Genome analysis and phylogenetic characterization of two deformed wing virus strains from Apis cerana in Vietnam

Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽

10.1139/g91-098 ◽

1991 ◽

Vol 34 (4) ◽

pp. 644-651 ◽

Cited By ~ 16

Author(s):

Kenneth Koo ◽

W. Dorsey Stuart

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Neurospora Crassa ◽

Rna Binding ◽

Signal Sequence ◽

Average Length ◽

Open Reading Frame ◽

Mrna Transcript ◽

S1 Nuclease ◽

Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

Sequence and expression of the dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.6.5.1711-1721.1986 ◽

1986 ◽

Vol 6 (5) ◽

pp. 1711-1721

Author(s):

E M McIntosh ◽

R H Haynes

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequences ◽

Open Reading Frame ◽

Northern Analysis ◽

Hindiii Site ◽

Reading Frame ◽

Hindiii Restriction Site ◽

Cycle Dependent

The dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae has been isolated by screening a Sau3A clone bank for complementation of the dUMP auxotrophy exhibited by dcd1 dmp1 haploids. Plasmid pDC3, containing a 7-kilobase (kb) Sau3A insert, restores dCMP deaminase activity to dcd1 mutants and leads to an average 17.5-fold overproduction of the enzyme in wild-type cells. The complementing activity of the plasmid was localized to a 4.2-kb PvuII restriction fragment within the Sau3A insert. Subcloning experiments demonstrated that a single HindIII restriction site within this fragment lies within the DCD1 gene. Subsequent DNA sequence analysis revealed a 936-nucleotide open reading frame encompassing this HindIII site. Disruption of the open reading frame by integrative transformation led to a loss of enzyme activity and confirmed that this region constitutes the dCMP deaminase gene. Northern analysis indicated that the DCD1 mRNA is a 1.15-kb poly(A)+ transcript. The 5' end of the transcript was mapped by primer extension and appears to exhibit heterogeneous termini. Comparison of the amino acid sequence of the T2 bacteriophage dCMP deaminase with that deduced for the yeast enzyme revealed a limited degree of homology which extends over the entire length of the phage polypeptide (188 amino acids) but is confined to the carboxy-terminal half of the yeast protein (312 amino acids). A potential dTTP-binding site in the yeast and phage enzymes was identified by comparison of homologous regions with the amino acid sequences of a variety of other dTTP-binding enzymes. Despite the role of dCMP deaminase in dTTP biosynthesis, Northern analysis revealed that the DCD1 gene is not subject to the same cell cycle-dependent pattern of transcription recently found for the yeast thymidylate synthetase gene (TMP1).

Effect of Different Edaphic Crop Conditions on the Free Amino Acid Profile of PH-16 Dry Cacao Beans

Agronomy ◽

10.3390/agronomy11081637 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1637

Author(s):

Quintino Reis de Araujo ◽

Guilherme Amorim Homem de Abreu Loureiro ◽

Cid Edson Mendonça Póvoas ◽

Douglas Steinmacher ◽

Stephane Sacramento de Almeida ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Glutamic Acid ◽

Free Amino Acid ◽

Free Amino Acids ◽

Free Amino ◽

Principal Component ◽

Amino Acid Profile ◽

Gamma Aminobutyric Acid ◽

Significant Difference

Free amino acids in cacao beans are important precursors to the aroma and flavor of chocolate. In this research, we used inferential and explanatory statistical techniques to verify the effect of different edaphic crop conditions on the free amino acid profile of PH-16 dry cacao beans. The decreasing order of free amino acids in PH-16 dry cacao beans is leucine, phenylalanine, glutamic acid, alanine, asparagine, tyrosine, gamma-aminobutyric acid, valine, isoleucine, glutamine, lysine, aspartic acid, serine, tryptophan, threonine, glycine. With the exception of lysine, no other free amino acid showed a significant difference between means of different edaphic conditions under the ANOVA F-test. The hydrophobic free amino acids provided the largest contribution to the explained variance with 58.01% of the first dimension of the principal component analysis. Glutamic acid stands out in the second dimension with 13.09%. Due to the stability of the biochemical profile of free amino acids in this clonal variety, it is recommended that cacao producers consider the genotype as the primary source of variation in the quality of cacao beans and ultimately the chocolate to be produced.

Nucleotide and Amino Acid Sequences of the Metallo-β-Lactamase, ImiS, from Aeromonas veronii bv. sobria

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.2.436 ◽

1998 ◽

Vol 42 (2) ◽

pp. 436-439 ◽

Cited By ~ 22

Author(s):

T. R. Walsh ◽

W. A. Neville ◽

M. H. Haran ◽

D. Tolson ◽

D. J. Payne ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Active Site ◽

Amino Acid Sequences ◽

Open Reading Frame ◽

Reading Frame ◽

Aeromonas Veronii ◽

Putative Active Site ◽

Lactamase Gene ◽

Active Site Sequence

ABSTRACT The Aeromonas veronii bv. sobria metallo-β-lactamase gene, imiS, was cloned. The imiS open reading frame extends for 762 bp and encodes a protein of 254 amino acids with a secreted modified protein of 227 amino acids and a predicted pI of 8.1. To confirm the predicted sequence, purified ImiS was digested and the resulting peptides were identified, yielding an identical sequence for ImiS, with 98% identity to CphA. Both possessed the putative active-site sequence Asn-Tyr-His-Thr-Asp at positions 88 to 92, which is unique to the Aeromonas metallo-β-lactamases.

Trans-tegumental absorption of L-alanine and L-leucine by a monogenean, Diclidophora merlangi

Parasitology ◽

10.1017/s0031182000047363 ◽

1978 ◽

Vol 76 (1) ◽

pp. 29-37 ◽

Cited By ~ 21

Author(s):

D. W. Halton

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Amino Acid ◽

Sea Water ◽

Low Molecular Weight ◽

Acid Uptake ◽

Neutral Amino Acids ◽

Freeze Dried ◽

Significant Difference

SummaryAn in vitro investigation has been made of the relative roles of the gut and tegument in the absorption of the neutral amino acids L-alanine and L-leucine by a marine fish-gill parasite, Diclidophora merlangi. The use of ligatures to preclude oral ingestion of trace-labelled medium has proved inadequate, invariably damaging the tegument, as revealed by stereoscan electron microscopy, and resulting in artifactual levels of absorption. Three alternative procedures have given consistently reliable data on the route of entry of low molecular weight substrates. (1) Ultrastructural examination of worms previously incubated in electron-dense cationic tracers has shown that, in vitro, there is no oral intake of sea water. (2) The suspending of worms in trace-labelled medium with the mouth out of the medium and comparing amino acid uptake with that of worms totally immersed in medium has revealed no statistically significant difference in the absorption levels. (3) Application of section (freeze-dried) auto-radiography to detect diffusible isotope has demonstrated directly transtegumental absorption of a neutral amino acid. It is concluded from these experiments that Diclidophora has a tegumental transport system for absorbing certain neutral amino acids, and whilst, clearly, the worm is sanguinivorous and digests blood in a well-developed gut, it may also be capable of supplementing this diet with low molecular weight organic nutrient absorbed directly from sea water via the tegument.

Sequence of the Structural Gene for Xanthine Dehydrogenase (rosy Locus) in Drosophila melanogaster

Genetics ◽

10.1093/genetics/116.1.67 ◽

1987 ◽

Vol 116 (1) ◽

pp. 67-73

Author(s):

Tim P Keith ◽

Margaret A Riley ◽

Martin Kreitman ◽

R C Lewontin ◽

Daniel Curtis ◽

...

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Drosophila Melanogaster ◽

Amino Acid ◽

Nucleotide Sequence ◽

Structural Gene ◽

Xanthine Dehydrogenase ◽

Open Reading Frame ◽

Reading Frame ◽

Eco Ri

ABSTRACT We determined the nucleotide sequence of a 4.6-kb Eco RI fragment containing 70% of the rosy locus. In combination with information on the 5′ sequence, the gene has been sequenced in entirety. rosy cDNAs have been isolated and intron/exon boundaries have been determined. We find an open reading frame which spans four exons and would encode a protein of 1335 amino acids. The molecular weight of the encoded protein (xanthine dehydrogenase), based on the amino acid translation, is 146,898 daltons which agrees well with earlier biophysical estimates. Characteristics of the protein are discussed.

Homochirality May Not Be a Prerequisite for Protein Structure and Function: A Computational Model Investigation of Prebiotic Peptides

10.20944/preprints202003.0005.v1 ◽

2020 ◽

Author(s):

Jianxun Shen ◽

Pauline M. Schwartz ◽

Carl Barratt

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Hierarchical Cluster ◽

Building Blocks ◽

Beta Sheets ◽

Folding Energy ◽

Primitive Earth ◽

C Terminus ◽

Significant Difference ◽

Prebiotic Amino Acids

On the primitive Earth, both L- and D-amino acids would have been present. However, only L-amino acids are essential blocks to construct proteins in modern life. To study the relative stability of homochiral and heterochiral peptides, a variety of computational methods were employed. 10 prebiotic amino acids (Gly, Ala, Asp, Glu, Ile, Leu, Pro, Ser, Thr, and Val) were previously determined by multiple previous meteorite, spark discharge, and hydrothermal vent studies. We focused on what had been reported as primary early Earth polypeptide analogs: 1ARK, 1PPT, 1ZFI, and 2LZE. Tripeptide composed of only Asp, Ser, and Val exemplified that different positions (i.e., N-terminus, C-terminus, and middle) made a difference in minimal folding energy of peptides, while the classification of amino acid (hydrophobic, acidic, or hydroxylic) did not show significant difference. Hierarchical cluster analysis for dipeptides with all possible combinations of the proposed 10 prebiotic amino acids and their D-amino acid substituted derivatives generated five clusters. Prebiotic polypeptides were built up to test the significance of molecular fluctuations, secondary structure occupancies, and folding energy differences based on these clusters. Most interestingly, among 129 residues, mutation sensitivity profiles presented that the ratio of more stable to less stable to equally stable D-amino acids was about 1:1:1. In conclusion, some combinations of a mixture of L- and D-amino acids can act as essential building blocks of life. Peptides with α-helices, long β-sheets, and long loops are usually less sensitive to D-amino acid replacements in comparison to short β-sheets.

Amino Acid and Mineral Supplementation in Fermentation Process of Concentrate Protein of Jatropha Seed Cake (Jatropha curcas L.)

ANIMAL PRODUCTION ◽

10.20884/1.anprod.2016.18.3.574 ◽

2016 ◽

Vol 18 (3) ◽

pp. 141 ◽

Cited By ~ 1

Author(s):

Titin Widiyastuti ◽

Tri Rahardjo Sutardi

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Fermentation Process ◽

Crude Fiber ◽

Seed Cake ◽

Significant Difference ◽

Gross Energy ◽

Calcium And Phosphorus ◽

Jatropha Seed ◽

Optimization Of Fermentation

The purpose of this study is to assess the optimization of fermentation process by adding a minerals and amino acids so that the potential of protein of Concentrate Protein-Jatropha seed cake (CP-JSC) can be optimally used as a substitute for soybean meal. The method used was completely randomized design. The treatment consisted of F1: Fermentation CP-BBJ + methionine-lysine (0.25%: 0.25%), F2: Fermentation CP-JSC + methionine-lysine (0.5%: 0.5%), F3: F1 + 0.45% Dicalsium Phosphate, F4: F2 + 0.45% Dicalsium Phosphate. Each treatment was repeated four times, When treatment significantly continued by Least Significant Difference (LSD), variables observed are the levels of antinutrients (phorbolester, antitrypsin), the levels of nutrients (fat, protein, crude fiber, Ca, P and gross energy) and amino acid. Results of analysis of variance showed that the addition of amino acids and minerals Ca, P in the fermentation process was highly significant effect on the levels of crude fiber and phosphorus (P <0.01) and significantly affected the gross energy content of CP-JSC post-fermentation (P <0.05). Dry matter, crude protein, crude lipid and calcium are not affected by supplementation of methionine and lysine as well as calcium and phosphorus. Supplementation of methionine and lysine in the fermentation substrate showed good levels of essential amino acids and non essential higher than previous studies although not statistically significant (P> 0.05). While the levels obtained phorbolester range of 0.055% - 0.08%. It was concluded that the optimization of fermentation can be done without adding the amino acid supplementation of minerals calcium and phosphorus. Supplementation significantly affect a significant increase or decrease in some nutrients (crude fiber, gross energy, phosphor) and capable of suppressing a decrease in amino acids. Supplementation of amino acids Lysine and Methionin 0.05% is the best treatment.

Evidence for Production of a New Lantibiotic (Butyrivibriocin OR79A) by the Ruminal Anaerobe Butyrivibrio fibrisolvensOR79: Characterization of the Structural Gene Encoding Butyrivibriocin OR79A

Applied and Environmental Microbiology ◽

10.1128/aem.65.5.2128-2135.1999 ◽

1999 ◽

Vol 65 (5) ◽

pp. 2128-2135 ◽

Cited By ~ 32

Author(s):

M. L. Kalmokoff ◽

D. Lu ◽

M. F. Whitford ◽

R. M. Teather

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Gel Filtration ◽

Culture Fluid ◽

Northern Blotting ◽

Coding Region ◽

Gene Encoding ◽

Butyrivibrio Fibrisolvens ◽

Reading Frame ◽

Significant Homology

ABSTRACT The ruminal anaerobe Butyrivibrio fibrisolvens OR79 produces a bacteriocin-like activity demonstrating a very broad spectrum of activity. An inhibitor was isolated from spent culture fluid by a combination of ammonium sulfate and acidic precipitations, reverse-phase chromatography, and high-resolution gel filtration. N-terminal analysis of the isolated inhibitor yielded a 15-amino-acid sequence (G-N/Q-G/P-V-I-L-X-I-X-H-E-X-S-M-N). Two different amino acid residues were detected in the second and third positions from the N terminus, indicating the presence of two distinct peptides. A gene with significant homology to one combination of the determined N-terminal sequence was cloned, and expression of the gene was confirmed by Northern blotting. The gene (bvi79A) encoded a prepeptide of 47 amino acids and a mature peptide, butyrivibriocin OR79A, of 25 amino acids. Significant sequence homology was found between this peptide and previously reported lantibiotics containing the double-glycine leader peptidase processing site. Immediately downstream of bvi79Awas a second, partial open reading frame encoding a peptide with significant homology to proteins which are believed to be involved in the synthesis of lanthionine residues. These findings indicate that the isolated inhibitory peptides represent new lantibiotics. Results from both total and N-terminal amino acid sequencing indicated that the second peptide was identical to butyrivibriocin OR79A except for amino acid substitutions in positions 2 and 3 of the mature lantibiotic. Only a single coding region was detected when restriction enzyme digests of total DNA were probed either with an oligonucleotide based on the 5′ region of bvi79A or with degenerate oligonucleotides based on the predicted sequence of the second peptide.

Sequence and expression of the dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.6.5.1711 ◽

1986 ◽

Vol 6 (5) ◽

pp. 1711-1721 ◽

Cited By ~ 38

Author(s):

E M McIntosh ◽

R H Haynes

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequences ◽

Open Reading Frame ◽

Northern Analysis ◽

Hindiii Site ◽

Reading Frame ◽

Hindiii Restriction Site ◽

Cycle Dependent

The dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae has been isolated by screening a Sau3A clone bank for complementation of the dUMP auxotrophy exhibited by dcd1 dmp1 haploids. Plasmid pDC3, containing a 7-kilobase (kb) Sau3A insert, restores dCMP deaminase activity to dcd1 mutants and leads to an average 17.5-fold overproduction of the enzyme in wild-type cells. The complementing activity of the plasmid was localized to a 4.2-kb PvuII restriction fragment within the Sau3A insert. Subcloning experiments demonstrated that a single HindIII restriction site within this fragment lies within the DCD1 gene. Subsequent DNA sequence analysis revealed a 936-nucleotide open reading frame encompassing this HindIII site. Disruption of the open reading frame by integrative transformation led to a loss of enzyme activity and confirmed that this region constitutes the dCMP deaminase gene. Northern analysis indicated that the DCD1 mRNA is a 1.15-kb poly(A)+ transcript. The 5' end of the transcript was mapped by primer extension and appears to exhibit heterogeneous termini. Comparison of the amino acid sequence of the T2 bacteriophage dCMP deaminase with that deduced for the yeast enzyme revealed a limited degree of homology which extends over the entire length of the phage polypeptide (188 amino acids) but is confined to the carboxy-terminal half of the yeast protein (312 amino acids). A potential dTTP-binding site in the yeast and phage enzymes was identified by comparison of homologous regions with the amino acid sequences of a variety of other dTTP-binding enzymes. Despite the role of dCMP deaminase in dTTP biosynthesis, Northern analysis revealed that the DCD1 gene is not subject to the same cell cycle-dependent pattern of transcription recently found for the yeast thymidylate synthetase gene (TMP1).