Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Genetic investigation of formaldehyde-induced DNA damage response in Schizosaccharomyces pombe


Formaldehyde is a common environmental pollutant and is associated with adverse health effects. Formaldehyde is also considered to be a carcinogen because it can form DNA adducts, leading to genomic instability. How these adducts are prevented and removed is not fully understood. In this study, we used the fission yeast Schizosaccharomyces pombe as a model organism to investigate cellular tolerance pathways against formaldehyde exposure. We show that Fmd1 is a major formaldehyde dehydrogenase that functions to detoxify formaldehyde and that Fmd1 is critical to minimize formaldehyde-mediated DNA lesions. Our investigation revealed that nucleotide excision repair and homologous recombination have major roles in cellular tolerance to formaldehyde, while mutations in the Fanconi anemia, translesion synthesis, and base excision repair pathways also render cells sensitive to formaldehyde. We also demonstrate that loss of Wss1 or Wss2, proteases involved in the removal of DNA–protein crosslinks, sensitizes cells to formaldehyde and leads to replication defects. These results suggest that formaldehyde generates a variety of DNA lesions, including interstrand crosslinks, DNA–protein crosslinks, and base adducts. Thus, our genetic studies provide a framework for future investigation regarding health effects resulting from formaldehyde exposure.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7



Base excision repair


DNA–protein crosslink


Fanconi anemia


Fork protection complex


Homologous recombination


Interstrand crosslink


Nucleotide excision repair


Translesion synthesis


  1. Alfa C, Fantes P, Hyams J, McLeod M, Warbrick E (1993) Experiments with fission yeast: a laboratory course manual cold spring harbor laboratory press, Cold Spring Harbor, NY

  2. al-Khodairy F, Fotou E, Sheldrick KS, Griffiths DJ, Lehmann AR, Carr AM (1994) Identification and characterization of new elements involved in checkpoint and feedback controls in fission yeast. Mol Biol Cell 5:147–160

  3. Ansbach AB, Noguchi C, Klansek IW, Heidlebaugh M, Nakamura TM, Noguchi E (2008) RFCCtf18 and the Swi1-Swi3 complex function in separate and redundant pathways required for the stabilization of replication forks to facilitate sister chromatid cohesion in Schizosaccharomyces pombe. Mol Biol Cell 19:595–607.

  4. Baber-Furnari BA, Rhind N, Boddy MN, Shanahan P, Lopez-Girona A, Russell P (2000) Regulation of mitotic inhibitor Mik1 helps to enforce the DNA damage checkpoint. Mol Biol Cell 11:1–11

  5. Brooks PJ, Zakhari S (2014) Acetaldehyde and the genome: beyond nuclear DNA adducts and carcinogenesis. Environ Mol Mutagen 55:77–91.

  6. Carr AM, Schmidt H, Kirchhoff S, Muriel WJ, Sheldrick KS, Griffiths DJ, Basmacioglu CN, Subramani S, Clegg M, Nasim A et al (1994) The rad16 gene of Schizosaccharomyces pombe: a homolog of the RAD1 gene of Saccharomyces cerevisiae. Mol Cell Biol 14:2029–2040

  7. Ceccaldi R, Sarangi P, D'Andrea AD (2016) The Fanconi anaemia pathway: new players and new functions. Nat Rev Mol Cell Biol 17:337–349.

  8. Corcoles-Saez I, Dong K, Cha RS (2019) Versatility of the Mec1(ATM/ATR) signaling network in mediating resistance to replication, genotoxic, and proteotoxic stresses. Curr Genet 65:657–661.

  9. Corkins ME, May M, Ehrensberger KM, Hu YM, Liu YH, Bloor SD, Jenkins B, Runge KW, Bird AJ (2013) Zinc finger protein Loz1 is required for zinc-responsive regulation of gene expression in fission yeast. Proc Natl Acad Sci USA 110:15371–15376.

  10. Coulon S, Gaillard PHL, Chahwan C, McDonald WH, Yates JR 3rd, Russell P (2004) Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell 15:71–80.

  11. de Graaf B, Clore A, McCullough AK (2009) Cellular pathways for DNA repair and damage tolerance of formaldehyde-induced DNA-protein crosslinks. DNA Repair 8:1207–1214.

  12. Duxin JP, Dewar JM, Yardimci H, Walter JC (2014) Repair of a DNA-protein crosslink by replication-coupled proteolysis. Cell 159:346–357.

  13. Fontebasso Y, Etheridge TJ, Oliver AW, Murray JM, Carr AM (2013) The conserved Fanconi anemia nuclease Fan1 and the SUMO E3 ligase Pli1 act in two novel Pso2-independent pathways of DNA interstrand crosslink repair in yeast. DNA Repair 12:1011–1023.

  14. Forsburg SL, Rhind N (2006) Basic methods for fission yeast. Yeast 23:173–183.

  15. Gadaleta MC, Das MM, Tanizawa H, Chang YT, Noma K, Nakamura TM, Noguchi E (2016) Swi1timeless prevents repeat instability at fission yeast telomeres. PLoS Genet 12:e1005943.

  16. Hoffman CS, Wood V, Fantes PA (2015) An ancient yeast for young geneticists: a primer on the Schizosaccharomyces pombe model system. Genetics 201:403–423.

  17. Hustedt N, Gasser SM, Shimada K (2013) Replication checkpoint: tuning and coordination of replication forks in s phase. Genes 4:388–434.

  18. Iborra FJ, Renau-Piqueras J, Portoles M, Boleda MD, Guerri C, Pares X (1992) Immunocytochemical and biochemical demonstration of formaldhyde dehydrogenase (class III alcohol dehydrogenase) in the nucleus. J Histochem Cytochem 40:1865–1878.

  19. IARC (2004) IARC classifies formaldehyde as carcinogenic to humans

  20. Kawanishi M, Matsuda T, Yagi T (2014) Genotoxicity of formaldehyde: molecular basis of DNA damage and mutation. Front Environ Sci 2:36

  21. Klages-Mundt NL, Li L (2017) Formation and repair of DNA-protein crosslink damage. Sci China Life Sci 60:1065–1076.

  22. Krawchuk MD, Wahls WP (1999) High-efficiency gene targeting in Schizosaccharomyces pombe using a modular, PCR-based approach with long tracts of flanking homology. Yeast 15:1419–1427.;2-q

  23. Lambert S, Watson A, Sheedy DM, Martin B, Carr AM (2005) Gross chromosomal rearrangements and elevated recombination at an inducible site-specific replication fork barrier. Cell 121:689–702.

  24. Lopez-Mosqueda J, Maddi K, Prgomet S, Kalayil S, Marinovic-Terzic I, Terzic J, Dikic I (2016) SPRTN is a mammalian DNA-binding metalloprotease that resolves DNA-protein crosslinks. Elife 510.7554:eLife.21491

  25. Lu K, Ye W, Zhou L, Collins LB, Chen X, Gold A, Ball LM, Swenberg JA (2010) Structural characterization of formaldehyde-induced cross-links between amino acids and deoxynucleosides and their oligomers. J Am Chem Soc 132:3388–3399.

  26. Luch A, Frey FC, Meier R, Fei J, Naegeli H (2014) Low-dose formaldehyde delays DNA damage recognition and DNA excision repair in human cells. PLoS ONE 9:e94149.

  27. Moreno S, Klar A, Nurse P (1991) Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol 194:795–823

  28. Moriel-Carretero M, Pasero P, Pardo B (2019) DDR Inc., one business, two associates. Curr Genet 65:445–451.

  29. Nakano T, Morishita S, Katafuchi A, Matsubara M, Horikawa Y, Terato H, Salem AM, Izumi S, Pack SP, Makino K, Ide H (2007) Nucleotide excision repair and homologous recombination systems commit differentially to the repair of DNA-protein crosslinks. Mol Cell 28:147–158.

  30. Nakano T, Katafuchi A, Matsubara M, Terato H, Tsuboi T, Masuda T, Tatsumoto T, Pack SP, Makino K, Croteau DL, Van Houten B, Iijima K, Tauchi H, Ide H (2009) Homologous recombination but not nucleotide excision repair plays a pivotal role in tolerance of DNA-protein cross-links in mammalian cells. J Biol Chem 284:27065–27076.

  31. Nandi S, Whitby MC (2012) The ATPase activity of Fml1 is essential for its roles in homologous recombination and DNA repair. Nucleic Acids Res 40:9584–9595.

  32. Noguchi E (2010) The DNA Replication Checkpoint and Preserving Genomic Integrity During DNA Synthesis. Nature Educ 3:46

  33. Noguchi E, Noguchi C, Du LL, Russell P (2003) Swi1 prevents replication fork collapse and controls checkpoint kinase Cds1. Mol Cell Biol 23:7861–7874

  34. Noguchi E, Ansbach AB, Noguchi C, Russell P (2009) Assays used to study the DNA replication checkpoint in fission yeast. Methods Mol Biol 521:493–507.

  35. Noguchi C, Rapp JB, Skorobogatko YV, Bailey LD, Noguchi E (2012) Swi1 associates with chromatin through the DDT domain and recruits Swi3 to preserve genomic integrity. PLoS ONE 7:e43988.

  36. Noguchi C, Grothusen G, Anandarajan V, Martinez-Lage Garcia M, Terlecky D, Corzo K, Tanaka K, Nakagawa H, Noguchi E (2017) Genetic controls of DNA damage avoidance in response to acetaldehyde in fission yeast. Cell Cycle 16:45–58.

  37. Pommier Y (2006) Topoisomerase I inhibitors: camptothecins and beyond. Nat Rev Cancer 6:789–802.

  38. Pommier Y, Barcelo JM, Rao VA, Sordet O, Jobson AG, Thibaut L, Miao ZH, Seiler JA, Zhang H, Marchand C, Agama K, Nitiss JL, Redon C (2006) Repair of topoisomerase I-mediated DNA damage. Prog Nucleic Acid Res Mol Biol 81:179–229.

  39. Pontel LB, Rosado IV, Burgos-Barragan G, Garaycoechea JI, Yu R, Arends MJ, Chandrasekaran G, Broecker V, Wei W, Liu L, Swenberg JA, Crossan GP, Patel KJ (2015) Endogenous formaldehyde is a hematopoietic stem cell genotoxin and metabolic carcinogen. Mol Cell 60:177–188.

  40. Rapp JB, Noguchi C, Das MM, Wong LK, Ansbach AB, Holmes AM, Arcangioli B, Noguchi E (2010) Checkpoint-dependent and -independent roles of Swi3 in replication fork recovery and sister chromatid cohesion in fission yeast. PLoS ONE 5:e13379.

  41. Ren X, Ji Z, McHale CM, Yuh J, Bersonda J, Tang M, Smith MT, Zhang L (2013) The impact of FANCD2 deficiency on formaldehyde-induced toxicity in human lymphoblastoid cell lines. Arch Toxicol 87:189–196.

  42. Rodel C, Kirchhoff S, Schmidt H (1992) The protein sequence and some intron positions are conserved between the switching gene swi10 of Schizosaccharomyces pombe and the human excision repair gene ERCC1. Nucleic Acids Res 20:6347–6353

  43. Rosado IV, Langevin F, Crossan GP, Takata M, Patel KJ (2011) Formaldehyde catabolism is essential in cells deficient for the Fanconi anemia DNA-repair pathway. Nat Struct Mol Biol 18:1432–1434.

  44. Schmidt H, Kapitza-Fecke P, Stephen ER, Gutz H (1989) Some of the swi genes of Schizosaccharomyces pombe also have a function in the repair of radiation damage. Curr Genet 16:89–94.

  45. Sheedy DM, Dimitrova D, Rankin JK, Bass KL, Lee KM, Tapia-Alveal C, Harvey SH, Murray JM, O'Connell MJ (2005) Brc1-mediated DNA repair and damage tolerance. Genetics 171:457–468.

  46. Stingele J, Schwarz MS, Bloemeke N, Wolf PG, Jentsch S (2014) A DNA-dependent protease involved in DNA-protein crosslink repair. Cell 158:327–338.

  47. Stingele J, Bellelli R, Alte F, Hewitt G, Sarek G, Maslen SL, Tsutakawa SE, Borg A, Kjaer S, Tainer JA, Skehel JM, Groll M, Boulton SJ (2016) Mechanism and regulation of DNA-protein crosslink repair by the DNA-dependent metalloprotease SPRTN. Mol Cell 64:688–703.

  48. Sugimoto T, Igawa E, Tanihigashi H, Matsubara M, Ide H, Ikeda S (2005) Roles of base excision repair enzymes Nth1p and Apn2p from Schizosaccharomyces pombe in processing alkylation and oxidative DNA damage. DNA Repair 4:1270–1280.

  49. Swenberg JA, Kerns WD, Mitchell RI, Gralla EJ, Pavkov KL (1980) Induction of squamous cell carcinomas of the rat nasal cavity by inhalation exposure to formaldehyde vapor. Cancer Res 40:3398–3402

  50. Swenberg JA, Moeller BC, Lu K, Rager JE, Fry RC, Starr TB (2013) Formaldehyde carcinogenicity research: 30 years and counting for mode of action, epidemiology, and cancer risk assessment. Toxicol Pathol 41:181–189.

  51. Vaz B, Popovic M, Newman JA, Fielden J, Aitkenhead H, Halder S, Singh AN, Vendrell I, Fischer R, Torrecilla I, Drobnitzky N, Freire R, Amor DJ, Lockhart PJ, Kessler BM, McKenna GW, Gileadi O, Ramadan K (2016) Metalloprotease SPRTN/DVC1 orchestrates replication-coupled DNA-protein crosslink repair. Mol Cell 64:704–719.

  52. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Dusterhoft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880.

Download references


We thank Drs. Amanda Bird, Shogo Ikeda, Matthew O’Connel, Matthew Whitby, and National BioResource Project Japan for S. pombe strains. We also thank Sofia Acchione for technical assistance. The members of the Noguchi laboratory are thanked for their support and encouragement. This work was supported by Drexel University College of Medicine and the Aging Initiative at Drexel University College of Medicine (to E.N.).

Author information

Correspondence to Eishi Noguchi.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Communicated by M. Kupiec.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Anandarajan, V., Noguchi, C., Oleksak, J. et al. Genetic investigation of formaldehyde-induced DNA damage response in Schizosaccharomyces pombe. Curr Genet (2020).

Download citation


  • Formaldehyde
  • Environmental toxin
  • Formaldehyde dehydrogenase
  • Fmd1
  • DNA damage
  • DNA repair
  • Replication fork
  • Crosslink
  • Interstrand crosslink
  • ICL
  • DNA–protein crosslink
  • DPC
  • Fanconi anemia
  • Nucleotide excision repair
  • NER
  • Base excision repair