Genetic Incorporation Research Articles

Genetic incorporation of D-Lysine into diketoreductase in Escherichia coli cells

AbstractD-Lysine has been genetically introduced into diketoreductase in E. coli cells by utilization of an orthogonal Ph tRNA /Lysyl-tRNA synthetase pair. This is the first report on the genetic incoporation of D-amino acids into proteins, which may be generally applicable to a wide variety of applications.

Genetically Encoding Bioorthogonal Functional Groups for Site-selective Protein Labeling

Site-selective protein labeling is an indispensible approach in the currently intense chemical biology research area. Studies involving site-selective protein labeling span from the protein dynamic analysis in vitro to the proteinprotein interaction investigation in living cells. In the past decade, multiple methods have been introduced to achieve site-selective protein labeling. These include genetic fusion of green fluorescent protein and its derivatives, selective chemical labeling of proteins with fusion tags, and site-specific modification of noncanonical amino acids that are genetically encoded. Using evolved orthogonal aminoacyl-tRNA synthetase-nonsense suppressor tRNA pairs, noncanonical amino acids with bioorthogonal functional groups such as azide, alkyne, tetrazine, alkene, keto, phenylhalide, etc. have been genetically incorporated into proteins in E. coli, yeast, and mammalian cells. Genetic encoding of these noncanonical amino acids enables multiple ways for site-selective protein labeling both in vitro and in vivo, allowing diverse strategies to interrogate protein functions. This review intends to provide a brief introduction to the genetic noncanonical amino acid incorporation technique and recent progresses in applying this technique to achieve site-selective protein labeling.

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites

Stop codons have been exploited for genetic incorporation of unnatural amino acids (Uaas) in live cells, but the efficiency is low possibly due to competition from release factors, limiting the power and scope of this technology. Here we show that the reportedly essential release factor 1 can be knocked out from Escherichia coli by fixing release factor 2. The resultant strain JX33 is stable and independent, and reassigns UAG from a stop signal to an amino acid when a UAG-decoding tRNA/synthetase pair is introduced. Uaas were efficiently incorporated at multiple UAG sites in the same gene without translational termination in JX33. We also found that amino acid incorporation at endogenous UAG codons is dependent on RF1 and mRNA context, which explains why E. coli tolerates apparent global suppression of UAG. JX33 affords a unique autonomous host for synthesizing and evolving novel protein functions by enabling Uaa incorporation at multiple sites.

Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal‐Binding Site into Green Fluorescent Protein

Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal‐Binding Site into Green Fluorescent Protein

Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal‐Binding Site into Green Fluorescent Protein

Development of a Selective, Sensitive, and Reversible Biosensor by the Genetic Incorporation of a Metal‐Binding Site into Green Fluorescent Protein

Molecular and morphological diversity in Japanese rice germplasm

Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the He value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher's method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.

Probing Local Environments with the Infrared Probe: l-4-Nitrophenylalanine

The genetic incorporation of unnatural amino acids (UAAs) with high efficiency and fidelity is a powerful tool for the study of protein structure and dynamics with site-specificity in a relatively nonintrusive manner. Here, we illustrate the ability of L-4-nitrophenylalanine to serve as a sensitive IR probe of local protein environments in the 247 residue superfolder green fluorescent protein (sfGFP). Specifically, the nitro symmetric stretching frequency of L-4-nitrophenylalanine was shown to be sensitive to both solvents that mimic different protein environments and (15)N isotopic labeling of the three-atom nitro group of this UAA. (14)NO(2) and (15)NO(2) variants of this UAA were incorporated utilizing an engineered orthogonal aminoacyl-tRNA synthetase/tRNA pair into a solvent exposed and a partially buried position in sfGFP with high efficiency and fidelity. The combination of isotopic labeling and difference FTIR spectroscopy permitted the nitro symmetric stretching frequency of L-4-nitrophenylalanine to be experimentally measured at either site in sfGFP. The (14)NO(2) symmetric stretching frequency red-shifted 7.7 cm(-1) between the solvent exposed and partially buried position, thus illustrating the ability of this UAA to serve as an effective IR probe of local protein environments.

Genetic Incorporation of Human Metallothionein into the Adenovirus Protein IX for Non-Invasive SPECT Imaging

As the limits of existing treatments for cancer are recognized, clearly novel therapies must be considered for successful treatment; cancer therapy using adenovirus vectors is a promising strategy. However tracking the biodistribution of adenovirus vectors in vivo is limited to invasive procedures such as biopsies, which are error prone, non-quantitative, and do not give a full representation of the pharmacokinetics involved. Current non-invasive imaging strategies using reporter gene expression have been applied to analyze adenoviral vectors. The major drawback to approaches that tag viruses with reporter genes is that these systems require initial viral infection and subsequent cellular expression of a reporter gene to allow non-invasive imaging. As an alternative to conventional vector detection techniques, we developed a specific genetic labeling system whereby an adenoviral vector incorporates a fusion between capsid protein IX and human metallothionein. Our study herein clearly demonstrates our ability to rescue viable adenoviral particles that display functional metallothionein (MT) as a component of their capsid surface. We demonstrate the feasibility of 99mTc binding in vitro to the pIX-MT fusion on the capsid of adenovirus virions using a simple transchelation reaction. SPECT imaging of a mouse after administration of a 99mTc-radiolabeled virus showed clear localization of radioactivity to the liver. This result strongly supports imaging using pIX-MT, visualizing the normal biodistribution of Ad primarily to the liver upon injection into mice. The ability we have developed to view real-time biodistribution in their physiological milieu represents a significant tool to study adenovirus biology in vivo.

Genetic Incorporation of an Unnatural Fluorescent Amino Acid in a Plant H-ATPase Expressed in Yeast

Fluorescence labeling provides an important tool to study the structure and function of proteins. Typically, fluorescence labeling involves either chemical modification or protein fusion with fluorescent probes. These techniques, however, have several significant drawbacks. First, the degree to which fluorescent probes interfere with protein folding and function is a concern. Second, many protein domains are difficult to target specifically. In the particular case of integral membrane proteins, few fluorescent probes can be targeted specifically to transmembrane domains without significantly disturbing protein function. Thus, small fluorescent probes that minimally perturb the structure and function of integral membrane proteins are needed. In this study, we genetically incorporated Anap, an environmentally-sensitive fluorescent unnatural amino acid, into specific locations in the Arabidopsis thaliana type 2 H+-ATPase (AHA2) expressed in Saccharomyces cerevisiae. The nonsense stop codon TAG was substituted for Trp codons to incorporate the unnatural amino acid into specific sites within the first two transmembrane alpha helices of AHA2 using an engineered suppressor tRNA that carries the artificial amino acid and is orthogonal to natural amino acids. Culture conditions were varied to maximize expression of a fluorescent 97 kDa protein in yeast that was only observed when Anap was included in the culture media. By taking advantage of the environmentally sensitive properties of this fluorescent unnatural amino acid, the resultant labeled protein can be used to study conformational dynamics during the enzyme cycle that may result from changes in the local environment surrounding the incorporated fluorescent probe. Fluorescence labeling of membrane proteins using this approach should allow detailed studies of local conformational kinetics that will shed new light on structure function relationships in this class of enzymes.

Probing Local Protein Environments with the Infrared Probe: L-4-Nitrophenylalanine

The genetic incorporation of unnatural amino acids (UAAs) with high efficiency and fidelity is a powerful tool for the study of protein structure and dynamics with site-specificity in a relatively nonintrusive manner. Here, we illustrate the ability of l-4-nitrophenylalanine to serve as a sensitive IR probe of local protein environments in the 247 residue superfolder green fluorescent protein (sfGFP). Specifically, the nitro symmetric stretching frequency of l-4-nitrophenylalanine was shown to be sensitive to both solvents that mimic different protein environments and 15N isotopic labeling of the three-atom nitro group of this UAA. 14NO2 and 15NO2 variants of this UAA were incorporated utilizing an engineered orthogonal aminoacyl−tRNA synthetase/tRNA pair into a solvent exposed and a partially buried position in sfGFP with high efficiency and fidelity. The combination of isotopic labeling and difference FTIR spectroscopy permitted the nitro symmetric stretching frequency of l-4-nitrophenylalanine to be ex...

Synthesis of proteins with defined posttranslational modifications using the genetic noncanonical amino acid incorporation approach

Posttranslational modifications modulate the activities of most eukaryotic proteins and play a critical role in all aspects of cellular life. Understanding functional roles of these modifications requires homogeneously modified proteins that are usually difficult to purify from their natural sources. An emerging powerful tool for synthesis of proteins with defined posttranslational modifications is to genetically encode modified amino acids in living cells and incorporate them directly into proteins during the protein translation process. Using this approach, homogenous proteins with tyrosine sulfation, tyrosine phosphorylation mimics, tyrosine nitration, lysine acetylation, lysine methylation, and ubiquitination have been synthesized in large quantities. In this review, we provide a brief introduction to protein posttranslational modifications and the genetic noncanonical amino acid (NAA) incorporation technique, then discuss successful applications of the genetic NAA incorporation approach to produce proteins with defined modifications, and end with challenges and ongoing methodology developments for synthesis of proteins with other modifications.

The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of l-phenylalanine and its derivatives

Using evolved pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs, L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine have been genetically incorporated into proteins at amber mutation sites in E. coli.

Palladium-mediated site-selective Suzuki–Miyaura protein modification at genetically encoded aryl halides

Site-specific genetic incorporation of unnatural p-halophenylalanine amino acid residues as 'tags' coupled with Pd(0)-mediated Suzuki-Miyuara 'modification' has been enabled by discovery of an effective small molecule palladium scavenger.

Genetic Incorporation of a Photo-Crosslinkable Amino Acid Reveals Novel Protein Complexes with GRB2 in Mammalian Cells

Cell signaling pathways are essentially organized through the distribution of various types of binding domains in signaling proteins, with each domain binding to specific target molecules. Although identification of these targets is crucial for mapping the pathways, affinity-based or copurification methods are insufficient to distinguish between direct and indirect interactions in a cellular context. In the present study, we developed another approach involving the genetic encoding of a photo-crosslinkable amino acid. p-Trifluoromethyl-diazirinyl- l-phenylalanine was thus incorporated at a defined site in the Src homology 2 (SH2) domain of the adaptor protein GRB2 in human embryonic kidney cells. These cells were exposed to 365-nm light after an epidermal growth factor stimulus, and the crosslinkable GRB2-SH2 domain exclusively formed covalent bonds with directly interacting proteins. Proteomic mass spectrometry analysis identified these direct binders of GRB2-SH2 separately from the proteins noncovalently bound to the Src homology 3 domains of GRB2. In addition to two signaling-associated proteins (GIT1 and AF6), the heterogeneous nuclear ribonucleoproteins F, H1, and H2 were thus identified as novel direct binders. The results revealed a connection between the cell signaling protein and the nuclear machinery involved in mRNA processing, and demonstrated the usefulness of genetically encoded photo-crosslinkers for mapping protein–protein interactions in cells.

Oncolytic Adenovirus Research And Applications

Cancer treatments have improved steadily, but still only few metastatic solid tumors can be cured. Apoptosis-resistant clones frequently develop following standard treatments. Resistance factors are shared between different treatment regimens and, therefore, loss of response can occur rapidly, despite changing the drug, and there is a tendency for crossresistance between modalities. Therefore, new agents with novel mechanisms of action are desperately needed. Oncolytic adenoviruses, featuring cancer-selective cell lysis and spread, constitute an interesting drug platform aimed towards the goals of tumor specificity, and have been engineered in a variety of ways to improve their selectivity and efficacy. They allow rational drug development by the genetic incorporation of targeting mechanisms that can exert their function at different stages of the viral replication cycle. Owing to their immunogenicity, adenoviruses are particularly attractive for immunostimulatory purposes.

A biosynthetic route to photoclick chemistry on proteins.

Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural amino acid, p-(2-tetrazole)phenylalanine (p-Tpa), into myoglobin site-specifically in E. coli by evolving an orthogonal tRNA/aminoacyl-tRNA synthetase pair and the use of p-Tpa as a bioorthogonal chemical "handle" for fluorescent labeling of p-Tpa-encoded myoglobin via the photoclick reaction. Moreover, we elucidated the structural basis for the biosynthetic incorporation of p-Tpa into proteins by solving the X-ray structure of p-Tpa-specific aminoacyl-tRNA synthetase in complex with p-Tpa. The genetic encoding of this photoreactive amino acid should make it possible in the future to photoregulate protein function in living systems.

Genetic Incorporation of Unnatural Amino Acids into Proteins in Mycobacterium tuberculosis

New tools are needed to study the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), to facilitate new drug discovery and vaccine development. We have developed methodology to genetically incorporate unnatural amino acids into proteins in Mycobacterium smegmatis, BCG and Mtb, grown both extracellularly in culture and inside host cells. Orthogonal mutant tRNATyr/tyrosyl-tRNA synthetase pairs derived from Methanococcus jannaschii and evolved in Escherichia coli incorporate a variety of unnatural amino acids (including photocrosslinking, chemically reactive, heavy atom containing, and immunogenic amino acids) into proteins in response to the amber nonsense codon. By taking advantage of the fidelity and suppression efficiency of the MjtRNA/pIpaRS pair in mycobacteria, we are also able to use p-iodophenylalanine to induce the expression of proteins in mycobacteria both extracellularly in culture and inside of mammalian host cells. This provides a new approach to regulate the expression of reporter genes or mycobacteria endogenous genes of interest. The establishment of the unnatural amino acid expression system in Mtb, an intracellular pathogen, should facilitate studies of TB biology and vaccine development.

A genetically encoded photocaged Nε-methyl-l-lysine

A photocaged N(epsilon)-methyl-L-lysine has been genetically incorporated into proteins at amber codon positions in Escherichia coli using an evolved pyrrolysyl-tRNA synthetase-pylT pair. Its genetic incorporation and following photolysis to recover N(epsilon)-methyl-L-lysine at physiological pH provide a convenient method for the biosynthesis of proteins with monomethylated lysines at specific sites.

A convenient method for genetic incorporation of multiple noncanonical amino acids into one protein in Escherichia coli

By overexpressing the C-terminal domain of the ribosomal protein L11 to decrease release factor 1-mediated termination of protein translation, enhanced amber suppression is achieved in E. coli. This enhanced amber suppression efficiency allows the genetic incorporation of three N(epsilon)-acetyl-l-lysines into one GFP(UV) protein in E. coli.

Genetic incorporation of an aliphatic keto-containing amino acid into proteins for their site-specific modifications

2-Amino-8-oxononanoic acid has been genetically incorporated into proteins in Escherichia coli by the use of an evolved pyrrolysyl-tRNA synthetase/pylT pair. The direct usage of the exclusive reactivity of the keto group in this amino acid with hydrazide- and alkoxyamine-bearing compounds to site-specifically label proteins under a mild condition close to physiological pH exhibited a very high efficiency.