Substrate Recognition Properties Research Articles

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae.

Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.

Demonstrating the utility of sugar-phosphate phosphatases in coupled enzyme assays: galactose-1-phosphate uridylyltransferase as proof-of-concept.

During our biochemical characterization of select bacterial phosphatases belonging to the haloacid dehalogenase superfamily of hydrolases, we discovered a strong bias of Salmonella YidA for glucose-1-phosphate (Glc-1-P) over galactose-1-phosphate (Gal-1-P). We sought to exploit this ability of YidA to discriminate these two sugar-phosphate epimers in a simple coupled assay that could be a substitute for current cumbersome alternatives. To this end, we focused on Gal-1-P uridylyltransferase (GalT) that is defective in individuals with classical galactosemia, an inborn disorder. GalT catalyzes the conversion of Gal-1-P and UDP-glucose to Glc-1-P and UDP-galactose. When recombinant YidA was coupled to GalT, the final orthophosphate product (generated from selective hydrolysis of Glc-1-P by YidA) could be easily measured using the inexpensive malachite green reagent. When this new YidA-based colorimetric assay was benchmarked using a recombinant Duarte GalT variant, it yielded kcat/Km values that are ~2.5-fold higher than the standard coupled assay that employs phosphoglucomutase and glucose-6-phosphate dehydrogenase. Although the simpler design of our new GalT coupled assay might find appeal in diagnostics, a testable expectation, we spotlight the GalT example to showcase the untapped potential of sugar-phosphate phosphatases with distinctive substrate-recognition properties for measuring the activity of various metabolic enzymes (e.g. trehalose-6-phosphate synthase, N-acetyl-glucosamine-6-phosphate deacetylase, phosphofructokinase).

Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter.

Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and acetamide in the Aspergillus nidulans urea transporter, UreA. To deepen the structural characterization of UreA, we employed the artificial intelligence (AI) based AlphaFold2 (AF2) program. In this analysis, the resulting AF2 models lacked inward- and outward-facing cavities, suggesting a structural intermediate state of UreA. Moreover, the orientation of the W82, W84, N279, and T282 side chains showed a large variability, which in the case of W82 and W84, may operate as a gating mechanism in the ligand pathway. To test this hypothesis non-conservative and conservative substitutions of these amino acids were introduced, and binding and transport assessed for urea and its toxic analogue 2-thiourea, as well as binding of the structural analogue acetamide. As a result, residues W82, W84, N279, and T282 were implicated in substrate identification, selection, and translocation. Using molecular docking with Autodock Vina with flexible side chains, we corroborated the AF2 theoretical intermediate model, showing a remarkable correlation between docking scores and experimental affinities determined in wild-type and UreA mutants. The combination of AI-based modeling with classical docking, validated by comprehensive mutational analysis at the binding region, would suggest an unforeseen option to determine structural level details on a challenging family of proteins.

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS‐CoV‐2 Main Protease

The SARS‐CoV‐2 main protease (MPro) is responsible for cleaving viral polypeptides to generate functional viral proteins, but like other viral proteases, MPro may also actively target and cleaave endogenous human host proteins during infection. Here we show that a human tRNA methyltransferase, TRMT1, can be recognized and cleaved by SARS‐CoV‐2 MPro. TRMT1 is a SAM‐dependent methyltransferase that installs the N 2,N 2‐dimethylguanosine (m2,2G) modification onto position G26 of human tRNAs. This abundant m2,2G modification is important for global protein synthesis, cellular redox homeostasis, and has been linked to neurodevelopmental defects. Early in the COVID‐19 pandemic, a host‐virus protein interaction map identified a putative interaction between SARS‐CoV‐2 MPro and human TRMT1. We carried out kinetic assays that show both a short peptide sequence in TRMT1 as well as endogenous, full‐length TRMT1 are actively cleaved by recombinant SARS‐CoV‐2 MPro in vitro. Cleavage of full‐length TRMT1 results in loss of its C‐terminal zinc finger domain thought to be critical for tRNA binding. Furthermore, we determined the co‐crystal structure of the human TRMT1 peptide in complex with SARS‐CoV‐2 MPro, which shows that the bound TRMT1 peptide substrate adopts a unique conformation in the protease active site. These results suggest that tRNA methyltransferase TRMT1 is a viable substrate for SARS‐CoV‐2 MPro, provide new structural insights into the diverse substrate recognition properties of the viral protease, and raise the possibility that TRMT1 cleavage during SARS‐CoV‐2 infection could contribute to downregulation of host protein synthesis or other phenotypes of viral infection.

Dissecting Monomer-Dimer Equilibrium of an RNase P Protein Provides Insight Into the Synergistic Flexibility of 5' Leader Pre-tRNA Recognition.

Ribonuclease P (RNase P) is a universal RNA-protein endonuclease that catalyzes 5’ precursor-tRNA (ptRNA) processing. The RNase P RNA plays the catalytic role in ptRNA processing; however, the RNase P protein is required for catalysis in vivo and interacts with the 5’ leader sequence. A single P RNA and a P protein form the functional RNase P holoenzyme yet dimeric forms of bacterial RNase P can interact with non-tRNA substrates and influence bacterial cell growth. Oligomeric forms of the P protein can also occur in vitro and occlude the 5’ leader ptRNA binding interface, presenting a challenge in accurately defining the substrate recognition properties. To overcome this, concentration and temperature dependent NMR studies were performed on a thermostable RNase P protein from Thermatoga maritima. NMR relaxation (R1, R2), heteronuclear NOE, and diffusion ordered spectroscopy (DOSY) experiments were analyzed, identifying a monomeric species through the determination of the diffusion coefficients (D) and rotational correlation times (τc). Experimental diffusion coefficients and τc values for the predominant monomer (2.17 ± 0.36 * 10−10 m2/s, τ c = 5.3 ns) or dimer (1.87 ± 0.40* 10−10 m2/s, τ c = 9.7 ns) protein assemblies at 45°C correlate well with calculated diffusion coefficients derived from the crystallographic P protein structure (PDB 1NZ0). The identification of a monomeric P protein conformer from relaxation data and chemical shift information enabled us to gain novel insight into the structure of the P protein, highlighting a lack of structural convergence of the N-terminus (residues 1–14) in solution. We propose that the N-terminus of the bacterial P protein is partially disordered and adopts a stable conformation in the presence of RNA. In addition, we have determined the location of the 5’ leader RNA in solution and measured the affinity of the 5’ leader RNA–P protein interaction. We show that the monomer P protein interacts with RNA at the 5’ leader binding cleft that was previously identified using X-ray crystallography. Data support a model where N-terminal protein flexibility is stabilized by holoenzyme formation and helps to accommodate the 5’ leader region of ptRNA. Taken together, local structural changes of the P protein and the 5’ leader RNA provide a means to obtain optimal substrate alignment and activation of the RNase P holoenzyme.

Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex

The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.

The structural characteristics and the substrate recognition properties of RNase ZS1

TMS5 encodes an RNase ZS1 protein that can process ubiquitin-60S ribosomal protein L40 family (UbL40) mRNAs to regulate thermo-sensitive genic male sterility in rice. Despite the importance of this protein, the structural characteristics and substrate recognition properties of RNase ZS1 remain unclear. Here, we found that the variations in several conservative amino acids alter the activation of RNase ZS1, and its recognition of RNA substrates depends on the structure of RNA. RNase ZS1 acts as a homodimer. The conserved amino acids in or adjacent to enzyme center play a critical role in the enzyme activity of RNase ZS1 and the conserved amino acids that far from active center have little impact on its enzyme activity. The cleavage efficiency of RNase ZS1 for pre-tRNA-MetCAU35 and UbL401 mRNA with cloverleaf-like structure was higher than that of pre-tRNA-AspAUC9 and UbL404 mRNA with imperfect cloverleaf-like structure. This difference implies that the enzyme activity of RNase ZS1 depends on the cloverleaf-like structure of the RNA. Furthermore, the RNase ZS1 activity was not inhibited by the 5′ leader sequence and 3’ CCA motif of pre-tRNA. These findings provide new insights for studying the cleavage characteristics and substrate recognition properties of RNase ZS.

Chlamydia trachomatis Oligopeptide Transporter Performs Dual Functions of Oligopeptide Transport and Peptidoglycan Recycling.

Peptidoglycan, the sugar-amino acid polymer that composes the bacterial cell wall, requires a significant expenditure of energy to synthesize and is highly immunogenic. To minimize the loss of an energetically expensive metabolite and avoid host detection, bacteria often recycle their peptidoglycan, transporting its components back into the cytoplasm, where they can be used for subsequent rounds of new synthesis. The peptidoglycan-recycling substrate binding protein (SBP) MppA, which is responsible for recycling peptidoglycan fragments in Escherichia coli, has not been annotated for most intracellular pathogens. One such pathogen, Chlamydia trachomatis, has a limited capacity to synthesize amino acids de novo and therefore must obtain oligopeptides from its host cell for growth. Bioinformatics analysis suggests that the putative C. trachomatis oligopeptide transporter OppABCDF (OppABCDF Ct ) encodes multiple SBPs (OppA1 Ct , OppA2 Ct , and OppA3 Ct ). Intracellular pathogens often encode multiple SBPs, while only one, OppA, is encoded in the E. coliopp operon. We hypothesized that the putative OppABCDF transporter of C. trachomatis functions in both oligopeptide transport and peptidoglycan recycling. We coexpressed the putative SBP genes (oppA1Ct , oppA2Ct , oppA3Ct ) along with oppBCDFCt in an E. coli mutant lacking the Opp transporter and determined that all three chlamydial OppA subunits supported oligopeptide transport. We also demonstrated the in vivo functionality of the chlamydial Opp transporter in C. trachomatis Importantly, we found that one chlamydial SBP, OppA3 Ct , possessed dual substrate recognition properties and is capable of transporting peptidoglycan fragments (tri-diaminopimelic acid) in E. coli and in C. trachomatis These findings suggest that Chlamydia evolved an oligopeptide transporter to facilitate the acquisition of oligopeptides for growth while simultaneously reducing the accumulation of immunostimulatory peptidoglycan fragments in the host cell cytosol. The latter property reflects bacterial pathoadaptation that dampens the host innate immune response to Chlamydia infection.

Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry.

Cross-linking mass spectrometry has become an important approach for studying protein structures and protein–protein interactions. The amino acid compositions of some protein regions impede the detection of cross-linked residues, although it would yield invaluable information for protein modeling. Here, we report on a sequential-digestion strategy with trypsin and elastase to penetrate regions with a low density of trypsin-cleavage sites. We exploited intrinsic substrate-recognition properties of elastase to specifically target larger tryptic peptides. Our application of this protocol to the TAF4–12 complex allowed us to identify cross-links in previously inaccessible regions.

A Supramolecular Palladium Catalyst Displaying Substrate Selectivity by Remote Control.

Inspired by enzymes such as cytochrome P-450, the study of the reactivity of metalloporphyrins continues to attract major interest in the field of homogeneous catalysis. However, little is known about benefitting from the substrate-recognition properties of porphyrins containing additional, catalytically relevant active sites. Herein, such an approach is introduced by using supramolecular ligands derived from metalloporphyrins customized with rigid, palladium-coordinating nitrile groups. According to different studies (NMR and UV/Vis spectroscopy, XRD, control experiments), the supramolecular ligands are able to accommodate pyridine derivatives as substrates inside the porphyrin pocket while the reactivity occurs at the peripheral side. By simply tuning a remote metal center, different binding events result in different catalyst reactivity, and this enzyme-like feature leads to high degrees of substrate selectivity in representative palladium-catalyzed Suzuki-Miyaura reactions.

Probing substrate recognition of bacterial lipoprotein signal peptidase using FRET reporters.

Lipoprotein signal peptidase (Lsp) is a transmembrane aspartic acid protease with a pivotal role in the bacterial lipoprotein maturation pathway. Despite the universal use of Lsp across the Bacterial Kingdom and its potential as an antibiotic target, the substrate recognition patterns of Lsp are poorly understood. Here, we investigated the substrate recognition and biochemical properties of Lsp from Gram- (Escherichia coli) and Gram+ (Streptococcus pyogenes) bacteria, using synthetic peptide-based FRET reporters. Didecanoyl glycerol was found to be an optimal lipid length, and Lsp demonstrated exclusive enantio-selectivity for the (R)-form of the diacylglycerol. Our study will facilitate the iterative optimization of in vitro Lsp assays, as well as provide the first chemical interrogation into the substrate scope of Lsp.

Fabrication of poly (1, 4-dioxa-7, 12-diazacyclotetradecane-8, 11-dione) macrocyclic functionalized hydrogel for high selective adsorption of Cr, Cu and Ni

Synthesis of hydrogel adsorbent for high selectivity and strong chelate removal of transition metals Cr, Cu and Ni was accomplished via sol-gel method using ligand monomers maleic acid and (2, 2′ ethylenedioxy) bis (ethylamine) reagent. We obtained a 14-membered macrocyclic functional unit called poly (1, 4-dioxa-7, 12-diazacyclotetradecane-8, 11-dione) as the main active sites for metal adsorption. The new adsorbent's cross-linked polymer chains was clearly visualized using SEM spectroscopy; whereas the FTIR, 13C NMR and EDX techniques demonstrated its structural and functional groups. With an improved chelating power, this macrocyclic hydrogel was able to ignore non-target substrates, instead showing high specificity for only Cu, Cr and Ni from both single and multi-ion competitive aqueous solutions, in the order Cr > Cu > Ni. Pseudo-second order kinetic model aptly described the adsorption process, revealing chemisorption as the main mechanism which proceeded based on the host-guest chelation principle of metal ions onto the gel's macrocyclic active sites. Thus a high performance, high selectivity adsorbent system was achieved using active sites bearing substrate recognition and isolation properties.

Engineered Polymerases with Altered Substrate Specificity: Expression and Purification

Polymerase engineering is making it possible to synthesize xeno-nucleic acid polymers (XNAs) with diverse backbone structures and chemical functionality. The ability to copy genetic information back and forth between DNA and XNA has led to a new field of science known as synthetic genetics, which aims to study the genetic concepts of heredity and evolution in artificial genetic polymers. Since many of the polymerases needed to synthesize XNA polymers are not available commercially, researchers must express and purify these enzymes as recombinant proteins from E. coli. This unit details the steps needed to express, purify, and evaluate the activity of engineered polymerases with altered substrate recognition properties. The protocol requires 6 days to complete and will produce ∼20mg of pure, nuclease-free polymerase per liter of E. coli bacterial culture. © 2017 by John Wiley & Sons, Inc.

How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs.

Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X-ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain-RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA-binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs.

TheTCP1γ subunit ofLeishmania donovaniforms a biologically active homo‐oligomeric complex

Chaperonins are a class of molecular chaperons that encapsulate nascent or stress-denatured proteins and assist their intracellular assembly and folding in an ATP-dependent manner. The ubiquitous eukaryotic chaperonin, TCP1 ring complex is a hetero-oligomeric complex comprising two rings, each formed of eight subunits that may have distinct substrate recognition and ATP hydrolysis properties. In Leishmania, only the TCP1γ subunit has been cloned and characterized. It exhibited differential expression at various growth stages of promastigotes. In the present study, we expressed the TCP1γ subunit in Escherichia coli to investigate whether it forms chaperonin-like complexes and plays a role in protein folding. LdTCP1γ formed high-molecular-weight complexes within E. coli cells as well as in Leishmania cell lysates. The recombinant protein is arranged into two back-to-back rings of seven subunits each, as predicted by homology modelling and observed by negative staining electron microscopy. This morphology is consistent with that of the oligomeric double-ring group I chaperonins found in mitochondria. The LdTCP1γ homo-oligomeric complex hydrolysed ATP, and was active as assayed by luciferase refolding. Thus, the homo-oligomer performs chaperonin reactions without partner subunit(s). Further, co-immunoprecipitation studies revealed that LdTCP1γ interacts with actin and tubulin proteins, suggesting that the complex may have a role in maintaining the structural dynamics of the cytoskeleton of parasites.

3P032 抗HIV 因子APOBEC3G の基質認識及びスライディング機構の実時間NMR 解析(01B. 蛋白質:構造機能相関,ポスター,第52回日本生物物理学会年会(2014年度))

3P032 抗HIV 因子APOBEC3G の基質認識及びスライディング機構の実時間NMR 解析(01B. 蛋白質:構造機能相関,ポスター,第52回日本生物物理学会年会(2014年度))

Designed peptides for biomineral polymorph recognition: a case study for calcium carbonate.

With their unique ability for substrate recognition and their sequence-specific self-assembly properties, peptides play an important role in controlling the mineralization of inorganic materials in natural systems and in controlling the assembly of soft materials into complex structures required for biological functions. Here we report the use of an engineered heptapeptide that can differentiate between the crystalline anhydrous polymorphs of calcium carbonate. This peptide contains the positively charged amino acid arginine as well as proline rather than the prototypical negatively charged aspartate or glutamate units. Its affinity to vaterite compared to aragonite was demonstrated by fluorescence microscopy using biotinylated peptides. Crystallization experiments in the presence of the vaterite-affine peptide afforded only vaterite, whereas a mutant peptide, where a proline residue was replaced by glycine, exclusively leads to the formation of calcite.

Human CCT4 and CCT5 Chaperonin Subunits Expressed in Escherichia coli Form Biologically Active Homo-oligomers

Chaperonins are a family of chaperones that encapsulate their substrates and assist their folding in an ATP-dependent manner. The ubiquitous eukaryotic chaperonin, TCP-1 ring complex (TRiC), is a hetero-oligomeric complex composed of two rings, each formed from eight different CCT (chaperonin containing TCP-1) subunits. Each CCT subunit may have distinct substrate recognition and ATP hydrolysis properties. We have expressed each human CCT subunit individually in Escherichia coli to investigate whether they form chaperonin-like double ring complexes. CCT4 and CCT5, but not the other six CCT subunits, formed high molecular weight complexes within the E. coli cells that sedimented about 20S in sucrose gradients. When CCT4 and CCT5 were purified, they were both organized as two back-to-back rings of eight subunits each, as seen by negative stain and cryo-electron microscopy. This morphology is consistent with that of the hetero-oligomeric double-ring TRiC purified from bovine testes and HeLa cells. Both CCT4 and CCT5 homo-oligomers hydrolyzed ATP at a rate similar to human TRiC and were active as assayed by luciferase refolding and human γD-crystallin aggregation suppression and refolding. Thus, both CCT4 and CCT5 homo-oligomers have the property of forming 8-fold double rings absent the other subunits, and these complexes carry out chaperonin reactions without other partner subunits.

Involvement of Ser94 in RNase HIII from Chlamydophila pneumoniae in the recognition of a single ribonucleotide misincorporated into double-stranded DNA

We recently provided the first report that RNase HIII can cleave a DNA-rN1-DNA/DNA substrate (rN1, one ribonucleotide) in vitro. In the present study, mutagenesis analyses and molecular dynamics (MD) simulations were performed on RNase HIII from Chlamydophila pneumoniae AR39 (CpRNase HIII). Our results elucidate the mechanism of ribonucleotide recognition employed by CpRNase HIII, indicating that the G95/K96/G97 motif of CpRNase HIII represents the main surface interacting with single ribonucleotides, in a manner similar to that of the GR(K)G motif of RNase HIIs. However, CpRNase HIII lacks the specific tyrosine required for RNase HII to recognize single ribonucleotides in double-stranded DNA (dsDNA). Interestingly, MD shows that Ser94 of CpRNase HIII forms a stable hydrogen bond with the deoxyribonucleotide at the (5')RNA–DNA(3') junction, moving this nucleotide away from the chimeric ribonucleotide. This movement appears to deform the nucleic acid backbone at the RNA–DNA junction and allows the ribonucleotide to interact with the GKG motif. Based on the inferences drawn from MD simulations, biochemical results indicated that Ser94 was necessary for catalytic activity on the DNA-rN1-DNA/DNA substrate; mutant S94V could bind this substrate but exhibited no cleavage. Mismatches opposite the single ribonucleotide misincorporated in dsDNA inhibited cleavage by CpRNase HIII to varying degrees but did not interfere with CpRNase/substrate binding. Further MD results implied that mismatches impair the interaction between Ser94 and the deoxyribonucleotide at the RNA–DNA junction. Consequently, recognition of the misincorporated ribonucleotide was disturbed. Our results may help elucidate the distinct substrate-recognition properties of different RNase Hs.

The Multiple Substrate Recognition Properties of Ribonuclease P

Ribonuclease P is an essential enzyme that is responsible for catalyzing the 5’end maturation of transfer RNA. In Bacteria, the RNase P holoenzyme is composed of a large RNA (∼400nt) and a smaller (∼100aa) protein. RNase P RNA contains the enzyme active site and interacts with tRNA; however, the protein subunit is essential in vivo because it binds the pre-tRNA leader sequence and increases active site metal ion binding. Unlike most enzymes, RNase P processes multiple structurally distinct substrates. Although the processing kinetics of individual substrates have been examined, comparison of processing kinetics and kinetic competition between substrates has not been explored. To understand the basis for multiple substrate recognition by the holoenzyme we determined kinetic schemes forpre-tRNA608MET, a consensus pre-tRNA, and pretRNA605fmet, a non-consensus pre-tRNA, using fluorescence assays and standard discontinuous assays. Remarkably, the results show processing kinetics to be uniform with the rate limiting step being association. To obtain a complete and comprehensive understanding of how sequence and structure influence processing rates and competition between substrates, we undertook two complementary directions. First, we directly examined the competition between pre-tRNA608MET and pre-tRNA605fmet distinguishing products using different leader sequence length. Second, we designed a high throughput method to determine the effects, if any, of differences in pre-tRNA leader sequence and structure by using deep sequencing to follow the range in distribution of different substrate sequence variants in the same reaction.