Phosphorylation and Acetylation of Acyl-CoA Synthetase- I

Long chain acyl-CoA synthetase 1 (ACSL1) contributes 50 to 90% of total ACSL activity in liver, adipose tissue, and heart and appears to direct the use of long chain fatty acids for energy. Although the functional importance of ACSL1 is becoming clear, little is understood about its post-translational regulation. In order to investigate the post-translational modifications of ACSL1 under different physiological conditions, we overexpressed ACSL1 in hepatocytes, brown adipocytes, and 3T3-L1 differentiated adipocytes, treated these cells with different hormones, and analyzed the resulting phosphorylated and acetylated amino acids by mass spectrometry. We then compared these results to the post-translational modifications observed in vivo in liver and brown adipose tissue after mice were fasted or exposed to a cold environment. We identified universal N-terminal acetylation, 15 acetylated lysines, and 25 phosphorylation sites on ACSL1. Several unique acetylation and phosphorylation sites occurred under conditions in which fatty acid β-oxidation is normally enhanced. Thirteen of the acetylated lysines had not previously been identified, and none of the phosphorylation sites had been previously identified. Site-directed mutagenesis was used to introduce mutations at three potential acetylation and phosphorylation sites believed to be important for ACSL1 function. At the ATP/AMP binding site and at a highly conserved site near the C terminus, modifications of Ser278 or Lys676, respectively, totally inhibited ACSL1 activity. In contrast, mutations of Lys285 that mimicked acetylation (Lys285Ala and Lys285Gln) reduced ACSL activity, whereas full activity was retained by Lys285Arg, suggesting that acetylation of Lys285 would be likely to decrease ACSL1 activity. These results indicate that ACSL1 is highly modified post-translationally. Several of these modifications would be expected to alter enzymatic function, but others may affect protein stability or protein-protein interactions.

Acyl-coenzyme A synthetases in metabolic control

PURPOSE OF REVIEW

The 11 long-chain (ACSL) and very long chain acyl-coenzyme A (acyl-CoA) synthetases [(ACSVL)/fatty acid transport protein] are receiving considerable attention because it has become apparent that their individual functions are not redundant.

RECENT FINDINGS

Recent studies have focused on the structure of the acyl-CoA synthetases, their post-translational modification, their ability to activate fatty acids of varying chain lengths, and their role in directing fatty acids into different metabolic pathways. An unsettled controversy focuses on the ACSVL isoforms and whether these have both enzymatic and transport functions. Another issue is whether conversion of a fatty acid to an acyl-CoA produces an increase in the AMP/ATP ratio that is sufficient to activate AMP-activated kinase.

SUMMARY

Future studies are required to determine the subcellular location of each ACSL and ACSVL isoform and the functional importance of phosphorylation and acetylation. Purification and crystallization of mammalian ACSL and ACSVL isoforms is needed to confirm the mechanism of action and discover how these enzymes differ in their affinity for fatty acids of different chain lengths. Functionally, it will be important to learn how the ACSL isoforms can direct their acyl-CoA products toward independent downstream pathways.

Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry

Posttranslational modifications such as glycosylation can play a fundamental role in signaling pathways that transform an ordinary cell into a malignant one. The development of a protocol to detect these changes in the preliminary stages of disease can lead to a sensitive and specific diagnostic for the early detection of malignancies such as ovarian cancer in which differential glycan patterns are linked to etiology and progression. Small variations in instrument parameters and sample preparation techniques are known to have significant influence on the outcome of an experiment. For an experiment to be effective and reproducible, these parameters must be optimized for the analyte(s) under study. We present a detailed examination of sample preparation and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) analysis of O-linked glycans globally cleaved from mucin glycoproteins. Experiments with stable isotope-labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI-FT-ICR-MS of oligosaccharides. Quadrupole ion guide optimization studies with mucin glycans identified conditions for the comprehensive analysis of the entire mass range of O-linked carbohydrates in this glycoprotein. Separately optimized experimental parameters were integrated in a method that allowed for the effective study of O-linked glycans.

Achieving Augmented Limits of Detection for Peptides with Hydrophobic Alkyl Tags

The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.

Understanding the influence of post-excite radius and axial confinement on quantitative proteomic measurements using Fourier transform ion cyclotron resonance mass spectrometry

Early studies of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) explored many of the fundamental issues surrounding the potential of the technique to provide quantitative data. Improvements in instrument technology and the analysis of larger molecules in increasingly complex mixtures warrant not only a revisit to some of these earlier studies, but a more comprehensive examination of the influence of various instrument parameters on quantitative (absolute and relative) measurements in proteomics. We present a detailed examination of the role that acquisition time, excite voltage (i.e. excite radius), trapping voltage, and the type of excitation waveform have on the ability of FT-ICR to accurately quantify biological molecules. The use of a stable-isotope-labeled and unlabeled phenyl isocyanate derivatized peptide allows us to ascribe the effects of FT-ICR-MS on quantification, thus eliminating the contribution of ionization differences to ion abundance. To adequately assess the multiple parameters in the large dataset, we develop a multiplicative quality factor that encompasses the total ion abundance, as well as the accuracy and the precision of abundance ratios. This assessment allows facile determination of optimal instrument parameters for quantitative measurements.

Nucleic Acid analysis by fourier transform ion cyclotron resonance mass spectrometry at the beginning of the twenty-first century

Mass spectrometers measure an intrinsic property (i.e., mass) of a molecule, which makes it an ideal platform for nucleic acid analysis. Importantly, the unparalleled capabilities of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry further extend its usefulness for nucleic acid analysis. The beginning of the twenty-first century has been marked with notable advances in the field of FT-ICR mass spectrometry analysis of nucleic acids. Some of these accomplishments include fundamental studies of nucleic acid properties, improvements in sample clean up and preparation, better methods to obtain higher mass measurement accuracy, analysis of noncovalent complexes, tandem mass spectrometry, and characterization of peptide nucleic acids. This diverse range of studies will be presented herein.

Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry

The number and wide dynamic range of components found in biological matrixes present several challenges for global proteomics. In this perspective, we will examine the potential of zero-dimensional (0D), one-dimensional (1D), and two-dimensional (2D) separations coupled with Fourier-transform ion cyclotron resonance (FT-ICR) and time-of-flight (TOF) mass spectrometry (MS) for the analysis of complex mixtures. We describe and further develop previous reports on the space occupied by peptides, to calculate the theoretical peak capacity available to each separations-mass spectrometry method examined. Briefly, the peak capacity attainable by each of the mass analyzers was determined from the mass resolving power (RP) and the m/z space occupied by peptides considered from the mass distribution of tryptic peptides from National Center for Biotechnology Information's (NCBI's) nonredundant database. Our results indicate that reverse-phase-nanoHPLC (RP-nHPLC) separation coupled with FT-ICR MS offers an order of magnitude improvement in peak capacity over RP-nHPLC separation coupled with TOF MS. The addition of an orthogonal separation method, strong cation exchange (SCX), for 2D LC-MS demonstrates an additional 10-fold improvement in peak capacity over 1D LC-MS methods. Peak capacity calculations for 0D LC, two different 1D RP-HPLC methods, and 2D LC (with various numbers of SCX fractions) for both RP-HPLC methods coupled to FT-ICR and TOF MS are examined in detail. Peak capacity production rates, which take into account the total analysis time, are also considered for each of the methods. Furthermore, the significance of the space occupied by peptides is discussed.

Leveling response factors in the electrospray ionization process using a heated capillary interface

Several investigators have observed a discrepancy in electrospray response of complementary strands from denatured DNA, which has been attributed to the difference in hydrophobicity between the two strands; the more hydrophobic species tend to have higher ion abundances. The implementation of a heated electrospray source has allowed us to "level" the electrospray response for two equimolar complementary strands with different hydrophobicities. As the temperature was increased, the ratio of ion abundances of the less hydrophobic noncoding strand to the more hydrophobic coding strand approached unity. Furthermore, the heated electrospray source was used to denature amplicons containing 7-deaza purines, which can be used to facilitate sequencing by mass spectrometry.