N-terminal Fatty Acyl Research Articles

Evolutionary Relationships and Protein Domain Architecture in an Expanded Calpain Superfamily in Kinetoplastid Parasites

Employing whole-genome analysis we have characterized a large family of genes coding for calpain-related proteins in three kinetoplastid parasites. We have defined a total of 18 calpain-like sequences in Trypanosoma brucei, 27 in Leishmania major, and 24 in Trypanosoma cruzi. Sequence characterization revealed a well-conserved protease domain in most proteins, although residues critical for catalytic activity were frequently altered. Many of the proteins contain a novel N-terminal sequence motif unique to kinetoplastids. Furthermore, 24 of the sequences contain N-terminal fatty acid acylation motifs indicating association of these proteins with intracellular membranes. This extended family of proteins also includes a group of sequences that completely lack a protease domain but is specifically related to other kinetoplastid calpain-related proteins by a highly conserved N-terminal domain and by genomic organization. All sequences lack the C-terminal calmodulin-related calcium-binding domain typical of most mammalian calpains. Our analysis emphasizes the highly modular structure of calpains and calpain-like proteins, suggesting that they are involved in diverse cellular functions. The discovery of this surprisingly large family of calpain-like proteins in lower eukaryotes that combines novel and conserved sequence modules contributes to our understanding of the evolution of this abundant protein family.

Chemo- and regioselective peptide cyclization triggered by the N-terminal fatty acid chain length: the recombinant cyclase of the calcium-dependent antibiotic from Streptomyces coelicolor.

Here we report the first biochemical characterization of a recombinant nonribosomal peptide cyclase of a streptomycete, the model actinomycete Streptomyces coelicolor A3(2). This bacterium produces the calcium-dependent antibiotic (CDA), which is a branched cyclic macrolactone belonging to the group of acidic lipopeptides. The recombinant CDA3 cyclase from CDA synthetase efficiently catalyzes ring formation of linear peptidyl thioester substrates based on a sequence analogous to natural CDA. Four leaving groups were attached to the C-terminus of the undecapeptide: coenzyme A (CoA), phosphopantetheine, N-acetylcysteamine (SNAC), and thiophenol. The best rates for cyclization were determined for the thiophenol substrate, revealing that chemical reactivity is more important than cofactor recognition. The cyclase catalyzes the formation of two regioisomeric macrolactones, which arise from simultaneous nucleophilic attack of the two adjacent Thr(2) and Ser(1) residues onto the C-terminus of the acyl-enzyme intermediate. This relaxed regioselectivity has not been observed for any other recombinant NRPS or PKS cyclases so far. Substitution of either Ser(1) or Thr(2) by alanine led to selective formation of a decapeptide or undecapeptide lactone ring. In contrast to that, CDA3 cyclase strictly retains stereoselectivity for both nucleophiles, accepting only l-configured Ser(1) and Thr(2) for cyclization. Further, our studies provide evidence for the crucial role of N-terminal fatty acyl groups of lipopeptides in controlling the regio- and chemoselectivity of enzyme-catalyzed macrocyclization. Elongation of the fatty acyl group of our thioester substrate from C(2) to C(6) as in CDA turned the relaxed regioselectivity into a strict regioselectivity, yielding solely the decapeptide lactone ring with a significantly improved cyclization-to-hydrolysis ratio.

N-terminal protein acylation confers localization to cholesterol, sphingolipid-enriched membranes but not to lipid rafts/caveolae.

When variably fatty acylated N-terminal amino acid sequences were appended to a green fluorescent reporter protein (GFP), chimeric GFPs were localized to different membranes in a fatty acylation-dependent manner. To explore the mechanism of localization, the properties of acceptor membranes and their interaction with acylated chimeric GFPs were analyzed in COS-7 cells. Myristoylated GFPs containing a palmitoylated or polybasic region colocalized with cholesterol and ganglioside GM(1), but not with caveolin, at the plasma membrane and endosomes. A dipalmitoylated GFP chimera colocalized with cholesterol and GM(1) at the plasma membrane and with caveolin in the Golgi region. Acylated GFP chimeras did not cofractionate with low-density caveolin-rich lipid rafts prepared with Triton X-100 or detergent-free methods. All GFP chimeras, but not full-length p62(c-yes) and caveolin, were readily solubilized from membranes with various detergents. These data suggest that, although N-terminal acylation can bring GFP to cholesterol and sphingolipid-enriched membranes, protein-protein interactions are required to localize a given protein to detergent-resistant membranes or caveolin-rich membranes. In addition to restricting acceptor membrane localization, N-terminal fatty acylation could represent an efficient means to enrich the concentration of signaling proteins in the vicinity of detergent-resistant membranes and facilitate protein-protein interactions mediating transfer to a detergent-resistant lipid raft core.

Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana.

Ara6 of Arabidopsis thaliana is a novel member of the Rab/Ypt GTPase family with unique structural features. It resembles Rab5 GTPases best, but lacks a large part of the C-terminal hypervariable region and the cysteine motif, and instead harbors an extra stretch of amino acid residues containing myristoylation and palmitoylation sites at the N-terminus. Ara6 is tightly associated with membranes and is expressed constitutively. In contrast, the conventional Rab5 ortholog, Ara7, is highly expressed only in actively dividing cells. Examination of green fluorescent protein (GFP)-tagged proteins indicates that both Ara6 and Ara7 are distributed on a subpopulation of endosomes and suggests their roles in endosomal fusion. The endosomal localization of Ara6 requires N-terminal fatty acylation, nucleotide binding and the C-terminal amino acid sequence coordinately. Proteins similar to Ara6 are found only in higher plants and thus represent a novel class of Rab GTPases regulating endocytic function in a plant- specific manner.

Targeting proteins to plasma membrane and membrane microdomains by N-terminal myristoylation and palmitoylation

This chapter discusses the use of N-terminal fatty acylation sequences for targeting chimeric proteins to the plasma membrane.. The fatty acids myristate and palmitate are covalently linked to a wide variety of viral and cellular proteins. Sequence motifs located at the N terminus are responsible for conferring N-myristoylation of all known N-myristoylated proteins. In addition, signals for protein palmitoylation are often located at or near the N terminus. Many myristoylated proteins and nearly all dually fatty acylated proteins are attached to the inner leaflet of the cell plasma membrane. The N-terminal sequence motifs that direct fatty acylation have been shown to be both necessary and sufficient for conferring plasma membrane association. In addition to providing plasma membrane binding, palmitoylated sequences have been shown to confer targeting of proteins to specific plasma membrane microdomains The chapter describes the three general types of N-terminal fatty acylation motifs that are known to confer membrane binding. Type 1 motifs contain a “myristate plus basic” signal. These proteins are modified by covalent attachment of the 1Ccarbon fatty acid myristate to the N-terminal glycine residue. On the other hand, Type 2 and 3 N-terminal motifs are useful for conferring plasma membrane microdomain localization to proteins.

Testing the '+2 rule' for lipoprotein sorting in the Escherichia coli cell envelope with a new genetic selection.

We report a novel strategy for selecting mutations that mislocalize lipoproteins within the Escherichia coli cell envelope and describe the mutants obtained. A strain carrying a deletion of the chromosomal malE gene, coding for the periplasmic maltose-binding protein (MalE), cannot use maltose unless a wild-type copy of malE is present in trans. Replacement of the natural signal peptide of preMalE by the signal peptide and the first four amino acids of a cytoplasmic membrane-anchored lipoprotein resulted in N-terminal fatty acylation of MalE (lipoMalE) and anchoring to the periplasmic face of the cytoplasmic membrane, where it could still function. When the aspartate at position +2 of this protein was replaced by a serine, lipoMalE was sorted to the outer membrane, where it could not function. Chemical mutagenesis followed by selection for maltose-using mutants resulted in the identification of two classes of mutations. The single class I mutant carried a plasmid-borne mutation that replaced the serine at position +2 by phenylalanine. Systematic substitutions of the amino acid at position +2 revealed that, besides phenylalanine, tryptophan, tyrosine, glycine and proline could all replace classical cytoplasmic membrane lipoprotein sorting signal (aspartate +2). Analysis of known and putative lipoproteins encoded by the E. coli K-12 genome indicated that these amino acids are rarely found at position +2. In the class II mutants, a chromosomal mutation caused small and variable amounts of lipoMalE to remain associated with the cytoplasmic membrane. Similar amounts of another, endogenous outer membrane lipoprotein, NlpD, were also present in the cytoplasmic membrane in these mutants, indicating a minor, general defect in the sorting of outer membrane lipoproteins. Four representative class II mutants analysed were shown not to carry mutations in the lolA or lolB genes, known to be involved in the sorting of lipoproteins to the outer membrane.

Identification and Quantitation of the Fatty Acids Composing the CoA Ester Pool of Bovine Retina, Heart, and Liver

Several proteins found in retinal photoreceptor cells (guanylate cyclase activating protein, protein kinase A, recoverin, and transducin) are N-terminally modified with the fatty acids 12:0, 14:0, 14:1n-9, and 14:2n-6, whereas similar proteins in other tissues contain only 14:0. It has been hypothesized that the acyl-CoA pool of the retina contains amounts of 12:0, 14:1n-9, and 14:2n-6 elevated over 14:0, in comparison to other tissues, and this accounts for the specificity of N-terminal fatty acylation. To test this hypothesis, we performed fatty acid analysis on total acyl-CoAs purified from bovine retina (light-adapted), heart, and liver. We also examined the N- and S-linked fatty acid composition of the total protein pools from these tissues. Acyl-CoAs were prepared from heart, liver, and retina and separated by high performance liquid chromatography (HPLC). Identities of peaks were based on HPLC of standard 12:0, 14:0, 14:1n-9, and 14:2n-6 CoAs. Total protein was subjected to base hydrolysis followed by acidic methanolysis to release S- and N-linked fatty acids, respectively, and fatty acid phenacyl esters were prepared for HPLC analysis. Retina had levels of 12:0 (2.7 +/- 2.1%), 14:1n-9 (2.9 +/- 2.2%), and 14:2n-6 (1.6 +/- 0.7%) CoAs below that of 14:0 CoA (7.0 +/- 1.8%). Likewise, heart levels of 14:2n-6 CoA (3.7 +/- 0.1%) were near and 12:0 (2.6 +/- 0. 6%) and 14:1n-9 (0.7 +/- 0.3%) CoAs were below that of 14:0 CoA (3.8 +/- 1.0%). Liver had levels of 12:0 (16.1 +/- 5.7%) and 14:2n-6 (8.1 +/- 1.2%) CoAs above and 14:1n-9 CoA (1.2 +/- 0.6%) below that of 14:0 CoA (5.9 +/- 0.8%). Fatty acid analysis of total protein showed that all tissues contained S-linked 16:0, 18:0, and 18:1n-9. Retina proteins contained N-linked 14:0, 14:1n-9, and 14:2n-6, whereas heart and liver had only 14:0. Our findings do not support the hypothesis that the CoA ester pool of the retina is enriched with 12:0, 14:1n-9, and 14:2n-6 over 14:0, in comparison to other tissues. This suggests that alternative models must be considered for the regulation of N-terminal fatty acylation of proteins in photoreceptor cells.

Calcium Binding, but Not a Calcium-Myristoyl Switch, Controls the Ability of Guanylyl Cyclase-activating Protein GCAP-2 to Regulate Photoreceptor Guanylyl Cyclase

Guanylyl cyclase-activating protein 2 (GCAP-2) is a recoverin-like calcium-binding protein that regulates photoreceptor guanylyl cyclase (RetGC) (Dizhoor, A. M., and Hurley, J. B. (1996) J. Biol. Chem. 271, 19346-19350). It was reported that myristoylation of a related protein, GCAP-1, was critical for its affinity for RetGC (Frins, S., Bonigk, W., Muller, F., Kellner, R., and Koch, K.-W. (1996) J. Biol. Chem. 271, 8022-8027). We demonstrate that the N terminus of GCAP-2, like those of other members of the recoverin family of Ca2+-binding proteins, is fatty acylated. However, unlike other proteins of this family, more GCAP-2 is present in the membrane fraction at low Ca2+ than at high Ca2+ concentrations. We investigated the role of the N-terminal fatty acyl residue in the ability of GCAP-2 to regulate RetGCs. Myristoylated or nonacylated GCAP-2 forms were expressed in Escherichia coli. Wild-type GCAP-2 and the Gly2 --> Ala2 GCAP-2 mutant, which is unable to undergo N-terminal myristoylation, were also expressed in mammalian HEK293 cells. We found that compartmentalization of GCAP-2 in photoreceptor outer segment membranes is Ca2+- and ionic strength-sensitive, but it does not require the presence of the fatty acyl group and does not necessarily directly reflect GCAP-2 interaction with RetGC. The lack of myristoylation does not significantly affect the ability of GCAP-2 to stimulate RetGC. Nor does it affect the ability of the Ca2+-loaded form of GCAP-2 to compete with the GCAP-2 mutant that constitutively activates RetGC. We conclude that while Ca2+ binding plays a major regulatory role in GCAP-2 function, it does not operate through a calcium-myristoyl switch similar to the one found in recoverin.

N-terminal fatty acylation of the α-subunit of the G-protein Gi1: only the myristoylated protein is a substrate for palmitoylation

The alpha-subunit of the G-protein Gi1 carries two fatty acyl moieties covalently bound to its N-terminal region: myristic acid is linked to glycine-2 and palmitic acid is linked to cysteine-3. Using site-directed mutagenesis on a cDNA construct of alpha i1 we have generated an alpha i1-G2A mutant, carrying alanine instead of glycine at position 2, and alpha i1-C3S mutant, in which serine replaced cysteine-3 and a double mutant with both substitutions (alpha i1-G2A/C3S). These constructs were individually expressed by transfection in Cos-7 cells, and incorporation of fatty acids into the various mutants was compared with wild-type alpha i1 monitoring metabolic labelling with [3H]palmitate or [3H]myristate. The disruption of the palmitoylation site in alpha i1-C3S did not influence myristoylation, whereas prevention of myristoylation in alpha i1-G2A also abolished palmitoylation. Co-translational myristoylation is thus an absolute requirement for alpha i1 to be post-translationally palmitoylated. The non-palmitoylated alpha i1-C3S showed reduced membrane binding to the same extent as the non-myristoylated/non-palmitoylated alpha i1-G2A and alpha i1-G2A/C3S mutants, indicating that the attachment of palmitic acid is necessary for proper interaction with the membrane.

Co-translational processing and intracellular transport of rat salivary mucus glycoprotein

A preparation of peptidyl-tRNA from intact microsomes of mucin-synthesizing polysomes of sublingual salivary gland cells contained fatty-acylated galactosamine-free and galactosamine-enriched peptidyl-tRNA fractions, whereas trypsin-chymotrypsin treated microsomes yielded predominantly the acylated galactosamine-enriched peptidyl-tRNA complexes. Radioscanning and chemical analyses revealed that palmitate was substituted on all nascent peptides, except those shorter than 20 amino-acid residues. In contrast, the [ 35S]-methionine label was detected only on galactosamine-free peptides containing up to 70 amino acids. On SDS-polyacrylamide gel, the peptides released from galactosamineenriched tRNA complexes separated into a multitude of bands ranging in size from 6000 to 60,000 dalton, whereas the total preparation afforded peptides ranging from 2000 to 60,000 dalton. Pulse-chase experiments, using radiolabelled methionine, palmitic acid and N-acetylgalactosamine, combined with chemical characterization of the radiolabelled fatty acids and carbohydrates from purified peptidyl-tRNA, confirmed that the N-terminal fatty acylation and the initial O-glycosylation with N-acetylgalactosamine are the co-translational processes taking place as soon as peptide is sufficiently large to be acylated, trimmed, and translocated to the luminal site of endoplasmic membrane.

Cotranslational fatty acylation of mucus glycoprotein. Addition of palmitic acid to peptidyl-tRNA occurs prior to peptide chain completion and its release

1. 1. The fatty acylation of mucus glycoprotein nascent peptides was investigated using [ 3H]palmitic acid and [ 35S]methionine-labeled peptidyl-tRNA of rat gastric mucous cells. 2. 2. The mucus glycoprotein peptidyl-tRNA fraction was found to contain covalently bound palmitic acid in its complexes. 3. 3. RNase digestion of the mucus glycoprotein peptidyl-tRNA released [ 3H]palmitic acid labeled peptides which, on SDS-polyacrylamide gel, separated into a multitude of bands ranging in size from 2000 to 60,000 Da. 4. 4. The analyses of low molecular weight peptides revealed that palmitic acid was present in methionine-labeled peptides containing 30–43 amino acids and those of 18–25 amino acids or larger devoid of methionine, but was not identified in methionine-labeled peptides containing 10–15 amino acids. 5. 5. The results indicate that the N-terminal fatty acylation of mucus glycoprotein nascent peptides is a cotranslational process which is occuring in an immediate vicinity of the signal peptide fragment.