1
|
Deng Z, Wang Y, Mao J, Ye M. Investigating the Relationship between the Substrates' Consumption and Their Abundances in a Complex Enzymatic System. Anal Chem 2017; 89:10644-10648. [PMID: 28972787 DOI: 10.1021/acs.analchem.7b03616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic process involving the incubation of a library of substrates with an enzyme is the key step for a few important experiments for bioanalytical chemistry including proteomics analysis, enzymatic labeling, substrate screening, etc. The relationship between the substrates' consumption and their abundances in a complex enzymatic system with a huge number of coexisting substrates of different abundances was not well-known. In this study, we have demonstrated theoretically and experimentally that the priority of substrate consumption depended on their specificity constants but not abundances. We derived the expression between the fractions of the substrates consumed (pi) and their specificity constants. Using the enzymatic system of five synthetic peptide substrates of trypsin, we validated through 24 experiments that the ln(1 - pi) values of competing substrates have linear correlation with their specificity constants, and thus, the priority of substrate depletion has no relation with their abundances. Using a state of the art quantitative proteomics approach, we found that the ln(1 - pi) values of 144 competing substrates between any two of four experiments have a linear relationship and the prioritization of substrates can be achieved by sorting their consumption rates in the experiment. This study will improve our understanding of the enzymatic kinetics in the complex system and will benefit the design of enzymatic analytical approaches.
Collapse
Affiliation(s)
- Zhenzhen Deng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian, Liaoning 116023, China
| |
Collapse
|
2
|
Niland CN, Anderson DR, Jankowsky E, Harris ME. The contribution of the C5 protein subunit of Escherichia coli ribonuclease P to specificity for precursor tRNA is modulated by proximal 5' leader sequences. RNA (NEW YORK, N.Y.) 2017; 23:1502-1511. [PMID: 28694328 PMCID: PMC5602109 DOI: 10.1261/rna.056408.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/14/2017] [Indexed: 05/03/2023]
Abstract
Recognition of RNA by RNA processing enzymes and RNA binding proteins often involves cooperation between multiple subunits. However, the interdependent contributions of RNA and protein subunits to molecular recognition by ribonucleoproteins are relatively unexplored. RNase P is an endonuclease that removes 5' leaders from precursor tRNAs and functions in bacteria as a dimer formed by a catalytic RNA subunit (P RNA) and a protein subunit (C5 in E. coli). The P RNA subunit contacts the tRNA body and proximal 5' leader sequences [N(-1) and N(-2)] while C5 binds distal 5' leader sequences [N(-3) to N(-6)]. To determine whether the contacts formed by P RNA and C5 contribute independently to specificity or exhibit cooperativity or anti-cooperativity, we compared the relative kcat/Km values for all possible combinations of the six proximal 5' leader nucleotides (n = 4096) for processing by the E. coli P RNA subunit alone and by the RNase P holoenzyme. We observed that while the P RNA subunit shows specificity for 5' leader nucleotides N(-2) and N(-1), the presence of the C5 protein reduces the contribution of P RNA to specificity, but changes specificity at N(-2) and N(-3). The results reveal that the contribution of C5 protein to RNase P processing is controlled by the identity of N(-2) in the pre-tRNA 5' leader. The data also clearly show that pairing of the 5' leader with the 3' ACCA of tRNA acts as an anti-determinant for RNase P cleavage. Comparative analysis of genomically encoded E. coli tRNAs reveals that both anti-determinants are subject to negative selection in vivo.
Collapse
Affiliation(s)
- Courtney N Niland
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - David R Anderson
- Zicklin School of Business, Baruch College, CUNY, New York, New York 10010, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| |
Collapse
|
3
|
Jankowsky E, Harris ME. Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing. Methods 2017; 118-119:111-118. [PMID: 28263887 DOI: 10.1016/j.ymeth.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/07/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022] Open
Abstract
To function in a biological setting, RNA binding proteins (RBPs) have to discriminate between alternative binding sites in RNAs. This discrimination can occur in the ground state of an RNA-protein binding reaction, in its transition state, or in both. The extent by which RBPs discriminate at these reaction states defines RBP specificity landscapes. Here, we describe the HiTS-Kin and HiTS-EQ techniques, which combine kinetic and equilibrium binding experiments with high throughput sequencing to quantitatively assess substrate discrimination for large numbers of substrate variants at ground and transition states of RNA-protein binding reactions. We discuss experimental design, practical considerations and data analysis and outline how a combination of HiTS-Kin and HiTS-EQ allows the mapping of RBP specificity landscapes.
Collapse
Affiliation(s)
- Eckhard Jankowsky
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States; Department of Biochemistry, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States.
| | - Michael E Harris
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 1099 Euclid Ave Cleveland, OH 44106, United States
| |
Collapse
|
4
|
Niland CN, Jankowsky E, Harris ME. Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates. Anal Biochem 2016; 510:1-10. [PMID: 27296633 DOI: 10.1016/j.ab.2016.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/03/2016] [Indexed: 12/12/2022]
Abstract
Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High-throughput sequencing kinetics (HTS-Kin) uses high-throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigated the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we found that high-throughput sequencing and experimental reproducibility contribute to error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed.
Collapse
Affiliation(s)
- Courtney N Niland
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| |
Collapse
|
5
|
Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:70-6. [PMID: 26321598 DOI: 10.1016/j.bbapap.2015.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/07/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
Collapse
|
6
|
Kellerman DL, Simmons KS, Pedraza M, Piccirilli JA, York DM, Harris ME. Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Anal Biochem 2015; 483:12-20. [PMID: 25937290 DOI: 10.1016/j.ab.2015.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
Biological catalysis involves interactions distant from the site of chemistry that can position the substrate for reaction. Catalysis of RNA 2'-O-transphosphorylation by the hepatitis delta virus (HDV) ribozyme is sensitive to the identity of the N(-1) nucleotide flanking the reactive phosphoryl group. However, the interactions that affect the conformation of this position, and in turn the 2'O nucleophile, are unclear. Here, we describe the application of multiple substrate internal competition kinetic analyses to understand how the N(-1) nucleobase contributes to HDV catalysis and test the utility of this approach for RNA structure-function studies. Internal competition reactions containing all four substrate sequence variants at the N(-1) position in reactions using ribozyme active site mutations at A77 and A78 were used to test a proposed base-pairing interaction. Mutants A78U, A78G, and A79G retain significant catalytic activity but do not alter the specificity for the N(-1) nucleobase. Effects of nucleobase analog substitutions at N(-1) indicate that U is preferred due to the ability to donate an H-bond in the Watson-Crick face and avoid minor groove steric clash. The results provide information essential for evaluating models of the HDV active site and illustrate multiple substrate kinetic analyses as a practical approach for characterizing structure-function relationships in RNA reactions.
Collapse
Affiliation(s)
- Daniel L Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kandice S Simmons
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mayra Pedraza
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| |
Collapse
|