scholarly journals Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 921-939 ◽  
Author(s):  
J Callis ◽  
T Carpenter ◽  
C W Sun ◽  
R D Vierstra
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Tandem Repeats ◽  
Synonymous Substitution ◽  
Coding Region ◽  
Coding Regions ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Polyubiquitin Gene ◽  
Polyubiquitin Genes

Abstract The Arabidopsis thaliana ecotype Columbia ubiquitin gene family consists of 14 members that can be divided into three types of ubiquitin genes; polyubiquitin genes, ubiquitin-like genes and ubiquitin extension genes. The isolation and characterization of eight ubiquitin sequences, consisting of four polyubiquitin genes and four ubiquitin-like genes, are described here, and their relationships to each other and to previously identified Arabidopsis ubiquitin genes were analyzed. The polyubiquitin genes, UBQ3, UBQ10, UBQ11 and UBQ14, contain tandem repeats of the 228-bp ubiquitin coding region. Together with a previously described polyubiquitin gene, UBQ4, they differ in synonymous substitutions, number of ubiquitin coding regions, number and nature of nonubiquitin C-terminal amino acid(s) and chromosomal location, dividing into two subtypes; the UBQ3/UBQ4 and UBQ10/UBQ11/UBQ14 subtypes. Ubiquitin-like genes, UBQ7, UBQ8, UBQ9 and UBQ12, also contain tandem repeats of the ubiquitin coding region, but at least one repeat per gene encodes a protein with amino acid substitutions. Nucleotide comparisons, Ks value determinations and neighbor-joining analyses were employed to determine intra- and intergenic relationships. In general, the rate of synonymous substitution is too high to discern related repeats. Specific exceptions provide insight into gene relationships. The observed nucleotide relationships are consistent with previously described models involving gene duplications followed by both unequal crossing-over and gene conversion events.

scholarly journals Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

2017 ◽  
Author(s):  
Anuj Kumar ◽  
Aditi Chauhan ◽  
Mansi Sharma ◽  
Sai Kumar Kompelli ◽  
Vijay Gahlaut ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Full Length ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genome Wide ◽  
Varying Length

AbstractSimple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

Isolation and characterization of the pea cytochrome c oxidase Vb gene

Genome ◽  
2006 ◽  
Vol 49 (11) ◽  
pp. 1481-1489 ◽  
Author(s):  
Nakao Kubo ◽  
Shin-ichi Arimura ◽  
Nobuhiro Tsutsumi ◽  
Koh-ichi Kadowaki ◽  
Masashi Hirai
Keyword(s):  
Amino Acid ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Fluorescent Proteins ◽  
Amino Acid Sequences ◽  
Homology Search ◽  
Coding Region ◽  
Angiosperm Evolution ◽  
Isolation And Characterization ◽  
Duplication Events

Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.

scholarly journals Amino Acid Starvation Enhances Programmed Ribosomal Frameshift in Metavirus Ty3 of Saccharomyces cerevisiae

2016 ◽  
Vol 2016 ◽  
pp. 1-6
Author(s):  
Sezai Türkel
Keyword(s):  
Amino Acid ◽  
Amino Acid Starvation ◽  
Yeast Cells ◽  
Dependent Manner ◽  
Coding Region ◽  
Coding Regions ◽  
In The Wild ◽  
Amino Acid Depletion ◽  
A Site ◽  
Wild Type Yeast

Ty3 is a retroviral-like element and propagates with a retroviral-like mechanism within the yeast cells. Ty3 mRNA contains two coding regions, which are GAG3 and POL3. The coding region POL3 is translated as a GAG3-POL3 fusion protein by a +1 programmed frameshift. In this study, it was shown that the Ty3 frameshift frequency is significantly increased by amino acid starvation in a Gcn2p complex dependent manner. When the yeast cells were subjected to amino acid starvation, the frameshift frequency of Ty3 increased more than 2-fold in the wild-type yeast cells, mostly independent of Gcn4p. However, Ty3 frameshift frequency remained at basal level in the gcn1, gcn20, or gcn2 mutant yeast cells in amino acid starved yeasts. Gcn1p forms a complex with Gcn2p and Gcn20p and is involved in the sensing of uncharged tRNAs on the ribosomal A-site during translation. Increases in uncharged tRNA levels due to amino acid depletion lead to ribosomal pauses. These ribosomal pauses are significant actors in the regulation of Ty3 frameshift frequency. Results of this research revealed that frameshift frequency in Ty3 is regulated by the Gcn2p complex in response to amino acid starvation in yeast.

scholarly journals Isolation and Characterization of the Genes Encoding Basic and Acidic Chitinase in Arabidopsis thaliana

1990 ◽  
Vol 93 (3) ◽  
pp. 907-914 ◽  
Author(s):  
Deborah A. Samac ◽  
Cathy M. Hironaka ◽  
Peter E. Yallaly ◽  
Dilip M. Shah
Keyword(s):  
Arabidopsis Thaliana ◽  
Isolation And Characterization ◽  
Genes Encoding

Isolation and characterization of an expressed napin gene fromBrassica rapa

1991 ◽  
Vol 1 (4) ◽  
pp. 209-219 ◽  
Author(s):  
Jean C. Kridl ◽  
David W. McCarter ◽  
Ronald E. Rose ◽  
Donna E. Scherer ◽  
Deborah S. Knutzon ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Storage Protein ◽  
Protein Gene ◽  
Coding Region ◽  
Coding Regions ◽  
Endogenous Expression ◽  
Isolation And Characterization ◽  
Glucuronidase Reporter ◽  
Transgenic Rapeseed

AbstractAn expressed napin storage protein gene fromBrassica rapa, BcNA1, has been cloned and sequenced. The gene is a member of a family of four to seven napin genes inB. rapaand is highly expressed in developing seeds. An expression cassette containing the DNA flanking the napin coding region of BcNA1 has been engineered and demonstrated to function appropriately, as compared with the gene's endogenous expression, in transgenic rapeseed using the β-glucuronidase reporter gene. TheB. rapaBcNA1 gene and aB. napusnapin gene, gNa, share extremely high nucleotide homology not only throughout their coding regions, but over a DNA locus comprising 4.3 kb. We suggest the gNa gene was contributed by the originalB. rapaprogenitor of the amphidiploidB. napus.

NUCLEOTIDE SEQUENCE OF THE STAPHYLOCOAGULASE GENE FROM STAPHYLOCOCCUS AUREUS STRAIN BB

1987 ◽  
Author(s):  
S Kaida ◽  
T Miyata ◽  
S Kawabata ◽  
T Morita ◽  
Y Yoshizawa ◽  
...  
Keyword(s):  
Amino Acids ◽  
Staphylococcus Aureus ◽  
Amino Acid ◽  
Tandem Repeats ◽  
Molar Ratio ◽  
Clotting Factor ◽  
Aureus Strain ◽  
Activation Process ◽  
Coding Region ◽  
Flanking Region

Staphylocoagulase (SC) is a secretary protein produced by several strains of Staphylococcus aureus (S. aureus). This protein forms a molecular complex ("staphylothrombin") with human prothrombin in a molar ratio of 1:1. The complex displays the ability to clot fibrinogen and to hydrolyze the synthetic tripeptide substrates for α-thrombin. The formation of staphylothrombin does not require proteolytic cleavage of the prothrombin molecule, and this mechanism differs markedly from the activation process by either blood-clotting factor Xa or snake venom procoagulant.In the present studies, a pAT153 library containing partial Mbo I-digested DNA prepared from aureus strain BB has been screened with a fibrin gel formation method. The identity of these clones with SC was confirmed by DNA sequence analysis and by comparison of the derived amino acid sequence with that determined for the purified SC protein. One of the positive colonies was isolated and 3.1 Kb of the insert DNA was determined by the dideoxy chain termination method. The results indicated that the insert DNA consists of 148 bp 5' flanking region, protein coding region of 715 amino acids and 746 bp 3' flanking region, and that SC from strain BB is synthesized as a precursor with a signal peptide of 26 amino acids. Thus, the mature form was composed of 689 amino acids with a molecular weight of 77,337- The NH2-terminal sequence (324 amino acids) of SC isolated from S. aureus strain 213 (S. Kawabata et al. (1986): J. Biol. Chem. 261, 527-531) was compared with that of SC derived from strain BB. The sequence homology between them was found to show 57 %. It was also found that SC derived from strain BB was composed of 8 tandem repeats (27 amino acid residues in length) in the COOH-terminal region, although their functions are not known.

scholarly journals Human carboxypeptidase E. Isolation and characterization of the cDNA, sequence conservation, expression and processing in vitro

1990 ◽  
Vol 267 (2) ◽  
pp. 517-525 ◽  
Author(s):  
E Manser ◽  
D Fernandez ◽  
L Loo ◽  
P Y Goh ◽  
C Monfries ◽  
...  
Keyword(s):  
Amino Acid ◽  
Membrane Protein ◽  
Sequence Similarity ◽  
Coding Region ◽  
Sequence Comparisons ◽  
Brain Membrane ◽  
Carboxypeptidase E ◽  
Isolation And Characterization ◽  
Microsomal Membranes

Carboxypeptidase E (CPE), which cleaves C-terminal amino acid residues and is involved in neuropeptide processing, is itself subject to intracellular processing. Human CPE cDNA was isolated and sequence comparisons were made with those of a previously isolated brain cDNA (M1622) encoding rat CPE and of other human carboxypeptidases (M and N). Human (2.5 kb) and rat (2.1 kb) CPE cDNAs approximated to the size of their respective mRNAs; additional sequences were located in putative 5′ and 3′ untranslated regions of human CPE mRNA. There is 79% sequence similarity between human and rat CPE cDNAs, with greater similarity (89%) over the coding region and short sections of the non-coding sequence. The predicted 476-amino acid-residue sequences of human and rat preproCPEs are highly conserved (96% identity), with lower degree of similarity of the N-terminal signal peptide (76%). Human CPE showed 51% and 43% sequence similarity to human CPN and CPM respectively, with discrete regions of divergence dispersed between the highly conserved mechanistically implicated regions. Antiserum generated from a fusion protein, synthesized in Escherichia coli from constructs of the human cDNA, recognized an approx. 50 kDa membrane protein and a smaller soluble protein in rat and human brain preparations, corresponding to the two forms of native CPE. Human CPE mRNA transcripts directed the synthesis in reticulocyte lysate of a 54 kDa translation product, which in the presence of dog pancreas microsomal membranes was co-translationally processed with cleavage, insertion into membranes and glycosylation. Three processed forms were generated, the largest (56 kDa) and smallest (52 kDa) being equally glycosylated. The membrane association of the processed translation products and of native brain membrane CPE, detected immunologically, was resistant to moderate alkali but not pH 11.5 extraction. These results are consistent with secondary-structure predictions that CPE is a peripheral membrane protein. The dissimilar regions of human carboxypeptidases may provide information on sequences responsible for their different cellular disposition.

scholarly journals Evidence that Spt2/Sin1, an HMG-Like Factor, Plays Roles in Transcription Elongation, Chromatin Structure, and Genome Stability in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (4) ◽  
pp. 1496-1509 ◽  
Author(s):  
Amine Nourani ◽  
Francois Robert ◽  
Fred Winston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Stability ◽  
Transcription Elongation ◽  
Coding Region ◽  
Elongation Factors ◽  
Chromatin Dynamics ◽  
Coding Regions ◽  
Genome Wide ◽  
Genes Encoding ◽  
Approaches To Study

ABSTRACT Spt2/Sin1 is a DNA binding protein with HMG-like domains that has been suggested to play a role in chromatin-mediated transcription in Saccharomyces cerevisiae. Previous studies have suggested models in which Spt2 plays an inhibitory role in the initiation of transcription of certain genes. In this work, we have taken several approaches to study Spt2 in greater detail. Our results have identified previously unknown genetic interactions between spt2Δ and mutations in genes encoding transcription elongation factors, including members of the PAF and HIR/HPC complexes. In addition, genome-wide and gene-specific chromatin immunoprecipitation analyses suggest that Spt2 is primarily associated with coding regions in a transcription-dependent fashion. Furthermore, our results show that Spt2, like other elongation factors, is required for the repression of transcription from a cryptic promoter within a coding region and that Spt2 is also required for repression of recombination within transcribed regions. Finally, we provide evidence that Spt2 plays a role in regulating the levels of histone H3 over transcribed regions. Taken together, our results suggest a direct link for Spt2 with transcription elongation, chromatin dynamics, and genome stability.

scholarly journals Isolation and characterization of cDNA clones encoding pig gastric mucin

1995 ◽  
Vol 308 (1) ◽  
pp. 89-96 ◽  
Author(s):  
B S Turner ◽  
K R Bhaskar ◽  
M Hadzopoulou-Cladaras ◽  
R D Specian ◽  
J T LaMont
Keyword(s):  
Amino Acid ◽  
Tandem Repeats ◽  
Consensus Sequence ◽  
Gastric Gland ◽  
Repeat Sequence ◽  
Gastric Mucin ◽  
Gastric Epithelium ◽  
Cdna Clones ◽  
Repeat Region ◽  
Isolation And Characterization

Polyclonal antibodies raised to deglycosylated pig gastric mucin were used to screen a cDNA library constructed with pig stomach mucosal mRNA. Immunocytochemistry indicated that the antibody recognizes intracellular and secreted mucin in surface mucous cells of pig gastric epithelium. A total of 70 clones producing proteins immunoreactive to this antibody were identified, two of which (PGM-2A,9B) were fully sequenced from both ends. Clone PGM-9B hybridized to a polydisperse mRNA (3-9 kb) from pig stomach, but not liver, intestine or spleen, nor to mRNA from human, mouse, rabbit or rat stomach. Sequence analysis indicated that PGM-9B encodes 33 tandem repeats of a 16-amino-acid consensus sequence rich in serine (46%) and threonine (17%). Using the restriction enzyme MwoI, which has a single target site in the repeat, it was demonstrated that PGM-9B consists entirely of this tandem repeat. Southern-blot analysis indicated that the repeat region is contained in a 20 kb HindIII-EcoRI fragment, and BamHI digestion suggested that most of the repeats are contained in a 10 kb fragment. In situ hybridization with an antisense probe to PGM-9B showed an intense signal in the entire gastric gland. Clone PGM-2A also contains the same repeat sequence as 9B, but, in addition, has a 64-amino-acid-long non-repeat region at its 5′ end. Interestingly the non-repeat region of PGM-2A has five cysteine residues, the arrangement of which is identical with that reported for human intestinal mucin gene MUC2.

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