scholarly journals Isolation and classification of a family of cyclin gene homologues in Lupinus luteus.

1997 ◽  
Vol 44 (1) ◽  
pp. 37-42 ◽  
Author(s):  
J Deckert ◽  
J Jeleńska ◽  
Z Zaborowska ◽  
A B Legocki
Keyword(s):  
Cell Cycle ◽  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid Sequences ◽  
Lupinus Luteus ◽  
Cdna Clones ◽  
Conserved Residues ◽  
The Press ◽  
Cyclin Gene

The lupine (Lupinus luteus cv. Ventus) cDNA clones encoding homologues of cyclin (CycB1;2, CycB1;3, CycB1;4) have been isolated from cDNA library prepared from roots inoculated with Bradyrhizobium lupini. Comparison of the deduced amino-acid sequences of CycB1;2, CycB1;3, CycB1;4 and previously described CycB1;1 (Deckert et al. 1996, Biochimie 78, 90-94) showed that they share 46-65% of identical amino acids. The presence of conserved residues (Renaudin et. al., in The Plant Cell Cycle, in the press; Renaudin et al., Plant Mol. Biol, in the press) along with phylogenetic analysis of known plant cyclins revealed that the four lupine sequences belong to subgroup 1 of B-like mitotic cyclins.

Molecular characterization of MHC class II DRA cDNA in Deoni cattle

2018 ◽  
Author(s):  
K. Swathi ◽  
M. Gnana Prakash ◽  
D. Sakaram ◽  
T. Raghunandan ◽  
A. Sarat Chandra ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mhc Class Ii ◽  
Signal Peptide ◽  
Class Ii ◽  
Glycosylation Site ◽  
Amino Acid Sequences ◽  
Conserved Residues ◽  
A2 Domain

The present study was undertaken to clone and characterize DRA gene in Deoni cattle. The cDNA for the DRA gene was amplified by using specific primers designed based on available cattle sequences and purified products were cloned in competent E.coli (DH5á) strain. The full length 1013bp product of cDNA of DRA contained a single ORF of 762 nucleotides that coded for 253 amino acids translated product. Twenty four amino acids formed signal peptide while 229 constituted mature peptide. The deduced amino acid sequences resembled those of class II molecules of other species for all the conserved residues having critical functional role. But a single N-linked glycosylation site in á1 was observed in cattle and buffalo when compared to human and swine which contain a second site in á2 domain. The signal peptide was found more variable among the species compared. Comparison of nucleotide and amino acid sequences among related species and dendrogram constructed revealed that the cattle sequences are more similar to buffalo sequences.

scholarly journals Topological distribution of two connexin32 antigenic sites in intact and split rodent hepatocyte gap junctions.

1988 ◽  
Vol 107 (5) ◽  
pp. 1817-1824 ◽  
Author(s):  
D A Goodenough ◽  
D L Paul ◽  
L Jesaitis
Keyword(s):  
Amino Acids ◽  
Gap Junctions ◽  
Keyhole Limpet Hemocyanin ◽  
Cell Types ◽  
Cell Interaction ◽  
Amino Acid Sequences ◽  
Membrane Topology ◽  
Cdna Clones ◽  
Cleavage Sites ◽  
Mouse Hepatocyte

The membrane topology of connexin32, a principal polypeptide of gap junctions in diverse cell types, has been studied in rat and mouse hepatocyte gap junctions using site-specific antisera raised against synthetic oligopeptides corresponding to amino acid sequences deduced from cDNA clones. Based on published hydropathicity maps and identified protease-sensitive cleavage sites, oligopeptides were synthesized corresponding to two hydrophilic domains of connexin32, one predicted to face the cytoplasm, the other predicted to be directed extracellularly. Antisera were raised to keyhole limpet hemocyanin conjugates of the oligopeptides and used to map the distribution of their antigens using indirect immunocytochemistry on isolated gap junctions. The results directly demonstrated the cytoplasmic orientation of an antigen contained within amino acids 98-124 of the connexin32 sequence. The extracellular space in intact, isolated gap junctions is too small to permit binding of antibody molecules, necessitating the experimental separation of the junctional membranes to expose their extracellular surfaces using a urea/alkali procedure. While an antigen contained within amino acids 164-189 was visualized on the extracellular surfaces of some of the separated junctional membranes, variability in the observations and in the splitting procedure left ambiguities concerning the biological relevance of the observations after the denaturing conditions necessary to separate the junctional membranes. Using a different approach, however, the antigen could be exposed in intact liver using a hypertonic disaccharide junction-splitting procedure. The period of time of antigen exposure at the cell surface appears to peak at 30 s and disappear by 2-4 min. Taken together, these data demonstrate the extracellular orientation of an antigen contained within amino acids 164-189, which may be involved in cell-cell interaction within the gap junction.

scholarly journals Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing.

1990 ◽  
Vol 10 (4) ◽  
pp. 1729-1742 ◽  
Author(s):  
J P Lees-Miller ◽  
L O Goodwin ◽  
D M Helfman
Keyword(s):  
Amino Acids ◽  
Striated Muscle ◽  
Structural Characteristics ◽  
Single Gene ◽  
Transcription Unit ◽  
Amino Acid Sequences ◽  
Terminal Region ◽  
Cdna Clones ◽  
Alternative Promoters ◽  
Tropomyosin Isoforms

cDNA clones encoding three novel tropomyosins, termed TMBr-1, TMBr-2, and TMBr-3, were isolated and characterized from a rat brain cDNA library. All are derived from a single gene, which was previously found to express striated muscle alpha-tropomyosin and a number of other tropomyosin isoforms via an alternative splicing mechanism (N. Ruiz-Opazo and B. Nadal-Ginard, J. Biol. Chem. 262:4755-4765, 1987; D. F. Wieczorek, C. W. J. Smith, and B. Nadal-Ginard, Mol. Cell. Biol. 8:679-694, 1988). The derived amino acid sequences revealed that TMBr-1 contains 281 amino acids, TMBr-2 contains 251 amino acids, and TMBr-3 contains 245 amino acids. All three proteins contain a region that is identical to amino acids 81 through 258 of skeletal muscle alpha-tropomyosin. TMBr-1 is identical to striated muscle alpha-tropomyosin from amino acids 1 through 258 but contains a novel COOH-terminal region from amino acids 259 through 281. TMBr-2 and TMBr-3 both contain identical NH2-terminal sequences from amino acids 1 through 44 which were found to be expressed from a novel promoter. TMBr-3 contains the same COOH-terminal region as TMBr-1, whereas TMBr-2 contains a second novel COOH-terminal region. The genomic organization of the exons encoding TMBr-1, TMBr-2, and TMBr-3 were determined. These studies revealed a previously uncharacterized promoter located in the internal region of the alpha-TM gene as well as two novel COOH-terminal coding exons. The alpha-TM gene is a complex transcription unit containing 15 exons including two alternative promoters, two internal mutually exclusive exon cassettes, and four alternatively spliced 3' exons that encode four different COOH-terminal coding regions. A total of nine distinct mRNAs are known to be expressed from the alpha-TM gene in a cell type-specific manner in tissues such as striated muscle, smooth muscle, kidney, liver, brain, and fibroblasts. The mRNAs encoding TMBr-1, TMBr-2, and TMBr-3 were found to be expressed only in brain tissue, with TMBr-3 being expressed at much greater levels than TMBr-1 and TMBr-2. The individual structural characteristics of each brain alpha-tropomyosin isoform and their possible functions are discussed.

scholarly journals Classification of ‘Sarraceniospora aurea’ Furihata et al. 1989 as Actinocorallia aurea sp. nov.

2007 ◽  
Vol 57 (9) ◽  
pp. 2052-2055 ◽  
Author(s):  
Tomohiko Tamura ◽  
Kazunori Hatano ◽  
Ken-ichiro Suzuki
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics

Phylogenetic analysis of ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120, based on 16S rRNA gene sequences, revealed that these organisms are related to members of the genus Actinocorallia. These organisms contained glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and the menaquinones MK-9(H4), MK-9(H6) and MK-9(H8). The chemotaxonomic characteristics of the strains were consistent with those of the genus Actinocorallia. However, DNA–DNA hybridization and phenotypic characteristics revealed that the strains differed from the recognized species of the genus Actinocorallia. Therefore, we propose that ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120 be reclassified in the genus Actinocorallia as a novel species, Actinocorallia aurea sp. nov. (type strain NBRC 14752T=DSM 44434T).

scholarly journals 088 Differential Expression of Expansin Genes Isolated from Sweet Cherry (Prunus avium L.) during Fruit Ripening

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 403F-404
Author(s):  
Zhencai Wu ◽  
Paul A. Wiersma
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Fruit Development ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Low Level ◽  
Expansin Gene

Expansins are a class of proteins that stimulate the extension of plant cell walls. Expansins have been found in nearly all growing plant tissues, such as hycopotyls, young seedlings, fibers, internodes, flower petals, and ripening fruits. We isolated two full-length expansin cDNA clones, Pruav-Exp1 and Pruav-Exp2, from sweet cherry (Prunus avium L.) fruit. Pruav-Exp1 has 1048 nucleotides encoding 254 amino acids, while Pruav-Exp2 has 1339 nucleotides encoding 250 amino acids. Deduced amino acid sequences of sweet cherry Pruav-Exp1 and Pruav-Exp2 share 72% identity. A Blast search of the GenBank database with the deduced amino acid sequences of Pruav-Exp1 and Pruav-Exp2 indicated a high sequence identity with other plant expansin genes. Interestingly, Pruav-Exp1 shares 99% identity of amino acid sequence with that of apricot expansin Pav-Exp1. Fragments from the 3' ends of Pruav-Exp1 and Pruav-Exp2 were cloned to generate gene-specific probes. These probes were used to study expansin gene expression in different tissues and during fruit development. Northern blot analysis showed different mRNA expression patterns for each gene. The mRNA of Pruav-Exp1 was expressed at the pink and ripe stages, but not at the early green and yellow stages of fruit development. The mRNA of Pruav-Exp2 was present earlier, from a low level in yellow expanding fruit, increasing to a high level at the pink stage and remaining at this level through the ripe stage. Both mRNAs were also expressed at a low level in flower, but not present in other tissues such as roots, leaves and peduncles. Our study indicates an expansin gene family is present in sweet cherry and suggests that two expansin genes may have different roles during fruit development and ripening.

scholarly journals Complete chloroplast genome of Oryza sativa L. (B810s) and its phylogenetic analysis

2021 ◽  
pp. 895-901
Author(s):  
Kebao Song ◽  
Congtian Wang ◽  
Zhongbo Li ◽  
Peng Ning
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Oryza Sativa ◽  
Gene Annotation ◽  
Oryza Sativa L ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Protein Coding ◽  
Cp Genome ◽  
Rna Genes

The complete chloroplast (cp) genome of Oryza sativa L.(B810S) was 134546 bp in length in the study, which contains 149 genes including 99 coding protein genes, 41 transfer RNA genes, 8 ribosomal RNA genes and 1 non-coding region by gene annotation. A total of 20879 amino acids were encoded by this cp genome, TTT (Phe) and TTG (Leu) codon were the most frequent amino acids, whereas the ACC (Thr), GCC (Ala), CTC (Leu), and AAC (Asn) codon were the least frequent ones. The content of the four bases on the cp genome were 30.6% for A, 30.4% for T, 19.4% for C and 19.6% for G, respectively. Obviously, the A+T (61.0%) content is more higher than G+C (39.0%). The gene order and content are the same as those of previously reported cp genome of Rice. Phylogenetic analysis was implemented based on concatenated amino acid sequences of 99 protein-coding genes using Neighbor-Joining method (NJ) method. Therefore, the complete B810S cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny. Bangladesh J. Bot. 50(3): 895-901, 2021 (September) Special

scholarly journals Characterization and Construction of Functional cDNA Clones of Pariacoto Virus, the First Alphanodavirus Isolated outside Australasia

2000 ◽  
Vol 74 (11) ◽  
pp. 5123-5132 ◽  
Author(s):  
Karyn N. Johnson ◽  
Jean-Louis Zeddam ◽  
L. Andrew Ball
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Capsid Protein ◽  
Cultured Cells ◽  
Geographic Origin ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Homologous Proteins ◽  
Genomic Rnas ◽  
Rna Genome

ABSTRACT Pariacoto virus (PaV) was recently isolated in Peru from the Southern armyworm (Spodoptera eridania). PaV particles are isometric, nonenveloped, and about 30 nm in diameter. The virus has a bipartite RNA genome and a single major capsid protein with a molecular mass of 39.0 kDa, features that support its classification as aNodavirus. As such, PaV is the firstAlphanodavirus to have been isolated from outside Australasia. Here we report that PaV replicates in wax moth larvae and that PaV genomic RNAs replicate when transfected into cultured baby hamster kidney cells. The complete nucleotide sequences of both segments of the bipartite RNA genome were determined. The larger genome segment, RNA1, is 3,011 nucleotides long and contains a 973-amino-acid open reading frame (ORF) encoding protein A, the viral contribution to the RNA replicase. During replication, a 414-nucleotide long subgenomic RNA (RNA3) is synthesized which is coterminal with the 3′ end of RNA1. RNA3 contains a small ORF which could encode a protein of 90 amino acids similar to the B2 protein of other alphanodaviruses. RNA2 contains 1,311 nucleotides and encodes the 401 amino acids of the capsid protein precursor α. The amino acid sequences of the PaV capsid protein and the replicase subunit share 41 and 26% identity with homologous proteins of Flock house virus, the best characterized of the alphanodaviruses. These and other sequence comparisons indicate that PaV is evolutionarily the most distant of the alphanodaviruses described to date, consistent with its novel geographic origin. Although the PaV capsid precursor is cleaved into the two mature capsid proteins β and γ, the amino acid sequence at the cleavage site, which is Asn/Ala in all other alphanodaviruses, is Asn/Ser in PaV. To facilitate the investigation of PaV replication in cultured cells, we constructed plasmids that transcribed full-length PaV RNAs with authentic 5′ and 3′ termini. Transcription of these plasmids in cells recreated the replication of PaV RNA1 and RNA2, synthesis of subgenomic RNA3, and translation of viral proteins A and α.

Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing

1990 ◽  
Vol 10 (4) ◽  
pp. 1729-1742
Author(s):  
J P Lees-Miller ◽  
L O Goodwin ◽  
D M Helfman
Keyword(s):  
Amino Acids ◽  
Striated Muscle ◽  
Structural Characteristics ◽  
Single Gene ◽  
Transcription Unit ◽  
Amino Acid Sequences ◽  
Terminal Region ◽  
Cdna Clones ◽  
Alternative Promoters ◽  
Tropomyosin Isoforms

cDNA clones encoding three novel tropomyosins, termed TMBr-1, TMBr-2, and TMBr-3, were isolated and characterized from a rat brain cDNA library. All are derived from a single gene, which was previously found to express striated muscle alpha-tropomyosin and a number of other tropomyosin isoforms via an alternative splicing mechanism (N. Ruiz-Opazo and B. Nadal-Ginard, J. Biol. Chem. 262:4755-4765, 1987; D. F. Wieczorek, C. W. J. Smith, and B. Nadal-Ginard, Mol. Cell. Biol. 8:679-694, 1988). The derived amino acid sequences revealed that TMBr-1 contains 281 amino acids, TMBr-2 contains 251 amino acids, and TMBr-3 contains 245 amino acids. All three proteins contain a region that is identical to amino acids 81 through 258 of skeletal muscle alpha-tropomyosin. TMBr-1 is identical to striated muscle alpha-tropomyosin from amino acids 1 through 258 but contains a novel COOH-terminal region from amino acids 259 through 281. TMBr-2 and TMBr-3 both contain identical NH2-terminal sequences from amino acids 1 through 44 which were found to be expressed from a novel promoter. TMBr-3 contains the same COOH-terminal region as TMBr-1, whereas TMBr-2 contains a second novel COOH-terminal region. The genomic organization of the exons encoding TMBr-1, TMBr-2, and TMBr-3 were determined. These studies revealed a previously uncharacterized promoter located in the internal region of the alpha-TM gene as well as two novel COOH-terminal coding exons. The alpha-TM gene is a complex transcription unit containing 15 exons including two alternative promoters, two internal mutually exclusive exon cassettes, and four alternatively spliced 3' exons that encode four different COOH-terminal coding regions. A total of nine distinct mRNAs are known to be expressed from the alpha-TM gene in a cell type-specific manner in tissues such as striated muscle, smooth muscle, kidney, liver, brain, and fibroblasts. The mRNAs encoding TMBr-1, TMBr-2, and TMBr-3 were found to be expressed only in brain tissue, with TMBr-3 being expressed at much greater levels than TMBr-1 and TMBr-2. The individual structural characteristics of each brain alpha-tropomyosin isoform and their possible functions are discussed.

scholarly journals Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of apple chlorotic leaf spot virus are crucial for infectivity

2007 ◽  
Vol 88 (9) ◽  
pp. 2611-2618 ◽  
Author(s):  
Hajime Yaegashi ◽  
Masamichi Isogai ◽  
Hiroko Tajima ◽  
Teruo Sano ◽  
Nobuyuki Yoshikawa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Coat Protein ◽  
Leaf Spot ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Single Amino Acid ◽  
Cdna Clones ◽  
Spot Virus ◽  
Chlorotic Leaf

Amino acid sequences of apple chlorotic leaf spot virus (ACLSV) coat protein (CP) were compared between 12 isolates from apple, plum and cherry, and 109 cDNA clones that were amplified directly from infected apple tissues. Phylogenetic analysis based on the amino acid sequences of CP showed that the isolates and cDNA clones were separated into two major clusters in which the combinations of the five amino acids at positions 40, 59, 75, 130 and 184 (Ala40-Val59-Phe75-Ser130-Met184 or Ser40-Leu59-Tyr75-Thr130-Leu184) were highly conserved within each cluster. Site-directed mutagenesis using an infectious cDNA clone of ACLSV indicated that the combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) are necessary for infectivity to Chenopodium quinoa plants by mechanical inoculation. Moreover, an agroinoculation assay indicated that the substitution of a single amino acid (Ala40 to Ser40 or Phe75 to Tyr75) resulted in extreme reduction in the accumulation of viral genomic RNA, double-stranded RNAs and viral proteins (movement protein and CP) in infiltrated tissues, suggesting that the combinations of the two amino acids at positions 40 and 75 are important for effective replication in host plant cells.

scholarly journals Quantitative Analysis of Protein Evolution: The Phylogeny of Osteopontin

2021 ◽  
Vol 12 ◽  
Author(s):  
Xia Wang ◽  
Georg F. Weber
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Protein Evolution ◽  
Phylogenetic Trees ◽  
Building Blocks ◽  
Amino Acid Sequences ◽  
Systems Research ◽  
Physico Chemical ◽  
Box Counting Dimension

The phylogenetic analysis of proteins conventionally relies on the evaluation of amino acid sequences or coding sequences. Individual amino acids have measurable features that allow the translation from strings of letters (amino acids or bases) into strings of numbers (physico-chemical properties). When the letters are converted to measurable properties, such numerical strings can be evaluated quantitatively with various tools of complex systems research. We build on our prior phylogenetic analysis of the cytokine Osteopontin to validate the quantitative approach toward the study of protein evolution. Phylogenetic trees constructed from the number strings differentiate among all sequences. In pairwise comparisons, autocorrelation, average mutual information and box counting dimension yield one number each for the overall relatedness between sequences. We also find that bivariate wavelet analysis distinguishes hypermutable regions from conserved regions of the protein. The investigation of protein evolution via quantitative study of the physico-chemical characteristics pertaining to the amino acid building blocks broadens the spectrum of applicable research tools, accounts for mutation as well as selection, gives assess to multiple vistas depending on the property evaluated, discriminates more accurately among sequences, and renders the analysis more quantitative than utilizing strings of letters as starting points.

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