Abstract
Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion–dependent manner. However, a few metal ion–independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion–independent nucleases are presented and discussed.
Key Points
• Bacterial phospholipases (PLD-family) exhibit nucleolytic activity.
• Bacterial nucleases of the PLD-family are metal ion-independent.
• NSNs can be used in downstream processing approaches.
Similar content being viewed by others
References
Ahrenholtz I, Lorenz MG, Wackernagel W (1994) A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA. Appl Environ Microbiol 60:3746–3751
Anderson PM, Sung YC, Fuchs JA (1990) The cyanase operon and cyanate metabolism. FEMS Microbiol Rev 7:247–252
Araki T (1903) Enzymatic decomposition of nucleic acids. Z Physiol Chem 38:84–92
Ausubel L, Hall C, Sharma A, Shakeley R, Lopez P, Quezada V, Couture S, Laderman K, McMahon R, Huang P, Hsu D, Couture L (2012) Production of CGMP-grade lentiviral vectors. BioProcess Int 10:32–43
Balagurumoorthy P, Adelstein SJ, Kassis AI (2008) Method to eliminate linear DNA from mixture containing nicked circular, supercoiled, and linear plasmid DNA. Anal Biochem 381:172–174
Bao Y, Higgins L, Zhang P, Chan SH, Laget S, Sweeney S, Lunnen K, Xu SY (2008) Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants. Protein Expr Purif 58:42–52
Beiter K, Wartha F, Albiger B, Normark S, Zychlinsky A, Henriques-Normark B (2006) An endonuclease allows Streptococcus pneumoniae to escape from neutrophil extracellular traps. Curr Biol 16:401–407
Beliaeva MI, Kapranova MN, Vitol M, Golubenko IA, Leshchinskaia IB (1976) Nucleic acids utilized as the main source of bacterial nutrition. Mikrobiologiia 45:420–424
Belkebir A, Azeddoug H (2012) Characterization of LlaKI, a new metal ion-independent restriction endonuclease from Lactococcus lactis KLDS4. ISRN Biochem 2012:1–6
Benedik MJ, Strych U (1998) Serratia marcescens and its extracellular nuclease. FEMS Microbiol Lett 165:1–13
Binnenkade L, Kreienbaum M, Thormann KM (2018) Characterization of ExeM, an extracellular nuclease of Shewanella oneidensis MR-1. Front Microbiol 9:1761
Brnakova Z (2002) Microbial sugar non-specific nucleases. Biologia 57:677–687
Brown PH, Ho TH (1986) Barley aleurone layers secrete a nuclease in response to gibberellic acid : purification and partial characterization of the associated ribonuclease, deoxyribonuclease, and 3′-nucleotidase activities. Plant Physiol 82:801–806
Ceska TA, Sayers JR (1998) Structure-specific DNA cleavage by 5′ nucleases. Trends Biochem Sci 23:331–336
Chan SH, Bao Y, Ciszak E, Laget S, Xu SY (2007) Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities. Nucleic Acids Res 35:6238–6248
Chandrasegaran S, Carroll D (2016) Origins of programmable nucleases for genome engineering. J Mol Biol 428:963–989
Chang HH, Lieber MR (2016) Structure-specific nuclease activities of Artemis and the Artemis: DNA-PKcs complex. Nucleic Acids Res 44:4991–4997
Chase JW, Richardson CC (1974) Exonuclease VII of Escherichia coli. Purification and properties. J Biol Chem 249:4545–4552
Cincinnati Children’s Hospital (2019) Cincinnati children’s research flow cytometry core cell sorting guidelines. 1–8
Dang G, Cao J, Cui Y, Song N, Chen L, Pang H, Liu S (2016) Characterization of Rv0888, a novel extracellular nuclease from Mycobacterium tuberculosis. Sci Rep 6:19033
Dang G, Cui Y, Wang L, Li T, Cui Z, Song N, Chen L, Pang H, Liu S (2018) Extracellular sphingomyelinase Rv0888 of Mycobacterium tuberculosis contributes to pathological lung injury of Mycobacterium smegmatis in mice via inducing formation of neutrophil extracellular traps. Front Immunol 9:677
Davies DR, Interthal H, Champoux JJ, Hol WG (2004) Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes. J Med Chem 47:829–837
De Falco M, Catalano F, Rossi M, Ciaramella M, De Felice M (2015) NurA is endowed with endo- and exonuclease activities that are modulated by HerA: new insight into their role in DNA-end processing. PLoS One 10:e0142345
Dominguez K, Ward W (2009) A novel nuclease activity that is activated by Ca2+ chelated to EGTA. Syst Biol Reprod Med 55:193–199
Doronina NV, Kaparullina EN, Trotsenko YA, Nortemann B, Bucheli-Witschel M, Weilenmann HU, Egli T (2010) Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria. Int J Syst Evol Microbiol 60:1044–1051
Elleuche S, Pöggeler S (2008) A cyanase is transcriptionally regulated by arginine and involved in cyanate decomposition in Sordaria macrospora. Fungal Genet Biol 45:1458–1469
Elleuche S, Klippel B, von der Heyde A, Antranikian G (2013) Comparative analysis of two members of the metal ion-containing group III-alcohol dehydrogenases from Dickeya zeae. Biotechnol Lett 35:725–733
Elleuche S, Schröder C, Sahm K, Antranikian G (2014) Extremozymes--biocatalysts with unique properties from extremophilic microorganisms. Curr Opin Biotechnol 29:116–123
Elleuche S, Schäfers C, Blank S, Schröder C, Antranikian G (2015) Exploration of extremophiles for high temperature biotechnological processes. Curr Opin Microbiol 25:113–119
Espinosa-Cantu A, Ascencio D, Barona-Gomez F, DeLuna A (2015) Gene duplication and the evolution of moonlighting proteins. Front Genet 6:227
Eyler E (2013) Explanatory chaper: nuclease protection assays. In: Lorsch J (ed) Laboratory methods in enzymology: RNA, vol 530. Academic Press, Waltham, p 413
Filiminova MN, Garusov AV, Andreeva MA, Smetanina TA, Bogomolnya LM, Leshchinskaya IB (1996) Isoforms of Serratia marcescens nuclease. Comparative analysis of substrate specificity. Biochemistry (Mosc) 61:1274–1278
Friedhoff P, Gimadutdinow O, Pingoud A (1994) Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis. Nucleic Acids Res 22:3280–3287
Gomes J, Steiner W (2004) The biocatalytical potential of extremophiles and extremozymes. Food Technol Biotechnol 42:223–235
Gottlin EB, Rudolph AE, Zhao Y, Matthews HR, Dixon JE (1998) Catalytic mechanism of the phospholipase D superfamily proceeds via a covalent phosphohistidine intermediate. Proc Natl Acad Sci U S A 95:9202–9207
Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V (2005) Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. Proc Natl Acad Sci U S A 102:15797–15802
Horikoshi K, Antranikian G, Bull AT, Robb FT, Stetter KO (2011) Extremophiles handbook, 1st edn. Springer, Japan
Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA (1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98:397–408
Hsia KC, Li CL, Yuan HS (2005) Structural and functional insight into sugar-nonspecific nucleases in host defense. Curr Opin Struct Biol 15:126–134
Hu Y, Meng J, Shi C, Hervin K, Fratamico PM, Shi X (2013) Characterization and comparative analysis of a second thermonuclease from Staphylococcus aureus. Microbiol Res 168:174–182
Imagawa H, Toryu H, Ozawa T, Takino Y (1982) Purification and characterization of nucleases from tea leaves. Agric Biol Chem 46:1261–1269
Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I (2005) Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5′-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res 33:e112
Iwanoff L (1903) Über die fermentative Zersetzung der Thymonucleinsäure durch Schimmelpilze. Z Physiol Chem 39:31–37
Jeucken A, Helms JB, Brouwers JF (2018) Cardiolipin synthases of Escherichia coli have phospholipid class specific phospholipase D activity dependent on endogenous and foreign phospholipids. Biochim Biophys Acta Mol Cell Biol Lipids 1863:1345–1353
Jun SY, Lewis KM, Youn B, Xun L, Kang C (2016) Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase. Mol Microbiol 100:989–1003
Kamekura M, Hamakawa T, Onishi H (1982) Application of halophilic nuclease H of Micrococcus varians subsp. halophilus to commercial production of flavoring agent 5'-GMP. Appl Environ Microbiol 44:994–995
Knott GJ, Doudna JA (2018) CRISPR-Cas guides the future of genetic engineering. Science 361:866–869
Koonin EV (1996) A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. Trends Biochem Sci 21:242–243
Leiros I, Secundo F, Zambonelli C, Servi S, Hough E (2000) The first crystal structure of a phospholipase D. Structure 8:655–667
Li L, Rohrmann GF (2000) Characterization of a baculovirus alkaline nuclease. J Virol 74:6401–6407
Li L, Lin S, Yang F (2005) Functional identification of the non-specific nuclease from white spot syndrome virus. Virology 337:399–406
Li L, Krishnan M, Baseman JB, Kannan TR (2010) Molecular cloning, expression, and characterization of a Ca2+−dependent, membrane-associated nuclease of Mycoplasma genitalium. J Bacteriol 192:4876–4884
Linder T (2018) Cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts. World J Microbiol Biotechnol 35:3
Linn S, Robert RJ (1982) Nucleases. Cold Spring Harbor Laboratory Press, New York
Loenen WA, Dryden DT, Raleigh EA, Wilson GG, Murray NE (2014) Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 42:3–19
Lunin VY, Levdikov VM, Shlyapnikov SV, Blagova EV, Lunin VV, Wilson KS, Mikhailov AM (1997) Three-dimensional structure of Serratia marcescens nuclease at 1.7 a resolution and mechanism of its action. FEBS Lett 412:217–222
Luque-Almagro VM, Huertas MJ, Saez LP, Luque-Romero MM, Moreno-Vivian C, Castillo F, Roldan MD, Blasco R (2008) Characterization of the Pseudomonas pseudoalcaligenes CECT5344 cyanase, an enzyme that is not essential for cyanide assimilation. Appl Environ Microbiol 74:6280–6288
Ma F, Guo X, Fan H (2017) Extracellular nucleases of Streptococcus equi subsp zooepidemicus degrade neutrophil extracellular traps and impair macrophage activity of the host. Appl Environ Microbiol 83:e02468-16
Maciejewska N, Walkusz R, Olszewski M, Szymanska A (2019) New nuclease from extremely psychrophilic microorganism Psychromonas ingrahamii 37: identification and characterization. Mol Biotechnol 61:122–133
Maeda M, Taga N (1976) Extracellular nuclease produced by a marine bacterium. II. Purification and properties of extracellular nuclease from a marine Vibrio sp. Can J Microbiol 22:1443–1452
Martin CE, Wagner RP (1975) Two forms of a mitochondrial endonuclease in Neurospora crassa. Can J Biochem 53:823–825
Miller MD, Benedik MJ, Sullivan MC, Shipley NS, Krause KL (1991) Crystallization and preliminary crystallographic analysis of a novel nuclease from Serratia marcescens. J Mol Biol 222:27–30
Miltenyi S, Hübel T, Nölle V (2018) Process for sorting cells by microfabricated components using a nuclease. US 10, 018,541 B2, 10.07.2018
Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I (2007) Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res 35:1908–1918
Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T, Ito T, Kobayashi I, Tanokura M (2014) A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. Nat Commun 5:3178
Moon AF, Krahn JM, Lu X, Cuneo MJ, Pedersen LC (2016) Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic Acids Res 44:3946–3957
Mullis KB, Ferre F, Gibbs RA (1994) The polymerase chain reaction (PCR). Birkhäuser Verlag, Basel
Pan CQ, Lazarus RA (1998) Hyperactivity of human DNase I variants. Dependence on the number of positively charged residues and concentration, length, and environment of DNA. J Biol Chem 273:11701–11708
Pan Y, Xiao L, Li AS, Zhang X, Sirois P, Zhang J, Li K (2013) Biological and biomedical applications of engineered nucleases. Mol Biotechnol 55:54–62
Pandya C, Farelli JD, Dunaway-Mariano D, Allen KN (2014) Enzyme promiscuity: engine of evolutionary innovation. J Biol Chem 289:30229–30236
Panfilova ZI, Salganik RI (1983) Isolation of Serratia marcescens mutants superproducers of endonuclease by exposure to nitrosomethylurea in a synchronized culture. Mikrobiologiia 52:974–978
Pedersen J, Filimonova M, Roepstorff P, Biedermann K (1995) Nuclease isoforms of natural and recombinant strains of Serratia marcescens. Biokhimiia 60:450–461
Pinchuk GE, Ammons C, Culley DE, Li SM, McLean JS, Romine MF, Nealson KH, Fredrickson JK, Beliaev AS (2008) Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl Environ Microbiol 74:1198–1208
Pohlman RF, Liu F, Wang L, More MI, Winans SC (1993) Genetic and biochemical analysis of an endonuclease encoded by the IncN plasmid pKM101. Nucleic Acids Res 21:4867–4872
Pommer AJ, Wallis R, Moore GR, James R, Kleanthous C (1998) Enzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli. Biochem J 334:387–392
Ponting CP, Kerr ID (1996) A novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues. Protein Sci 5:914–922
Prazeres DM (2016) Considerations on the use of enzymes in downstream processing of biopharmaceuticals. Pharm Bioprocess 4:91–95
Rangarajan ES, Shankar V (2001) Sugar non-specific endonucleases. FEMS Microbiol Rev 25:583–613
Romier C, Dominguez R, Lahm A, Dahl O, Suck D (1998) Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Proteins 32:414–424
Rudolph AE, Stuckey JA, Zhao Y, Matthews HR, Patton WA, Moss J, Dixon JE (1999) Expression, characterization, and mutagenesis of the Yersinia pestis murine toxin, a phospholipase D superfamily member. J Biol Chem 274:11824–11831
Saez LP, Cabello P, Ibanez MI, Luque-Almagro VM, Roldan MD, Moreno-Vivian C (2019) Cyanate assimilation by the alkaliphilic cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344: mutational analysis of the cyn gene cluster. Int J Mol Sci 20
Saha SK, Saikot FK, Rahman MS, Jamal M, Rahman SMK, Islam SMR, Kim KH (2019) Programmable molecular scissors: applications of a new tool for genome editing in biotech. Mol Ther Nucleic Acids 14:212–238
Sasnauskas G, Zakrys L, Zaremba M, Cosstick R, Gaynor JW, Halford SE, Siksnys V (2010) A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3′-5′ and 5′-3′ strands by rotating a single active site. Nucleic Acids Res 38:2399–2410
Satomi M (2014) The family Shewanellaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, pp 597–625
Schmitz S, Börner P, Nölle V, Elleuche S (2019a) Comparative analysis of two non-specific nucleases of the phospholipase D family from the plant pathogen competitor bacterium Pantoea agglomerans. Appl Microbiol Biotechnol 103:2635–2648
Schmitz S, Nölle V, Elleuche S (2019b) A non-specific nucleolytic enzyme and its application potential in EDTA-containing buffer solutions. Biotechnol Lett 41:129–136
Schmitz S, Wieczorek M, Nölle V, Elleuche S (2020) Characterization of single amino acid variations in a cold-active and EDTA-tolerating non-specific nuclease from the ice-nucleating bacterium Pseudomonas syringae. Mol Biotechnol 62:67–78
Schwardmann LS, Schmitz S, Nölle V, Elleuche S (2019) Decoding essential amino acid residues in the substrate groove of a non-specific nuclease from Pseudomonas syringae. Catalysts 9:941
Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM (2000) Atomic structure of the Serratia marcescens endonuclease at 1.1 a resolution and the enzyme reaction mechanism. Acta Crystallogr D Biol Crystallogr 56:567–572
Smith JG, Liu X, Kaufhold RM, Clair J, Caulfield MJ (2001) Development and validation of a gamma interferon ELISPOT assay for quantitation of cellular immune responses to varicella-zoster virus. Clin Diagn Lab Immunol 8:871–879
Song Q, Zhang X (2008) Characterization of a novel non-specific nuclease from thermophilic bacteriophage GBSV1. BMC Biotechnol 8:43
Stuckey JA, Dixon JE (1999) Crystal structure of a phospholipase D family member. Nat Struct Biol 6:278–284
Vafina G, Zainutdinova E, Bulatov E, Filimonova MN (2018) Endonuclease from gram-negative bacteria Serratia marcescens is as effective as Pulmozyme in the hydrolysis of DNA in sputum. Front Pharmacol 9:114
Varley DL, Hitchcock AG, Weiss AM, Horler WA, Cowell R, Peddie L, Sharpe GS, Thatcher DR, Hanak JA (1999) Production of plasmid DNA for human gene therapy using modified alkaline cell lysis and expanded bed anion exchange chromatography. Bioseparation 8:209–217
Vassylyeva MN, Klyuyev S, Vassylyev AD, Wesson H, Zhang Z, Renfrow MB, Wang H, Higgins NP, Chow LT, Vassylyev DG (2017) Efficient, ultra-high-affinity chromatography in a one-step purification of complex proteins. Proc Natl Acad Sci U S A 114:E5138–E5147
Vitkute J, Maneliene Z, Petrusyte M, Janulaitis A (1998) BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3′. Nucleic Acids Res 26:3348–3349
Vlassov VV, Laktionov PP, Rykova EY (2007) Extracellular nucleic acids. Bioessays 29:654–667
Waite M (1999) The PLD superfamily: insights into catalysis. Biochim Biophys Acta 1439:187–197
Wang D, Miyazono KI, Tanokura M (2016) Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA. Sci Rep 6:35197
Witteveldt J, Van Hulten MC, Vlak JM (2001) Identification and phylogeny of a non-specific endonuclease gene of white spot syndrome virus of shrimp. Virus Genes 23:331–337
Wu SI, Lo SK, Shao CP, Tsai HW, Hor LI (2001) Cloning and characterization of a periplasmic nuclease of Vibrio vulnificus and its role in preventing uptake of foreign DNA. Appl Environ Microbiol 67:82–88
Xin XF, Kvitko B, He SY (2018) Pseudomonas syringae: what it takes to be a pathogen. Nat Rev Microbiol 16:316–328
Yang W (2011) Nucleases: diversity of structure, function and mechanism. Q Rev Biophys 44:1–93
Zhao Y, Stuckey JA, Lohse DL, Dixon JE (1997) Expression, characterization, and crystallization of a member of the novel phospholipase D family of phosphodiesterases. Protein Sci 6:2655–2658
Acknowledgements
We thank the members of the department “Recombinant proteins” at Miltenyi Biotec B.V. & Co. KG and especially Sarah Schmitz and Marek Wieczorek for discussion.
Author information
Authors and Affiliations
Contributions
Conceived and designed the concept: SE; Wrote the paper: LSS, SE; Reviewed and edited the manuscript: VN.
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Schwardmann, L.S., Nölle, V. & Elleuche, S. Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential. Appl Microbiol Biotechnol 104, 3293–3304 (2020). https://doi.org/10.1007/s00253-020-10459-5
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-020-10459-5