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

Antibiotics
Antibiotic precursors
- ACV-Tripeptide
Cytostatics
Immunosuppressants
- Ciclosporin (Cyclosporine A)
Siderophores
Pigments
- Indigoidine
Toxins
- Microcystins and
- Nodularins, cyanotoxins from cyanobacteria.
Nitrogen storage polymers
- Cyanophycin – produced by some cyanobacteria
Phytotoxins
- HC-toxin – a virulence factor made by the plant pathogenic fungus Cochliobolus (Helminthosporium) carbonum^[2]
- AM-toxin – made by the plant pathogenic fungus Alternaria alternata pv. Mali^[3]
- victorin – a chlorinated cyclic pentapeptide made by the pathogenic fungus Cochliobolus victoriae. Its nonribosomal synthesis has not been established.

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.^[5]

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.^[6]

Note that as many as 10% percent of bacterial NRPS are not laid out as large modular proteins, but as separate enzymes.^[6] Some NRPS modules deviate from the standard domain structure, and some extra domains have been described. There are also NRPS enzymes that serve as a scaffold for other modifications to the substrate to incorporate unusual amino acids.^[7]

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)
X: Recruits cytochrome P450 enzymes (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.^[8]^[9]
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, and rational protein design has yielded methodologies to computationally switch the specificities of A-domains.^[10] 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^[11] and NRPSpredictor2,^[12] have been developed to predict substrate specificity from DNA or protein 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 Carrier (PCP/ACP) domains of both types of synthetases, the mechanism of condensation is different from a chemical standpoint:

PKS, carbon-carbon bond formation through Claisen condensation reaction
NRPs, the C domain catalyzes the amide bond formation between the amino acid it adds to the chain (on the PCP of one module) and the nascent peptide(on the PCP of the next module).^[13]

References

^ Dai LX (2012). Ding K (ed.). Organic chemistry : breakthroughs and perspectives. Weinheim, Germany: Wiley-VCH. ISBN 9783527333776.
^ Walton JD (July 2006). "HC-toxin". Phytochemistry. 67 (14): 1406–13. Bibcode:2006PChem..67.1406W. doi:10.1016/j.phytochem.2006.05.033. PMID 16839576.
^ Johnson RD, Johnson L, Itoh Y, Kodama M, Otani H, Kohmoto K (July 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): 742–53. doi:10.1094/MPMI.2000.13.7.742. PMID 10875335. S2CID 36754751.
^ Turgay K, Krause M, Marahiel MA (February 1992). "Four homologous domains in the primary structure of GrsB are related to domains in a superfamily of adenylate-forming enzymes". Molecular Microbiology. 6 (4): 529–46. doi:10.1111/j.1365-2958.1992.tb01498.x. PMID 1560782. S2CID 25266991.
^ Fischbach MA, Walsh CT (August 2006). "Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms". Chemical Reviews. 106 (8): 3468–96. doi:10.1021/cr0503097. PMID 16895337. S2CID 29014161.
^ ^a ^b Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K (June 2014). "Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes". Proceedings of the National Academy of Sciences of the United States of America. 111 (25): 9259–64. Bibcode:2014PNAS..111.9259W. doi:10.1073/pnas.1401734111. PMC 4078802. PMID 24927540.
^ McErlean M, Overbay J, Van Lanen S (March 2019). "Refining and expanding nonribosomal peptide synthetase function and mechanism". Journal of Industrial Microbiology & Biotechnology. 46 (3–4): 493–513. doi:10.1007/s10295-018-02130-w. PMC 6460464. PMID 30673909.
^ Felnagle EA, Barkei JJ, Park H, Podevels AM, McMahon MD, Drott DW, Thomas MG (October 2010). "MbtH-like proteins as integral components of bacterial nonribosomal peptide synthetases". Biochemistry. 49 (41): 8815–7. doi:10.1021/bi1012854. PMC 2974439. PMID 20845982.
^ Zhang W, Heemstra JR, Walsh CT, Imker HJ (November 2010). "Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins". Biochemistry. 49 (46): 9946–7. doi:10.1021/bi101539b. PMC 2982891. PMID 20964365.
^ Chen CY, Georgiev I, Anderson AC, Donald BR (March 2009). "Computational structure-based redesign of enzyme activity". Proceedings of the National Academy of Sciences of the United States of America. 106 (10): 3764–9. Bibcode:2009PNAS..106.3764C. doi:10.1073/pnas.0900266106. PMC 2645347. PMID 19228942.
^ Chevrette MG, Aicheler F, Kohlbacher O, Currie CR, Medema MH (October 2017). "SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria". Bioinformatics. 33 (20): 3202–3210. doi:10.1093/bioinformatics/btx400. PMC 5860034. PMID 28633438.
^ Röttig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O (July 2011). "NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity". Nucleic Acids Research. 39 (Web Server issue): W362-7. doi:10.1093/nar/gkr323. PMC 3125756. PMID 21558170.
^ Bloudoff, Kristjan; Schmeing, Martin T. (2017). "Structural and functional aspects of the nonribosomal peptide synthetase condensation domain superfamily: discovery, dissection and diversity". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1865 (11): 1587–1604. doi:10.1016/j.bbapap.2017.05.010. PMID 28526268.