Methanococcus jannaschii prolyl-cysteinyl-tRNA synthetase possesses overlapping amino acid binding sites

The protein translation apparatus of Methanococcus jannaschii possesses the unusual enzyme prolyl-cysteinyl-tRNA synthetase (ProCysRS), a single enzyme that attaches two different amino acids, proline and cysteine, to their cognate tRNA species. Measurement of the ATP-PP(i) exchange reaction revealed that amino acid activation, the first reaction step, differs for the two amino acids. While Pro-AMP can be formed in the absence of tRNA, Cys-AMP synthesis is tRNA-dependent. Studies with purified tRNAs indicate that tRNA(Cys) promotes cysteine activation. The k(cat) values of wild-type ProCysRS for tRNA prolylation (0.09 s(-1)) and cysteinylation (0.02 s(-1)) demonstrate that both aminoacyl-tRNAs are synthesized with comparable rates, the cysteinyl-tRNA synthetase activity being only 4.5-fold lower than prolyl-tRNA synthetase activity. Kinetic analysis of ProCysRS mutant enzymes, generated by site-directed mutagenesis, shows glutamate at position 103 to be critical for proline binding, and proline at position 100 to be involved in cysteine binding. The proximity in ProCysRS of amino acid residues affecting binding of either cysteine or proline strongly suggests that structural elements of the two amino acid binding sites overlap.     

Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA

Transfer RNA can play a role in amino acid activation by aminoacyl-tRNA synthetases. For the prolyl-tRNA synthetase (ProRS) of Methanococcus jannaschii, which activates both proline and cysteine, the role of tRNA in amino acid selection and activation is of interest in the effort to understand the mechanism of the dual-specificity. While activation of proline does not require tRNA, whether or not tRNA is required in the activation of cysteine has been a matter of debate. Here, investigation of a series of buffer conditions shows that activation of cysteine occurs without tRNA in a wide-range of buffers. However, the extent of cysteine activation is strongly buffer-dependent, varying over a 180-fold range. In contrast, the extent of proline activation is much less sensitive to buffer conditions, varying over only a 36-fold range. We also find that addition of tRNA has a small threefold stimulatory effect on cysteine activation. The lack of a major role of tRNA in activation of cysteine suggests that the dual-specificity enzyme must distinguish cysteine from proline directly, without the assistance of each cognate tRNA, to achieve the necessary specificity required for protein synthesis.     

Metabolism of a proline analogue, l-thiazolidine-4-carboxylic acid, by Escherichia coli

Unger, Leon (University of Illinois, Urbana), and R. D. DeMoss. Metabolism of a proline analogue, l-thiazolidine-4-carboxylic acid, by Escherichia coli. J. Bacteriol. 91:1564-1569. 1966.-Resting cells of Escherichia coli K-12, pregrown in a proline- and thioproline-free medium, oxidize the proline analogue, l-thiazolidine-4-carboxylic acid (l-thioproline), without a lag with the consumption of 1 atom of oxygen per mole of thioproline. The organism also oxidizes cysteine and formaldehyde, the chemical precursors of thioproline. The total oxygen consumed is the same whether the substrate is thioproline, cysteine, formaldehyde, or an equimolar mixture of cysteine and formaldehyde. The results suggest that neither cysteine nor formaldehyde are free intermediates in the oxidative pathway. Thioproline is available as a metabolic carbon source for the synthesis of the ribonucleic acid bases, guanine and uracil.     

Survival, fecundity and fertility of Bactrocera oleae, as affected by amino acid analogues

The effect of twenty five amino acid analogues at various concentrations upon the adult olive fruit fly Bactrocera oleae Gmelin (Diptera: Tephritidae), was tested. Insect survival was significantly shortened by the following amino acid analogues: (in parentheses are indicated the antagonized amino acids) D-cycloserine (alanine), L-glutamic acid--hydrazide (glutamine), DL-allyl-glycine (cysteine), L-canavanine (arginine), L-methionine-DL-sulfoximine (methionine) and 3,4-dehydro-DL-proline (proline). Fecundity was significantly reduced by the same analogues plus aminoethanesulfonic acid (glycine), taurine (alanine), L-norvaline (leucine), a-methyl-DL-serine (serine), DL-hydroxyglutamic acid (glutamic acid), (S)-2-(aminoethyl)-L-cysteine (lysine), a-methyl-DL-methionine (methionine) and a-methyl-DL-histidine (histidine). All the above amino acid analogues also depressed egg-hatching with the exception of taurine, DL-hydroxyglutamic acid, DL-allyl glycine, a-methyl-DL-methionine and a-methyl-DL-histidine. Finally, y-glutamyl-p-nitroanilide (glutamic acid), crotyl-glycine (methionine), DL-7-azatryptophan and 5-methyl-DL-tryptophan (tryptophan), DL-1,2,4 triazole-3-alanine (histidine) and DL-pipecolic acid (proline) did not affect any of the parameters tested.     

Cloning and expression of amino acid transporters from broad bean

This work describes the isolation of a full-length (VfAAP2) and three partial amino acid transporter genes (VfAAPa, VfAAPb, VfAAPc) from broad bean (Vicia faba L.). The function of VfAAP2 was tested by heterologous expression in a yeast mutant deficient in proline uptake. VfAAP2 mediates proton-dependent proline uptake with an apparent K_m of about 1 mM. Analysis of substrate specificity by competition experiments showed that aromatic amino acids, neutral aliphatic acids and L-citrulline are the best competitors, whereas basic amino acids do not compete with proline. Northern analysis indicates that all VfAAPs exhibit different patterns of expression. VfAAP2 is most strongly expressed in the stem and at a lower level in sink leaves and pods. VfAAPa, VfAAPb and VfAAPc are most strongly expressed in the flowers, but their expression in the other organs varies.     

Stimulatory effects of amino acids and oleic acid on poly(3-hydroxybutyric acid) synthesis by recombinant Escherichia coli

Addition of cysteine, isoleucine, methionine, or proline promoted poly(3-hydroxybutyric acid) [PHB] synthesis by recombinant Escherichia coli more than two-fold. Oleic acid also enhanced PHB synthesis more than three-fold. A PHB concentration of 70 g/l could be obtained by fed-batch culture of recombinant E. coli in a defined medium supplemented with small amounts of isoleucine, methionine, and proline. The stimulatory effects of amino acids and oleic acid on PHB synthesis seems to be due to the availability of more acetyl-CoA and/or NADPH.     

Generation of a cysteine sulfinic acid analog for incorporation in peptides using solid phase peptide synthesis

The sulfinic acid analog of aspartic acid, cysteine sulfinic acid, introduces a sulfur atom that perturbs the acidity and oxidation properties of aspartic acid. Cysteine sulfinic acids are often introduced in peptides and proteins by oxidation of cysteine, but this method is limited as all cysteine residues are oxidized and cysteine residues are often oxidized to sulfonic acids. To provide the foundation for the specific incorporation of cysteine sulfinic acids in peptides and proteins, we synthesized a 9-fluorenylmethyloxycarbonyl (Fmoc) benzothiazole sulfone analog. Oxidation conditions to generate the sulfone were examined and oxidation of the Fmoc-protected sulfide (3) with NbC in hydrogen peroxide provided the corresponding sulfone (4) in the highest yield and purity. Reduction with sodium borohydride generated the cysteine sulfinic acid (5) suggesting this approach may be an efficient method to incorporate a cysteine sulfinic acid in biomolecules. A model tripeptide bearing a cysteine sulfinic acid was synthesized using this approach. Future studies are aimed at using this method to incorporate cysteine sulfinic acids in peptide hormones and proteins for use in the study of biological function.     

SLC36A4 (hPAT4) is a high affinity amino acid transporter when expressed in Xenopus laevis oocytes

The SLC36 family of transporters consists of four genes, two of which, SLC36A1 and SLC36A2, have been demonstrated to code for human proton-coupled amino acid transporters or hPATs. Here we report the characterization of the fourth member of the family, SLC36A4 or hPAT4, which when expressed in Xenopus laevis oocytes also encodes a plasma membrane amino acid transporter, but one that is not proton-coupled and has a very high substrate affinity for the amino acids proline and tryptophan. hPAT4 in Xenopus oocytes mediated sodium-independent, electroneutral uptake of [(3)H]proline, with the highest rate of uptake when the uptake medium pH was 7.4 and an affinity of 3.13 μM. Tryptophan was also an excellently transported substrate with a similarly high affinity (1.72 μM). Other amino acids that inhibited [(3)H]proline were isoleucine (K(i) 0.23 mM), glutamine (0.43 mM), methionine (0.44 mM), and alanine (1.48 mM), and with lower affinity, glycine, threonine, and cysteine (K(i) >5 mM for all). Of the amino acids directly tested for transport, only proline, tryptophan, and alanine showed significant uptake, whereas glycine and cysteine did not. Of the non-proteogenic amino acids and drugs tested, only sarcosine produced inhibition (K(i) 1.09 mM), whereas γ-aminobutyric acid (GABA), β-alanine, L-Dopa, D-serine, and δ-aminolevulinic acid were without effect on [(3)H]proline uptake. This characterization of hPAT4 as a very high affinity/low capacity non-proton-coupled amino acid transporter raises questions about its physiological role, especially as the transport characteristics of hPAT4 are very similar to the Drosophila orthologue PATH, an amino acid "transceptor" that plays a role in nutrient sensing.     

Neutral amino acid transport in Leishmania promastigotes

Neutral amino acid transport was investigated in Leishmania promastigotes. Proline and alanine transport occur against their concentration gradient although there is a very rapid (40% at 30 min) conversion of proline to alanine. Uptake of these amino acids occurs by a sodium-independent route which is completely eliminated by addition of CCCP or KCN. $\text{K}{}_{\mathrm{<mtext>m</mtext>}}$ values for proline and alanine are 80 μM and 63 μM with $\text{V}{}_{\mathrm{<mtext>max</mtext>}}$ values of 6.4 and 7.2 nmol/min per mg dry weight, respectively. Countertransport of proline, alanine and phenylalanine was measured by loading the cells with a variety of neutral amino acids and proline analogs, followed by CCCP addition. The effect of aminooxyacetic acid, an inhibitor of alanine aminotransferase (EC 2.6.1.2), on proline and alanine countertransport was also examined. The results obtained are consistent with the presence of at least two systems for neutral amino acid transport in Leishmania promastigotes.     

Amino acid requirements of Eikenella corrodens

The amino acid requirements of asaccharolytic Eikenella corrodens strains were investigated and a minimal amino acid medium was developed. Single amino acid deletions performed in a chemically defined medium indicated that these strains required arginine, cysteine, histidine, lysine, and proline, and partially required tyrosine. These six amino acids plus aspartic acid, glutamic acid, and glycine supported growth of E. corrodens in a medium containing only inorganic salts and vitamins.     

Effects of weak acids on proline accumulation in barley leaves: a comparison between abscisic acid and isobutyric acid

Abstract. When isobutyric acid (IBA) or abscisic acid (ABA) are supplied to leaf sections a similar rapid and marked decrease in the intracellular pH is observed. This acidification is accompanied by an increase in proline level which is about the same for both 3 mol m⁻³ IBA and 1 mol m⁻³ ABA treatments.
Fusicoccin (FC), known to act at the proton pump level, almost completely suppresses the ABA-induced acidification of the cell sap, whereas it only partially counteracts the acidifying effect of IBA, in particular during short periods of treatment. This effect of FC is paralleled by a similar inhibition of the induced proline accumulation: in fact, FC completely suppresses the ABA-induced increase in proline during short treatment periods, whereas it is only effective in inhibiting the IBA-induced proline accumulation after long treatment periods.
These data seem to suggest that the ABA- and IBA-induced changes in proline level might be mediated by changes in the intracellular pH.     

Abscisic acid and proline improve desiccation tolerance and increase fatty acid content of celery somatic embryos

Desiccation tolerance of celery (Apium graveolens L.) somatic embryos was increased by supplementation of embryo-production medium with 1 M abscisic acid (ABA) or 1 mM proline, with highest survival obtained with a combination of 1 M ABA and 1 mM proline. Addition of ABA and proline increased fatty acid accumulation by somatic embryos; the effect on fatty acid composition was inconsistent. Somatic embryos capable of germination differed from mature zygotic embryos by greater size, lower fatty acid level, and substantially lower proportion of oleic acid (18:1) as compared to linoleic acid (18:2).     

The amino acid sequence of avian thymic hormone, a parvalbumin

The complete amino acid sequence of 'avian thymic hormone' (ATH), a protein from thymus tissue that appears to promote immune maturation in chicken bone marrow cells in culture, is presented. The sequence was obtained from sequences of ATH peptides isolated by HPLC after tryptic, chymotryptic, peptic or S aureus V8 protease digestions. The protein is a parvalbumin consisting of 108 residues with a blocked amino terminus, a single cysteine, tyrosine, proline and arginine and no histidine, methionine or tryptophan. This is the first amino acid sequence of a parvalbumin which is not derived from muscle tissue.     

A theoretical study of zinc(II) interactions with amino acid models and peptide fragments

Density functional theory calculations have been employed to study the interaction between the Zn²⁺ ion and some standard amino acid models. The highest affinities towards the Zn²⁺ ion are predicted for serine, cysteine, and histidine. Relatively high affinities are reported also for proline and glutamate/aspartate residues. It was found that the zinc complexes with cysteine adopt a tetrahedral conformation. Conversely, complexes with one or two histidine moieties remain in an octahedral geometry, while those with three or more histidine groups adopt a square-planar geometry. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Amino acid transport via the red cell anion transport system

Evidence is presented that the red cell anion-exchange transport (Band 3) can selectively transport small neutral amino acids, including glycine, serine and cysteine, but not alanine, proline, valine and threonine. This transport is inhibited by micromolar concentrations of SITS (4-acetamido-4′-isothiocyanostilbene-2,2′-disulphonate), and increased by raising the pH from 6.5 to 8.5.     

Amino acid sequence of a four-iron-four-sulphur ferredoxin isolated from Bacillus stearothermophilus.

1. The primary structure of a 4Fe-4S ferredoxin from Bacillus stearothermophilus was determined and shown to consist of a single polypeptide chain of 81 amino acid residues. The molecular weight of the holoprotein is about 9120. 2. There are only four cysteine residues in the molecule; three of these are located near the N-terminus as a Cys-X-X-Cys-X-X-Cys segment, and the fourth cysteine residue is followed by a proline and located in the C-terminal half. 3. The Fe-S chromophore in B. stearothermophilus ferredoxin was previously well characterized and was shown to consist of a single 4Fe-4S cluster. This ferredoxin sequence establishes for the first time the relative location of the four cysteine residues necessary to bind the 4Fe-4S cluster of a 4Fe ferredoxin, and is in agreement with the criteria for the relative positions of the cysteines proposed from X-ray-crystallographic studies on an 8Fe (two 4Fe-4S clusters) ferredoxin. 4. The sequence of B. stearothermophilus ferredoxin is homologous in many segments to that of other bacterial ferredoxins, the degree of homology being greater towards ferredoxins from Desulfovibrio gigas and photosynthetic bacteria than to Clostridial ferredoxins. 5. The presence of a relatively higher number of glutamic acid and lower number of cysteine residues in the molecule may explain the greater thermal stability and oxygen-insenstivity of this ferredoxin.     

High degree of homology between primary structure of human lysosomal acid phosphatase and human prostatic acid phosphatase

Alignment of the amino-acid sequences of the human lysosomal acid phosphatase (LAP) and human prostatic acid phosphatase (PAP) yielded an extensive homology between the two mature polypeptide chains. In the overlapping part, which extends over the entire PAP sequence and the N-terminal 90% of the LAP sequence, the identity is 49.1%. The LAP has an additional C-terminal sequence, which is encoded by the last exon of the LAP gene. This sequence contains the transmembrane domain of LAP, which is lacking in the secretory PAP. All six cysteine residues as well as 20 out of 27 (LAP) and 26 (PAP) proline residues present in the overlapping part of the proteins are conserved, suggesting that they are involved in stabilization of the tertiary structure of both proteins. Only two out of 8 N-glycosylation sites in LAP and 3 in PAP are conserved, suggesting that the dense N-glycosylation of LAP is related to its function in lysosomes.     

A single amino acid substitution affects substrate specificity in cysteine proteinases from Fasciola hepatica

The trematode Fasciola hepatica secretes a number of cathepsin L-like proteases that are proposed to be involved in feeding, migration, and immune evasion by the parasite. To date, six full cDNA sequences encoding cathepsin L preproproteins have been identified. Previous studies have demonstrated that one of these cathepsins (L2) is unusual in that it is able to cleave substrates with a proline in the P2 position, translating into an unusual ability (for a cysteine proteinase) to clot fibrinogen. In this study, we report the sequence of a novel cathepsin (L5) and compare the substrate specificity of a recombinant enzyme with that of recombinant cathepsin L2. Despite sharing 80% sequence identity with cathepsin L2, cathepsin L5 does not exhibit substantial catalytic activity against substrates containing proline in the P2 position. Molecular modeling studies suggested that a single amino acid change (L69Y) in the mature proteinases may account for the difference in specificity at the S2 subsite. Recombinant cathepsin L5/L69Y was expressed in yeast and a substantial increase in the ability of this variant to accommodate substrates with a proline residue in the P2 position was observed. Thus, we have identified a single amino acid substitution that can substantially influence the architecture of the S2 subsite of F. hepatica cathepsin L proteases.     

Structure of the catalytic domain of protein tyrosine phosphatase sigma in the sulfenic acid form

Protein tyrosine phosphatase sigma (PTPσ) plays a vital role in neural development. The extracellular domain of PTPσ binds to various proteoglycans, which control the activity of 2 intracellular PTP domains (D1 and D2). To understand the regulatory mechanism of PTPσ, we carried out structural and biochemical analyses of PTPσ D1D2. In the crystal structure analysis of a mutant form of D1D2 of PTPσ, we unexpectedly found that the catalytic cysteine of D1 is oxidized to cysteine sulfenic acid, while that of D2 remained in its reduced form, suggesting that D1 is more sensitive to oxidation than D2. This finding contrasts previous observations on PTPα. The cysteine sulfenic acid of D1 was further confirmed by immunoblot and mass spectrometric analyses. The stabilization of the cysteine sulfenic acid in the active site of PTP suggests that the formation of cysteine sulfenic acid may function as a stable intermediate during the redox-regulation of PTPs.     

Salicylic acid alleviates adverse effects of heat stress on photosynthesis through changes in proline production and ethylene formation

We investigated the potential of salicylic acid (SA) in alleviating the adverse effects of heat stress on photosynthesis in wheat (Triticum aestivum L.) cv WH 711. Activity of ribulose 1,5-bisphosphate carboxylase (Rubisco), photosynthetic-nitrogen use efficiency (NUE), and net photosynthesis decreased in plants subjected to heat stress (40°C for 6 h), but proline metabolism increased. SA treatment (0.5 mM) alleviated heat stress by increasing proline production through the increase in γ-glutamyl kinase (GK) and decrease in proline oxidase (PROX) activity, resulting in promotion of osmotic potential and water potential necessary for maintaining photosynthetic activity. Together with this, SA treatment restricted the ethylene formation in heat-stressed plants to optimal range by inhibiting activity of 1-aminocyclopropane carboxylic acid (ACC) synthase (ACS). This resulted in improved proline metabolism, N assimilation and photosynthesis. The results suggest that SA interacts with proline metabolism and ethylene formation to alleviate the adverse effects of heat stress on photosynthesis in wheat.