Searching genomes for noncoding RNA using FastR

The discovery of novel noncoding RNAs has been among the most exciting recent developments in biology. It has been hypothesized that there is, in fact, an abundance of functional noncoding RNAs (ncRNAs) with various catalytic and regulatory functions. However, the inherent signal for ncRNA is weaker than the signal for protein coding genes, making these harder to identify. We consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. The results are two orders of magnitude better than the currently available software for the problem. We applied FastR to the discovery of novel riboswitches, which are a class of RNA domains found in the untranslated regions. They are of interest because they regulate metabolite synthesis by directly binding metabolites. We searched all available eubacterial and archaeal genomes for riboswitches from purine, lysine, thiamin, and riboflavin subfamilies. Our results point to a number of novel candidates for each of these subfamilies and include genomes that were not known to contain riboswitches.     

The distributions,mechanisms, and structures of metabolite-binding riboswitches

Background  

Riboswitches are noncoding RNA structures that appropriately regulate genes in response to changing cellular conditions. The expression of many proteins involved in fundamental metabolic processes is controlled by riboswitches that sense relevant small molecule ligands. Metabolite-binding riboswitches that recognize adenosylcobalamin (AdoCbl), thiamin pyrophosphate (TPP), lysine, glycine, flavin mononucleotide (FMN), guanine, adenine, glucosamine-6-phosphate (GlcN6P), 7-aminoethyl 7-deazaguanine (preQ₁), and S-adenosylmethionine (SAM) have been reported.     

褐稻虱饲料稻株中数种氨基酸的营养效应

本研究初步证实饲料稻株中甘氨酸、赖氨酸和酪氨酸含量的高低,同褐稻虱(Nilaparvata lugens Stal)的发育进度、存活率、短翅型出现率和单雌产卵量关系极为密切,它们是褐稻虱赖以正常生长发育和繁殖的重要氨基酸。     

A kinetic spectrophotometric method for simultaneous determination of glycine and lysine by artificial neural networks

A spectrophotometric method for simultaneous analysis of glycine and lysine is proposed by application of neural networks on the spectral kinetic data. The method is based on the reaction of glycine and lysine with 1,2-naphthoquinone-4-sulfonate (NQS) in slightly basic medium. On the basis of the difference in the rate between the two reactions, these two amino acids can be determined simultaneously in binary mixtures. Feed-forward neural networks have been trained to quantify considered amino acids in mixtures under optimum conditions. In this way, a one-layer network was trained. Sigmoidal and linear transfer functions were used in the hidden and output layers, respectively. Linear calibration graphs were obtained in the concentration range of 1 to 25microgml(-1) for glycine and 1 to 19microgml(-1) for lysine. The analytical performance of this method was characterized by the relative standard error. The proposed method was applied to the determination of considered amino acids in synthetic samples.     

Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis

Riboswitches are structured mRNA elements that regulate gene expression upon binding specific cellular metabolites. It is thought that the highly conserved metabolite-binding domains of riboswitches undergo conformational change upon binding their cognate ligands. To investigate the generality of such a mechanism, we employed small-angle X-ray scattering (SAXS). We probed the nature of the global metabolite-induced response of the metabolite-binding domains of four different riboswitches that bind, respectively, thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), lysine, and S-adenosyl methionine (SAM). We find that each RNA is unique in its global structural response to metabolite. Whereas some RNAs exhibit distinct free and bound conformations, others are globally insensitive to the presence of metabolite. Thus, a global conformational change of the metabolite-binding domain is not a requirement for riboswitch function. It is possible that the range of behaviors observed by SAXS, rather than being a biophysical idiosyncrasy, reflects adaptation of riboswitches to the regulatory requirements of their individual genomic context.     

D-serine dehydratase from Escherichia coli. DNA sequence and identification of catalytically inactive glycine to aspartic acid variants

We have identified two glycyl residues whose integrity is essential for the catalytic competence of a model pyridoxal 5'-phosphate requiring enzyme, D-serine dehydratase from Escherichia coli. This was accomplished by isolating and sequencing the structural gene from wild type E. coli and from two mutant strains that produce inactive D-serine dehydratase. DNA sequencing indicated the presence of a single glycine to aspartic acid replacement in each variant. The amino acid replacements lie in a glycine-rich region of D-serine dehydratase well removed from pyridoxal 5'-phosphate-binding lysine 118 in the primary structure of the enzyme. The striking effect of these two glycine to aspartic acid replacements on catalytic activity, the conservation of the glycine-rich region in several pyridoxal 5'-phosphate-dependent enzymes that catalyze alpha/beta-eliminations, and the placement of similar glycine-rich sequences in well-characterized active site structures suggest that the glycine-rich region interacts with the cofactor at the active site of the enzyme.     

Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase that compensate for the formylation defect of a mutant tRNA aminoacylated with lysine

The specific formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for the initiation of protein synthesis in eubacteria such as Escherichia coli. In addition to the determinants for formylation present in the initiator tRNA, the nature of the amino acid attached to the tRNA is also important for formylation. We showed previously that a mutant tRNA aminoacylated with lysine was an extremely poor substrate for formylation. As a consequence, it was essentially inactive in initiation of protein synthesis in E. coli. In contrast, the same tRNA, when aminoacylated with methionine, was a good substrate for formylation and was, consequently, quite active in initiation. Here, we report on the isolation of suppressor mutations in MTF which compensate for the formylation defect of the mutant tRNA aminoacylated with lysine. The suppressor mutant has glycine 178 changed to glutamic acid. Mutants with glycine 178 of MTF changed to aspartic acid, lysine, and leucine were generated and were found to be progressively weaker suppressors. Studies on allele specificity of suppression using different mutant tRNAs as substrates suggest that the Gly178 to Glu mutation compensates for the nature of the amino acid attached to the tRNA. We discuss these results in the framework of the crystal structure of the MTF.fMet-tRNA complex published recently.     

Study of structure-activity relationship among similar analogues of GSB-106, a dipeptide mimetic of a brain-derived neurotrophic factor

In the previous work, we synthesized a dimeric dipeptide mimetic of the 4th loop of BDNF, i.e., hexamethylenediamide bis(N-monosuccinil-L-seryl-L-lysine) (GSB-106), which has neuroprotective activity in vitro in a concentration range of 10^?5–10^?8 M and antidepressant activity in vivo at intraperitoneal doses of 0.1 and 1 mg/kg in rats. We studied the structural and functional relationships among analogues of GSB-106. A glycine scan was performed, and a number of corresponding compounds were synthesized: GT-105 (where lysine was replaced by glycine), GT-107 (where serine was replaced by glycine), and GT-106Ac (where the monosuccinic radical was replaced by the acetyl group). We studied the dependence of the activity on the configuration of amino acid residues in the following compounds: GT-107D (D-enantiomer of GT-107), GT-106DL (L-serine was replaced by D-serine), GT-106LD (L-lysine was replaced by D-lysine). The investigation of these compounds in the HT22 cell culture in conditions of oxidative stress showed that only two analogues of GSB-106 had the neuroprotective effect, i.e., in the case of the replacement of serine by glycine and the succinic radical by the acetic group. This effect disappeared when the lysine residue was replaced by glycine or D-lysine and the L-serine residue, by D-serine. The results indicate the key role of the lysine side group in GSB-106 for its neuroprotective activity. The L-configuration is necessary for both the lysine and serine residues. The configuration of the lysine residue remains critical in the absence of the serine side group. Thus, the minimum neuroprotective pharmacophore of the beta-turn of the 4th loop of BDNF is the following fragment: HOOC-CH₂-CH₂-CO-NH-(S)CH(CH2OH)-CO-NH-(S)CH((CH₂)₄NH₂)-CO-NH-(CH₂)₃ Only GT-106Ac out of two analogues of GSB-106 having the neuroprotective activity showed the antidepressant activity. This indicates more stringent structural requirements for the manifestation of the antidepressant activity. The results can be useful for designing new active mimetics of BDNF.     

The importance of dietary amino acids on the reproduction and longevity of adult Dacus oleae (Gmelin) (Diptera Tephritidae)

When the amino-acid mixture of an effective chemically defined diet was replaced by single amino acids, keeping the total nitrogen at the same level, the egg production of Dacus oleae was minimal with all the 19 amino acids tested. Male survival was adversely affected by the amino acids : alanine, aspartic acid, glutamic acid, glycine, hydroxyproline, lysine, serine and tyrosine, while female survival was shortened when the amino acids : glycine, hydroxyproline and lysine were added. The creation of amino-acid imbalances, by deleting the 19 amino acids individually, from the complete amino-acid mixture, showed that the amino acids : arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tryptophane and valine were indispensable to the adult Dacus oleae flies, as far as egg production is concerned. Survival of the male flies was significantly shortened when the amino acids : alanine, hydroxyproline and tryptophane were omitted. Significant differences in longevity between males and females were scored, when the amino acids : alanine, aspartic acid, cystine, glycine and tryptophane, were omitted.     

Acyl-CoA: glycine N-acyltransferase: in vitro studies on the glycine conjugation of straight- and branched-chained acyl-CoA esters in human liver

Apparent kinetic constants (Km and Vmax values) were determined for human liver acyl-CoA: glycine acyltransferase (glycine-N-acylase) towards isobutyryl-CoA, 2-methyl butyryl-CoA, isovaleryl-CoA, butyryl-CoA, hexanoyl-CoA, octanoyl-CoA, and decanoyl-CoA. These acyl-CoA esters were selected because of their relevance to the human diseases with cellular accumulation of these esters, i.e., especially to metabolic defects in the acyl-CoA dehydrogenation steps of the branched-chain amino acids, lysine, 5-hydroxy lysine, tryptophan, and fatty acid oxidation pathways. With the acyl-CoA ester as the fixed substrate, the Km value for glycine ranged from 0.5 to 2.9 mole/liter, and with glycine as fixed substrate, the Km values for the acyl-CoA esters varied from 0.3 to 5.6 mmole/liter. It is concluded that the substrate concentration is decisive for the glycine conjugate formation and that the occurrence in urine of acylglycines reflects an intramitochondrial accumulation of the corresponding acyl-CoA ester.     

Identification of amino acids in the leader peptide of Methanococcus voltae preflagellin that are important in posttranslational processing

Archaeal flagellins are made initially as preproteins with short, positively charged leader peptides. Analysis of all available archaeal preflagellin sequences indicates that the -1 position is always held by a glycine while the -2 and -3 positions are almost always held by charged amino acids. To evaluate the importance of these and other amino acids in the leader peptides of archaeal flagellins for processing by a peptidase, Methanococcus voltae mutant FlaB2 preflagellin genes were generated by PCR and the proteins tested in a methanogen preflagellin peptidase assay that detects the removal of the leader peptide from preflagellin. When the -1 position was changed from glycine to other amino acids tested, no cleavage was observed by the peptidase, with the exception of a change to alanine at which poor, partial processing was observed. Amino acid substitutions at the -2 lysine position resulted in a complete loss of processing by the peptidase, while changes at the -3 lysine resulted in partial processing. A mutant preflagellin with a leader peptide shortened from 12 amino acids to 6 amino acids was not processed. When the invariant glycine residue present at position +3 was changed to a valine, no processing of this mutant preflagellin was observed. The identification of critical amino acids in FlaB2 required for proper processing suggests that a specific preflagellin peptidase may cleave archaeal flagellins by recognition of a conserved sequence of amino acids.     

The Amino Acid Requirements of Acanthamoeba sp. Neff

SYNOPSIS. Acanthamoeba sp. Neff can synthesize 4 of the 10 essential amino acids, namely, histidine, lysine, threonine and tryptophan. However, in this minimal medium, the non-essential amino acid glycine was also required for growth. Serine or threonine could replace glycine, but the growth rate was reduced.     

The first seven amino acids encoded by the v-src oncogene act as a myristylation signal: lysine 7 is a critical determinant.

The transforming protein of Rous sarcoma virus, pp60v-src, is covalently coupled to myristic acid by an amide linkage to glycine 2. Myristylation promotes the association of pp60v-src with cellular membranes, and this subcellular location is essential for transforming activity. The findings presented here, in conjunction with the previous reports of others, imply that the seventh amino acid encoded by v-src might be important in the myristylation reaction. Replacement of lysine 7 by asparagine greatly reduced the myristylation, membrane association, and transforming activity of pp60v-src. In contrast, substitution of arginine at residue 7 had no effect on any of these properties of pp60v-src. Addition of amino acids 1 to 7 encoded by v-src was sufficient to cause myristylation of a src-pyruvate kinase fusion protein. We conclude that the recognition sequence for myristylation of pp60v-src comprises amino acids 1 to 7 and that lysine 7 is a critical component of this sequence.     

Plasma amino acids and sports injuries

Summary. The aim of this study was to explore the relationship between changes in plasma amino acids and the incidence of sports injuries during a soccer season. Fourteen plasma amino acids were assayed at monthly intervals in 12 young soccer players during a whole soccer season. Based on the number and severity of injuries the soccer players were divided into an injury-prone and a non-injury-prone group. The mean plasma level of the amino acid glycine was significantly lower (P=0.009) in the injury-prone group than the other group, while the mean plasma levels of tyrosine, tryptophan and lysine were higher in the injury-prone group during this period (P<0.05). However there were no significant differences in the calculated plasma tryptophan and tyrosine/large neutral amino acids ratios. Significant linear time trends were observed for taurine, ornithine, lysine and the tryptophan/large neutral amino acids ratio.These results indicate that the plasma concentrations of glycine and to a lesser extent those of tyrosine, tryptophan and lysine may be promising peripheral markers for injury-proneness in young soccer players. Whether a role for glycine substitution will be indicative to reduce the occurrence of sports injuries will need to be investigated in future studies.     

Functional roles of amino acid residues involved in forming the alpha-helix-turn-alpha-helix operator DNA binding motif of Tet repressor from Tn10.

The Tn10 derived Tet repressor contains an amino acid segment with high homology to the alpha-helix-turn-alpha-helix motif (HTH) of other DNA binding proteins. The five most conserved amino acids in HTH are probably involved in structural formation of the motif. Their functional role was probed by saturation mutagenesis yielding 95 single amino acid replacement mutants of Tet repressor. Their binding efficiencies to tet operator were quantitatively determined in vivo. All functional mutants contain amino acid substitutions consistent with their proposed role in a HTH. In particular, only the two smallest amino acids (serine, glycine) can substitute a conserved alanine in the proposed first alpha-helix without loss of activity. The last position of the first alpha-helix, the second position in the turn, and the fourth position in the second alpha-helix require mostly hydrophobic residues. The proposed C-terminus of the first alpha-helix is supported by a more active asparagine compared to glutamine replacement mutant of the wt leucine residue. The turn is located close to the protein surface as indicated by functional lysine and arginine replacements for valine. A glycine residue at the first position in the turn can be replaced by any amino acid yielding mutants with at least residual tet operator affinity. A structural model of the HTH of Tet repressor is presented.