scholarly journals Molecular Characterization and Functional Analysis of an AGAMOUS-like Gene CiAG from Pecan

HortScience ◽  
2016 ◽  
Vol 51 (6) ◽  
pp. 664-668 ◽  
Author(s):  
Jiyu Zhang ◽  
Min Wang ◽  
Zhenghai Mo ◽  
Gang Wang ◽  
Zhongren Guo
Keyword(s):  
Flower Development ◽  
Carya Illinoinensis ◽  
Open Reading Frame ◽  
Base Pairs ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
Reading Frame ◽  
Vegetative Tissues ◽  
Current Growth

The floral homeotic C-function gene AGAMOUS (AG) has been shown to be critical in the determination of stamen and carpel identity in Arabidopsis. In the present study, a new homologue of AGAMOUS gene from pecan [Carya illinoinensis (Wangenh.) K. Koch], denoted by CiAG, was isolated and its function was characterized. The complementary DNA (cDNA) of CiAG contains an open reading frame of 687 base pairs (bp) encoding 227 amino acids. Multiple sequence comparisons revealed that CiAG had the typical MIKC structure. Phylogenetic analysis indicated that CiAG is closely related to C-lineage AG. The expression of CiAG was highly accumulated in the reproductive tissues (staminate flowers, pistillate flowers, and fruitlets) than in vegetative tissues (leaves and current-growth branches). Arabidopsis overexpressing CiAG exhibited earlier flowering. The homeotic transformations of petals into stamen organs were observed in 35S::CiAG transgenic plants. All these results indicated that CiAG plays a key role in the process of flower development of pecan.

scholarly journals One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

1988 ◽  
Vol 8 (9) ◽  
pp. 3898-3905 ◽  
Author(s):  
C Huxley ◽  
T Williams ◽  
M Fried
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
The Other ◽  
Base Pairs ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Processed Pseudogenes ◽  
Dna Fragment ◽  
Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

Primary structure of the nuclear PUT2 gene involved in the mitochondrial pathway for proline utilization in Saccharomyces cerevisiae

1984 ◽  
Vol 4 (12) ◽  
pp. 2837-2842
Author(s):  
K A Krzywicki ◽  
M C Brandriss
Keyword(s):  
Rna Synthesis ◽  
Signal Sequence ◽  
Mitochondrial Pathway ◽  
Open Reading Frame ◽  
Amino Terminus ◽  
Transcript Mapping ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Reading Frame ◽  
Proline Utilization

The PUT2 gene, believed to encode delta 1-pyrroline-5-carboxylate dehydrogenase, has been completely sequenced. The DNA contains an open reading frame of 1,725 base pairs encoding a protein of 575 amino acids. Transcript mapping with both S1 nuclease and primer extension methods revealed numerous initiation sites of RNA synthesis 50 to 80 base pairs downstream from several TATA boxes. The deduced amino acid sequence of delta 1-pyrroline-5-carboxylate dehydrogenase contains a highly basic amino terminus that may serve as the signal sequence that targets this protein to the mitochondrion.

scholarly journals IRA1, an inhibitory regulator of the RAS-cyclic AMP pathway in Saccharomyces cerevisiae.

1989 ◽  
Vol 9 (2) ◽  
pp. 757-768 ◽  
Author(s):  
K Tanaka ◽  
K Matsumoto ◽  
A Toh-E
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cyclic Amp ◽  
Nitrogen Starvation ◽  
Open Reading Frame ◽  
Large Open Reading Frame ◽  
Ras Proteins ◽  
Base Pairs ◽  
Reading Frame ◽  
Phosphoprotein Phosphatase ◽  
Cdc25 Protein

A mutation in the gene IRA1 (formerly called PPD1) was originally characterized as a deficiency of a phosphoprotein phosphatase. The IRA1 gene has been cloned and sequenced. A large open reading frame (8,817 base pairs) which can encode a protein of 2,938 amino acids was found. Northern (RNA) blot analysis detected a message of about 10 kilobases, and nuclease S1 protection demonstrated mRNA start points at 97 and 98 base pairs upstream from the putative initiator ATG codon. Disruption of the IRA1 gene resulted in sensitivity to nitrogen starvation and heat shock. Diploids homozygous for the disrupted IRA1 gene were deficient in sporulation. Disruption of the IRA1 gene suppressed the lethality of the cdc25 mutation but did not suppress the lethality of either the ras1 ras2 or the cyr1 mutations. Deficiency of the phosphoprotein phosphatase was not reproducible in the disruption mutant of the IRA1 gene. Moreover, the ira1 mutant showed an increased level of cyclic AMP. Our results suggest that the IRA1 protein inhibits the function of the RAS proteins in a fashion antagonistic to the function of the CDC25 protein in the RAS-cyclic AMP pathway in Saccharomyces cerevisiae.

scholarly journals A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas sp. Strain U2

1998 ◽  
Vol 180 (9) ◽  
pp. 2522-2530 ◽  
Author(s):  
Sergio L. Fuenmayor ◽  
Mark Wild ◽  
Alastair L. Boyes ◽  
Peter A. Williams
Keyword(s):  
Single Gene ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Gas Chromatography Mass Spectrometry ◽  
Nucleotide Sequencing ◽  
Naphthalene Dioxygenase ◽  
Sequence Comparisons ◽  
Reading Frame ◽  
Selective Enrichment ◽  
E Coli

ABSTRACT Pseudomonas sp. strain U2 was isolated from oil-contaminated soil in Venezuela by selective enrichment on naphthalene as the sole carbon source. The genes for naphthalene dioxygenase were cloned from the plasmid DNA of strain U2 on an 8.3-kbBamHI fragment. The genes for the naphthalene dioxygenase genes nagAa (for ferredoxin reductase), nagAb(for ferredoxin), and nagAc and nagAd (for the large and small subunits of dioxygenase, respectively) were located by Southern hybridizations and by nucleotide sequencing. The genes for nagB (for naphthalenecis-dihydrodiol dehydrogenase) and nagF (for salicylaldehyde dehydrogenase) were inferred from subclones by their biochemical activities. Between nagAa and nagAbwere two open reading frames, homologs of which have also been identified in similar locations in two nitrotoluene-using strains (J. V. Parales, A. Kumar, R. E. Parales, and D. T. Gibson, Gene 181:57–61, 1996; W.-C. Suen, B. Haigler, and J. C. Spain, J. Bacteriol. 178:4926–4934, 1996) and a naphthalene-using strain (G. J. Zylstra, E. Kim, and A. K. Goyal, Genet. Eng. 19:257–269, 1997). Recombinant Escherichia coli strains with plasmids carrying this region were able to convert salicylate to gentisate, which was identified by a combination of gas chromatography-mass spectrometry and nuclear magnetic resonance. The first open reading frame, designated nagG, encodes a protein with characteristics of a Rieske-type iron-sulfur center homologous to the large subunits of dihydroxylating dioxygenases, and the second open reading frame, designatednagH, encodes a protein with limited homology to the small subunits of the same dioxygenases. Cloned together inE. coli, nagG, nagH, andnagAb, were able to convert salicylate (2-hydroxybenzoate) into gentisate (2,5-dihydroxybenzoate) and therefore encode a salicylate 5-hydroxylase activity. Single-gene knockouts ofnagG, nagH, and nagAb demonstrated their functional roles in the formation of gentisate. It is proposed that NagG and NagH are structural subunits of salicylate 5-hydroxylase linked to an electron transport chain consisting of NagAb and NagAa, although E. coli appears to be able to partially substitute for the latter. This constitutes a novel mechanism for monohydroxylation of the aromatic ring. Salicylate hydroxylase and catechol 2,3-dioxygenase in strain U2 could not be detected either by enzyme assay or by Southern hybridization. However growth on both naphthalene and salicylate caused induction of gentisate 1,2-dioxygenase, confirming this route for salicylate catabolism in strain U2. Sequence comparisons suggest that the novel gene ordernagAa-nagG-nagH-nagAb-nagAc-nagAd-nagB-nagF represents the archetype for naphthalene strains which use the gentisate pathway rather than the meta cleavage pathway of catechol.

A comparison of GABAC and ρ subunit receptors from the white perch retina

1997 ◽  
Vol 14 (5) ◽  
pp. 843-851 ◽  
Author(s):  
Aohua Qian ◽  
George Hyatt ◽  
Andres Schanzer ◽  
Rohan Hazra ◽  
Abigail S. Hackam ◽  
...  
Keyword(s):  
Amino Acids ◽  
White Perch ◽  
Partial Agonist ◽  
Reversal Potential ◽  
Open Reading Frame ◽  
Retinal Neurons ◽  
Base Pairs ◽  
Reading Frame ◽  
A Value ◽  
Gabac Receptors

AbstractThere is increasing evidence that GABAC receptors are composed of GABA ρ subunits. In this study, we compared the properties of native GABAC receptors with those of receptors composed of a GABA ρ subunit. A homologue of the GABA ρ gene was cloned from a white perch (Roccus americana) retinal cDNA library. The clone (perch-s) has an open reading frame of 1422 nucleotide base pairs and encodes a predicted protein of 473 amino acids. It is highly homologous to GABA ρ subunits cloned from human and rat retinas. The receptors (perch-s receptor) expressed by this gene in Xenopus oocytes show properties similar to those of the GABAC receptors present on white perch retinal neurons. GABA induced a sustained response that had a reversal potential of –27.1 +minus; 3.6 mV. The EC50 for the response was 1.74 +− 1.25 μM, a value similar to that reported for GABAC receptors. Pharmacologically, the responses were bicuculline insensitive and not modulated by either diazepam or pentobarbital as is the case for GABAc receptors. There were, however, some distinct differences between native GABAc and perch-s receptors. I4AA acts as a partial agonist on perch-s receptors whereas it is strictly an antagonist on native GABAC receptors. Picrotoxin inhibition is noncompetitive on perch-s receptors, but both competitive and noncompetitive on GABAC receptors. We conclude that GABAC receptors are formed by GABA p subunits but that native GABAc receptors probably consist of a mixture of GABA ρ subunits.

scholarly journals Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator

1986 ◽  
Vol 234 (1) ◽  
pp. 111-117 ◽  
Author(s):  
N J Gay ◽  
V L Tybulewicz ◽  
J E Walker
Keyword(s):  
Escherichia Coli ◽  
Transposable Elements ◽  
Protein Sequence ◽  
Open Reading Frame ◽  
Base Pairs ◽  
Transcriptional Terminator ◽  
Reading Frame ◽  
High Frequencies ◽  
Unique Site ◽  
Dyad Symmetry

The transposon Tn7 is unusual as it transposes at high frequencies from episomal elements to a unique site in the Escherichia coli chromosome. This unique site is within a region of dyad symmetry that we have demonstrated to be the transcriptional terminator of the glmS gene which encodes the glutamine amidotransferase, glucosamine synthetase. Transposition of Tn7 abolishes termination of glmS transcription at this site; the transcripts now extend into the left end of Tn7 and terminate at a new site, tm, 127 base pairs from the left end of Tn7. This region of the transposon contains a long open reading frame which encodes a protein sequence that is significantly related to the transposase proteins of the transposable elements IS1 and Tn3. A weak transcript has been identified that emanates from a promoter on the 5′ side of this reading frame. This promoter is over-run by glmS transcripts and so it appears that expression of the Tn7 transposase may be regulated by promoter occlusion.

scholarly journals Primary structure of the nuclear PUT2 gene involved in the mitochondrial pathway for proline utilization in Saccharomyces cerevisiae.

1984 ◽  
Vol 4 (12) ◽  
pp. 2837-2842 ◽  
Author(s):  
K A Krzywicki ◽  
M C Brandriss
Keyword(s):  
Rna Synthesis ◽  
Signal Sequence ◽  
Mitochondrial Pathway ◽  
Open Reading Frame ◽  
Amino Terminus ◽  
Transcript Mapping ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Reading Frame ◽  
Proline Utilization

The PUT2 gene, believed to encode delta 1-pyrroline-5-carboxylate dehydrogenase, has been completely sequenced. The DNA contains an open reading frame of 1,725 base pairs encoding a protein of 575 amino acids. Transcript mapping with both S1 nuclease and primer extension methods revealed numerous initiation sites of RNA synthesis 50 to 80 base pairs downstream from several TATA boxes. The deduced amino acid sequence of delta 1-pyrroline-5-carboxylate dehydrogenase contains a highly basic amino terminus that may serve as the signal sequence that targets this protein to the mitochondrion.

scholarly journals Sequence analysis and genomic organization of a new insect picorna-like virus, Ectropis obliqua picorna-like virus, isolated from Ectropis obliqua

2004 ◽  
Vol 85 (5) ◽  
pp. 1145-1151 ◽  
Author(s):  
Xiaochun Wang ◽  
Jiamin Zhang ◽  
Jie Lu ◽  
Fuming Yi ◽  
Chuanfeng Liu ◽  
...  
Keyword(s):  
Genome Organization ◽  
Genomic Organization ◽  
Sequence Similarity ◽  
Open Reading Frame ◽  
Large Open Reading Frame ◽  
Structural Genes ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Comparisons ◽  
Reading Frame ◽  
Consensus Sequences

The complete nucleotide sequence of a new insect picorna-like virus, Ectropis obliqua picorna-like virus (EoPV), which causes a fatal infection of Ectropis obliqua larvae, has been determined. The genomic RNA of EoPV is 9394 nt in length and contains a single, large open reading frame (nt 391–9351) encoding a polyprotein of 2987 aa. Sequence comparisons with other viral polyproteins revealed that the consensus sequences for picornavirus RNA helicase, protease and RNA-dependent RNA polymerase proteins are found on the genome in order in the 5′→3′ direction. All structural genes were located at the 5′ terminus. In terms of sequence similarity, identity and genome organization, EoPV resembles mammalian picornaviruses and three other insect picorna-like viruses: Infectious flacherie virus of silkworm, Sacbrood virus of honeybee and Perina nuda picorna-like virus (PnPV). Phylogenetic analysis showed that EoPV is most closely related to PnPV and suggests that these four insect picorna-like viruses might constitute a new group of insect-infectious RNA viruses.

scholarly journals Determination of the attP and attB sites of phage ϕCD27 from Clostridium difficile NCTC 12727

2013 ◽  
Vol 62 (9) ◽  
pp. 1439-1443 ◽  
Author(s):  
Rachel Williams ◽  
Emma Meader ◽  
Melinda Mayer ◽  
Arjan Narbad ◽  
Adam P. Roberts ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Abc Transporter ◽  
Low Frequency ◽  
Toxin Production ◽  
Protein Export ◽  
Open Reading Frame ◽  
The Other ◽  
Reading Frame ◽  
Circular Molecule

The attP region of the Clostridium difficile phage ϕCD27 was identified, located immediately downstream of the putative recombinase. The phage could integrate into two specific sites (attB) in the C. difficile genome, one of which was in an open reading frame encoding a putative ATPase of an ABC transporter and the other in an open reading frame encoding a putative ATPase of the flagella protein export apparatus. The prophage was capable of excision and formation of a circular molecule and phages were spontaneously released at a low frequency during growth. Infection and lysogeny of a C. difficile strain previously shown to be sensitive to ϕCD27 were demonstrated, leading to a reduction in toxin production. Finally, a putative repressor was identified which is likely to be involved in maintaining lysogeny in these strains.

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