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Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid–type III polyketide synthase

Nature Chemical Biology volume 2, pages 494–502 (2006)Cite this article

Abstract

Differentiation-inducing factors (DIFs) are well known to modulate formation of distinct communal cell types from identical Dictyostelium discoideum amoebas, but DIF biosynthesis remains obscure. We report complimentary in vivo and in vitro experiments identifying one of two ∼3,000-residue D. discoideum proteins, termed 'steely', as responsible for biosynthesis of the DIF acylphloroglucinol scaffold. Steely proteins possess six catalytic domains homologous to metazoan type I fatty acid synthases (FASs) but feature an iterative type III polyketide synthase (PKS) in place of the expected FAS C-terminal thioesterase used to off load fatty acid products. This new domain arrangement likely facilitates covalent transfer of steely N-terminal acyl products directly to the C-terminal type III PKS active sites, which catalyze both iterative polyketide extension and cyclization. The crystal structure of a steely C-terminal domain confirms conservation of the homodimeric type III PKS fold. These findings suggest new bioengineering strategies for expanding the scope of fatty acid and polyketide biosynthesis.

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Figure 1: Biosynthesis of D. discoideum DIF-1.
Figure 2: D. discoideum type III PKSs occur as C-terminal domains of steely FAS-PKS hybrids.
Figure 3: Hexanoyl-primed in vitro product specificity of steely C-terminal type III PKS domains.
Figure 4: Steely gene expression and DIF-1 synthesis by steely− null mutants.
Figure 5: Development of Steely2− mutant and rescue by DIF-1.
Figure 6: Crystal structure of Steely1 C-terminal domain confirms conservation of the PKS III fold, homodimeric assembly and internal active site cavity.
Figure 7: Steely1 type III PKS homodimer suggests functional similarity of steely hybridization interface to modular type I PKS interfaces.

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Acknowledgements

D. discoideum genomic DNA was a gift from R. Firtel and S. Merlot (University of California, San Diego). We also thank S. Horinouchi and N. Funa (University of Tokyo) for providing the synthetic PCP authentic standard, R. Schaloske (University of California, San Diego) for discussion of (A+T)-rich PCR and T. Baiga (Salk Institute) and N. Funa for discussion of LC-MS-MS. Use of the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. This work was supported by the National Institutes of Health Grant AI52443 (B.S.M. and J.P.N.), the Hayashi Memorial Foundation (T.S.) and core support from the Medical Research Council (R.R.K.). J.P.N. is an investigator of the Howard Hughes Medical Institute.

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Author notes

  1. Michael B Austin and Tamao Saito: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, 92037, California, USA

    Michael B Austin, Marianne E Bowman & Joseph P Noel

  2. Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan

    Tamao Saito & Atsushi Kato

  3. Biochemistry Department, University of Cambridge, Cambridge, CB2 1QW, UK

    Stephen Haydock

  4. Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, 92037-0634, California, USA

    Bradley S Moore

  5. Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

    Robert R Kay

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Contributions

M.B.A., conceptualization of project, in vitro experimental design, bioinformatic analysis from raw sequencing contigs, execution and analysis of the in vitro data including enzyme assays and structural elucidation, and substantial drafting of the manuscript; T.S., conceptualization of project, experimental design, execution and analysis of in vivo data including knockouts and complementation, and drafting of manuscript; M.E.B., expression, purification and crystallization of steely proteins; S.H., genome annotation, data analysis and interpretation; A.K., experimental assistance; B.S.M., funding and manuscript editing; R.R.K. and J.P.N., principal investigators of the project, experimental concept and design, data analysis, manuscript editing and funding.

Corresponding authors

Correspondence to Robert R Kay or Joseph P Noel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

In metazoan type 1 FASs and related type 1 PKSs, a C-terminal TE domain catalyzes the hydrolytic release of enzymatic products from the prosthetic Ppant arm of the adjacent ACP domain. (PDF 236 kb)

Supplementary Fig. 2

Acyl-thioester starter specificities of steely C-terminal type 3 PKS domains in comparison to alfalfa CHS. (PDF 456 kb)

Supplementary Fig. 3

LC-MS-MS analysis of all hexanoyl-primed products of in vitro enzyme assays with malonyl-CoA. (PDF 405 kb)

Supplementary Fig. 4

LC-MS-MS analysis of all butanoyl-primed products of in vitro enzyme assays with malonyl-CoA. (PDF 381 kb)

Supplementary Fig. 5

Transformed clones were screened for disruption of the Steely1 (stlA) and Steely2 (stlB) loci by genomic PCR using primers. (PDF 77 kb)

Supplementary Table 1

Data collection and refinement statistics. (PDF 70 kb)

Supplementary Methods (PDF 110 kb)

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Austin, M., Saito, T., Bowman, M. et al. Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid–type III polyketide synthase. Nat Chem Biol 2, 494–502 (2006). https://doi.org/10.1038/nchembio811

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