Skip to main content

Hydrophobic Modifications of Biomolecules: An Introduction

  • Reference work entry
  • First Online:
Cellular Ecophysiology of Microbe: Hydrocarbon and Lipid Interactions

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

  • 945 Accesses

Abstract

Nucleic acids and proteins, the biomolecules that carry all necessary information for life in the cell, undergo very often modifications in the primary coding elements of their sequences. Some of the bases in the DNA and RNA and the majority of the amino acids in the protein can incorporate new functional groups through a covalent addition. By means of these modifications, the genetically encoded functions of active proteins or the expression patterns of the DNA are affected, leading to changes at the physiological level. These modifications are generally catalyzed by one of the most abundant enzyme families in the cell, the transferases. The importance of this enzyme family is evidenced by the fact that many of them are subject to a strict regulation since they are implicated in key cellular mechanisms. Most of these modifications cause a local increase in hydrophobicity at the biomolecule that leads to changes in protein-protein and protein-nucleic acid interactions. A relevant example for nucleic acid modification is the methylation, while alkylation, lipidation, acetylation, and ubiquitination are frequent hydrophobic modifications of proteins.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bah A, Forman-Kay JD (2016) Modulation of intrinsically disordered protein function by post-translational modifications. J Biol Chem 291(13):6696–6705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biggar KK, Li SS (2015) Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 16(1):5–17

    Article  CAS  PubMed  Google Scholar 

  • Bijlmakers MJ, Marsh M (2003) The on-off story of protein palmitoylation. Trends Cell Biol 13(1):32–42

    Article  CAS  PubMed  Google Scholar 

  • Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72:291–336

    Article  CAS  PubMed  Google Scholar 

  • Bouziane M, Miao F, Ye N, Holmquist G, Chyzak G, O’Connor TR (1998) Repair of DNA alkylation damage. Acta Biochim Pol 45(1):191–202

    CAS  PubMed  Google Scholar 

  • Boyes J, Bird A (1991) DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64(6):1123–1134

    Article  CAS  PubMed  Google Scholar 

  • Capili AD, Lima CD (2007) Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways. Curr Opin Struct Biol 17(6):726–735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Zhao BS, He C (2016) Nucleic acid modifications in regulation of gene expression. Cell Chem Biol 23(1):74–85

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke SG (2013) Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem Sci 38(5):243–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cole PA (2008) Chemical probes for histone-modifying enzymes. Nat Chem Biol 4(10):590–597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drablos F, Feyzi E, Aas PA, Vaagbo CB, Kavli B, Bratlie MS, Pena-Diaz J, Otterlei M, Slupphaug G, Krokan HE (2004) Alkylation damage in DNA and RNA – repair mechanisms and medical significance. DNA Repair (Amst) 3(11):1389–1407

    Article  CAS  Google Scholar 

  • Ehrlich M, Wilson GG, Kuo KC, Gehrke CW (1987) N4-methylcytosine as a minor base in bacterial DNA. J Bacteriol 169(3):939–943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Engelbergs J, Thomale J, Rajewsky MF (2000) Role of DNA repair in carcinogen-induced ras mutation. Mutat Res 450(1–2):139–153

    Article  CAS  PubMed  Google Scholar 

  • Farazi TA, Waksman G, Gordon JI (2001) The biology and enzymology of protein N-myristoylation. J Biol Chem 276(43):39501–39504

    Article  CAS  PubMed  Google Scholar 

  • Guan KL, Xiong Y (2011) Regulation of intermediary metabolism by protein acetylation. Trends Biochem Sci 36(2):108–116

    Article  CAS  PubMed  Google Scholar 

  • Hallgrimsson B, Hall BK (2011) Epigenetics: linking genotype and phenotype in development and evolution. University of California Press, Oakland

    Google Scholar 

  • Hazelbauer GL, Falke JJ, Parkinson JS (2008) Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci 33(1):9–19

    Article  CAS  PubMed  Google Scholar 

  • Hentschel A, Zahedi RP, Ahrends R (2016) Protein lipid modifications – more than just a greasy ballast. Proteomics 16(5):759–782

    Article  CAS  PubMed  Google Scholar 

  • Hubbard SR, Miller WT (2007) Receptor tyrosine kinases: mechanisms of activation and signaling. Curr Opin Cell Biol 19(2):117–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeltsch A, Jurkowska RZ (2014) New concepts in DNA methylation. Trends Biochem Sci 39(7):310–318

    Article  CAS  PubMed  Google Scholar 

  • Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13(7):484–492

    Article  CAS  PubMed  Google Scholar 

  • Karijolich J, Yu YT (2010) Spliceosomal snRNA modifications and their function. RNA Biol 7(2):192–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knorre DG, Kudryashova NV, Godovikova TS (2009) Chemical and functional aspects of posttranslational modification of proteins. Acta Nat 1(3):29–51

    CAS  Google Scholar 

  • Korlach J, Turner SW (2012) Going beyond five bases in DNA sequencing. Curr Opin Struct Biol 22(3):251–261

    Article  CAS  PubMed  Google Scholar 

  • Kumar R, Rao DN (2013) Role of DNA methyltransferases in epigenetic regulation in bacteria. Subcell Biochem 61:81–102

    Article  CAS  PubMed  Google Scholar 

  • Lee YH, Stallcup MR (2009) Minireview: protein arginine methylation of nonhistone proteins in transcriptional regulation. Mol Endocrinol 23(4):425–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li G, Weis RM (2000) Covalent modification regulates ligand binding to receptor complexes in the chemosensory system of Escherichia coli. Cell 100(3):357–365

    Article  CAS  PubMed  Google Scholar 

  • Li M, Luo J, Brooks CL, Gu W (2002) Acetylation of p53 inhibits its ubiquitination by Mdm2. J Biol Chem 277(52):50607–50611

    Article  CAS  PubMed  Google Scholar 

  • Liyanage VR, Zachariah RM, Delcuve GP, Davie JR, Rastegar M (2012) New developments in chromatin research: an epigenetic perspective. In: Simpson NM, Stewart VJ (eds) New developments in chromatin research. Nova Science Publishers, Hauppauge, pp 29–58

    Google Scholar 

  • Liyanage VR, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR (2014) DNA modifications: function and applications in normal and disease states. Biology (Basel) 3(4):670–723

    CAS  Google Scholar 

  • Marinus MG, Casadesus J (2009) Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33(3):488–503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Massenet S, Mougin A, Branlant C (1998) Posttranscriptional modifications in the U small nuclear RNAs. In: Grosjean H, Benne R (eds) Modification and Editing of RNA. ASM Press, Washington, DC, pp 201–227

    Chapter  Google Scholar 

  • Molina-Serrano D, Schiza V, Kirmizis A (2013) Cross-talk among epigenetic modifications: lessons from histone arginine methylation. Biochem Soc Trans 41(3):751–759

    Article  CAS  PubMed  Google Scholar 

  • Moore LD, Le T, Fan G (2013) DNA methylation and its basic function. Neuropsychopharmacology 38(1):23–38

    Article  CAS  PubMed  Google Scholar 

  • Nadolski MJ, Linder ME (2007) Protein lipidation. FEBS J 274(20):5202–5210

    Article  CAS  PubMed  Google Scholar 

  • Ndlovu MN, Denis H, Fuks F (2011) Exposing the DNA methylome iceberg. Trends Biochem Sci 36(7):381–387

    CAS  PubMed  Google Scholar 

  • Phizicky EM, Hopper AK (2015) tRNA processing, modification, and subcellular dynamics: past, present, and future. RNA 21(4):483–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ratel D, Ravanat JL, Berger F, Wion D (2006) N6-methyladenine: the other methylated base of DNA. BioEssays 28(3):309–315

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Razin A, Riggs AD (1980) DNA methylation and gene function. Science 210(4470):604–610

    Article  CAS  PubMed  Google Scholar 

  • Resh MD (1999) Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim Biophys Acta 1451(1):1–16

    Article  CAS  PubMed  Google Scholar 

  • Shen L, Song CX, He C, Zhang Y (2014) Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu Rev Biochem 83:585–614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smotrys JE, Linder ME (2004) Palmitoylation of intracellular signaling proteins: regulation and function. Annu Rev Biochem 73:559–587

    Article  CAS  PubMed  Google Scholar 

  • Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45

    Article  CAS  PubMed  Google Scholar 

  • Takai Y, Sasaki T, Matozaki T (2001) Small GTP-binding proteins. Physiol Rev 81(1):153–208

    Article  CAS  PubMed  Google Scholar 

  • Walsh D (2005) Posttranslational modification of proteins: expanding nature’s inventory. Roberts & Company Publishers, Englewood

    Google Scholar 

  • Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 44(45):7342–7372

    Article  CAS  PubMed  Google Scholar 

  • Wyatt GR (1951) Recognition and estimation of 5-methylcytosine in nucleic acids. Biochem J 48(5):581–584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang FL, Casey PJ (1996) Protein prenylation: molecular mechanisms and functional consequences. Annu Rev Biochem 65:241–269

    Article  CAS  PubMed  Google Scholar 

  • Zhang K, Williams KE, Huang L, Yau P, Siino JS, Bradbury EM, Jones PR, Minch MJ, Burlingame AL (2002) Histone acetylation and deacetylation: identification of acetylation and methylation sites of HeLa histone H4 by mass spectrometry. Mol Cell Proteomics 1(7):500–508

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Álvaro Ortega .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Ortega, Á. (2018). Hydrophobic Modifications of Biomolecules: An Introduction. In: Krell, T. (eds) Cellular Ecophysiology of Microbe: Hydrocarbon and Lipid Interactions. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50542-8_17

Download citation

Publish with us

Policies and ethics