Dietary fats are the major source of fatty acids in humans. They are absorbed in the intestine and transported to the liver by chilomicrons* (CMs). Beyond that the liver is the major organ capable of synthesis of fatty acids. In this case fatty acids are synthesized from acetyl coenzyme A* (acetyl-CoA) derived from glucose. Fatty acids are oxidized to generate energy for several tissues. In the liver adipocytes, fatty acids are esterified to glycerol to form triaglycerol (TG) for storage and transport. Dietary fat has a dual role in human physiology: a) it functions as a source of energy and structural components for cells; b) it functions as a regulator of gene expression that impacts lipid, carbohydrate, and protein metabolism, as well as cell growth and differentiation. Fatty acid effects on gene expression are cell-specific and influenced by fatty acid structure and metabolism. Fatty acids interact with the genome through several mechanisms. They regulate the activity or nuclear abundance of several transcription factors, including PPAR, LXR, HNF-4, NFκB, and SREBP. Fatty acids or their metabolites bind directly to specific transcription factors to regulate gene transcription. Alternatively, fatty acids indirectly act on gene expression through their effects on a) specific enzyme-mediated pathways, such as cyclooxygenase, lipoxygenase, protein kinase C, or sphingomyelinase signal transduction pathways; or b) pathways that involve changes in membrane lipid/lipid raft composition that affect G-protein receptor or tyrosine kinase-linked receptor signaling. 

Fatty acids/triacylglycerols may originate from four sources (pool input): De novo lipogenesis, cytoplasmic triacylglycerol stores, fatty acids derived from triacylglycerols of lipoprotein remnants directly taken up by the liver, and plasma non-esterified fatty acids (NEFA) released by adipose tissue.  

The triacylglycerol content of hepatocytes is regulated by the activity of cellular molecules that facilitates hepatic fatty acid uptake, fatty acid synthesis, and esterification (‘input’) and hepatic fatty acid oxidation and triacylglycerol export (‘output’).

Moreover, and interestingly, fatty acids regulate overall lipid metabolism by binding nuclear receptors that modulate gene transcription.  

Regulation at molecular level

Fatty acids regulate gene expression by controlling the activity or abundance of key transcription factors (Jump et al., 2005), which at the molecular level play a crucial role; this has been particularly illustrated by the link between alterations in their functions and the occurrence of major metabolic diseases. Many transcription factors have been identified as prospective targets for fatty acid regulation, including peroxisome proliferator-activated receptors (PPARα, β and γ) (Schoonjans et al., 1996), SREBP-1c (Xu et al., 1999), retinoid X receptor (RXRα) (Dubuquoy et al., 2002), and LXRα (Zelcer and Tontonoz, 2006). They integrate signals from various pathways and coordinate the activity of the metabolic machinery necessary for fatty acid metabolism with the supply of energy and fatty acids.

Nuclear receptors and transcription factors

Retinoid X receptors (RXRs) play an important regulatory role in metabolic signaling pathways (glucose, fatty acid and cholesterol metabolism) (Ahuja et al., 2003). These receptors activate transcription as homodimers or as obligate heterodimeric partners of numerous other nuclear receptors; especially PPARs and LXRs that belong to the nuclear receptor superfamily of ligand-activated transcription factors and which have been implicated in diverse pathways of lipid metabolism (Barish, 2006; Zelcer and Tontonoz, 2006). Similarly to other nuclear receptors, they interact with nuclear proteins known as co-activators and co-repressors. Activated PPARs or LXRs heterodimerize with RXR (PPAR-RXR or LXR-RXR complex). The heterodimers modulate the transcription of target genes by binding to their promoter region on a specific DNA sequence termed the peroxisome proliferator responsive element (PPRE); this consists of a direct repeat of the nuclear receptor hexameric DNA core recognition (AGGTCA) motif spaced by one nucleotide (Latruffe et al., 2001). Liver X receptors bind to cognate LXR response element (LXRE) sequences that typically consist of a direct repeat of TGACCT spaced by four nucleotides (Willy and Mangelsdorf, 1997). PPARs and LXRs act as key messengers responsible for the translation of nutritional, metabolic and pharmacological stimuli into changes in the expression of genes, especially those genes involved in lipid metabolism.

PPAR-α is highly expressed in the liver and in those tissues that use a lot of lipid-derived energy, where it regulates a set of enzymes crucial for fatty acid oxidation. Indeed, its primary role is to increase the cellular capacity to mobilize and catabolize fatty acids. It increases transcription and expression of proteins and enzymes necessary to transport and catabolize fatty acids (FABP, FAT, CPT-I etc.). It also participates in the regulation of mitochondrial and peroxisomal fatty acid β-oxidation systems, microsomal ω-oxidation system (acyl-CoA oxidase, CYP4A1 and CYP4A6 etc.), and the production of apolipoproteins (Everett et al., 2000). PPAR-α functions as a sensor for fatty acids and ineffective PPAR-α sensing (or PPAR-α null phenotype) can lead to reduced energy burning, resulting in hepatic steatosis. The DNA-binding properties of PPARα and other transcription factors (RXRs) on the PPRE of the mitochondrial HMG-CoA synthase promoter have revealed that ketogenesis can be regulated by fatty acids. Interestingly HMG-CoA synthase can react with PPARα and thus autoregulate its own transcription. PPARγ activation is followed by overexpression of lipogenic enzymes (acetylCoA carboxylase, FAS, GPAT) and FATP. Liver X receptors are master regulators of whole-body cholesterol homeostasis. CYP7a1, which is another member of the cytochrome P450 enzyme family and the rate-limiting enzyme in the pathway of bile acid synthesis is the first direct target of LXRs. Their target genes also include the ATP-binding cassette (ABC) subfamilies (ABCA1 and G1: cholesterol efflux, G5 and G8: bile acid excretion and intestinal cholesterol absorption). In addition to their role in cholesterol metabolism, LXRs are also key regulators of hepatic lipogenesis through the upregulation of the master regulator of hepatic lipogenesis, SREBP-1c, as well as induction of FAS and acyl-CoA carboxylase (Zelcer and Tontonoz, 2006). Sterol regulatory element binding proteins-1 has also been identified as a potent activator of lipogenic gene expression. The regulation of its gene expression by dietary and hormonal factors has already been mentioned. Moreover, polyunsaturated fatty acids suppress SREBP-1c gene expression and inhibit SREBP-1c protein maturation, which results in suppression of its target genes (such as FAS and GPAT) resulting in reduced fatty acid and triglyceride synthesis (Kim et al., 2002).

Nuclear factors and Gene regulation

Nuclear factors play a crucial role in the regulation of lipid metabolism. Indeed, fatty acid metabolism is transcriptionally regulated by two main systems under the control of either LXRs or PPARs. Liver X receptors activate expression of SREBP-1c, an already mentioned dominant lipogenic gene regulator, whereas genes encoding peroxisomal, microsomal and some mitochondrial fatty acid metabolizing enzymes in the liver are transcriptionally regulated by PPARα. An intricate network of nutritional transcription factors with mutual interactions has been proposed, resulting in efficient reciprocal regulation of lipid degradation and lipogenesis. LXR activation, either by overexpression of LXR or its ligand would cause suppression of PPARα signaling, by RXRα competition between PPAR and LXR (Ide et al., 2003). Reciprocally, PPARα activation would suppress the LXR-SREBP-1c pathway through reduction of LXR/RXRα formation (Yoshikawa et al., 2003). As LXRα and PPARα regulate alternate pathways of fatty acid synthesis and catabolism, these nuclear receptors would ‘cross-talk’ to ensure that antagonistic pathways are not simultaneously activated. Other studies have not shown this cross-talk, but some work indicates that PPARα and LXRα activate an overlapping set of genes involved in both fatty acid catabolism and synthesis (Anderson et al., 2004). Hepatic peroxisomal fatty acid β-oxidation would especially be regulated by LXRα, and this process might serve as a counterregulatory mechanism for responding to extreme situations such as hypertriglyceridaemia and liver steatosis (Hu et al., 2005). In such unusual situations, PPARγ expression which is usually low in liver (10–30% of expression in adipose tissue) would nevertheless be capable of selectively upregulating a subset of the lipogenic enzymes in hepatocytes, thus enhancing both lipid synthesis and accumulation leading to steatosis (Coleman and Lee, 2004). PPARγ has been reported to activate LXRα gene expression (Tsukamoto, 2005) which could in turn activate SREBP-1c gene expression and downregulate PPARα, leading to speculation that these four factors could form an auto-loop controlling the activation of adipogenesis and the inactivation of oxidation.

Fatty acids and Gene regulation

Receptors and transcription factors drive liver lipid metabolism. In turn, long chain fatty acids, acyl-CoAs, and other fatty acid-derived compounds (e.g., eicosanoids) are the ligands of nuclear factors and are responsible for their activation, thus acting as metabolic regulators of gene transcription. Fatty acids induce changes in the activity or abundance of at least four transcription factor families: PPARs, LXRs, hepatic nuclear factor 4, and SREBP (Pegorier et al., 2004; Jump et al., 2005). Long chain polyunsaturated fatty acids are strong ligands, while monounsaturated fatty acids are only weak ligands and saturated fatty acids poor ligands. Moreover, downregulation of gene expression by fatty acids would be restricted to polyunsaturated fatty acids, whereas upregulation would be independent of the degree of saturation (Pegorier et al., 2004). Differences might involve differential metabolism (oxidative pathways, kinetics etc.) and selective transport of fatty acids to the nucleus. Table 1 shows some genes involved in lipid metabolism whose expression is regulated by fatty acids. An abundance of polyunsaturated fatty acids regulates numerous PPARα target genes, especially those involved in fatty acid oxidation, while they block the ligand-dependent activation of LXR. Long chain (polyunsaturated) fatty acids suppress SREBP-1c activity, leading to a reduction in liver triacylglycerol content; directly by reducing the nuclear abundance of SREBP-1c, and indirectly because of inactivation of LXR.

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Free fatty acids are first activated by linking to acetyl-CoA by acyl-CoA synthetase to form fatty acyl-CoA, which is transported into mitochondria through a carnitine-dependent transport system in the outer mitochondrial membrane. CPTI tranfers a carnitine to fatty acyl-CoA to form fatty acylcarnitine, which is then transported across the inner mitochondrial membrane by carnitine: acylcarnitine translocase. Once inside the mitochondrial matrix, fatty acylcarnitine converts to to fatty acyl-CoA to release a free carnitine. Fatty acyl-CoA enters the Beta-oxidation cycle to release an acetyl-CoA and produce one each of NADH and FADH2, which generate a total of 5 ATP. Each acetym-CoA entering into the tricarboxylic cycle produces 12 ATP. Complete oxidation of one palmitoryl CoA produces 131 ATP. CPTI is the rate-determinating step in fatty acid oxidation and is inhibited by malonyl-CoA. The rate of ATP utilization controls the rate of the electron-transport chain, which regulates Beta oxidation of fatty acids and the TCA cycle. A high ATP/ADP or NADH/NAD+ ratio signals high energy stae and inhibits fatty acid oxidation. Peroxisomes are involved in oxidation of long chain and very long chain fatty acids. The peroxisomal fatty acid Beta oxidation pathway is similar to the mitochondrial pathway, but enzymes involved (Acyl-CoA oxidase, bifunctional enzyme, and thiolase) are different, and the pathway does not produce ATP. Long chain fatty acids are shortened to short and median-chain fatty acyl-CoAs in peroxisomes, which are further oxidized in the mitochondria. The liver, muscle, and heart preferentially utilize fatty acids and spare glucose for use by the brain and red blood cells.

Non-esterified acyl-CoA may be oxidized, either in the mitochondria or peroxisomes. Mitochondrial oxidation may be either complete or incomplete. Incomplete oxidation leads to formation of ketone bodies.

The two main factors regulating the degree to which fatty acids are oxidized by the liver are the supply of fatty acids to the liver (via lipolysis), and the partitioning between oxidation and microsomal esterification.  

Very long chain fatty acids are also metabolized by the cytochrome P450 CYP4A ω-oxidation system to dicarboxylic acids. Indeed, the CYP4A enzymes are especially capable of hydroxylating the terminal ω-carbon and, to a lesser extent the (ω-1) position of fatty acids. Ω-hydroxylation is followed by cytosolic oxidation to produce long chain dicarboxylic acids (Simpson, 1997). These acids cannot be readily metabolized by the mitochondria, whereas they are the preferred substrate for the peroxisomal β-oxidation pathway. They are thus taken up by the peroxisomes and oxidized to fatty acids, which can then be shortened even further by the mitochondria. The induction of this system would be an adaptive response by the hepatocyte to maintain cellular lipid homeostasis. It is important during fatty acid overload of the mitochondrial β-oxidation system with the microsomal CYP4A-mediated ω-oxidation and peroxisomal β-oxidation being co-operatively regulated to achieve fatty acid metabolism in the liver. 

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Ketogenesis

Under conditions of increased fatty acid uptake, the liver often produces large amounts of the ketone bodies, acetoacetate and β-hydroxybutyrate, in a process known as ketogenesis. Ketogenesis is enhanced in times of increased NEFA uptake by the liver, when low insulin levels cause activation of CPT-I, allowing extensive uptake of fatty acids into mitochondria.

Conversion of acetyl-CoA to ketone bodies, rather than complete oxidation in the TCA cycle, results in the formation of less ATP/mole of fatty acid oxidized (e. g. five times less in the case of palmitate: 129 vs. 27 ATP/mole, TCA and oxidative phosphorylation in the electron transport chain vs. conversion of acetyl-CoA to ketone bodies). Ketogenesis therefore allows the liver to metabolize about five times more fatty acids (for the same ATP yield), and conversion of fatty acids into water-soluble fuels may be an important short-term strategy to redistribute energy.

Ketogenesis (as well as cholesterol biosynthesis) is controlled indirectly by CPT-I (McGarry et al., 1989) and directly by the activity of the mitochondrial key regulatory enzyme 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (Hegardt, 1999). The enzyme is regulated by two systems: succinylation in the short term, and transcriptional regulation in the long term (prolonged energy deficit). When the succinyl-CoA pool size increases as a result of an increased flux of glucogenic metabolites, a succinyl group is added to a regulatory sub-unit of HMG-CoA synthase, which inactivates the enzyme. Both control mechanisms are influenced by nutritional and hormonal factors, which explain the incidence of ketogenesis.