Biosynthesis and biotechnological application of non-canonical amino acids: Complex and unclear

Compared with the better-studied canonical amino acids, the distribution, metabolism and functions of natural non-canonical amino acids remain relatively obscure. Natural non-canonical amino acids have been mainly discovered in plants as secondary metabolites that perform diversified physiological functions. Due to their specific characteristics, a broader range of natural and artificial non-canonical amino acids have recently been applied in the development of functional materials and pharmaceutical products. With the rapid development of advanced methods in biotechnology, non-canonical amino acids can be incorporated into peptides, proteins and enzymes to improve the function and performance relative to their natural counterparts. Therefore, biotechnological application of non-canonical amino acids in artificial bio-macromolecules follows the central goal of synthetic biology to: create novel life forms and functions. However, many of the non-canonical amino acids are synthesized via chemo- or semi-synthetic methods, and few non-canonical amino acids can be synthesized using natural in vivo pathways. Therefore, further research is needed to clarify the metabolic pathways and key enzymes of the non-canonical amino acids. This will lead to the discovery of more candidate non-canonical amino acids, especially for those that are derived from microorganisms and are naturally bio-compatible with chassis strains for in vivo biosynthesis. In this review, we summarize representative natural and artificial non-canonical amino acids, their known information regarding associated metabolic pathways, their characteristics and their practical applications. Moreover, this review summarizes current barriers in developing in vivo pathways for the synthesis of non-canonical amino acids, as well as other considerations, future trends and potential applications of non-canonical amino acids in advanced biotechnology.     

Synthesis and Structure-activity Relationships of Amastatin Analogues,Inhibitors of Aminopeptidase A

Stereoisomers and analogues of amastatin, [(2S,3R)-3-amino-2-hydroxy-5-methylhexanoyl]-l-Val-l-Val-l-Asp, were synthesized and their inhibitory activities towards aminopeptidase A (AP-A) and other arylamidases tested. Among the four stereoisomers of a new amino acid residue in amastatin, the 2S stereoisomers exhibited strong activity. In a series of compounds in which the C-terminal amino acid of amastatin was substituted by other amino acids, the one containing Asp or Glu showed the strongest activity towards AP-A. In a series of compounds in which the second or third residue from the amino terminal of amastatin was substituted by other amino acids, the one containing hydrophobic amino acids showed strong activity. In the study of the relationship of the length of the peptide chain and inhibitory activity, the activity towards AP-A was seen to increase until the length of the peptide reached that of a tetrapeptide.     

Analysis of tyrosine- and methionine-containing neuropeptides by fast atom bombardment mass spectrometry

A simple and unambiguous method for the detection of the amino acids tyrosine and methionine in peptide structures has been developed. The procedure, which was applied in studies of opioid peptides, is based on continuous-flow fast atom bombardment mass spectrometry (CF-FAB-MS) following chemical modification of the residue to be analyzed. Thus, for the detection of tyrosine, modification reactions such as acetylation or non-radioactive iodination were performed prior to analysis by CF-FAB-MS. O-Acetylation of the tyrosine residue with N-acetylimidazole was accompanied by a shift of 42 Da in the molecular mass of the peptide under investigation. This modification was reversed by treatment with hydroxylamine hydrochloride. Incorporation of iodine resulted in a molecular weight shift of 126 Da per iodine atom. Methionine residues were detected in methionine-enkephalin-containing peptides following S-oxidation with hydrogen peroxide. The procedures described may have a wide application in peptide chemistry, particularly for the identification of peptide fragments containing the above residues, e.g. in studies of processing or degradation of the enkephalins or other neuropeptides (e.g. endorphins and tachykinins).     

Non-canonical amino acids in protein engineering

Methods for engineering proteins that contain non-canonical amino acids have advanced rapidly in the past few years. Novel amino acids can be introduced into recombinant proteins in either a residue-specific or site-specific fashion. The methods are complementary: residue-specific incorporation allows engineering of the overall physical and chemical behavior of proteins and protein-like macromolecules, whereas site-specific methods allow mechanistic questions to be probed in atomistic detail. Challenges remain in the engineering of the translational apparatus and in the design of schemes that can be used to encode both canonical and non-canonical amino acids.     

Synthesis of novel unnatural amino acid as a building block and its incorporation into an antimicrobial peptide

Considering the biological mechanism and in vivo stability of antimicrobial peptides, we designed and synthesized novel unnatural amino acids with more positively charged and bulky side chain group than lysine residue. The unusual amino acids, which were synthesized by either solution phase or solid phase, were incorporated into an antimicrobial peptide. Its effect on the stability, activity, and the structure of the peptide was studied to evaluate the potential of these novel unnatural amino acids as a building block for antimicrobial peptides. The incorporation of this unusual amino acid increased the resistance of the peptide against serum protease more than three times without a decrease in the activity. Circular dichroism spectra of the peptides indicated that all novel unnatural amino acids must have lower helical forming propensities than lysine. Our results indicated that the unnatural amino acids synthesized in this study could be used not only as a novel building block for combinatorial libraries of antimicrobial peptides, but also for structure–activity relationship studies about antimicrobial peptides.     

Novel tRNA aminoacylation mechanisms

In nature, ribosomally synthesized proteins can contain at least 22 different amino acids: the 20 common amino acids as well as selenocysteine and pyrrolysine. Each of these amino acids is inserted into proteins codon-specifically via an aminoacyl-transfer RNA (aa-tRNA). In most cases, these aa-tRNAs are biosynthesized directly by a set of highly specific and accurate aminoacyl-tRNA synthetases (aaRSs). However, in some cases aaRSs with relaxed or novel substrate specificities cooperate with other enzymes to generate specific canonical and non-canonical aminoacyl-tRNAs.     

Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog

Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins.     

Evaluation and biosynthetic incorporation of chlorotyrosine into recombinant proteins

Recently, non-canonical amino acids (NCAA) incorporation was developed to enhance the functional properties of proteins. Incorporation of NCAA containing chlorine atom is conceptually an attractive approach to prepare pharmacologically active substances, which is a difficult task since chlorine is bulky atom. In this study, we evaluated the efficiency and extent of in vivo incorporation of tyrosine analogue 3-chlorotyrosine [(3-Cl)Tyr] into the recombinant proteins GFP and GFPHS (highly stable GFP). The incorporation of (3-Cl)Tyr into GFP leads to dramatic reduction in the expression level of protein. On the other hand, the incorporation of (3-Cl)Tyr into GFPHS was expressed well as a soluble form. In addition we used bioinformatics tools for the analysis to explore the possible constraints in micro-environment of each natural amino acid residue to be replaced with chlorine atom accommodation into GFPHS. In conclusion, our approaches are reliable and straightforward way to enhance the translation of chlorinated amino acids into proteins.     

Chemoenzymatic methods for site-specific protein modification

In the past decade, numerous chemical technologies have been developed to allow the site-specific post-translational modification of proteins. Traditionally covalent chemical protein modification has been accomplished by the attachment of synthetic groups to nucleophilic amino acids on protein surfaces. These chemistries, however, are rarely sufficiently selective to distinguish one residue within a literal sea of chemical functionality. One solution to this problem is to introduce a unique chemical handle into the target protein that is orthogonal to the remainder of the proteome. In practice, this handle can be a novel peptide sequence, which forms a 'tag' that is selectively and irreversibly modified by enzymes. Furthermore, if the enzymes can tolerate substrate analogs, it becomes possible to engineer chemically modified proteins in a site-specific fashion. This review details the significant progress in creating techniques for the chemoenzymatic generation of protein-small molecule constructs and provides examples of novel applications of these methodologies.     

High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology

Incorporation of noncanonical amino acids (ncAAs) can endow proteins with novel functionalities, such as crosslinking or fluorescence. In ion channels, the function of these variants can be studied with great precision using standard electrophysiology, but this approach is typically labor intensive and low throughput. Here, we establish a high-throughput protocol to conduct functional and pharmacological investigations of ncAA-containing human acid-sensing ion channel 1a (hASIC1a) variants in transiently transfected mammalian cells. We introduce 3 different photocrosslinking ncAAs into 103 positions and assess the function of the resulting 309 variants with automated patch clamp (APC). We demonstrate that the approach is efficient and versatile, as it is amenable to assessing even complex pharmacological modulation by peptides. The data show that the acidic pocket is a major determinant for current decay, and live-cell crosslinking provides insight into the hASIC1a–psalmotoxin 1 (PcTx1) interaction. Further, we provide evidence that the protocol can be applied to other ion channels, such as P2X2 and GluA2 receptors. We therefore anticipate the approach to enable future APC-based studies of ncAA-containing ion channels in mammalian cells.

This study describes a method to rapidly screen hundreds of ion channel variants containing non-canonical amino acids. A proof-of-principle introducing photocrosslinking non-canonical amino acids into the human ion channel hASIC1a shows how this approach can provide insights into function and pharmacology.     

Applications of Genetic Code Expansion in Studying Protein Post-translational Modification

Various post-translational modifications can naturally occur on proteins, regulating the activity, subcellular localization, interaction, or stability of the proteins. However, it can be challenging to decipher the biological implication or physiological roles of site-specific modifications due to their dynamic and sub-stoichiometric nature. Genetic code expansion method, relying on an orthogonal aminoacyl-tRNA synthetase/tRNA pair, enables site-specific incorporation of non-canonical amino acids. Here we focus on the application of genetic code expansion to study site-specific protein post-translational modification in vitro and in vivo. After a brief introduction, we discuss possibilities of incorporating non-canonical amino acids containing post-translational modifications or their mimics into target proteins. This approach is applicable for Ser/Thr/Tyr phosphorylation, Tyr sulfation/nitration/hydroxylation, Lys acetylation/acylation, Lys/His mono-methylation, as well as Arg citrullination. The next section describes the use of a precursor non-canonical amino acid followed by chemical and/or enzymatic reactions to afford the desired modification, such as Cys/Lys acylation, ubiquitin and ubiquitin-like modifications, as well as Lys/Gln methylation. We also discuss means for functional regulation of enzymes involving in post-translational modifications through genetically incorporated non-canonical amino acids. Lastly, the limitations and perspectives of genetic code expansion in studying protein post-translational modification are described.     

Synthesis and Mass Spectrometry Analysis of Mimosine-Containing Peptides

Non-proteinogenic amino acids are widely explored group of compounds due to their chemical properties and great potential of application in the combinatorial chemistry, medicinal investigation etc. Therefore the synthetic methods of their incorporation to the peptide chain are required. l-Mimosine, (S)-α-amino-β-(3-hydoxy-4-oxo-1,4-dihydropyridin-1-yl)-propanoic acid), is a plant amino acid, known to induce apoptosis in human pancreatic cancer xenografts. Here we present our investigations on the synthesis of mimosine-containing peptide and their ESI-MS/MS analysis. We successfully applied Fmoc-protected mimosine a with a free hydroxy ketone group for efficient peptide synthesis in the presence of HATU as a coupling reagent without the formation of side products. Additionally the tandem mass spectrometry analysis revealed the characteristic loss of the heterocyclic ring from mimosine residue side chain. The described method allows insertion of mimosine residue at any endo-position within a peptide sequence. The obtained results may be useful in the synthesis and mass spectrometry analysis of various mimosine-containing peptides.

     

Amino acid sequence of the phosphorylation site of isocitrate dehydrogenase fromEscherichia coli

InEscherichia coli, NADP⁺-specific isocitrate dehydrogenase (EC 1.1.1.42) may undergo a phosphorylation catalyzed by a cAMP-independent protein kinase, with a concomitant decrease in catalytic activity. In this report, we describe the purification and amino acid sequence of a³²P-labeled peptide obtained from in vivo³²P-labeled isocitrate dehydrogenase. The³²P-labeled peptide was isolated from a tryptic digest and found to contain seven amino acids, including a single serine residue. Following automated Edman degradation and reversephase high-pressure liquid chromatography of the phenylthiohydantoin-amino acids, the sequence of this peptide was established to be-Ser(P)-Leu-Asn-Val-Ala-Leu-Arg.     

Recombinant hBMP4 incorporated with non-canonical amino acid for binding to hydroxyapatite

A novel growth factor containing non-canonical amino acids was designed and synthesized to enhance the binding to hydroxyapatite (HA). The designed protein was human bone morphogenetic protein 4 (hBMP4) incorporating diphosporylated serines (pSpS) that was found in salivary protein statherin and was reported to be responsible for binding to HA. Recombinant hBMP4 and a short peptide sequences containing pSpS were ligated by enzymatice reaction of sortase A, which exchanges the terminal amino acids of two polypeptides. Resulting hBMP4 containing pSpS (hBMP4-pSpS) bound HA more efficiently than hBMP-4 tagged with canonical serines (hBMP4-SS). The HA-bound hBMP-4-pSpS exhibited osteogenesis inducing activity to multipotential mesenchyme cells (C3H10T1/2) as evidenced by increased expression of osteogenic markers, which was not seen by hBMP4-SS. This novel protein with non-canonical serines will be applicable to bone regeneration materials in combination with HA.     

Analytical Procedures for the Sequential Extraction of 14C-Labeled Constituents from Leaves, Bark and Wood of Cottonwood Plants

A procedure for the extraction, separation, and measurement of photosynthetically fixed ¹⁴C in up to 8 chemical fractions (CHCl), amino acids, organic acids, sugars, protein, starch, hemicellulose, and residue) from small samples (1 to 100 mg) of cottonwood (Populus deltoides Bartr.) leaf material is described. The different chemical fractions are extracted in a sequence of chemical, ion exchange, and enzymatic steps. The ¹⁴C-activity in these major fractions is then determined with liquid scintillation spectrometry. These major fractions (e.g., sugars, amino acids, organic acids) can be further separated into their individual chemical components by standard thin-layer or gas- chromatographic methods for quantitative analysis if specific activities are desired. The major advantage of the procedure is that many chemical fractions can be sequentially separated with good reproducibility from a small amount of plant material without transfer of the material from the original homogenizer or centrifuge tube.     

The amino acid sequence of the peptide moiety of the pseudomurein from Methanobacterium thermoautotrophicum

The amino acid sequence of the peptide subunits of the peptide moiety of the sacculus polymer (pseudomurein) of Methanobacterium thermoautotrophicum was elucidated by analysing overlapping peptides obtained from partial acid hydrolysates of isolated sacculi. It is suggested that the peptide subunits are attached to glycan strands via one of their glutamyl residues. Another glutamyl residue may crosslink two adjacent peptide subunits to form a dimer. The calculated molar ratios of the amino acids and the percentages of the N-or C-terminal amino acid residues of the supposed dimers are compatible with those actually found in the sacculus polymer.     

AlLTPs from Allium species represent a novel class of lipid transfer proteins that are localized in endomembrane compartments

Lipid transfer proteins (LTPs) are widely distributed in the plant kingdom, but their functions remain elusive. The proteins AlLTP2-4 were isolated from three related Allium plants: garlic (A. sativum L.), Welsh onion (A. fistulosum L.), and Nanking shallot (A. ascalonicum L.). These novel proteins comprise a new class of LTPs associated with the Ace-AMP1 from onion (A. cepa L.). The AlLTP genes encode proteins harboring 132 common amino acids and also share a high level of sequence identity. Protein characteristics and phylogenetic analysis suggest that LTPs could be classified into five distinct groups. The AlLTPs were clustered into the most distantly related plant LTP subfamily and appeared to be restricted to the Allium species. In particular, the number of amino acids existing between the fourth and fifth Cys residue was suggested as a conserved motif facilitating the categorization of all the LTP-related proteins in the family. Unlike other LTPs, AlLTPs harboring both the putative C-terminal propeptide and N-terminal signal peptide were predicted to be localized to cytoplasmic vacuoles. When a chimeric GFP protein fused with both N-terminal and C-terminal AlLTP2 signal peptides was expressed in rice cells, the fluorescence signal was detected in the endomembrane compartments, thereby confirming that AlLTPs are an unprecedented intracellular type of LTP. Collectively, our present data demonstrate that AlLTPs are a novel type of LTP associated with the Allium species.     

Differences between ranamargarin and other tachykinins in the stimulation of ion transport in frog skin

In frog skin, tachykinins stimulate ion transport by interaction with NK1-like receptors. The structural requirements of the peptide are the presence of the C-terminal sequence Phe-X-Gly-Leu-Met-NH₂ and at least one Pro residue in the N-terminal sequence. In this paper, we demonstrate that the C-terminal amino acid must be amidated but it can be different from Met, and that the sequence cannot be longer or shorter than 11–12 amino acids. Unexpectedly, Ranamargarin (14 amino acids, no Pro residue) increased the short circuit current value by 48 ± 0.3%. On the basis of considerable experimental evidence, we suggest that Ranamargarin interacts with a receptor different from those of other tachykinins.     

Improved antimicrobial activity of h‐lysozyme (107–115) by rational Ala substitution

The most challenging target in the design of new antimicrobial agents is the development of antibiotic resistance. Antimicrobial peptides are good candidates as lead compounds for the development of novel anti‐infective drugs. Here we propose the sequential substitution of each Ala residue present in a lead peptide with known antimicrobial activity by specific amino acids, rationally chosen, that could enhance the activity of the resultant peptide. Taking the fragment 107–115 of the human lysozyme as lead, two‐round screening by sequentially replacing both Ala residues (108 and 111) by distinct amino acids resulted in a novel peptide with 4‐ and 20‐fold increased antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, respectively. These results reinforce the strategy proposed, which, in combination with simple and easy screening tools, will contribute to the rapid development of new therapeutic peptides required by the market. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.