Improved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides

Methylotroph Quorum Sensing Signal Identification by Inverse Stable Isotopic Labeling

Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a ¹³C-carbon source and then identifying ¹²C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate that this method identifies N-acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously detect five previously unidentified signals produced by a methylotroph and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive ¹³C-carbon sources.

Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments

Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH₄ emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH₄) emission, since CH₄ production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH₄ emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH₄ cycling and ultimately to predicting future CH₄ emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH₄, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH₄-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH₄-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH₄ oxidation in anaerobic lake sediments.

Preparative separation of ribonucleoside monophosphates by ion-pair reverse-phase HPLC

Structural and dynamic investigations of RNA by nuclear magnetic resonance (NMR) spectroscopy strongly benefit from isotopic-labeling strategies. Among these, nucleotide-specific and site-specific labeling methods can help tremendously in simplifying complex NMR data, while providing unique opportunities for structural investigation of larger RNAs. Such methods generally require separation of individual isotopically labeled ribonucleoside monophosphates prior to their conversion into nucleoside triphosphates and selective incorporation of these nucleoside triphosphates into the RNA. This chapter provides the experimental details for preparative separation of ribonucleoside monophosphates by ion-pair reverse-phase HPLC. It also describes a quick procedure for clean-up and quality control of the individual ribonucleoside monophosphates.

Synthesis of (6-(13)C)pyrimidine nucleotides as spin-labels for RNA dynamics

We present a (13)C-based isotope labeling protocol for RNA. Using (6-(13)C)pyrimidine phosphoramidite building blocks, site-specific labels can be incorporated into a target RNA via chemical oligonucleotide solid-phase synthesis. This labeling scheme is particularly useful for studying milli- to microsecond dynamics via NMR spectroscopy, as an isolated spin system is a crucial prerequisite to apply Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion type experiments. We demonstrate the applicability for the characterization and detection of functional dynamics on various time scales by incorporating the (6-(13)C)uridine and -cytidine labels into biologically relevant RNAs. The refolding kinetics of a bistable terminator antiterminator segment involved in the gene regulation process controlled by the preQ(1) riboswitch class I was investigated. Using (13)C CPMG relaxation dispersion NMR spectroscopy, the milli- to microsecond dynamics of the HIV-1 transactivation response element RNA and the Varkud satellite stem loop V motif was addressed.

Enzymatic de novo pyrimidine nucleotide synthesis

The use of stable isotope labeling has revolutionized NMR studies of nucleic acids, and there is a need for methods of incorporation of specific isotope labels to facilitate specific NMR experiments and applications. Enzymatic synthesis offers an efficient and flexible means to synthesize nucleoside triphosphates from a variety of commercially available specifically labeled precursors, permitting isotope labeling of RNAs prepared by in vitro transcription. Here, we recapitulate de novo pyrimidine biosynthesis in vitro, using recombinantly expressed enzymes to perform efficient single-pot syntheses of UTP and CTP that bear a variety of stable isotope labeling patterns. Filtered NMR experiments on (13)C, (15)N, (2)H-labeled HIV-2 TAR RNA demonstrate the utility and value of this approach. This flexible enzymatic synthesis will make implementing detailed and informative RNA stable isotope labeling schemes substantially more cost-effective and efficient, providing advanced tools for the study of structure and dynamics of RNA molecules.

13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides

We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of (13)C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, (13)C-direct detected NMR methods constitute useful complements to the conventional (1)H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.

Key labeling technologies to tackle sizeable problems in RNA structural biology

The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (< or =2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as (2)H, (13)C, (15)N, and (19)F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined.

RNA structure determination by NMR

This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.

New RNA Labeling Methods Offer Dramatic Sensitivity Enhancements in 2H NMR Relaxation Spectra

A new labeling strategy is presented that greatly facilitates the measurement of 2H spin relaxation rates in RNA molecules as a probe of pico- to nanosecond time scale dynamics. In this labeling scheme the sugar positions are uniformly 13C-labeled, with position 2' protonated and all other sites on the sugar deuterated. Pulse sequences are presented for measurement of 2H R1 and R2 relaxation rates at positions 1', 3', and 4' with sensitivity gains that are on the order of 5-fold relative to previous methods that employed random fractional deuteration. The improved sensitivity is transformative and facilitates the study of motion in moderately sized RNA molecules with good sensitivity. The utility of the approach is demonstrated with an application to HIV-2 TAR, where the site-specific measures of molecular dynamics at sugar positions obtained here complement previous studies of dynamics at aromatic sites in the molecule.

A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics

A suite of (2)H-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly (13)C, randomly fractionally deuterated ( approximately 50%) RNA molecules. The experiments quantify (2)H R(1) and R(2) relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity permitting, the consistency of the data can be evaluated by measuring all five rates that are accessible for a spin 1 particle and establishing that the rates obey relations that are predicted from theory. The utility of the methodology is demonstrated with studies of the dynamics of a 14-mer RNA containing the UUCG tetraloop at temperatures of 25 and 5 degrees C. The high quality of the data, even at 5 degrees C, suggests that the experiments will be of use for the study of RNA molecules that are as large as 30 nucleotides.

Structural characterization of the complex of the Rev response element RNA with a selected peptide

INTRODUCTION

The RSG-1.2 peptide was selected for specific binding to the Rev response element RNA, as the natural Rev peptide does. The RSG-1.2 sequence has features incompatible with the helical structure of the bound Rev peptide, indicating that it must bind in a different conformation.

RESULTS

The binding of the RSG-1.2 peptide to the Rev response element RNA was characterized using multinuclear, multidimensional NMR. The RSG-1.2 peptide is shown to bind with the N-terminal segment of the peptide along the major groove in an extended conformation and turn preceding a C-terminal helical segment, which crosses the RNA groove in the region widened by the presence of purine-purine base pairs. These features make the details of the bound state rather different than that of the Rev peptide which targets the same RNA sequence binding as a single helix along the groove axis.

CONCLUSIONS

These studies further demonstrate the versatility of arginine-rich peptides in recognition of specific RNA elements and the lack of conserved structural features in the bound state.

Heterologous expression of a deuterated membrane-integrated receptor and partial deuteration in methylotrophic yeasts

Methylotrophic yeast has previously been shown to be an excellent system for the cost-effective production of perdeuterated biomass and for the heterologous expression of membrane receptors. A protocol for the expression of 85% deuterated, functional human mu-opiate receptor was established. For partially deuterated biomass, deuteration level and distribution were determined for fatty acids, amino acids and carbohydrates. It was shown that prior to biosynthesis of lipids and amino acids (and of carbohydrates, to a lower extent), exchange occurs between water and methanol hydrogen atoms, so that 80%-90% randomly deuterated biomass and over-expressed proteins may be obtained using only deuterated water.

The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins

During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.

Solution NMR spectroscopy beyond 25 kDa

Improvements in NMR instrumentation, higher magnetic field strengths, novel NMR experiments and new deuterium-labeling strategies have significantly increased the scope of structural problems that can now be addressed by solution NMR methods. To date, a number of structures of proteins of 30 kDa have been solved using multidimensional 15N,13C,2H NMR techniques, and this molecular weight limit will probably be surpassed in the near future.

Comparison of H5 and H8 relaxation rates of a 2H/13C/15N labeled RNA oligonucleotide with selective protonation at C5 and C8

Uniformly 13C/15N enriched ribonucleotide monophosphates have been prepared with extensive deuterium enrichment of the non-exchangeable positions. The purine C8 and pyrimidine C5 base positions were selectively protonated prior to incorporation of the individual nucleotide triphosphates into an RNA oligonucleotide. The longitudinal and transverse relaxation rates of the H8 and H5 resonances of this deuterated molecule were compared with the relaxation rates of the corresponding protonated, 13C/15N enriched RNA molecule. Deuteration disrupts the efficiency of 1H-1H dipolar relaxation and reduces the longitudinal and transverse magnetization relaxation rates on average to 25% and 68%, respectively, of the values measured for the non-deuterated RNA molecule. Importantly, the longitudinal relaxation rates remain sufficiently rapid (> 1s[-1]) to permit the use of short recovery delays in multidimensional NMR experiments without significant loss of sensitivity.