Amino acid-selective isotope labeling of proteins for nuclear magnetic resonance study: Proteins secreted by Brevibacillus choshinensis

Here we report the first application of amino acid-type selective (AATS) isotope labeling of a recombinant protein secreted by Brevibacillus choshinensis for a nuclear magnetic resonance (NMR) study. To prepare the ¹⁵N-AATS-labeled protein, the transformed B. choshinensis was cultured in ¹⁵N-labeled amino acid-containing C.H.L. medium, which is commonly used in the Escherichia coli expression system. The analyses of the ¹H-¹⁵N heteronuclear single quantum coherence (HSQC) spectra of the secreted proteins with a ¹⁵N-labeled amino acid demonstrated that alanine, arginine, asparagine, cysteine, glutamine, histidine, lysine, methionine, and valine are suitable for selective labeling, although acidic and aromatic amino acids are not suitable. The ¹⁵N labeling for glycine, isoleucine, leucine, serine, and threonine resulted in scrambling to specific amino acids. These results indicate that the B. choshinensis expression system is an alternative tool for AATS labeling of recombinant proteins, especially secretory proteins, for NMR analyses.     

Genetic tools for selective labeling of proteins with α-15N-amino acids

Summary A collection of genetic tools that can be used to manipulate amino acid metabolism in Escherichia coli is described. The set comprises 21 strains of bacteria, each containing a different genetic defect that is closely linked to a selectable transposon marker. These tools can be used to construct strains of E. coli with ideal genotypes for residue-specific, selective labeling of proteins with nearly any ¹⁵N-amino acid. By using strains which have been modified to contain the appropriate genetic lesions to control amino acid biosynthesis, dilution of the isotope by endogenous amino acid biosynthesis and scrambling of the label to other types of residues can be avoided.Abbreviations ¹⁵N-amino acid -¹⁵N-amino acid - Cam^R chloramphenicol-resistant - DPA diaminopimelic acid - Hfr high-frequency recombinant - LB Luria broth - Kan^R kanamycin resistant - P1 bacteriophage P1 - pfu plaque-forming units - Str^R streptomycin-resistant - Tet^R tetracycline-resistant     

Topograph,a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Defects in protein turnover have been implicated in a broad range of diseases, but current proteomics methods of measuring protein turnover are limited by the software tools available. Conventional methods require indirect approaches to differentiate newly synthesized protein when synthesized from partially labeled precursor pools. To address this, we have developed Topograph, a software platform which calculates the fraction of peptides that are from newly synthesized proteins and their turnover rates. A unique feature of Topograph is the ability to calculate amino acid precursor pool enrichment levels which allows for accurate calculations when the precursor pool is not fully labeled, and the approach used by Topograph is applicable regardless of the stable isotope label used. We validate the Topograph algorithms using data acquired from a mouse labeling experiment and demonstrate the influence that precursor pool corrections can have on protein turnover measurements.Methods of measuring protein synthesis and degradation using stable or radioactive isotope labels have existed for decades. The isotope label is introduced in the form of a labeled amino acid or amino acid precursor, and the incorporation or removal of that label from protein is used to estimate average protein turnover rates (1, 2). Historically, the amount of stable isotope label incorporated into a protein is measured by enriching for the protein (e.g. affinity chromatography, gel electrophoresis, and other biochemical methods), hydrolyzing the protein to amino acids, derivatizing the amino acids, and measuring the labeled amino acid by gas chromatography-mass spectrometry or gas chromatography-combustion-isotope ratio mass spectrometry (3, 4). More recently, proteomics methods have been developed that measure the labeled amino acid on the peptide level, eliminating the need for a protein enrichment step and enabling the monitoring of many proteins in a single experiment (5).Proteomics approaches to measuring protein turnover rates in mice have been accomplished by the introduction of a ¹⁵N stable isotope label. The labeled diets were created by supplementing a protein-free diet with a ¹⁵N enriched protein source. Price et al. (6) generated ¹⁵N-labeled protein from the alga, Spirulina platensis and Zhang et al. (7) introduced ¹⁵N-label in the form of lysate from the bacterium, Ralstonia eutropha. An advantage of using complete ¹⁵N labeling is the rapid incorporation of ¹⁵N and separation of isotope distributions between labeled and natural isotope abundance peptides, which reduces the need to deconvolute the two distributions. However, current methods require that the dietary protein content be derived from bacterial or alga lysate, a diet that is not normally fed to laboratory mice. As a result, measurements of protein turnover may not reflect conventional mouse model systems because of effects of diet on protein and amino acid metabolism. A more recent work by Claydon et al. (8) demonstrated a stable isotope labeling method by supplementing labeled valine into a standard mouse diet.The complex data generated from these analyses creates a data processing and analysis challenge; exemplified by recent software platforms that have been developed. Guan et al. (9) and Hoopmann et al. (10) demonstrated data analysis pipelines for ¹⁵N labeled SILAM and SILAC experiments. Here we describe the software platform, Topograph, we have developed for the analysis of liquid chromatography-tandem MS (LC-MS/MS) data from samples with isotopic labels. Topograph is able to deconvolute the complex spectra that may result from overlapping isotope distributions, regardless of the isotope label used. More uniquely, Topograph is able to calculate the relative isotope abundance (RIA)¹ of the amino acid precursor pool, which is necessary to correctly determine the amount of newly synthesized peptide and to subsequently calculate peptide and protein turnover rates.     

Abstracts: Albany 2005, The 14th Conversation

Abstract

We report a cost efficient approach for amino-acid-type selective isotope labeling of proteins expressed in Leishmania tarentolae. The method provides an economically advantageous alternative to recently established protocol for isotopic labeling using expensive synthetic media. The method is based on cultivation of the L. tarentolae expression strain in a cheap complex medium supplemented with labeled amino acid(s). In this protocol, a labeled amino acid is deliberately diluted in the medium of undefined composition, which leads to a low-level isotope enrichment upon protein over-expression. The economic advantage of the protocol is achieved by avoiding large volumes of expensive synthetic medium. Decreased sensitivity of a NMR experiment due to low-level isotope enrichment is compensated by a five- to seven-fold increase of the yield of the recombinant protein in complex medium as compared to that in the synthetic medium. In addition, the decreased sensitivity can be compensated by using a higher magnetic field, cryo-detection system or higher number of transients during the NMR data acquisition. We show that enrichment as low as 5% does not compromise a NMR experiment and makes preparation of the recombinant proteins over- expressed in L. tarentolae economically viable. The method is demonstrated by selective labeling of the ～27 kDa enhanced green fluorescent protein (EGFP) with ¹⁵N-labeled valine.     

Affordable uniform isotope labeling with <Superscript>2</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N in insect cells

For a wide range of proteins of high interest, the major obstacle for NMR studies is the lack of an affordable eukaryotic expression system for isotope labeling. Here, a simple and affordable protocol is presented to produce uniform labeled proteins in the most prevalent eukaryotic expression system for structural biology, namely Spodoptera frugiperda insect cells. Incorporation levels of 80 % can be achieved for ¹⁵N and ¹³C with yields comparable to expression in full media. For ²H,¹⁵N and ²H,¹³C,¹⁵N labeling, incorporation is only slightly lower with 75 and 73 %, respectively, and yields are typically twofold reduced. The media were optimized for isotope incorporation, reproducibility, simplicity and cost. High isotope incorporation levels for all labeling patterns are achieved by using labeled algal amino acid extracts and exploiting well-known biochemical pathways. The final formulation consists of just five commercially available components, at costs 12-fold lower than labeling media from vendors. The approach was applied to several cytosolic and secreted target proteins.     

Selective <Superscript>15</Superscript>N labeling of barstar in a T7 polymerase system

The T7 RNA polymerase system for selective protein labeling, previously optimized for the time of introducing the ¹⁵N amino acid relative to the inducer (IPTG) and host polymerase inhibitor (rifampicin), was further improved by the use of a special growth medium enriched in particular amino acids and by administration of an aminotransferase inhibitor (α-aminooxyacetic acid); the latter prevented isotope redistribution (as required by NMR studies) even with readily metabolized leucine. The approach is shown to be successful for selective labeling of barstar with [¹⁵N]Trp and [¹⁵N]Leu; it can be used with any proteins expressed in the T7 system.     

Resonance assignment of 13C/15N labeled solid proteins by two- and three-dimensional magic-angle-spinning NMR

The comprehensive structure determination of isotopically labeled proteins by solid-state NMR requires sequence-specific assignment of ¹³C and ¹⁵ N spectra. We describe several 2D and 3D MAS correlation techniques for resonance assignment and apply them, at 7.0 Tesla, to ¹³C and ¹⁵N labeled ubiquitin to examine the extent of resonance assignments in the solid state. Both interresidue and intraresidue assignments of the ¹³C and ¹⁵N resonances are addressed. The interresidue assignment was carried out by an N(CO)CA technique, which yields N_i-C_i–1 connectivities in protein backbones via two steps of dipolar-mediated coherence transfer. The intraresidue connectivities were obtained from a new 3D NCACB technique, which utilizes the well resolved C chemical shift to distinguish the different amino acids. Additional amino acid type assignment was provided by a ¹³C spin diffusion experiment, which exhibits ¹³C spin pairs as off-diagonal intensities in the 2D spectrum. To better resolve carbons with similar chemical shifts, we also performed a dipolar-mediated INADEQUATE experiment. By cross-referencing these spectra and exploiting the selective and extensive ¹³ C labeling approach, we assigned 25% of the amino acids in ubiquitin sequence-specifically and 47% of the residues to the amino acid types. The sensitivity and resolution of these experiments are evaluated, especially in the context of the selective and extensive ¹³C labeling approach.     

Selective backbone labeling of proteins using {1,2-<Superscript>13</Superscript>C<Subscript>2</Subscript>}-pyruvate as carbon source

A simple isotope labeling approach for selective ¹³C/¹⁵N backbone labeling of proteins is described. Using {1,2-¹³C₂}-pyruvate as the sole carbon source in bacterial growth media, selective incorporation of ¹³C^α-¹³CO spin-pairs into the backbones of protein molecules with medium-to-high levels of ¹³C-enrichment is possible for a subset of 12 amino acids. The isotope labeling scheme has been tested on a pair of proteins—a 7-kDa immunoglobulin binding domain B1 of streptococcal protein G and an 82-kDa enzyme malate synthase G. A number of protein NMR applications are expected to benefit from the {1,2-¹³C₂}-pyruvate based protein production.     

Quantitative,Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture

An approach to proteomic analysis that combines bioorthogonal noncanonical amino acid tagging (BONCAT) and pulsed stable isotope labeling with amino acids in cell culture (pSILAC) provides accurate quantitative information about rates of cellular protein synthesis on time scales of minutes. The method is capable of quantifying 1400 proteins produced by HeLa cells during a 30 min interval, a time scale that is inaccessible to isotope labeling techniques alone. Potential artifacts in protein quantification can be reduced to insignificant levels by limiting the extent of noncanonical amino acid tagging. We find no evidence for artifacts in protein identification in experiments that combine the BONCAT and pSILAC methods.Methods for the analysis of cellular protein synthesis should be quantitative and fast. In 2006, Dieterich and coworkers introduced a proteomics discovery tool called bioorthogonal noncanonical amino acid tagging (BONCAT),¹ in which noncanonical amino acids (ncAAs) with bioorthogonal functional groups (e.g. azides or alkynes) are used as metabolic labels to distinguish new proteins from old (1, 2). Labeled proteins can be conjugated to fluorescent reporters for visualization or affinity tags for purification and subsequent identification by mass spectrometry (3). Because the ncAA probe can be introduced to cells in a well-defined “pulse,” affinity purification removes pre-existing proteins and provides both reduced sample complexity and excellent time resolution.The methionine (Met) surrogate l-azidohomoalanine (Aha) has become standard in the application of BONCAT methodologies. Using Aha and fluorescent tagging, Tcherkezian et al. observed co-localization of the DCC receptor with sites of protein synthesis, providing support for the role of netrin as a stimulant of extranuclear protein production in neurons (4). Combining Aha labeling and 2D gel electrophoresis, Yoon et al. discovered that the protein lamin B2 is synthesized in axons and crucial to mitochondrial function and axon maintenance in Xenopus retinal glial cells (5). Aha has also been used to study histone turnover (6), protein palmitoylation (7), pathogen amino acid uptake (8), inflammatory response (9), and local translation in neuronal dendrites and axons (10). These labeling techniques have been expanded to tissue and animal culture, where Aha has been used to profile protein synthesis in rat hippocampal brain slices (11, 12) and zebrafish embryos (13).The development of fast, reliable, quantitative BONCAT methods will enable new insights into proteome dynamics in response to biological stimuli. Recent work by Eichelbaum et al. combined Aha labeling with stable isotope labeling to measure lipopolysaccharide-stimulated protein secretion by macrophages (14). Using similar approaches, Somasekharan et al. identified a set of proteins that are translationally regulated by the Y-box binding protein-1 (YB-1) in TC-32 Ewing sarcoma cells (15), and Howden et al. monitored changes in protein expression following stimulation of primary T cells with phorbol 12-myristate 13-acetate and ionomycin (16).A concern that arises in the use of Aha (as it does for all chemical probes of biological processes) is that the protocols used for Aha labeling might perturb cellular protein synthesis. The development of ncAAs as reliable analytic tools hinges on our ability to understand and minimize such unintended effects. For Aha, previous work has shown that protein labeling does not visibly alter cellular morphology in dissociated hippocampal neurons or HEK293 cells, and 1D gels reveal no discrepancies between the proteomes of Aha- and Met-treated cells (1). These experiments, however, offer only coarse measures of effects on protein synthesis, and as Aha labeling is frequently coupled to mass spectrometry-based proteomic analysis, the biological effects of Aha treatment must be investigated with equivalent sensitivity and resolution.Here we report sound methods for fast, reliable measurement of proteome dynamics via noncanonical amino acid tagging. First, we use the quantitative proteomics technique pulsed stable isotope labeling with amino acids in cell culture (pSILAC) to investigate potential unintended effects of Aha labeling on protein abundance in HeLa cell cultures, and we develop a strategy for minimizing these effects. Second, we show that a combined BONCAT-pSILAC approach, capable of both enriching and quantifying newly synthesized proteins, yields detailed proteomic information on time scales that are inaccessible to isotope labeling techniques alone.     

Efficient identification of amino acid types for fast protein backbone assignments

We describe a procedure that allows for very efficient identification of amino acid types in proteins by selective ¹⁵N-labeling. The usefulness of selective incorporation of ¹⁵N-labeled amino acids into proteins for the backbone assignment has been recognized for several years. However, widespread use of this method has been hindered by the need to purify each selectively labeled sample and by the relatively high cost of labeling with ¹⁵N-labeled amino acids. Here we demonstrate that purification of the selectively ¹⁵N-labeled samples is not necessary and that background-free HSQC spectra containing only the peaks of the overexpressed heterologous protein can be obtained in crude lysates from as little as 100 ml cultures, thus saving time and money. This method can be used for fast and automated backbone assignment of proteins.     

A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility

An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract, similar protein amounts as with full media are obtained, without compromising on isotope incorporation. In single and dual amino acid labeling experiments incorporation ratios are consistently ≥90% for all amino acids tested. This enables NMR studies of eukaryotic proteins and their interactions even for proteins with low expression levels. We show applications with human kinases, where protein–ligand interactions are characterized by 2D [¹⁵N, ¹H]- and [¹³C, ¹H]-HSQC spectra.     

Stereospecific assignments of glycine in proteins by stereospecific deuteration and 15N labeling

Summary A method is described for stereospecifically assigning the -protons of glycine residues in proteins. The approach involves the stereospecific deuteration and ¹⁵N labeling of glycine and subsequent selective incorporation of this residue into the protein. The stereospecific assignments of the glycine -protons are obtained from a comparison of a 3D ¹⁵N-resolved TOCSY spectrum of the uniformly ¹⁵N-labeled protein with a 2D/3D ¹⁵N-edited TOCSY spectrum of the protein, containing the stereospecifically deuterated and ¹⁵N-labeled glycine. The approach is demonstrated by stereospecifically assigning the glycine -protons of the FK506 binding protein when bound to the immunosuppressant ascomycin.     

Residual backbone and side-chain <Superscript>13</Superscript>C and <Superscript>15</Superscript>N resonance assignments of the intrinsic transmembrane light-harvesting 2 protein complex by solid-state Magic Angle Spinning NMR spectroscopy

This study reports the sequence specific chemical shifts assignments for 76 residues of the 94 residues containing monomeric unit of the photosynthetic light-harvesting 2 transmembrane protein complex from Rhodopseudomonas acidophila strain 10050, using Magic Angle Spinning (MAS) NMR in combination with extensive and selective biosynthetic isotope labeling methods. The sequence specific chemical shifts assignment is an essential step for structure determination by MAS NMR. Assignments have been performed on the basis of 2-dimensional proton-driven spin diffusion ¹³C–¹³C correlation experiments with mixing times of 20 and 500 ms and band selective ¹³C–¹⁵N correlation spectroscopy on a series of site-specific biosynthetically labeled samples. The decreased line width and the reduced number of correlation signals of the selectively labeled samples with respect to the uniformly labeled samples enable to resolve the narrowly distributed correlation signals of the backbone carbons and nitrogens involved in the long -helical transmembrane segments. Inter-space correlations between nearby residues and between residues and the labeled BChl a cofactors, provided by the ¹³C–¹³C correlation experiments using a 500 ms spin diffusion period, are used to arrive at sequence specific chemical shift assignments for many residues in the protein complex. In this way it is demonstrated that MAS NMR methods combined with site-specific biosynthetic isotope labeling can be used for sequence specific assignment of the NMR response of transmembrane proteins.     

Cost-effective large-scale expression of proteins for NMR studies

We present protocols for high-level expression of isotope-labelled proteins in E. coli in cost-effective ways. This includes production of large amounts of unlabeled proteins and ¹³C-methyl methionine labeling in rich media, where yields of up to a gram of soluble protein per liter of culture are reached. Procedures for uniform isotope labeling of ²H, ¹³C and ¹⁵N using auto-induction or isopropyl-β-d-1-thiogalactopyranoside-induction are described, with primary focus on minimal isotope consumption and high reproducibility of protein expression. These protocols are based on high cell-density fermentation, but the key procedures are easily transferred to shake flask cultures.     

Measurement of the <Superscript>15</Superscript>N/<Superscript>14</Superscript>N ratio of phenylalanine in fermentation matrix by isotope ratio mass spectrometry

Objectives

To determine the origin of ¹⁵N-labeled phenylalanine in microbial metabolic flux analysis using ¹⁵N as a tracer, a method for measuring phenylalanine δ¹⁵N using HPLC coupled with elemental analysis-isotope ratio mass spectrometry (EA-IRMS) was developed.

Results

The original source of the ¹⁵N-labeled phenylalanine was determined using this new method that consists of three steps: optimization of the HPLC conditions, evaluation of the isotope fractionation effects, and evaluation of the effect of pre-processing on the phenylalanine nitrogen stable isotope. In addition, the use of a ¹⁵N-labeled inorganic nitrogen source, rather than ¹⁵N-labeled amino acids, was explored using this method.

Conclusions

The method described here can also be applied to the analysis of metabolic flux.

     

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective ‘unlabeling’ or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly ¹³C/¹⁵N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {¹²CO _i –¹⁵N _i+1}-filtered HSQC, which aids in linking the ¹H^N/¹⁵N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i − 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to ²H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of ¹⁴N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.     

Phase labeling of C−H and C−C spin-system topologies: Application in constant-time PFG-CBCA(CO)NH experiments for discriminating amino acid spin-system types

Summary Triple-resonance experiments facilitate the determination of sequence-specific resonance assignments of medium-sized ¹³C, ¹⁵N-enriched proteins. Some triple-resonance experiments can also be used to obtain information about amino acid spin-system topologies by proper delay tuning. The constant-time PFG-CBCA(CO)NH experiment allows discrimination between five different groups of amino acids by tuning (phase labeling) independently the delays for proton-carbon refocusing and carbon-carbon constant-time frequency labeling. The proton-carbon refocusing delay allows discrimination of spin-system topologies based on the number of protons attached to C and C atoms (i.e. C-H phase labeling). In addition, tuning of the carbon-carbon constant-time frequency-labeling delay discriminates topologies based on the number of carbons directly coupled to C and C atoms (i.e. C-C phase labeling). Classifying the spin systems into these five groups facilitates identification of amino acid types, making both manual and automated analysis of assignments easier. The use of this pair of optimally tuned PFG-CBCA(CO)NH experiments for distinguishing five spin-system topologies is demonstrated for the 124-residue bovine pancreatic ribonuclease A protein.