De Novo Sequencing of Nonribosomal Peptides
While nonribosomal peptides (NRPs) are of tremendous pharmacological importance, there is currently no technology capable of high-throughput sequencing of NRPs. Difficulties in sequencing NRPs slow down the progress in elucidating the non-ribosomal geneti
- PDF / 837,477 Bytes
- 15 Pages / 430 x 660 pts Page_size
- 60 Downloads / 203 Views
University of California, San Diego, USA University of California, Santa Cruz, USA [email protected]
Abstract. While nonribosomal peptides (NRPs) are of tremendous pharmacological importance, there is currently no technology capable of high-throughput sequencing of NRPs. Difficulties in sequencing NRPs slow down the progress in elucidating the non-ribosomal genetic code and negatively affect various screening programs aimed at the discovery of natural compounds of medical importance. We propose to employ multi-stage mass-spectrometry (MSn ) for the data acquisition, followed by alignment-based heuristic algorithms for data analysis. Since mass spectrometry based analysis of NRPs is fast and inexpensive, this approach opens the possibility of high-throughput sequencing of many unknown NRPs accumulated in large screening programs. Keywords: Cyclic Peptides Sequencing De novo Algorithm.
1
Introduction
The classical protein synthesis pathway (translation of template mRNA into proteins/peptides) is not the only mechanism for cells to assemble amino acids into peptides. The alternative Non Ribosomal Peptide Synthesis is performed by a large multi-enzyme complex (called Non Ribosomal Peptide Synthetase or NRPS) that represents both the biosynthetic machinery and the mRNA-free template for the biosynthesis of secondary metabolites (see [1,2,3] for recent reviews). NRPS gene clusters produce relatively short (up to 50 aa) nonribosomal peptides (NRP) that are not directly inscribed in the genomic DNA and thus cannot be inferred with traditional DNA-based sequencing techniques. NRPs are of tremendous pharmacological importance since they were optimized during millions of years of evolution to play important roles in chemical defense and communication for producing organisms. Starting from penicillin, NRPs and other natural products have an unparallel track record in pharmacology: 9 out of the top 20 best-selling drugs were either inspired by or derived from natural products. NRPs have some naturally evolved features that are applicable to the modulation of protein function in human systems, making them excellent lead compounds for the development of novel pharmaceutical agents. In particular, NRPs include antibiotics (penicillin, cephalosporin, vancomycin, M. Vingron and L. Wong (Eds.): RECOMB 2008, LNBI 4955, pp. 181–195, 2008. c Springer-Verlag Berlin Heidelberg 2008
182
N. Bandeira et al.
etc.), immunosuppressors (cyclosporin), antiviral agents (luzopeptin A), antitumor agents (bleomycin), toxins (thaxtomin), and many peptides with yet unknown functions. When DNA sequencing is not available, biologists use either Edman degradation or tandem mass spectrometry (MS2 ) to sequence ribosomal peptides. However, neither of these approaches works for nonribosomal peptides since they differ from ribosomal peptides in many respects: (i) they often represent non-linear structures of amino acids, e.g., cyclic, tree-like, and branch-cyclic peptides, (ii) they often contain non-standard amino acids increasing the number of pos
Data Loading...
