When peroxisomes were first identified over a half-century ago, they were considered by some to be vestigial organelles with little physiological significance. Work done over the last three to four decades has clearly demonstrated otherwise. In particular, peroxisomes carry out many essential processes involving fatty acid (FA) metabolism.
Essentially all cellular metabolic pathways in which FAs participate require that they first be activated to their CoA derivatives (). Among these pathways are the synthesis of triacylglycerol, phospholipids, plasmalogens, sphingolipids, and cholesterol esters, α-and β-oxidation of FA, FA elongation, conversion of FA to fatty alcohols, insertion and removal of double bonds, and protein acylation. Notable exceptions to the requirement for FA activation are the pathways for conversion of polyunsaturated FAs arachidonic acid and docosahexaenoic acid to bioactive eicosanoids and docosanoids, respectively. In addition, some bacteria, yeast, and plants use FA-acyl carrier protein thioesters instead of acyl-CoAs for certain metabolic processes [1
Metabolic fates of activated FAs
The ACS reaction is ATP-dependent. In the first half-reaction, the FA substrate is adenylated, releasing inorganic pyrophosphate (PPi):
The ubiquitous enzyme inorganic pyrophosphatase, which can be found in soluble, mitochondrial, peroxisomal, and other subcellular fractions [4
], rapidly cleaves PPi, effectively preventing reversal of this reaction. In the second half-reaction, CoA displaces AMP, forming a thioester bond to yield the activated FA:
The length of FA carbon chains varies from 2 to more than 30, significantly affecting FA hydrophobicity and solubility. These factors likely influenced the evolution of distinct families of ACSs that activate short-, medium-, long-, and very long-chain FA substrates. This was nicely demonstrated more than 40 years ago by Aas, who measured rat liver mitochondrial and microsomal ACS enzyme activity with FA substrates ranging in chain length from 2–20 carbons [5
]; four overlapping but distinct peaks of enzyme activity were observed. Although it was initially thought that there might be a single ACS responsible for activation of each FA chain length group, we now know the situation to be far more complex. Human and mouse genomes encode 26 ACSs [6
], while the plant Arabidopsis thaliana
has an estimated 64 acyl-activating enzyme genes [7
Identification of ACSs was facilitated by the recognition of two highly conserved domains; all enzymes with documented ACS activity contain these motifs () [6
]. This has allowed the identification of several new putative ACSs, and has facilitated the assignment of proteins to structurally-related subfamilies. Additional conserved domains found in some, but not all, ACS subfamilies have been identified. Twenty-two of the mammalian ACSs can be grouped into five subfamilies, which include the aforementioned short-, medium-, long-, and very long-chain activating enzymes, as well as a family containing two proteins homologous to the Drosophila melanogaster
“bubblegum” protein [6
]. Uniform ACS nomenclature has been established for four subfamilies, the short-chain (ACSS), medium-chain (ACSM), long-chain (ACSL), and bubblegum (ACSBG) families [10
]; the mammalian genes/proteins are listed in . The six very long-chain ACS family genes are currently designated SLC27A1-6. Members of this subfamily were investigated as fatty acid transport proteins (FATPs) as well as ACSs; the official gene nomenclature (S
arrier) reflects their putative transport function (). Four less structurally-related ACS enzymes are also represented in mammalian genomes.
Conserved domains in ACSs
Acyl-CoA Synthetase Nomenclature.
In addition to FAs, other compounds containing acyl side chains are substrates for ACSs. For example, the final step in the synthesis of bile acids requires the removal of three carbons from the cholesterol side chain, converting 27-carbon precursors to 24-carbon mature bile acids [11
]. In this process, a terminal carbon of the cholesterol aliphatic side chain is oxidized to a carboxylic acid, which must be activated to its CoA thioester before removal of a 3-carbon fragment via β-oxidation. Furthermore, many xenobiotic compounds, such as the hypolipidemic drug clofibrate and the non-steroidal anti-inflammatory drug ibuprofen, are ACS substrates [12
]. Enzymes of the ACSM family are primarily responsible for xenobiotic activation [13
]. Besides providing an acyl-CoA substrate for amino acid conjugation and elimination, xenobiotic-CoAs are substrates for lipid synthesis [12
In addition to classifying ACSs by their substrate chain length preference, these enzymes have also been categorized by their subcellular locations. There are numerous literature references to a “mitochondrial medium-chain ACS” or a “microsomal long-chain ACS”, without designating a specific enzyme. Many of these studies were done prior to the genomic era, at a time when our understanding of the diversity of the ACS subfamilies was far more limited.