Intracellular sensing of amino acids in Xenopus laevis oocytes stimulates p70 S6 kinase in a target of rapamycin-dependent manner.

Amino acids exert modulatory effects on proteins involved in control of mRNA translation in animal cells through the target of rapamycin (TOR) signaling pathway. Here we use oocytes of Xenopus laevis to investigate mechanisms by which amino acids are "sensed" in animal cells. Small ( approximately 48%) but physiologically relevant increases in intracellular but not extracellular total amino acid concentration (or Leu or Trp but not Ala, Glu, or Gln alone) resulted in increased phosphorylation of p70(S6K) and its substrate ribosomal protein S6. This response was inhibited by rapamycin, demonstrating that the effects require the TOR pathway. Alcohols of active amino acids substituted for amino acids with lower efficiency. Oocytes were refractory to changes in external amino acid concentration unless surface permeability of the cell to amino acids was increased by overexpression of the System L amino acid transporter. Amino acid-induced, rapamycin-sensitive activation of p70(S6K) was conferred when System L-expressing oocytes were incubated in extracellular amino acids, supporting intracellular localization of the putative amino acid sensor. In contrast to lower eukaryotes such as yeast, which possess an extracellular amino acid sensor, our findings provide the first direct evidence for an intracellular location for the putative amino acid sensor in animal cells that signals increased amino acid availability to TOR/p70(S6K).     

Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies.

We have investigated protein-rRNA cross-links formed in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus at the molecular level using UV and 2-iminothiolane as cross-linking agents. We identified amino acids cross-linked to rRNA for 13 ribosomal proteins from these organisms, namely derived from S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29 and L36. Several other peptide stretches cross-linked to rRNA have been sequenced in which no direct cross-linked amino acid could be detected. The cross-linked amino acids are positioned within loop domains carrying RNA binding features such as conserved basic and aromatic residues. One of the cross-linked peptides in ribosomal protein S3 shows a common primary sequence motif--the KH motif--directly involved in interaction with rRNA, and the cross-linked amino acid in ribosomal protein L36 lies within the zinc finger-like motif of this protein. The cross-linked amino acids in ribosomal proteins S17 and L6 prove the proposed RNA interacting site derived from three-dimensional models. A comparison of our structural data with mutations in ribosomal proteins that lead to antibiotic resistance, and with those from protein-antibiotic cross-linking experiments, reveals functional implications for ribosomal proteins that interact with rRNA.     

NH2-terminal amino acid distribution and amino acid composition of Streptococcus faecalis R soluble and ribosomal proteins

The NH(2)-terminal amino acid distribution of Streptococcus faecalis R soluble and ribosomal proteins isolated from cells at different stages of growth on either folate-sufficient or folate-deficient medium was determined by the dinitrophenyl method. The NH(2)-terminal residues do not follow the random distribution observed for the total amino acid composition of S. faecalis soluble and ribosomal proteins. Methionine and alanine occur most frequently; serine, threonine, aspartic and glutamic acids, and glycine are also present at the NH(2)-terminal position of S. faecalis R proteins. The absence of folic acid yields cells that are incapable of formylating methionyl-transfer ribonucelic acid tRNA(f) (Met), but does not affect either the qualitative or quantitative NH(2)-terminal distribution of total soluble or total ribosomal proteins compared to cells grown with folate. A small quantitative difference was observed in the frequency of distribution of certain amino acids at the NH(2)-termini between log and stationary phase soluble proteins. The amino acid residues found at the NH(2)-terminal position of S. faecalis proteins are qualitatively similar to those reported for several other organisms.     

S‐deficiency responsive accumulation of amino acids is mainly due to hydrolysis of the previously synthesized proteins – not to de novo synthesis in Brassica napus

To characterize the mechanisms of amino acid accumulation under sulphur (S)‐deficiency and its physiological significance in Brassica napus, stable isotopes ¹⁵N and ³⁴S were employed. The plants were exposed for 9 days to S‐deficient conditions (0.05 mM vs 1.5 mM sulphate). After 9 days of S‐deficiency, leaf‐osmotic potential and total chlorophyll content significantly decreased. S uptake decreased by 94%, whereas N uptake and biomass were not significantly changed. Using ¹⁵N and ³⁴S labelling, de novo synthesis of amino acids and proteins derived from newly absorbed NO₃^? and SO₄^2? and the content of N and S in the previously synthesized amino acids and proteins were quantified. At the whole plant level, S‐deficiency increased the pool of amino acids but resulted in strong decrease of incorporation of newly absorbed NO₃^? and SO₄^2? into amino acids by 22.2 and 76.6%, respectively, compared to the controls. Total amount of N and S incorporated into proteins also decreased by 28.8 and 62.1%, respectively. The levels of ¹⁴N‐ and ³²S‐proteins (previously synthesized proteins) strongly decreased, mainly in mature leaves. The data thus indicate that amino acid accumulation under short‐term S‐deficiency results from the degradation of previously synthesized proteins rather than from de novo synthesis.     

Purification and characterization of 30S ribosomal proteins from Bacillus subtilis: correlation to Escherichia coli 30S proteins

Summary Twenty proteins were isolated from the 30S ribosomal subunits of Bacillus subtilis and their amino acid compositions and amino-terminal amino acid sequences were determined. These results were compared with the data of Escherichia coli 30S ribosomal proteins and the structural correspondence of individual ribosomal proteins has been established between B. subtilis and E. coli.Post-translational modifications of amino-terminal amino acids of the ribosomal proteins which have been found in E. coli are almost absent in B. subtilis with the exception of acetylated forms of S9.     

Identification of residues in a hydrophilic loop of the Papaver rhoeas S protein that play a crucial role in recognition of incompatible pollen.

The self-incompatibility response involves S allele-specific recognition between stigmatic S proteins and incompatible pollen. This response results in pollen inhibition. Defining the amino acid residues within the stigmatic S proteins that participate in S allele-specific inhibition of incompatible pollen is essential for the elucidation of the molecular basis of the self-incompatibility response. We have constructed mutant derivatives of the S1 protein from Papaver rhoeas by using site-directed mutagenesis and have tested their biological activity. This has enabled us to identify amino acid residues in the stigmatic S proteins of P. rhoeas that are required for S-specific inhibition of incompatible pollen. We report here the identification of several amino acid residues in the predicted hydrophilic loop 6 of the P. rhoeas stigmatic S1 protein that are involved in the inhibition of S1 pollen. Mutation of the only hypervariable amino acid, which is situated in this loop, resulted in the complete loss of ability of the S protein to inhibit S1 pollen. This clearly demonstrates that this residue plays a crucial role in pollen recognition and may also participate in defining allelic specificity. We have also established the importance of highly conserved amino acids adjacent to this hypervariable site. Our studies demonstrate that both variable and conserved amino acids in the region of the S protein corresponding to surface loop 6 are key elements that play a role in the recognition and inhibition of incompatible pollen in the pollen-pistil self-incompatibility reaction.     

Transport of amino acids in the splanchnic bed by blood plasma and blood in the preruminant calf]

Three preruminant calves were fitted with catheters in portal and hepatic veins and in a mesenteric artery. Two electromagnetic flowmeter probes were clipped around the portal vein and the hepatic artery. The calves were fed either a diet with a low (L) or a high (R) abomasal emptying rate for dietary proteins. Blood flow and free amino acid levels in plasma (P) and blood (S) were determined before the morning meal and during the following 7 h. In the portal vein, for most amino acids P/S ratios were correlated to the net amino acid balance of the digestive tract measured in plasma. By contrast in the hepatic vein, these ratios were mainly correlated to hepatic balance measured in whole blood. Correlations between digestive tract and hepatic balance calculated using either plasma or whole blood pool were different for some amino acids. This suggests that amino acid exchange between plasma and blood cells is low and absorbed amino acids are mainly transported to the liver by plasma, whereas whole blood rather than plasma is concerned in amino acid exchanges in the liver.     

Zinc finger-like motifs in rat ribosomal proteins S27 and S29.

The primary structures of the rat 40S ribosomal subunit proteins S27 and S29 were deduced from the sequences of nucleotides in recombinant cDNAs and confirmed by determination of amino acid sequences in the proteins. Ribosomal protein S27 has 83 amino acids and the molecular weight is 9,339. Hybridization of cDNA to digests of nuclear DNA suggests that there are 4-6 copies of the S27 gene; the mRNA for the protein is about 620 nucleotides in length. Ribosomal protein S29 has 55 amino acids and the molecular weight is 6,541. There are 14-17 copies of the S29 gene and its mRNA is about 500 nucleotides in length. Rat ribosomal protein S29 is related to several members of the archaebacterial and eubacterial S14 family of ribosomal proteins. S27 and S29 have zinc finger-like motifs as do other proteins from eukaryotic, archaebacterial, eubacterial, and mitochondrial ribosomes. Moreover, ribosomes and ribosomal subunits appear to contain zinc and iron as well.     

Expansion of the Genetic Code Through the Use of Modified Bacterial Ribosomes

Biological protein synthesis is mediated by the ribosome, and employs ~20 proteinogenic amino acids as building blocks. Through the use of misacylated tRNAs, presently accessible by any of several strategies, it is now possible to employ in vitro and in vivo protein biosynthesis to elaborate proteins containing a much larger variety of amino acid building blocks. However, the incorporation of this broader variety of amino acids is limited to those species utilized by the ribosome. As a consequence, virtually all of the substrates utilized over time have been L-α-amino acids. In recent years, a variety of structural and biochemical studies have provided important insights into those regions of the 23S ribosomal RNA that are involved in peptide bond formation. Subsequent experiments, involving the randomization of key regions of 23S rRNA required for peptide bond formation, have afforded libraries of E. coli harboring plasmids with the rrnB gene modified in the key regions. Selections based on the use of modified puromycin derivatives with altered amino acids then identified clones uniquely sensitive to individual puromycin derivatives. These clones often recognized misacylated tRNAs containing altered amino acids similar to those in the modified puromycins, and incorporated the amino acid analogues into proteins. In this fashion, it has been possible to realize the synthesis of proteins containing D-amino acids, β-amino acids, phosphorylated amino acids, as well as long chain and cyclic amino acids in which the nucleophilic amino group is not in the α-position. Of special interest have been dipeptides and dipeptidomimetics of diverse utility.     

Changes in accumulation of seed nitrogen compounds in maize under conditions of sulphur deficiency

Maize ( Zea mays L., hybrid INRA 260) was grown in the greenhouse with mineral nutrition of different sulphate concentrations. Mature seeds from these plants were compared for their free amino acid and protein N forms. For the most S-deficient sample, the Asx (asparagine + aspartic acid) content increased by 30% as compared with control, while methionine and cysteine decreased (by 25 and 30%, respectively), as well as glycine, lysine, histidine, arginine and tryptophan. In seeds lowest in S the non-protein N to total N ratio was 77% higher than in the control. Free asparagine dominated in starved seeds (50 mol % of total free amino acids) and was ten-fold more concentrated than in the control, where proline was the predominant free amino acid. Thus the Asx of non-protein N reached 28% of the total mol Asx of the whole starved seed. Altered S nutrition had virtually no effect on the amino acid composition of the main protein fractions, but it significantly changed their ratios. Zeins, which are poor in S-containing amino acids, showed 25% higher level than in seeds supplied with normal S. As a counterbalance, two glutelin subfractions rich in S-containing amino acids, decreased by 36–71% under limiting S nutrition.
It is concluded that the plant reacts against S deficiency by modifying its N metabolism. Significant accumulation occurred of free asparagine, which is the main form of N transportation. The biosynthesis of seed storage protein occurred through the accumulation of the highest possible protein quantity allowed by the available S-containing amino acids, i.e. proteins low in S-containing amino acids were preferentially synthesized.     

Amino Acid Metabolic Origin as an Evolutionary Influence on Protein Sequence in Yeast

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor’s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Benjamin L. de Bivort and Ethan O. Perlstein have contributed equally to this work.     

圈卷产色链霉菌尼可霉素生物合成基因——sanH和sanI的研究

通过反向遗传学方法克隆到圈卷产色链霉菌尼可霉素生物合成基因簇中约7.0kb的DNA片段。该片段除含有尼可霉素生物合成基因sanF外,对sanF上游约22kb的BglⅡDNA片段进行序列测定及分析表明,还含有两个完整的开放阅读框(ORF)。ORF1由1233个核苷酸组成,ORF2由195个核苷酸组成,它们分别编码由410个氨基酸残基和64个氨基酸残基组成的蛋白质,依次命名为sanH和sanI。蛋白序列数据库比较结果表明,SanH和SanI与浅灰链霉菌(\%Streptomyces griseolus)\%中共转录的细胞色素P450(cytochrome P450)和铁氧还蛋白(ferredoxin)有较高的同源性,一致性分别为46%和56%,相似性分别为62%和70%。基因功能研究表明,sanH基因的破坏虽不影响圈卷产色链霉菌产生的尼可霉素的生物活性,但该基因可能参与了尼可霉素羟基化反应的生物合成。     

Identification of tyrosine residues that are susceptible to lactoperoxidase-catalyzed iodination on the surface of Escherichia coli 30S ribosomal subunit

The detailed surface topography of the Escherichia coli 30S ribosomal subunit has been investigated, with iodination catalyzed by immobilized lactoperoxidase as the surface probe. Under mild conditions, only proteins S3, S7, S9, S18, and S21 were iodinated to a significant and reproducible extent. These proteins were isolated from the iodinated subunits, and in each case, the individual tyrosine residues that had reacted were identified by standard protein sequencing techniques. The targets of iodination that could be positively established were as follows: in protein S3 (232 amino acids), the tyrosines at positions 167 and 192; in S7 (153 amino acids), tyrosines 84 and 152; in S9 (128 amino acids), tyrosine 89; in S18 (74 amino acids), tyrosine 3 (tentative); in S21 (70 amino acids), tyrosines 37 and 70. The results represent part of a broader program to investigate ribosomal topography at the amino acid-nucleotide level.     

The primary structure of rat ribosomal proteins: the amino acid sequences of L27a and L28 and corrections in the sequences of S4 and S12

The amino acid sequences of rat ribosomal proteins L27a and L28 were deduced from the sequences of nucleotides in recombinant cDNAs and confirmed from the NH2-terminal amino acid sequences of the proteins. L27a contains 147 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 16 476. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 18-22 copies of the L27a gene. The mRNA for the protein is about 600 nucleotides in length. L27a is homologous to mouse L27a (there are 3 amino acid changes) and to yeast L29. Rat ribosomal protein L28 has 136 amino acids (its NH2-terminal methionine is also processed after translation) and has a molecular weight of 15 707. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 9 or 10 copies of the L28 gene. The mRNA for the protein is about 640 nucleotides in length. L28 contains a possible internal duplication of 9 residues. Corrections are recorded in the sequences reported before for rat ribosomal proteins S4 and S12.     

Amino acid budgets in three aphid species using the same host plant

Abstract. Nutrient provisioning in aphids depends both on the composition of ingested phloem sap and on the biosynthetic capabilities of the aphid and its intracellular symbionts. Amino acid budgets for three aphid species, Rhopalosiphum padi (L.), Schizaphis graminum (Rondani) and Diuraphis noxia (Mordvilko), were compared on a single host plant species, wheat Triticum aestivum L. Ingestion of amino acids from phloem, elimination of amino acids in honeydew, and the content of amino acids in aphids tissue were measured. From these values, ingestion rates were estimated and compared to honeydew and to estimated composition of aphid proteins. Ingestion rate was lowest in D. noxia due to low growth rate and low honeydew production; intermediate in S. graminum due to higher growth rate and intermediate honeydew production; and highest in R. padi , which had the highest rates for both variables. Both D. noxia and S. graminum induced increases in the amino acid content of ingested phloem. These changes in phloem content, combined with differences in ingestion rates, resulted in large differences among aphids in estimated rates of ingestion of individual amino acids. In honeydew, most essential amino acids were found in low amounts compared with the amounts ingested, especially for methionine and lysine. A few amino acids (arginine, cystine, histidine and tryptophan) were more abundant in honeydew of some aphids, suggesting oversupply. Aphid species differed in the composition of free amino acids in tissue but showed very similar composition in protein, implying similar requirements among the aphids. In R. padi and D. noxia , most essential amino acids were ingested in amounts insufficient for growth, implying dependence on symbiont provisioning. In S. graminum , most amino acids were ingested in amounts apparently sufficient for growth.     

Comparison of the sequences and coding of La Crosse and snowshoe hare bunyavirus S RNA species.

The sequence of the S RNA of La Crosse bunyavirus was deduced from analyses of DNA copies cloned in the Escherichia coli plasmid pBR322. The S RNA is 984 nucleotides in length, has a base ratio of 31.8% U, 27.0% A, 23.2% C, and 18.0% G, and codes for two distinct gene products that are read from overlapping reading frames in the viral complementary strand. The larger gene product (N, 26.5 x 10(3) daltons) contains 235 amino acids, and the smaller gene product (NSS, 10.4 x 10(3) daltons) has 92 amino acids. Comparisons with the published sequences of the related snowshoe hare bunyavirus S RNA and its gene products (Bishop et al., Nucleic Acids Res. 10:3703-3713, 1982) indicate that there are a total of 114 nucleotide differences (6 additions or deletions and 108 substitutions). Also, there are 22 amino acid differences between the N proteins and 12 amino acid differences between the NSS proteins of the two S RNAs.     

How nutritionally imbalanced is phloem sap for aphids?

Aphids harbour intracellular symbionts (Buchnera) that provide their host with amino acids present in low amounts in their diet, phloem sap. To find out the extent to which aphids depend on their symbionts for synthesis of individual essential amino acids, we have evaluated how well phloem sap amino acid composition matches the aphids' needs. Amino acid compositions of the ingested phloem sap were compared to amino acids in aphid body proteins and also to available information about optimal diet composition for other plant feeding insects. Phloem sap data from severed stylets of two aphid species, Rhopalosiphum padi (L.) (Homoptera: Aphididae) feeding on wheat, and Uroleucon sonchi (L.) (Homoptera: Aphididae) feeding on Sonchus oleraceus (L.), together with published information on phloem sap compositions from other plant species were used.Phloem sap has in general only around 20% essential amino acids, with a range from 15–48%. Aphid body proteins and optimal diets for two other plant feeding insects have around 50%. The phloem sap of early flowering S. oleraceus ingested by U. sonchi contained 48%, which seems to be exceptional. Aphids feeding on different plants appear to be very differently dependent on their symbionts for their overall essential amino acid synthesis, due to the large variation in proportion of essential amino acids in phloem sap from different plants.The profile of the essential amino acids in phloem sap from different plant species corresponds rather well to profiles of both aphid body proteins and optimal diets determined for plant feeding insects. However, methionine and leucine in phloem sap are in general low in these comparisons, suggesting a higher dependence on the symbiont for synthesis of these amino acids. Concentrations of several essential amino acids in phloem from different plant species seem to vary together, suggesting that levels of symbiont provisioning of different amino acids are adjusted in parallel.