Zechel Lab

57. Pasternak, ARO; Balanus, MJ; Zechel DL*. Discovery of 3′-O-β-Glucosyltubercidin and the Nucleoside Specific Glycosyltransferase AvpGT through Genome Mining. ACS Chemical Biology, 2022, in press online, DOI: 10.1021/acschembio.2c00707. Highlighted as a supplementary cover!

56. Pasternak, ARO; Bechthold, A; Zechel, DL*. Identification of Genes Essential for Sulfamate and Fluorine Incorporation During Nucleocidin Biosynthesis. ChemBioChem 2022, 23, e202200140.  https://doi.org/10.1002/cbic.202200140. Featured on the cover and as a “Very Important Paper”!

55. Gama SR, Stankovic T, Hupp K, Hejami AA, McClean M, Evans A, Beauchemin D, Hammerschmidt F, Pallitsch K*, Zechel DL*, Biosynthesis of the Fungal Organophosphonate Fosfonochlorin Involves an Iron(II) and 2-(Oxo)glutarate Dependent Oxacyclase. ChemBioChem, 2022, 23, e202100352. https://doi.org/10.1002/cbic.202100352. Featured on cover!

54. Bernhardt, M., Berman, S., Zechel, D. L., and Bechthold, A*.  Role of Two Exceptional trans Adenylation Domains and MbtH‐like Proteins in the Biosynthesis of the Nonribosomal Peptide WS9324A from Streptomyces calvus ATCC 13382. ChemBioChem 2020, 21, 2659-2666.

53. Tsypik, O., Makitrynskyy, R., Frensch, B., Zechel, D. L., Paululat, T., Teufel, R., and Bechthold, A.  Oxidative Carbon Backbone Rearrangement in Rishirilide Biosynthesis. J. Am. Chem. Soc. 2020, 142, 5913–5917

52. Makitrynskyy, R., Tsypik, O., Nuzzo, D., Paululat, T., Zechel, D. L., and Bechthold, A.  Secondary nucleotide messenger c-di-GMP exerts a global control on natural product biosynthesis in streptomycetes. Nucleic Acids Res. 2020, 48, 1583–1598.

51. Zhu, J., Zhang, S., Zechel, D. L., Paululat, T., and Bechthold, A.* Rational Design of Hybrid Natural Products by Utilizing the Promiscuity of an Amide Synthetase. ACS Chem. Biol. 2019 14, 1793–1801.

50. Gama SR, Lo BSY, Séguin J, Pallitsch K, Hammerschmidt F, Zechel DL*. 2019. C-H Bond Cleavage Is Rate-Limiting for Oxidative C-P Bond Cleavage by the Mixed Valence Diiron-Dependent Oxygenase PhnZ. Biochemistry 2019, 58, 5271-5280.

We were delighted to be invited by John Gerlt (U. Illinois) to contribute this paper for a special issue on Mechanistic Enzymology. In this study we used a classical approach involving deuterium kinetic isotope effects, a proton inventory, and site directed mutagenesis to identify the rate-limiting step of the organophosphonate degrading enzyme PhnZ. Turns out that C-H bond cleavage, not C-P, is the tough step for PhnZ!

49. Gama SR, Vogt M, Kalina T, Hupp K, Hammerschmidt F, Pallitsch K*, Zechel DL*.  An Oxidative Pathway for Microbial Utilization of Methylphosphonic Acid as a Phosphate Source. ACS Chem Biol 2019, 14, 735–741.

48. Zhang, S.; Klementz, D.; Zhu, J.; Makitrynskyy, R.; Pasternak, A. R. O.; Günther, S.; Zechel, D. L.*; Bechthold, A*. Genome Mining Reveals the Origin of a Bald Phenotype and a Cryptic Nucleocidin Gene Cluster in Streptomyces asterosporus DSM 41452. J. Biotechnol. 2019, 292, 23–31.

For over 60 years, only Streptomyces calvus was known to produce nucleocidin, a rare example of a fluorinated secondary metabolite. This is a problem, as S. calvus is a terrible producer of this valuable molecule ( about 0.5 mg/L culture). Our genome mining approach sets the stage for finding better producers of nucleocidin or derivatives thereof. 

47. Sarwar, A; Latif, Z; Zhang, S; Zhu, J; Zechel, D; *Bechthold, A. Biological control of potato common scab with rare Isatropolone C compound produced by plant growth promoting Streptomyces A1RT. Front. Microbiol. 2018, 9, 1126.

46. Zhang, S.; Zhu, J.; Zechel, D. L.; Jessen-Trefzer, C.; Eastman, R. T.; Paululat, T.; Bechthold, A. New WS9326A Derivatives and One New Annimycin Derivative with Antimalarial Activity Are Produced by Streptomyces asterosporus DSM 41452 and Its Mutant. ChemBioChem 2018, 19, 272-279.

This paper provides intriguing insights into the biosynthesis of the non-ribosomal peptide WS9326A and annimycin from a new producer of these molecules. We previously documented these compounds in our favourite strain, S. calvus.

45. Horsman G* and Zechel DL*. Phosphonate Biochemistry. Chem. Rev. 2017, 118, 5704-5783.

I’m very excited about this joint effort with Geoff Horsman (Wilfrid Laurier U.). This is an invited review on the biosynthesis and catabolism of phosphonate natural products that will be part of a special thematic issue on “Unusual Enzymology in Natural Products Biosynthesis”, edited by Wilfred van der Donk (U. Illinois). One doesn’t need to look hard to find strange enzymes in the world of phosphonates!

44. Zechel DL*, PhnK: Another piece of the carbon-phosphorus lyase puzzle. Structure 2016, 24, 3-4.

My commentary on some very nice work by the Zhang and Raushel labs on the PhnGHIJK complex using cryo-electron microscopy.

43. Johnston CW, Skinnider MA, Wyatt MA, Li X, Ranieri MRM, Yang L, Zechel DL, Bin Ma, and Magarvey NA*. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nature Comms 2015, 6, 1–11.

An innovative combination of bioinformatics, chemoinformatics, and LC-MS/MS that allows one to predict the structures of bacterial natural products based on genetic information and then look for the corresponding molecules in culture extracts. Our favourite bacterium Streptomyces calvus figures prominently in this paper where we use this method to identify a non-ribosomal peptide encoded by an unusual NRPS gene cluster.

42. Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL*: Biosynthesis of the fluorinated natural product nucleocidin in Streptomyces calvus is dependent on the bldA specified Leu-tRNA(UUA) molecule. ChemBioChem 2015, 16, 2498-2506.

First discovered in 1956, nucleocidin was ‘re-discovered’ in S. calvus after correcting a mutation in the gene bldA. The genes encoding the biosynthetic pathway were also identified. The lack of production of this rare fluorinated natural product in by S. calvus had bedevilled researchers for decades, as well as thwarted investigations into the biosynthetic pathway. Fluorinated nucleosides are prized for their antiviral and antitumour activity, thus a precise enzymatic means to such compounds is highly desirable. Next stop: the nucleocidin fluorinase! 

41. Gessner A, Heitzler T, Zhang S, Klaus C, Murillo R, Zhao H, Vanner S, Zechel DL*, and Bechthold A*. Changing biosynthetic profiles by expressing bldA in Streptomyces strains. ChemBioChem 2015, 16, 2244-2252.

Turns out that constitutively expressing bldA in Streptomyces can frequently turn on sleeping biosynthetic genes, even when the strains contain native copies of bldA that are normal. This may relate to the prominence of TTA codons in biosynthetic genes and regulatory genes in Streptomyces. Add bldA to the growing list of techniques for activating ‘cryptic’ genes to discover new molecules.

40. van Staalduinen LM, McSorley FR, Schiessl K, Séguin J, Wyatt PB, Hammerschmidt F, Zechel DL*, Jia Z*: Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates. Proc. Natl Acad Sci USA 2014, 111, 5171-6.

Describes the structure of an enzyme that ‘burns’ through carbon-phosphorus bonds using iron and oxygen. Fun fact: PhnZ most closely resembles the structure of an enzyme called MIOX that burns through carbon-carbon bonds. PhnZ is from a marine bacterium. MIOX is from a mouse. Got to love evolution! Might also explain why MIOX researchers were inspired to work on PhnZ as well! See http://www.ncbi.nlm.nih.gov/pubmed/24198335.

39. Hove-Jensen B*, Zechel DL, Jochimsen B: Utilization of glyphosate as a phosphorus source: Biochemistry and genetics of bacterial carbon-phosphorus lyase. Microbiol. Mol. Biol. Rev. 2014, 78, 176-97.

Want to know how the active ingredient of RoundUp™, the most widely used herbicide on Earth, is degraded in the soil? Read this review by my good friend and collaborator Bjarne Hove-Jensen.

38. Kalan L, Gessner A, Thaker MN, Waglechner N, Zhu X, Szawiola A, Bechthold A, Wright GD, Zechel DL*: A cryptic polyene biosynthetic gene cluster in Streptomyces calvus is expressed upon complementation with a functional bldA gene. Chem. Biol. 2013, 20, 1214-1224.

The saga with Streptomyces calvus begins. Our interest in this strain was inspired by its former ability to produce a fluorinated natural product called nucleocidin. But we were faced with a big problem: S. calvus only produced nucleocidin during the 1950’s in the hands of the company that discovered it (American Cyanamid), whereas samples of the strain available to academics (e.g. ATCC 13382) failed to do so. Out of exasperation this fluorinated natural product was declared to be extinct! S. calvus was odd in another way as well, which provided a clue to as to why nucleocidin ‘disappeared’. S. calvus is strange because it cannot form fuzzy looking spores, thus colonies growing on solid media have a glossy, ‘bald’ appearance. Scientists from American Cyanamid were so struck by this trait that they christened it the ‘bald’ Streptomycete (calvus = Latin for bald). Turns out that S. calvus is bald due to a mutation in the gene bldA, which is well known to be important for sporulation and secondary metabolite production. Our hope at the end of this paper was that by correcting bldA in S. calvus, we could restore production nucleocidin. At this point we settled for an interesting polyketide, annimycin. We were also super excited to receive a commentary about this article by Keith Chater (John Innes Centre, UK), a pioneer in the field of Streptomyces genetics. 

37. Hove-Jensen B*, McSorley FR, Zechel DL*: Catabolism and detoxification of 1-aminoalkylphosphonic acids: N-acetylation by the phnO gene product. PLoS One 2012, 7, e46416.

PhnO performs N-acetylation of aminoalkylphosphonates as these compounds enter the carbon-phosphorus lyase pathway. It was not understood why, or even if, N-acetylation was required for CP-bond cleavage. Upon deleting phnO in E. coli we were surprised to learn that in only two cases was N-acetylation necessary for catabolism of aminoalkylphosphonates, these being aminomethylphosphophonate and (S)-1-aminoethylphosphonate. The latter is also bactericidal, but here too PhnO is useful neutralizing the compound through N-acetylation. Thus PhnO is necessary to allow CP-lyase to cleave the bonds of 1-aminoalkylphosphonates, and additionally provides a protection against toxic compounds.

36. McSorley FR, Wyatt PB, Martinez A, Delong EF, Hove-Jensen B, Zechel DL*: PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond. J. Am. Chem. Soc. 2012, 134, 8364-7.

In addition to the hydrolase and CP-lyase mechanisms, the PhnY-PhnZ pathway represents a third mechanism that is used by bacteria to extract inorganic phosphate from organophosphonates. This paper was highlighted as a ‘Spotlight’ article in JACS.

35. He S-M, Wathier M, Podzelinska K, Wong M, McSorley F, Asfaw, A, Hove-Jensen B, Jia Z, Zechel DL*: Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway. Biochemistry, 2011, 50, 8603-15.

An extensive kinetic, mutagenic, and crystallographic analysis of the phosphodiesterase that recycles a ‘dead-end’ intermediate in the CP-lyase pathway. Features a orthovanadate complex and a Bronsted analysis of leaving groups.

34. Jochimsen B, Lolle S, McSorely FR, Nabi M, Stougaard J, Zechel DL, Hove-Jensen B*: Five phn gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway for organophosphonate catabolism. Proc Natl Acad Sci USA, 2011, 108, 11393-8.

First evidence that CP-lyase is comprised, in part, of a multi-protein complex. The complexity of this enzyme system continues to surprise!

33. Härle J, Günther S, Lauinger B, Weber M, Kammerer B, Zechel DL, Luzhetskyy A, Bechthold A*: Rational design of an aryl-C-glycoside catalyst from a natural product O-glycosyltransferase. Chem Biol 2011, 18, 520-30.

32. Hove-Jensen B*, McSorley F, Zechel DL*: Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway. J. Am. Chem. Soc. 2011, 133, 3617-24.

Identification of the dead-end intermediate that is formed as a product of the CP-bond cleaving step catalyzed by CP-lyase. PhnP is shown to convert this intermediate into a metabolically useful compound. 

31. Groom K, Bhattacharya A, Zechel DL*: Rebeccamycin and staurosporine biosynthesis: Insight into the mechanisms of the flavin-dependent monooxygenases RebC and StaC. ChemBioChem 2011, 12, 396-400.

Indolocarbazole biosynthesis involves an interesting cascade of oxidative steps that involve electron rich indole rings. These steps can diverge, depending on the site of oxidation, leading to different products. In this paper we show how a key enzyme in this pathway can act as a gatekeeper to forming different oxidation products.

30. Podzelinska K, Latimer R, Bhattacharya A, Vining LC, Zechel DL*, Jia Z*: The structure of CmlS, a flavin-dependent halogenase involved in the biosynthesis of chloramphenicol. J. Mol. Biol. 2010, 397, 316-331.

Chloramphenicol is an iconic antibiotic and a deceptively simple molecule that belies its remarkable biosynthesis. This includes the dichloroacetyl group. In this paper we characterize the ‘halogenase’ that installs the two chlorine atoms.

29. Hove-Jensen B*, Rosenkrantz TJ, Zechel DL, Willemoes M: Accumulation of intermediates of the carbon-phosphorus lyase pathway for phosphonate degradation in phn mutants of Escherichia coli. J. Bacteriol. 2010, 192, 370-374.

28. Nelson GW, Perry M, He SM, Zechel DL, Horton JH*: Characterization of covalently bonded proteins on poly(methyl methacrylate) by X-ray photoelectron spectroscopy. Colloids. Surf. B Biointerfaces 2010, 78, 61-68.

27. Suits MDL, Zhu Y, Taylor EJ, Walton J, Zechel DL, Gilbert HJ, Davies GJ*: Structure and kinetic investigation of Streptococcus pyogenes family GH38 α-mannosidase. PLoS ONE 2010, 5, e9006.

26. Tailford LE, Ducros VM, Flint JE, Roberts SM, Morland C, Zechel DL, Smith N, Bjornvad ME, Borchert TV, Wilson KS, Davies GJ*, Gilbert HJ: Understanding how diverse β-mannanases recognize heterogeneous substrates. Biochemistry 2009, 48, 7009-7018.

25. Podzelinska K, He SM, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL*, Jia Z*: Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation. J. Biol. Chem. 2009, 284, 17216-17226.

24. Offen WA, Zechel DL, Withers SG, Gilbert HJ, Davies GJ*: Structure of the Michaelis complex of b-mannosidase, Man2A, provides insight into the conformational itinerary of mannoside hydrolysis. Chem. Commun. (Camb) 2009, 2484-2486.

23. Latimer R, Podzelinska K, Soares A, Bhattacharya A, Vining LC, Jia Z, Zechel DL*: Expression, purification and preliminary diffraction studies of CmlS. Acta. Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2009, 65, 260-263.

22. He SM, Luo Y, Hove-Jensen B, Zechel DL*: A fluorescent substrate for carbon-phosphorus lyase: towards the pathway for organophosphonate metabolism in bacteria. Bioorg. Med. Chem. Lett. 2009, 19, 5954-5957.

21. Podzelinska K, He S, Soares A, Zechel DL, Hove-Jensen B, Jia Z*: Expression, purification and preliminary diffraction studies of PhnP. Acta. Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2008, 64, 554-557.

20. Adams MA, Luo Y, Hove-Jensen B, He SM, van Staalduinen LM, Zechel DL*, Jia Z*: Crystal structure of PhnH: an essential component of carbon-phosphorus lyase in Escherichia coli. J. Bacteriol. 2008, 190, 1072-1083.

19. van Staalduinen LM, Bhattacharya A, Groom K, Zechel DL, Jia Z*: Expression, purification and preliminary X-ray diffraction studies of RebC. Acta. Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2007, 63, 980-982.

18. Gloster TM, Meloncelli P, Stick RV, Zechel DL, Vasella A, Davies GJ*: Glycosidase inhibition: an assessment of the binding of 18 putative transition-state mimics. J. Am. Chem. Soc. 2007, 129, 2345-2354.

17. Luo Y, Zechel DL*: A concise synthesis of α-D-ribofuranosyl alkylphosphonates: putative substrate intermediates for the carbon phosphorous lyase system. Can. J. Chem. 2006, 84, 743-747.

16. Matsuura T, Ernst A, Zechel DL, Pluckthun A*: Combinatorial approaches to novel proteins. ChemBioChem 2004, 5, 177-182.

15. Zechel DL, Boraston AB, Gloster T, Boraston CM, Macdonald JM, Tilbrook DM, Stick RV, Davies GJ*: Iminosugar glycosidase inhibitors: structural and thermodynamic dissection of the binding of isofagomine and 1-deoxynojirimycin to β-glucosidases. J. Am. Chem. Soc. 2003, 125, 14313-14323.

14. Varrot A, Tarling CA, Macdonald JM, Stick RV, Zechel DL, Withers SG, Davies GJ*: Direct observation of the protonation state of an imino sugar glycosidase inhibitor upon binding. J. Am. Chem. Soc. 2003, 125, 7496-7497.

13. Ducros VM, Tarling CA, Zechel DL, Brzozowski AM, Frandsen TP, von Ossowski I, Schulein M, Withers SG, Davies GJ*: Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants. Chem. Biol. 2003, 10, 619-628.

12. Davies GJ, Ducros VM, Varrot A, Zechel DL: Mapping the conformational itinerary of β-glycosidases by X-ray crystallography. Biochem. Soc. Trans. 2003, 31, 523-527.

11. Zechel DL, Reid SP, Stoll D, Nashiru O, Warren RA, Withers SG*: Mechanism, mutagenesis, and chemical rescue of a β-mannosidase from Cellulomonas fimi. Biochemistry 2003, 42, 7195-7204.

10. Ducros VM, Zechel DL, Murshudov GN, Gilbert HJ, Szabo L, Stoll D, Withers SG, Davies GJ*: Substrate distortion by a β-mannanase: snapshots of the Michaelis and covalent-intermediate complexes suggest a B^2,5 conformation for the transition state. Angew. Chem. Int. Ed. Engl. 2002, 41, 2824-2827.

9. Zechel DL, Withers SG*: Dissection of nucleophilic and acid-base catalysis in glycosidases. Curr. Opin. Chem. Biol. 2001, 5, 643-649.

8. Zechel DL, Reid SP, Nashiru O, Mayer C, Stoll D, Jakeman DL, Warren RA, Withers SG*: Enzymatic synthesis of carbon-fluorine bonds. J. Am. Chem. Soc. 2001, 123, 4350-4351.

7. Nashiru O, Zechel DL, Stoll D, Mohammadzadeh T, Warren RA, Withers SG*: β-Mannosynthase: synthesis of β-mannosides with a mutant β-mannosidase. Angew. Chem. Int. Ed. Engl. 2001, 40, 417-420.

6. Mayer C, Zechel DL, Reid SP, Warren RA, Withers SG*: The E358S mutant of Agrobacterium sp. β-glucosidase is a greatly improved glycosynthase. FEBS Lett. 2000, 466, 40-44.

5. Zechel DL, Withers SG*: Glycosidase mechanisms: anatomy of a finely tuned catalyst. Acc. Chem. Res. 2000, 33, 11-18.

4. Zechel DL, Konermann L, Withers SG, Douglas DJ*: Pre-steady state kinetic analysis of an enzymatic reaction monitored by time-resolved electrospray ionization mass spectrometry. Biochemistry 1998, 37, 7664-7669.

3. Zechel DL, He S, Dupont C, Withers SG*: Identification of Glu-120 as the catalytic nucleophile in Streptomyces lividans endoglucanase celB. Biochem. J. 1998, 336, 139-145.

2. D.L. Zechel, K.C. Hultzsch, R. Rulkens, D. Balaishis, Y. Ni, J.K. Pudelski, A.J. Lough, I. Manners, D.A. Foucher*.  Thermal and transition-metal-catalyzed ring-opening polymerization (ROP) of [1]silaferrocenophanes with chlorine substituents at silicon:  A route to tunable poly(ferrocenylsilanes).  Organometallics 1996, 15, 1972-1978.

1. D.L. Zechel, D.A. Foucher, J.K. Pudelski, G.P.A. Yap, A.L. Rheingold, I. Manners*.  Synthesis, structural characterization, electrochemical properties and polymerization behaviour of the first silicon-bridged [1.1]ferrocenophane [{Fe(h-C₅H₄)₂SiMe₂}₂].  J. Chem. Soc., Dalton Trans. 1995, 1893-1899.