular Biology. 1995;15(3):1564–72.

38. Ozcan S, Johnston M. Function and regulation of yeast hexose transporters. Microbiol Mol Biol Rev. 1999;63(3):554–69. Epub 1999/09/08. 10477308; PubMed Central PMCID: PMC103746.

39. Zhang Y, McCartney RR, Chandrashekarappa DG, Mangat S, Schmidt MC. Reg1 protein regulates phosphorylation of all three Snf1 isoforms but preferentially associates with the Gal83 isoform. Eukaryot Cell. 2011;10(12):1628–36. Epub 2011/10/18. doi: 10.1128/EC.05176-11 22002657; PubMed Central PMCID: PMC3232714.

40. Leech A, Nath N, McCartney RR, Schmidt MC. Isolation of mutations in the catalytic domain of the snf1 kinase that render its activity independent of the snf4 subunit. Eukaryot Cell. 2003;2(2):265–73. doi: 10.1128/ec.2.2.265-273.2003 12684376.

41. Chandrashekarappa DG, McCartney RR, O'Donnell AF, Schmidt MC. The beta subunit of yeast AMP-activated protein kinase directs substrate specificity in response to alkaline stress. Cell Signal. 2016;28(12):1881–93. doi: 10.1016/j.cellsig.2016.08.016 Epub Aug 31. 27592031

42. Boukouris AE, Zervopoulos SD, Michelakis ED. Metabolic Enzymes Moonlighting in the Nucleus: Metabolic Regulation of Gene Transcription. Trends Biochem Sci. 2016;41(8):712–30. doi: 10.1016/j.tibs.2016.05.013 Epub Jun 23. 27345518

43. Fernandez-Garcia P, Pelaez R, Herrero P, Moreno F. Phosphorylation of yeast hexokinase 2 regulates its nucleocytoplasmic shuttling. The Journal of biological chemistry. 2012;287(50):42151–64. Epub 2012/10/16. doi: 10.1074/jbc.M112.401679 23066030; PubMed Central PMCID: PMC3516761.

44. Fernandez R, Herrero P, Fernandez E, Fernandez T, Lopez-Boado YS, Moreno F. Autophosphorylation of yeast hexokinase PII. Journal of general microbiology. 1988;134(9):2493–8. Epub 1988/09/01. doi: 10.1099/00221287-134-9-2493 3076185.

45. Herrero P, Fernandez R, Moreno F. The hexokinase isoenzyme PII of Saccharomyces cerevisiae ia a protein kinase. Journal of general microbiology. 1989;135(5):1209–16. Epub 1989/05/01. doi: 10.1099/00221287-135-5-1209 2559946.

46. Herrero P, Martinez-Campa C, Moreno F. The hexokinase 2 protein participates in regulatory DNA-protein complexes necessary for glucose repression of the SUC2 gene in Saccharomyces cerevisiae. FEBS letters. 1998;434(1–2):71–6. Epub 1998/09/17. doi: 10.1016/s0014-5793(98)00872-2 9738454.

47. Amigoni L, Martegani E, Colombo S. Lack of HXK2 induces localization of active Ras in mitochondria and triggers apoptosis in the yeast Saccharomyces cerevisiae. Oxidative medicine and cellular longevity. 2013;2013:678473. Epub 2013/10/04. doi: 10.1155/2013/678473 24089630; PubMed Central PMCID: PMC3780702.

48. Yao Y, Tsuchiyama S, Yang C, Bulteau AL, He C, Robison B, et al. Proteasomes, Sir2, and Hxk2 form an interconnected aging network that impinges on the AMPK/Snf1-regulated transcriptional repressor Mig1. PLoS genetics. 2015;11(1):e1004968. Epub 2015/01/30. doi: 10.1371/journal.pgen.1004968 25629410; PubMed Central PMCID: PMC4309596.

49. Mulichak AM, Wilson JE, Padmanabhan K, Garavito RM. The structure of mammalian hexokinase-1. Nat Struct Biol. 1998;5(7):555–60. doi: 10.1038/811 9665168

50. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999;285(5429):901–6. doi: 10.1126/science.285.5429.901 10436161.

51. Rose MD, Winston F, Hieter P, editors. Methods in Yeast Genetics. Cold Spring Harbor: Cold Spring Harbor Laboratory; 1990.

52. Birkeland SR, Jin N, Ozdemir AC, Lyons RH Jr., Weisman LS, Wilson TE. Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing. Genetics. 2010;186(4):1127–37. Epub 2010/10/07. doi: 10.1534/genetics.110.123232 20923977; PubMed Central PMCID: PMC2998298.

53. Hoffman CS, Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 1987;57(2–3):267–72. Epub 1987/01/01. doi: 10.1016/0378-1119(87)90131-4 3319781.

54. Fisher CL, Pei GK. Modification of a PCR-based site-directed mutagenesis method. Biotechniques. 1997;23(4):570–4. Epub 1997/10/31. doi: 10.2144/97234bm01 9343663.

55. Southern JA, Young DF, Heaney F, Baumgartner WK, Randall RE. Identification of an epitope on the P and V proteins of simian virus 5 that distinguishes between two isolates with different biological characteristics. Journal of General Virology. 1991;72 (Pt 7):1551–7. doi: 10.1099/0022-1317-72-7-1551 1713260.

56. Sikorski RS, Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989;122(1):19–27. 2659436.

57. Goldstein A, Lampen JO. ß-D-Fructofuranoside fructohydrolase from yeast. Methods Enzymol. 1975;42C:504–11.

58. Zhang Y, Nijbroek G, Sullivan ML, McCracken AA, Watkins SC, Michaelis S, et al. Hsp70 molecular chaperone facilitates endoplasmic reticulum-associated protein degradation of cystic fibrosis transmembrane conductance regulator in yeast. Mol Biol Cell. 2001;12(5):1303–14. Epub 2001/05/22. doi: 10.1091/mbc.12.5.1303 11359923; PubMed Central PMCID: PMC34585.

59. McCartney RR, Garnar-Wortzel L, Chandrashekarappa DG, Schmidt MC. Activation and inhibition of Snf1 kinase activity by phosphorylation within the activation loop. Biochimica et biophysica acta. 2016;1864(11):1518–28. Epub 2016/08/16. doi: 10.1016/j.bbapap.2016.08.007 27524664; PubMed Central PMCID: PMC5018454.

60. Desai P, Person S. Molecular interactions between the HSV-1 capsid proteins as measured by the yeast two-hybrid system. Virology. 1996;220(2):516–21. Epub 1996/06/15. S0042-6822(96)90341-4 [pii] doi: 10.1006/viro.1996.0341 8661404.

61. Bartel PL, Fields S. Analyzing protein-protein interactions using two-hybrid system. Methods Enzymol. 1995;254:241–63. Epub 1995/01/01. doi: 10.1016/0076-6879(95)54018-0 8531690.

Článek A non-canonical RNAi pathway controls virulence and genome stability in Mucorales

Článek TaTLP1 interacts with TaPR1 to contribute to wheat defense responses to leaf rust fungus

Článek Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits

Článek Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat

Článek Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication

Článek Predicting longevity responses to dietary restriction: A stepping stone toward precision geroscience

Článek Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila

Článek Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host

Článek Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

Článek Brassinosteroids regulate root meristem development by mediating BIN2-UPB1 module in Arabidopsis

Článek The membrane protein ANKH is crucial for bone mechanical performance by mediating cellular export of citrate and ATP

Článek A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata