Introduction

Tyrocidine is a ten amino acid long nonribosomal peptide (NRP) produced by the tyrocidine synthetase. This nonribosomal synthetase (NRPS) is composed of ten modules with specificity for different proteinogenic and non-proteinogenic amino acids [1]. The tyrocidine pathway can be found e.g. in Brevibacillus parabrevis. The gene cluster ( Fig. 1 ) consists of: tycA, tycB and tycC. Those genes encode for different numbers of modules - tycA is a single module, tycB is composed of three, tycC of six modules. Only the complex of modules is able to produce a NRP, whereas a single module is not completely functional independently [2].
Every module is again subdivided into domains. Among the most common domains are the Adenylation domain, the Condensation domain and the Thiolation domain. Beside, there are Epimerization domains, Thio-Esterase domains and Communication domains [3] [4] [5].

During the synthesis of nonribosomal peptides, the growing peptide-chain is transferred from one module to the next. The domains within the modules fulfill distinct functions. An amino acid is first adenylated by the A domain and then bound to the T domain (also called Peptidyl-Carrier-Protein domain) via a thioester bond for subsequent reactions in the nascent NRP. The C domain then catalyzes the condensation of the already synthesized peptide chain (bound to the T domain) with the amino acid of the next module [7] [8]. The T domain itself does not exhibit any substrate specificity. Instead, it is merely a carrier domain to keep the peptide attached to the NRPS complex [4]. The core of every T domain is a conserved 4’-phosphopanthetheinylated (4’-PPT) Serine. The 4’-PPT residue is added by a 4’-PhosphoPanthetheinyl-Transferase (PPTase)activating the NRPS as a prosthetic group [9].

The remaining domains vary in their functions. Every NRPS is terminated by a TE domain that cleaves the thioester bond between the synthesized NRP and the last T domain [10]. E domains perform an epimerization reaction from the L- to the D-conformation or vice versa [11] [12]. Com domains are required for protein-protein interactions between subsequent modules that are not encoded on the same gene [13]. This is the case for the communication between the TycA and TycB1 module [14]. All of those six domain types mentioned above are present in the tyrocidine synthetase of B. parabrevis [6].

Results

Claims

Here we show that modules of NRPSs can be interchanged resulting in engineered enzymes with novel functionalities. In the following, we have three claims to propose.

1. Modules of NRPSs can be interchanged.
2. The enzyme modularity allows the synthesis of custom peptides.
3. Customized NRPs can be detected and are functional.

The establishment of a standard framework (RFC 100) for in-vivo synthesis of customized, novel NRPs by nonribosomal peptide synthetases required systematic investigation of NRPS modularity and compatibility. As proof of principle, we semi-rationally interchanged NRPS modules, a process we refer to as shuffling.

Shuffling Modules of a Single NRPS

Initially, we tried to interchange modules of the tyrocidine cluster of B. parabrevis in E. coli. The following criteria were considered important to be investigated in this context:

1. The initiation module TycA can be located at any position within a NRPS, when placing it behind a suitable C domain.
2. Any other module can be used as an Initiation module, when removing the C domain.
3. Non-proteinogenic amino acids can be introduced at any position.
4. Com domain interactions can be replaced by suitable linkers.

Assembling of a Synthetic NRPS

To obtain a basis for shuffling and creation of artificial peptide synthetases, the coding sequences for each individual module were amplified from the tyrocidine cluster by the use of primers optimized for a Gibson assembly strategy. The primers were annealed to the unconserved linker regions between the NRPS domains that were predicted by Pfam. We successfully validated the correct amplification of 12 single DNA fragments and corresponding pSB1C3 backbones by electrophoresis ( Fig. 2 ).

Since functionality of isolated modules cannot be shown, as they simply take up single amino acids without linking them to another monomer, we started to design small peptides of two to four amino acid long chains. To show the compatibility of the tyrocidine modules with one another, we put module genes into non-native order via Gibson Assembly. These constructs led to synthetic NRPSs and the production of five new peptides, i.e. one dipeptide, two tripeptides and two tetrapeptides.

We were able to successfully assemble all of our plasmids and continued our work with our synthetic dipeptide (Proline-Leucine) NRPS and tripeptide-I-NRPS (Phenylalanine-Ornithine-Leucine; Fig. 3 ) by transforming them into the E. coli strain BAPI.

Expression and Detection of the NRPS and its Products

The expression of the 212 kDa dipeptide synthetase and the 380 kDa tripeptide synthetase was shown by SDS-PAGE ( Fig. 4 ).

Since SDS-PAGE is not sensitive enough to detect small peptides, we wanted to assess the presence of the newly synthesized peptides at different time points by the use of mass spectrometry. Expression of the NRPSs was induced with Isopropyl β-D-1-thiogalactopyranoside (IPTG). Samples were taken at different time points post induction. Since residual salts could potentially disturb the acquisition of small peptide abundances, we washed our LB-Cm culture in M9 minimal medium to minimize this effect and improve the detection of our short NRPs. Supernatant and the bacterial pellet were processed separately. Final sample preparation for tandem mass-spectrometry was conducted at the neonate screening facility of the university medical center. There the peptides were hydrolyzed during the butylation reaction.

Finally the highly specific m/z profile allowed the identification of different amino acid abundances [16][17]. Since Ornithine is a non-proteinogenic amino acid that is incorporated in our tripeptide (Phe-Orn-Leu), we mainly focused on detecting Ornithine levels ( Fig. 5 ). The abundance of Ornithine in the tripeptide samples was strongly elevated with time compared to our dipeptide (Pro-Leu; Fig. 6 ). Due to variation of the general amino acid concentration in both used media and samples, we normalized the Ornithine values by the amount of all amino acids present in the respective medium.

The Ornithine level in the supernatant of the tripeptide samples peaked 21 hours upon induction. Afterwards concentrations returned to basal levels. Samples prepared from bacteria pellets showed minor increases in Ornithine levels in comparison to the pure medium and our negative control (untransformed BAPI). To aquire additional data on the existence of our short peptides we sent two samples to analysis via high-resolution electrospray ionization (HR-ESI) mass spectrometry at the mass spectrometry facility of the Institue for Chemistry, based on preliminary results from the Ornithine screening. However, we could not obtain conclusive data for our samples, because the background was too high (MS Results: dipeptide and Fig. 7 ).

In summary, we were able to amplify single modules from the tyrocidine NRPS cluster, and we shuffled them via Gibson Assembly. Two constructs coding for two entirely new NRPSs were successfully transformed. The synthetases are both well expressed on pSB1C3 in BAPI and their products, short NRPs, can be detected through tandem mass spectrometry finally confirming the functionality of the engineered NRPSs.

Discussion

Interchangeability of Modules

Module compatibility is the vital basis for any standardized work with NRPSs. Hence, the major objective of this project was to investigate flexible interchangeability of modules, which allows for customized synthesis of short peptides via NRPSs, as we propose in our standard (RFC 100). tyrocidine served as a paradigm for semi-rational rearrangements in the modular structure of NRPSs, a process, which we refer to as shuffling.

Here, we present a clear line of evidence stating that it is possible to shuffle modules to produce functional NRPs. Modules of NRPSs can be interchanged, as demonstrated by the creation of two different novel peptides through rearrangement of the respective modules that were amplified from B. parabrevis. The detection of these peptides was eased by the use of Ornithine, which is a non-proteinogenic amino acid and thus a proper marker for the synthesis of the desired peptide. Comparing the normalized levels of Ornithine in the different samples, we could conclude that the synthetic NRPS is in fact functional enabling the creation of customized peptides that can be detected via mass spectrometry.

Synthetic Peptides

Before our experiments, there was no evidence whether the synthetic peptides would be released to the medium or remained in the pellet. Showing that the resuspension of lyophilized supernatant in ethanol obtains a higher yield in ornithine content compared to the pellet samples, we can conclude that the small peptides are emitted into the medium. As salt concentrations did not seem to interfere with mass spectrometry measurements, the whole work up process has been successful. The final output of the tandem mass spectrometry demonstrated a highly elevated concentration of synthetic peptides in the medium compared to the cell interior, which leads to an improved protocol for standardized purification of short nonribosomal peptides (RFC 100).

Furthermore, we found that there was no need to provide additional Ornithine to the media since it was incorporated from E. coli as an intermediate product from L-glutamate. Moreover, this assay accounted for the functional incorporation of non-proteinogenic amino acids into artificial nonribosomal peptides. A high variety of non-proteinogenic amino acids as constituents has already been described in literature [19].

Interestingly, the Ornithine concentration in the samples peaked at the first day upon induction but dropped rapidly during the second day to basal level. The transient enrichment of Ornithine could reflect the stability of the NRPS or the synthesized tripeptide. Most likely Ornithine is cleaved by the endogenous enzyme ornithine decarboxylase encoded by the speC gene to form CO₂ and Putrescine [20]. As ornithine abundance and acidic conditions serve as activators for the expression of the Ornithine decarboxylase respectively , this would explain the time-shift due to increased expression. Although this decarboxylase cannot cleave Ornithine incorporated in peptides, it could contribute to the decay process of free ornithine. In addition, the products could be toxic for the cells and are therefore degraded faster. The kinetics of Ornithine as a proxy for the production of the tripeptide synthesis would thus imply that harvest of the peptide after one day would give optimal yield. Computational metabolic analysis could provide more insights into processes leading to peptide decay and instability. Metabolic reconstruction can give new insights to correlations at gene regulation and therefore provide new insights integrated in a biological context [21].

In the future, synthesized nonribosomal peptides could be elongated even further. Therefore, a stepwise-assembly strategy should be considered since the complexity of cloning will increase with the number and size of DNA fragments as well. Of course, additional modules for shuffling will increase the amount of opportunities to create comprehensive constructs. Such an approach is guided by the NRPS Designer, which frames our proposed standard (RFC 100).

Detection Methods

Mass spectrometry often requires several tries and iterations of sample work up procedures to acquire good results. Since the synthetic peptides assembled by our artificial nonribosomal peptide synthetases were rather small, their properties would not differ significantly from other salts in the solution. As we were able to cut salt concentrations significantly with our purification techniques, no problems of signal interference by the salty background occured at the tandem mass spectrometry of the neonate screening facility. The butylation reaction allowed a highly specific compound detection making this method less prone to high salt backgrounds. This technique could be the reason for the proper detection as it makes the product more distinctive. For other Mass Spectrometry measurements an improved purification procedure could lead to the spectra that were expected. In addition to contaminants disturbing a clear signal, a non-ionizability of our target compounds, several other adducts resulting from interactions with other remaining molecules or charge states, which we did not anticipate, could contribute to the inconclusive results. The fragmentation of molecules at the thought target mass did not display significant decay products. The results of the differential approaches were measured at two different facilities minimizing the risk of the mass spectrometre itself as an source of errors. We ourselves thought of using methods such as Click-Chemistry for the purification of the short, synthetic peptides. Increased masses and easy cleavage enable high purities and can be determined via HPLC with UV and ESI-MS detection [22]. This approach, however, does not offer any opportunity to evaluate expression in vivo’ [23].

Combinatorial Usage

Combinatorial chemistry gained significant recognition over the last decades. Screening of large libraries enables a target-oriented approach of compound research. Exhibiting the manifoldness of nonribosomal Peptides in combinatorial biology even short NRP sequences result in an impressive number of possible differentially composed products. As approximately 500 different monomers for NRPS exist even a dipeptide would result in possible 500²=250.000 possible combinations of which, of course only a fraction would obtain a reasonable function. Calculating the number of possible combinations of a product composed of 3 monomers, as we assembled, already leads to 500³ = 125 million. These simple numbers would increase even more with longer sequences and the introduction of possible modifications, as branching or cyclization. To stack this number up against the number of possible combinations assembled by the ribosome (22³ = 10.648) the potential of NRPS for in-vivo peptide production becomes even more vivid (tab. 1). Although most of the products won´t inhabit specific features, for instance customized production of toxins, siderophores, pigments, antibiotics, cytostatics, and immunosuppressants would be facilitated. That even small peptides are functional can be seen from the success of peptide therapeutics [24] and from various natural products like the peptide enterobactin, for example. Databases like Norine [25] and Software as the NRPS Designer developed by us will assist these purposes.

Tab. 1: Comparison of possible combinations for peptides of different sequence lengths for Ribosomal and Nonribosomal Peptides

Sequence Length	Possible Nonribosomal Peptide Combinations*	Possible Ribosomal Peptide Combinations
2	250.000	484
3	125.000.000	10.648
4	62.500.000.000	234.256

*on basis of estimations of 500 possible monomers and exclusion of modifications as branching.

Conclusion

We can prove all claims mentioned above since we have:

1. Exchanged modules of of the tyrocidine synthetase
2. Constructed a custom dipeptide- and a custom tripeptide-NRPS
3. Detected both the engineered NRPSs and the synthetic peptides via SDS-PAGE and mass spectrometry

In Conclusion we were able to prove interchangeability and recombinational potential of modules deriving from a single NRPS. The proper expression of the synthetase was shown by SDS-PAGES and an indirect prove of incorporation of non-proteinogenic amino acids accounting for a functional production of the desired target peptide. Thus, we were able to reproduce the work of Marahiel et al. [26] and could open up the diversity of NRPS to the iGEM community. Proving inter-species compatibility of different modules, we were able to confirm all four claims mentioned above. The achievements were enabled through and fed back to the NRPS Designer. This software tool incorporates a database utilizing our experimental on NRPS modules for guiding through user-oriented design of NRPSs.