scholarly journals Nucleotide sequence, organization and characterization of the atp genes and the encoded subunits of Mycoplasma gallisepticum ATPase

1992 ◽  
Vol 285 (3) ◽  
pp. 881-888 ◽  
Author(s):  
O F Rasmussen ◽  
M H Shirvan ◽  
H Margalit ◽  
C Christiansen ◽  
S Rottem
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Close Association ◽  
Mycoplasma Gallisepticum ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Alpha Helices ◽  
B Subunit ◽  
C Subunit ◽  
Delta Subunit

The nucleotide sequence of a 7.8 kbp DNA fragment from the genome of Mycoplasma gallisepticum has been determined. The fragment contains a cluster of nine tightly linked genes coding for the subunits of the M. gallisepticum ATPase. The gene order is I (I-subunit), B (a-subunit), E (c-subunit), F (b-subunit), H (delta-subunit), A (alpha-subunit), G (gamma-subunit), D (beta-subunit) and C (epsilon-subunit). Two open reading frames were identified in the flanking regions; one (ORFU), preceding the I gene, encodes at least 110 amino acids and the other (ORFS), following the C gene, encodes at least 90 amino acids. The deduced amino acid sequences of the various subunits are presented and discussed with regard to the structure, function and differing sensitivity of the M. gallisepticum enzyme to dicyclohexylcarbodiimide and aurovertin. The alpha- and beta-subunits of the F1 portion are well conserved (51% and 65% identity with those of Escherichia coli), whereas the gamma-, delta- and epsilon-subunits, as well as the F0-subunits, show a low percentage identity. Nonetheless, the secondary structure of the F0-subunits show a high degree of similarity to the corresponding subunits of E. coli. Two very strong potential amphipathic alpha-helices are predicted in the delta-subunit and the N-terminus of the b-subunit contains two hydrophobic helical stretches. The possible roles of these structural properties in the close association of the F1 and F0 multisubunit complexes among mycoplasmas are discussed.

Nucleotide sequences of the 2-oxoacid ferredoxin oxidoreductase and ferredoxin genes fromFrankiastrain EuIK1, a symbiont ofElaeagnus umbellataroot nodules

1999 ◽  
Vol 77 (9) ◽  
pp. 1279-1286
Author(s):  
Won Young Yoo ◽  
Si Bum Sung ◽  
Chung Sun An
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Genomic Library ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Amino Acid Sequences ◽  
Elaeagnus Umbellata ◽  
Ferredoxin Oxidoreductase ◽  
B Subunit ◽  
A Subunit

A genomic clone, pEuNIFII, was isolated by screening a genomic library of Frankia strain EuIK1, a symbiont of Elaeagnus umbellata Thunb. root nodules. A 1.5-kb fragment of pEuNIF4.0, which contained ORF2 and N-terminal part of nifS, was used as a probe. A 7.2-kb BamHI fragment of pEuNIFII, which was proven to be adjacent to the probe, was subjected to sequence determination. The sequence analysis suggested one partial ORF followed by three open reading frames (ORFs). Two ORFs next to nifS encodes an a subunit (672 amino acids) and b subunit (347 amino acids) of a 2-oxoacid ferredoxin oxidoreducatase (OR), respectively. The third ORF encodes 114 amino acids of a 7Fe-type ferredoxin (Fdx). All ORFs are transcribed in the same direction as other nif genes. Alignment of the deduced amino acid sequences from frankiae OR revealed the motifs of gamma and alpha domains seen in other ORs in the a subunit, and the beta domain in the b subunit. Frankia or shows about 44% nucleotide sequence similarity with nifJ from Klebsiella pneumoniae, while frankiae fdx shows about 56% similarity with fdxI from Azotobacter vinelandii. These genes are reported for the first time in Frankia, and putative roles of their products in symbiosis is discussed in relation to nitrogen fixation and carbohydrate metabolism.Key words: 2-oxoacid ferredoxin oxidoreductase, ferredoxin, nucleotide sequence, Frankia EuIK1.

scholarly journals Nucleotide Sequence and Genetic Structure of a Novel Carbaryl Hydrolase Gene (cehA) from Rhizobium sp. Strain AC100

2002 ◽  
Vol 68 (3) ◽  
pp. 1220-1227 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Mitsuru Fukui ◽  
Kouichi Hayano ◽  
Masahito Hayatsu
Keyword(s):  
Nucleotide Sequence ◽  
Insertion Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Homology Search ◽  
Sequencing Analysis ◽  
Terminal Sequence ◽  
Homologous Sequences ◽  
Naphthyl Acetate ◽  
Reading Frames

ABSTRACT Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.

scholarly journals Nucleotide and derived amino acid sequences of a cDNA coding for pre-uteroglobin from the lung of the hare (Lepus capensis)

1986 ◽  
Vol 235 (3) ◽  
pp. 895-898 ◽  
Author(s):  
M S López de Haro ◽  
A Nieto
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Untranslated Regions ◽  
Coding Region ◽  
Homologous Proteins ◽  
Lepus Capensis ◽  
Rabbit Gene

An almost full-length cDNA coding for pre-uteroglobin from hare lung was cloned and sequenced. The derived amino acid sequence indicated that hare pre-uteroglobin contained 91 amino acids, including a signal peptide of 21 residues. Comparison of the nucleotide sequence of hare pre-uteroglobin cDNA with that previously reported for the rabbit gene indicated five silent point substitutions and six others leading to amino acid changes in the coding region. The untranslated regions of both pre-uteroglobin mRNAs were very similar. The amino acid changes observed are discussed in relation to the different progesterone-binding abilities of both homologous proteins.

Molecular Heterogeneity of the L-1 Metallo-β-Lactamase Family from Stenotrophomonas maltophilia

1998 ◽  
Vol 42 (5) ◽  
pp. 1245-1248 ◽  
Author(s):  
François Sanschagrin ◽  
Julien Dufresne ◽  
Roger C. Levesque
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Stenotrophomonas Maltophilia ◽  
Amino Acid Sequences ◽  
Molecular Heterogeneity ◽  
Gene Encoding ◽  
Class B

ABSTRACT We have determined the nucleotide sequence of the blaSgene encoding the carbapenem-hydrolyzing L-1 β-lactamase fromStenotrophomonas maltophilia GN12873. Analysis of the DNA and deduced amino acid sequences identified a product of 290 amino acids. Comparisons of the L-1 amino acid sequence with those of other zinc β-lactamases showed 88.6% identity with the L-1 enzyme fromS. maltophilia IID1275 and less than 20% identity with other class B metalloenzymes.

scholarly journals Human Herpesvirus 6B Genome Sequence: Coding Content and Comparison with Human Herpesvirus 6A

1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Genomic Sequence ◽  
Human Herpesvirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
T Cell Lines ◽  
The Right

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.

scholarly journals Differences in editing of mitochondrial nad3 transcripts from CMS and fertile carrots.

2001 ◽  
Vol 48 (3) ◽  
pp. 711-717 ◽  
Author(s):  
M Rurek ◽  
M Szklarczyk ◽  
N Adamczyk ◽  
B Michalik ◽  
H Augustyniak
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Sequence Conservation ◽  
Open Reading Frames ◽  
Male Sterile ◽  
Nucleotide Substitutions ◽  
Cytoplasmic Male Sterile ◽  
Fertile Line ◽  
High Level ◽  
Reading Frames

A high level of the nucleotide sequence conservation was found for mitochondrial nad3 gene of carrot. Three silent nucleotide substitutions differentiate nad3 open reading frames from cytoplasmic male sterile and male fertile carrots. All these differences are preserved on the RNA level. Partial and silent editing also distinguished both carrots. Three of the C to U conversions were specific to the fertile line. In the two examined carrot lines editing did not affect the mode of alteration of encoded amino acids.

scholarly journals Cloning, Sequencing, and Characterization of the Iturin A Operon

2001 ◽  
Vol 183 (21) ◽  
pp. 6265-6273 ◽  
Author(s):  
Kenji Tsuge ◽  
Takanori Akiyama ◽  
Makoto Shoda
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Fatty Acid Synthetase ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Upstream Sequence ◽  
Flanking Sequence ◽  
Coding Region ◽  
Iturin A ◽  
Peptide Synthetases

ABSTRACT Bacillus subtilis RB14 is a producer of the antifungal lipopeptide iturin A. Using a transposon, we identified and cloned the iturin A synthetase operon of RB14, and the sequence of this operon was also determined. The iturin A operon spans a region that is more than 38 kb long and is composed of four open reading frames, ituD, ituA, ituB, and ituC. The ituD gene encodes a putative malonyl coenzyme A transacylase, whose disruption results in a specific deficiency in iturin A production. The second gene, ituA, encodes a 449-kDa protein that has three functional modules homologous to fatty acid synthetase, amino acid transferase, and peptide synthetase. The third gene, ituB, and the fourth gene, ituC, encode 609- and 297-kDa peptide synthetases that harbor four and two amino acid modules, respectively. Mycosubtilin, which is produced by B. subtilis ATCC 6633, has almost the same structure as iturin A, but the amino acids at positions 6 and 7 in the mycosubtilin sequence ared-Ser→l-Asn, while in iturin A these amino acids are inverted (i.e., d-Asn→l-Ser). Comparison of the amino acid sequences encoded by the iturin A operon and the mycosubtilin operon revealed that ituD, ituA, andituB have high levels of homology to the counterpart genesfenF (79%), mycA (79%), and mycB(79%), respectively. Although the overall level of homology of the amino acid sequences encoded by ituC andmycC, the counterpart of ituC, is relatively low (64%), which indicates that there is a difference in the amino acid sequences of the two lipopeptides, the levels of homology between the putative serine adenylation domains and between the asparagine adenylation domains in the two synthetases are high (79 and 80%, respectively), implying that there is an intragenic domain change in the synthetases. The fact that the flanking sequence of the iturin A synthetase coding region was highly homologous to the flanking sequence that of xynD of B. subtilis 168 and the fact that the promoter of the iturin A operon which we identified was also conserved in an upstream sequence of xynD imply that horizontal transfer of this operon occurred. When the promoter was replaced by the repU promoter of the plasmid pUB110 replication protein, production of iturin A increased threefold.

Characterization of a dispersed repetitive DNA sequence associated with the CCDD genome of wild rice

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 681-688 ◽  
Author(s):  
M. C. Kiefer-Meyer ◽  
A. S. Reddy ◽  
M. Delseny
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequence ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Wild Rice ◽  
Repeated Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Repetitive Dna Sequence ◽  
Wild Rice Species

A HindII repetitive fragment (pOD3) was isolated and cloned from the genomic DNA of an accession of Oryza latifolia, a wild rice species that possesses a tetraploid CCDD genome. Southern blot analysis using this clone as a probe demonstrated that this repetitive DNA sequence had a dispersed organization in the CCDD genome and seemed to be highly specific for this genome type. This fragment is the first CCDD-specific repeated DNA sequence to be described. The hybridization pattern is similar for most CCDD accessions tested, although a few showed no hybridization signal. The nucleotide sequence of the element cloned in pOD3 was determined and analysed. The 1783 base pair long repeated sequence shows no homology with other known nucleotide sequences. In addition, none of the amino acid sequences deduced from the potential open reading frames contained in the pOD3 repeat is homologous to any known protein. The nucleotide sequence presents several internal repeats, direct or inverted, but their significance remains unknown.Key words: rice, dispersed repetitive DNA sequences, genome-specific sequences.

scholarly journals The resistant ability to weevils and the characteristics of VrPDF1 gene of some mungbean cultivars (Vigna radiata L.Wilczek)

2016 ◽  
Vol 14 (1) ◽  
pp. 105-113
Author(s):  
Hoàng Thị Thao ◽  
Hồ Mạnh Tường ◽  
Nguyễn Thị Ngọc Lan ◽  
Nguyễn Vũ Thanh Thanh ◽  
Nguyễn Văn Sơn ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amylase Activity ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Transformation Vector ◽  
Plant Defensins ◽  
Intron Region ◽  
Comparative Results

Plant defensins play a role against the seed-feeding insects. Defensin associates with the center of α-amylase activity in the gut of weevils, thus inhibiting the digestion of starch by weevils. In this study, the resistance of eight mungbean cultivars to weevils was evaluated by the method of artificial weevils infection. The Tam TH cultivar had lowest index of susceptibility to weevils (634.63) and DX22 cultivar had highest index (1058.72), and the highest resistance to weevils was found in Tam TH and DX22 was found to have the lowest resistance. VrPDF1 genes isolated from mungbean cultivars are 356 bp in length with two exons interrupted by an intron. The coding region of the VrPDF1 gene is 228 bp in length, encoding 75 amino acids. The comparative results of the nucleotide sequence of cDNA between Tam TH  and DX22 showed that there was a difference in 13 nucleotides and comparison of amino acid sequences of the deduced protein indicated that there was a difference in 9 amino acids. Within the intron region of the VrPDF1 genes there was difference in 5 nucleotides. The genetic distance based on nucleotide sequences of the coding region of VrPDF1 gene of DX22 and seven other mungbean cultivars is 6.2% and based on the amino acid sequence deduced is 7.7%. The coding region of the VrPDF1 gene of DX22 was used to create a transformation vector aimed at creating weevil-resistant transgenic mungbean.

scholarly journals Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site

2002 ◽  
Vol 83 (12) ◽  
pp. 3075-3084 ◽  
Author(s):  
Afjal Hossain Khan ◽  
Kouichi Morita ◽  
Maria del Carmen Parquet ◽  
Futoshi Hasebe ◽  
Edward G. M. Mathenge ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chikungunya Virus ◽  
Genomic Sequence ◽  
Adenine Nucleotides ◽  
Repeated Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Sequence Elements

In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3′ non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5′ cap nucleotide, an I-poly(A) tract and the 3′ poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5′ NTR and repeated sequence elements (RSEs) within the 3′ NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o’nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as ‘polymerase slippage’, as has been reported for vesicular stomatitis virus.

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