Vitamin B6 enzymes participating in selenium amino acid metabolism

Various vitamin B6 enzymes play important roles in mammalian and microbial metabolism of selenium amino acids. Selenocysteine is synthesized from selenohomocysteine by catalysis of cystathionine beta-synthase and cystathionine gamma-lyase, which both require pyridoxal phosphate. Selenocysteine beta-lyase, a new B6-enzyme, exclusively catalyzes beta-elimination of selenocysteine, and occurs in mammalian systems and bacteria. Methionine gamma-lyase, cysteine desulfurase, cysteine sulfinate desulfinase, and D-selenocystine alpha,beta-lyase, which are B6-enzymes, act on cysteine, cysteine sulfinate, D-cystine, and their derivatives, and their selenium counterparts indiscriminately. Their reaction mechanisms are comparatively described.     

Specific incorporation of selenium into lysine- and glutamate- accepting tRNAs from Escherichia coli

Amino acid transfer nucleic acids (tRNAs) that contain selenium-modified bases are synthesized by Escherichia coli in the presence of low levels (0.1-0.5 microM) of [75Se]selenite or [75Se]selenate. The amount of selenium incorporated (1-2 g atoms/100 mol of tRNA) was unchanged by 10-20-fold variations in selenium or sulfate concentrations or by the addition of 1 mM cysteine, sulfide, or sulfite. Specific incorporation of selenium (as opposed to nonspecific substitution for sulfur) was further indicated by the different reversed phase chromatographic elution patterns of 35S- and 75Se-labeled tRNAs isolated from cells labeled with 35SO2-4 and 75SeO2-4. Also, E. coli mutants unable to synthesize an abundant sulfur-modified base, 4-thiouracil, nevertheless produced normal levels of selenium-modified tRNAs. Two different methods of distinguishing between aminoacylated and nonaminoacylated tRNA, one which examined mobility during reversed phase chromatography and another which employed anti-AMP antibodies, indicated that over 50% of the selenium-containing tRNA had lysine or glutamate acceptor activity.     

Reactions of selenium dioxide free radicals with amino acids and enzymes

Pulse radiolysis of selenium dioxide in aqueous solution has shown the presence of three selenite radicals in acid-base equilibrium within well defined pH ranges: (formula; see text) The selenite radicals react selectively with amino acids, preferentially with the aromatic ones in the order tryptophan greater than tyrosine greater than histidine, independently of the acid-base structure of the radical. Kinetic and spectroscopic data on the reaction of selenite radicals with some proteins and parallel inactivation studies generally reflect knowledge on the amino acid residues mainly involved in the radical attack. The investigations at different pH values on the reactivity of selenite radicals with amino acids and proteins and on the transient spectra of the reaction products exhibit different behaviour for the various acid-base structures of the selenite radicals, reflecting the influence of particular ionizable groups in the reacting molecules and the structure modifications at the level of proteins.     

Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes

If the enzymes responsible for biosynthesis of a given amino acid are repressed and the cognate amino acid pool suddenly depleted, then derepression of these enzymes and replenishment of the pool would be problematic, if the enzymes were largely composed of the cognate amino acid. In the proverbial "Catch 22", cells would lack the necessary enzymes to make the amino acid, and they would lack the necessary amino acid to make the needed enzymes. Based on this scenario, we hypothesize that evolution would lead to the selection of amino acid biosynthetic enzymes that have a relatively low content of their cognate amino acid. We call this the "cognate bias hypothesis". Here we test several implications of this hypothesis directly using data from the proteome of Escherichia coli. Several lines of evidence show that low cognate bias is evident in 15 of the 20 amino acid biosynthetic pathways. Comparison with closely related Salmonella typhimurium shows similar results. Comparison with more distantly related Bacillus subtilis shows general similarities as well as significant differences in the detailed profiles of cognate bias. Thus, selection for low cognate bias plays a significant role in shaping the amino acid composition for a large class of cellular proteins.     

Diversity of amino acid converting enzymes in wild lactic acid bacteria

A total of 156 lactic acid bacteria isolates belonging to the genera Lactococcus, Lactobacillus and Leuconostoc were analysed for the amino acid converting enzymes aminotransferases, glutamate dehydrogenase, and α-ketoisovalerate decarboxylase. All isolates showed aminotransferase activity towards phenylalanine (substrate for the aromatic aminotransferase AraT) and isoleucine (substrate for the branched-chain aminotransferase BcaT). Although there was a high variability inter- and intra-species, the lactococcal strains showed the highest values for both aminotransferase activities. Moreover, α-ketoisovalerate decarboxylase (Kivd) activity was only found in lactococcal isolates, although at low relative numbers (16%). On the other hand, glutamate dehydrogenase (Gdh) activity values were highest in facultative heterofermentative lactobacilli (FHL) and the activity was found at high relative numbers (50%) in leuconostocs. Results showed a high variability in amino acid convertase activities within the wild LAB isolates assayed, therefore the utilisation in the dairy industry of new strains with high flavour-forming abilities could be a powerful tool to enhance cheese aroma development.     

Levels of tRNAs in bacterial cells as affected by amino acid usage in proteins.

Transfer RNAs of Mycoplasma capricolum were separated by two-dimensional polyacrylamide gel electrophoresis, and the relative abundance of each of the 28 known tRNA species was measured. There existed a correlation between the relative amount of isoacceptor tRNAs and the frequency in choosing synonymous codons that could be translated by the isoacceptors. Furthermore, it was observed that the total amount of tRNAs for a particular amino acid was paralleled by the composition of the amino acid in ribosomal proteins. A similar relationship was obtained from reexamination of the previous data on Escherichia coli tRNAs, suggesting that the amount of tRNAs for an amino acid is affected by the usage of the amino acid in proteins.     

Pyridoxal phosphate-dependent enzymes of sulfur amino acid metabolism

Cystathionine beta-synthase and gamma-cystathionase, the two major enzymes of the transsulfuration pathway of methionine metabolism, are described. These enzymes are responsible for inborn errors, e.g., homocystinuria and cystathioninuria. The interaction of gamma-cystathionase with the cofactor, substrates and inhibitors of the general formula RONH2 containing structural fragments of substrates has been studied. A non-radioactive avidin-biotin system for the microdetection of gamma-cystathionase in dot blots has been developed. This system was applied for immunoscreening of a rat liver cDNA library in the prokaryotic expression vector lambda gt 11.     

大豆含硫氨基酸相关酶基因发掘

大豆(Glycine max)含硫氨基酸合成途径中的酶基因是含硫氨基酸组分的重要调控基因,发掘相关酶基因对高含硫氨基酸分子育种具有重要意义。文章采用大豆物理与遗传整合图谱,通过BioMercator2.1将113个含硫氨基酸合成途径酶基因及33个控制含硫氨基酸含量的QTL整合到遗传图谱Consensus Map 4.0上,依据酶基因位点与QTL的一致性以及QTL的效应值,初步筛选到16个与含硫氨基酸合成相关的候选基因。通过生物信息学方法对候选基因进行拷贝数、SNP、表达谱等分析,鉴定到12个相关酶基因,分别位于D1a、M、A2、K和G等8个连锁群上。生物信息学分析显示这些基因所在QTL可解释含硫氨基酸遗传变异的6.0%~38.5%,其中9个基因的间接效应值超过10%。12个相关酶基因参与含硫氨基酸代谢的重要途径,且多在子叶、花中高丰度表达,存在丰富的SNP。这些基因可作为候选基因进行功能标记开发,将为大豆分子设计育种奠定基础。     

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Proper recognition of tRNAs by their aminoacyl-tRNA synthetase is essential for translation accuracy. Following evidence that the enzymes can recognize the correct tRNA even when anticodon information is masked, we search for additional nucleotide positions within the tRNA molecule that potentially contain information for amino acid identification. Analyzing 3936 sequences of tRNA genes from 86 archaeal species, we show that the tRNAs’ cognate amino acids can be identified by the information embedded in the tRNAs’ nucleotide positions without relying on the anticodon information. We present a small set of six to 10 informative positions along the tRNA, which allow for amino acid identification accuracy of 90.6% to 97.4%, respectively. We inspected tRNAs for each of the 20 amino acid types for such informative positions and found that tRNA genes for some amino acids are distinguishable from others by as few as one or two positions. The informative nucleotide positions are in agreement with nucleotide positions that were experimentally shown to affect the loaded amino acid identity. Interestingly, the knowledge gained from the tRNA genes of one archaeal phylum does not extrapolate well to another phylum. Furthermore, each species has a unique ensemble of nucleotides in the informative tRNA positions, and the similarity between the sets of positions of two distinct species reflects their evolutionary distance. Hence, we term this set of informative positions a “tRNA cipher.” It is tempting to suggest that the diverging code identified here might also serve the aminoacyl tRNA synthetase in the task of tRNA recognition.     

Effect of diet and essential amino acids gavage on young rat amino acid metabolism enzymes

• 1.1. The effects of a high-fat, high-energy diet and essential plus semi-essential amino acid gavage on pup rats have been studied (60–65 animals).
• 2.2. The activities of alanine transaminase, adenylate deaminase, glutamine synthetase and serine dehydratase have been tested in liver and muscle.
• 3.3. Plasma was used for the estimation of proteins, urea, amino acids, glucose, lactate, 3-hydroxy-butyrate and acetoacetate.
• 4.4. Liver and muscle glutamine synthetase activities are increased by diet and gavage administered. Hepatic serine dehydratase is inhibited by a cafeteria diet but activated by amino acid gavage. Adenylate deaminase is inhibited by diet and gavage in the liver, but gavage does not affect this enzyme activity in muscle. Liver alanine transaminase is increased by the diet; in the muscle, cafeteria diet and amino acid gavage showed the highest values for this enzyme.
• 5.5. In the plasma, the increase in lactate produced by the diet is inhibited by the amino acids provided. Cafeteria-fed pups showed lower urea levels and higher 3-hydroxybutyrate concentrations in the plasma.
• 6.6. Intracellular glucose is diminished by cafeteria diet. In contrast, the blood cell amino acid concentration increases with diet and gavage supplied.

     

Assays for amino acid decarboxylase enzymes using ion-exchange cartridges

A general radiochemical method for estimating the activity of amino acid decarboxylases is reported. This method utilizes ion-exchange cartridges to separate unreacted radiolabeled amino acid substrates from product amines, which can then readily be quantitated by liquid scintillation counting. The assay is simple, rapid, and more sensitive than standard 14CO2 trapping procedures if uniformly labeled amino acid substrates are utilized. Acidic, basic, and aromatic amino acid decarboxylases can be assayed with the appropriate choice of cation or anion exchangers. The utility of the method is demonstrated for aspartate-alpha-decarboxylase, tyrosine decarboxylase, and lysine decarboxylase where kinetic parameters are comparable to values obtained by standard radiochemical 14CO2 trapping assays.     

Widespread occurrence of mycosporine-like amino acid compounds in scleractinians from French Polynesia

 A survey of 23 species of scleractinians, belonging to seven families and 8 genera, collected from two different areas in French Polynesia, showed that all specimens possessed between four and seven UV-absorbing compounds, identified as mycosporine-like amino acids (MAAs). In all, 11 different MAAs molecules were found, of which two were previously unknown. Palythine and mycosporine-glycine were the most abundant MAAs in the corals. With few exceptions, most specimens of each species possessed the same pattern of MAAs. Similarly, species from the same genus also had very similar qualitative composition of MAAs, although quantities of individuals MAAs varied from specimen to specimen. This suggests that MAAs are ancient and evolutionarily well conserved. Accepted: 22 October 1996     

Specific and non-specific purine trap in the T-loop of normal and suppressor tRNAs

To elucidate the general constraints imposed on the structure of the D and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions in these loops were randomized. Analysis of the nucleotide sequences of the selected clones demonstrates that most of them contain combination U54-A58 allowing the formation of the standard reverse-Hoogsteen base-pair 54-58 in the T-loop. With only one exception, all these clones fall into two groups, each characterized by a distinct sequence pattern. Analysis of these two groups has allowed us to suggest two different types of nucleotide arrangement in the DT region. The first type, the so-called specific purine trap, is found in 12 individual tRNA clones and represents a generalized version of the standard D-T loop interaction. It consists of purine 18 sandwiched between the reverse-Hoogsteen base-pair U54-A58 and purine 57. The identity of purine 18 is restricted by the specific base-pairing with nucleotide 55. Depending on whether nucleotide 55 is U or G, purine 18 should be, respectively, G or A. The second structural type, the so-called non-specific purine trap, corresponds to the nucleotide sequence pattern found in 16 individual tRNA clones and is described here for the first time. It consists of purine 18 sandwiched between two reverse-Hoogsteen base-pairs U54-A58 and A55-C57 and, unlike the specific purine trap, requires the T-loop to contain an extra eighth nucleotide. Since purine 18 does not form a base-pair in the non-specific purine trap, both purines, G18 and A18, fit to the structure equally well. The important role of both the specific and non-specific purine traps in the formation of the tRNA L-shape is discussed.     

Activities of enzymes of amino acid metabolism in rat brown adipose tissue

There was a nil arginase and serine dehydratase activities in interscapular brown adipose tissue, but the activity of adenylate deaminase, glutamine synthetase, glutamate dehydrogenase and the aspartate, alanine and branched chain amino acid transaminases was higher than those of white adipose tissue; the differences were diminished when expressed per unit of protein weight. Brown adipose tissue enzyme activities were in a range between those of liver and muscle. The high amino acid handling capabilities, together with its physiological role, suggest that brown adipose tissue can metabolize significant amounts of amino acids, its enzyme pattern being different both from white adipose tissue, as well as of liver and muscle.