Nonribosomal peptide

Nonribosomal peptides (NRP) are a class of peptide secondary metabolites, usually produced by microorganisms like bacteria and fungi. Nonribosomal peptides are also found in higher organisms, such as nudibranchs, but are thought to be made by bacteria inside these organisms.[1] While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as discussed in this article.

Nonribosomal peptides are synthesized by nonribosomal peptide synthetases, which, unlike the ribosomes, are independent of messenger RNA. Each nonribosomal peptide synthetase can synthesize only one type of peptide. Nonribosomal peptides often have cyclic and/or branched structures, can contain non-proteinogenic amino acids including D-amino acids, carry modifications like N-methyl and N-formyl groups, or are glycosylated, acylated, halogenated, or hydroxylated. Cyclization of amino acids against the peptide "backbone" is often performed, resulting in oxazolines and thiazolines; these can be further oxidized or reduced. On occasion, dehydration is performed on serines, resulting in dehydroalanine. This is just a sampling of the various manipulations and variations that nonribosomal peptides can perform. Nonribosomal peptides are often dimers or trimers of identical sequences chained together or cyclized, or even branched.

Nonribosomal peptides are a very diverse family of natural products with an extremely broad range of biological activities and pharmacological properties. They are often toxins, siderophores, or pigments. Nonribosomal peptide antibiotics, cytostatics, and immunosuppressants are in commercial use.

Examples

Biosynthesis

Nonribosomal peptides are synthesized by one or more specialized nonribosomal peptide-synthetase (NRPS) enzymes. The NRPS genes for a certain peptide are usually organized in one operon in bacteria and in gene clusters in eukaryotes. However the first fungal NRP to be found was ciclosporin. It is synthesized by a single 1.6MDa NRPS.[4] The enzymes are organized in modules that are responsible for the introduction of one additional amino acid. Each module consists of several domains with defined functions, separated by short spacer regions of about 15 amino acids.

The biosynthesis of nonribosomal peptides shares characteristics with the polyketide and fatty acid biosynthesis. Due to these structural and mechanistic similarities, some nonribosomal peptide synthetases contain polyketide synthase modules for the insertion of acetate or propionate-derived subunits into the peptide chain.

Modules

The order of modules and domains of a complete nonribosomal peptide synthetase is as follows:

  • Initiation or Starting module: [F/NMT]-A-PCP-
  • Elongation or Extending modules: -(C/Cy)-[NMT]-A-PCP-[E]-
  • Termination or Releasing module: -(TE/R)

(Order: N-terminus to C-terminus; []: optionally; (): alternatively)

Domains

  • F: Formylation (optional)
  • A: Adenylation (required in a module)
  • PCP: Thiolation and Peptide Carrier Protein with attached 4'-phospho-pantetheine (required in a module)
  • C: Condensation forming the amide bond (required in a module)
  • Cy: Cyclization into thiazoline or oxazolines (optional)
  • Ox: Oxidation of thiazolines or oxazolines to thiazoles or oxazoles (optional)
  • Red: Reduction of thiazolines or oxazolines to thiazolidines or oxazolidines (optional)
  • E: Epimerization into D-amino acids (optional)
  • NMT: N-methylation (optional)
  • TE: Termination by a thio-esterase (only found once in a NRPS)
  • R: Reduction to terminal aldehyde or alcohol (optional)

Starting stage

  • Loading: The first amino acid is activated with ATP as a mixed acyl-phosphoric acid anhydride with AMP by the A-domain and loaded onto the serine-attached 4'-phospho-pantethine (4'PP) sidechain of the PCP-domain catalyzed by the PCP-domain (thiolation).
  • Some A domains require interaction with MbtH-like proteins for their activity.[5][6]
  • Sometimes the amino group of the bound amino acid is formylated by an F-domain or methylated by an NMT-domain.

Elongation stages

  • Loading: Analogous to the starting stage, each module loads its specific amino acid onto its PCP-domain.
  • Condensation: The C-domain catalyzes the amide bond formation between the thioester group of the growing peptide chain from the previous module with the amino group of the current module. The extended peptide is now attached to the current PCP-domain.
  • Condensation-Cyclization: Sometimes the C-domain is replaced by a Cy-domain, which, in addition to the amide bond formation, catalyzes the reaction of the serine, threonine, or cysteine sidechain with the amide-N, thereby forming oxazolidines and thiazolidine, respectively.
  • Epimerization: Sometimes an E-domain epimerizes the innermost amino acid of the peptide chain into the D-configuration.
  • This cycle is repeated for each elongation module.

Termination stage

  • Termination: The TE-domain (thio-esterase domain) hydrolyzes the completed polypeptide chain from the PCP-domain of the previous module, thereby often forming cyclic amides (lactams) or cyclic esters (lactones).
  • Also, the peptide can be released by an R-domain that reduces the thioester bond to terminal aldehyde or alcohol.

Processing

The final peptide is often modified, e.g., by glycosylation, acylation, halogenation, or hydroxylation. The responsible enzymes are usually associated to the synthetase complex and their genes are organized in the same operons or gene clusters.

Priming and deblocking

To become functional, the 4'-phospho-pantetheine sidechain of acyl-CoA molecules has to be attached to the PCP-domain by 4'PP transferases (Priming) and the S-attached acyl group has to be removed by specialized associated thioesterases (TE-II) (Deblocking).

Substrate specificities

Most domains have a very broad substrate specificity and usually only the A-domain determines which amino acid is incorporated in a module. Ten amino acids that control substrate specificity and can be considered the 'codons' of nonribosomal peptide synthesis have been identified. The condensation C-domain is also believed to have substrate specificity, especially if located behind an epimerase E-domain-containing module where it functions as a 'filter' for the epimerized isomer. Computational methods, such as SANDPUMA[7] and NRPSpredictor2[8], have been developed to predict substrate specificity from DNA sequence data.

Mixed with polyketides

Due to the similarity with polyketide synthases (PKS), many secondary metabolites are, in fact, fusions of NRPs and polyketides. In essence, this occurs when PK modules follow NRP modules, and vice versa. Although there is high degree of similarity between the PCP domains of both types of sythetases, the mechanism of condensation is different from a chemical standpoint (claisen vs. transamidation).

See also

References

  1. ↑ Dai, Li-Xin (2012). Ding, Kuiling, ed. Organic chemistry : breakthroughs and perspectives. Weinheim, Germany: Wiley-VCH. ISBN 9783527333776.
  2. ↑ J.D. Walton (2006). "HC-toxin". Phytochemistry. 67 (14): 1406–1413. doi:10.1016/j.phytochem.2006.05.033. PMID 16839576.
  3. ↑ R.D. Johnson; L. Johnson; Y. Itoh; M. Kodama; H. Otani; K. Kohmoto (2000). "Cloning and Characterization of a Cyclic Peptide Synthetase Gene from Alternaria alternata Apple Pathotype Whose Product Is Involved in AM-Toxin Synthesis and Pathogenicity". Molecular Plant-Microbe Interactions. 13 (7): 742–753. doi:10.1094/MPMI.2000.13.7.742. PMID 10875335.
  4. ↑ K. Turgay, M. Krause and M. A. Marahiel, Mol. Microbiol., 1992, 6, 529.
  5. ↑ Elizabeth A. Felnagle; John J. Barkei; Hyunjun Park; Angela M. Podevels; Matthew D. McMahon; Donald W. Drott; Michael G. Thomas (2010). "MbtH-Like Proteins as Integral Components of Bacterial Nonribosomal Peptide Synthetases". Biochemistry. 49: 8815–8817. doi:10.1021/bi1012854. PMC 2974439. PMID 20845982.
  6. ↑ Wenjun Zhang; John R. Heemstra Jr.; Christopher T. Walsh; Heidi J. Imker (2010). "Activation of the Pacidamycin PacL Adenylation Domain by MbtH-like Proteins". Biochemistry. 49: 9946–9947. doi:10.1021/bi101539b. PMC 2982891. PMID 20964365.
  7. ↑ Chevrette, Marc G.; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R.; Medema, Marnix H. (2017-10-15). "SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria". Bioinformatics. 33 (20): 3202–3210. doi:10.1093/bioinformatics/btx400. ISSN 1367-4803.
  8. ↑ Röttig, Marc; Medema, Marnix H.; Blin, Kai; Weber, Tilmann; Rausch, Christian; Kohlbacher, Oliver (2011-07-01). "NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity". Nucleic Acids Research. 39 (suppl_2): W362–W367. doi:10.1093/nar/gkr323. ISSN 0305-1048.

Literature

  • Dirk Schwarzer; Robert Finking; Mohamed A. Marahiel (2003). "Nonribosomal peptides: from genes to products". Nat. Prod. Rep. 20 (3): 275–87. doi:10.1039/b111145k. PMID 12828367.
  • Mohamed A. Marahiel; Torsten Stachelhaus; Henning D. Mootz (1997). "Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis". Chem. Rev. 97 (7): 2651–2674. doi:10.1021/cr960029e. PMID 11851476.
  • Segolene Caboche; Maude Pupin; Valerie Leclere; Arnaud Fontaine; Philippe Jacques; Gregory Kucherov (2008). "NORINE: a database of nonribosomal peptides". Nucleic Acids Research. 36 (Database issue): D326–31. doi:10.1093/nar/gkm792. PMC 2238963. PMID 17913739.
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