Nonribosomal peptide

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Overview

Nonribosomal peptides (NRP) are a class of secondary metabolites, usually produced by microorganisms like bacteria and fungi. These are also often found in higher organisms, such as nudibranchs but they are thought to be made by bacteria inside these organisms. Note that although there are many peptides which are not made on the ribosome, nonribosomal peptide typically refers to a very specific set of these as discussed in this article.

Unlike polypeptides synthesized on the ribosome, these peptides are synthesized by nonribosomal peptide synthetases (NRPS) from amino acids. NRPS can be thought of as preassembled, modular, molecular factories. Unlike the ribosome, which is fed an mRNA code and can make an arbitrary sequence of peptides, an NRPS does not accept a code and is preset to make one peptide. As a class, NRPS can make a wider diversity of peptides than can ribosomes.

NRPs often have a cyclic and/or branched structure, 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. Occasionally dehydration is performed on serines resulting on dehydroalanine. This is just a sampling of the various manipulations and variations that NRPS can perform. NRPs are often dimers or trimers of identical sequences chained together or cyclized, or even branched.

Nonribosomal peptides are structurally 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. The enzymes are organized in modules that are responsible for the indroduction 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 similarities 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/NMe]-A-PCP-
  • Elongation or Extending modules: -(C/Cy)-[NMe]-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-pantethein (required in a module)
  • C: Condensation forming the amide bond (required in a module)
  • Cy: Cylization 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)
  • 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-pantethein (4'PP) sidechain of the PCP-domain catalyzed by the PCP-domain (thiolation) .
  • Sometimes the amino group of the bound amino acid is formylated by an F-domain or methylated by an NMe-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.
  • 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 ACP-domain of the previous module, thereby often forming cyclic amides (lactams) or cyclic esters (lactones).
  • Alternatively, 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-pantethein 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 have been identified that control substrate specificity and can be considered the 'codons' of nonribosomal peptide synthesis. 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.

Mixed with Polyketides

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

See also

Literature

  • "Nonribosomal peptides: from genes to products" by Dirk Schwarzer, Robert Finking, and Mohamed A. Marahiel in Nat. Prod. Rep. 20(3):275-287 (2003) DOI: 10.1039/b111145k
  • "Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis" by Mohamed A. Marahiel, Torsten Stachelhaus, and Henning D. Mootz in Chem. Rev. 97(7):2651-2673 (1997) DOI: 10.1021/cr960029e



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