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.

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.

Characterization of the mouse thyrotrophin-releasing hormone receptor gene: an exon corresponds to a deletion in the rat cDNA

1993 ◽  
Vol 11 (2) ◽  
pp. 141-149 ◽  
Author(s):  
S M Duthie ◽  
P L Taylor ◽  
K A Eidne
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Stop Codon ◽  
Amino Acid Sequences ◽  
R Gene ◽  
Coding Region ◽  
Thyrotrophin Releasing Hormone ◽  
Exon 2 ◽  
Exon 4

ABSTRACT The cloning and characterization of the mouse TRH receptor (TRH-R) gene revealed an untranslated exon (exon 1), a single intron and an upstream dinucleotide repeat sequence (d(TG)16.d(AG)21) in the 5′ untranslated region (UTR). The coding region was contained almost entirely on a second exon (exon 2), with the final amino acid and stop codon at the COOH terminus of the gene encoded by a third exon (exon 3) flanked by two introns. The 3′ UTR was contained on the remainder of exon 3 and on the final exon (exon 4). Exon 3 (228 bp) corresponds exactly to a 228 bp deletion that exists in the rat TRH-R cDNA, but not in the mouse cDNA. The mouse TRH-R cDNA encodes a protein of 393 amino acids which is 96% homologous to the rat TRH-R protein of 412 amino acids, but is 19 amino acids shorter at its COOH terminus. The coding sequence for these 19 amino acids (plus 1 extra amino acid) does exist in the mouse TRH-R gene, but the sequence is encoded by exon 4, separated from the rest of the coding region by the stop codon and 223 bp of 3′ UTR on exon 3. Splicing of exon 3 in the mouse TRH-R gene would remove the last amino acid, the stop codon and the 223 bp of 3′ UTR, allowing transcription to continue into the 3′ UTR on exon 4, which encodes the 19 extra amino acids found in the rat cDNA. This would then result in an alternative 412 amino acid version of the mouse TRH-R protein, with 95% homology to the rat TRH-R. This study focused on the structural differences in the intracellular COOH-terminal tail of the receptor, which is known to be a functionally important domain in other members of the G protein-coupled receptor family. We have also recently characterized the human TRH-R cDNA, which revealed a third variant at the COOH terminus. Comparisons between mouse, rat and human TRH-Rs show that the amino acid sequences are virtually identical. However, significant differences between these species exist at the COOH terminus, with each TRH-R having a unique form of the COOH-terminal tail, beginning at exactly the same site and encoding 1, 20 and 6 amino acids in the mouse, rat and human respectively.

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.

scholarly journals Molecular characterization of CDC42, a Saccharomyces cerevisiae gene involved in the development of cell polarity.

1990 ◽  
Vol 111 (1) ◽  
pp. 143-152 ◽  
Author(s):  
D I Johnson ◽  
J R Pringle
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Amino Acid ◽  
Biochemical Properties ◽  
Amino Acid Sequences ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Rho Proteins ◽  
Coding Region ◽  
High Degree

The Saccharomyces cerevisiae CDC42 gene product is involved in the morphogenetic events of the cell division cycle; temperature-sensitive cdc42 mutants are unable to form buds and display delocalized cell-surface deposition at the restrictive temperature (Adams, A. E. M., D. I. Johnson, R. M. Longnecker, B. F. Sloat, and J. R. Pringle. 1990. J. Cell Biol. 111:131-142). To begin a molecular analysis of CDC42 function, we have isolated the CDC42 gene from a yeast genomic DNA library. The use of the cloned DNA to create a deletion of CDC42 confirmed that the gene is essential. Overexpression of CDC42 under control of the GAL10 promoter was not grossly deleterious to cell growth but did perturb the normal pattern of selection of budding sites. Determination of the DNA and predicted amino acid sequences of CDC42 revealed a high degree of similarity in amino acid sequence to the ras and rho (Madaule, P., R. Axel, and A. M. Myers. 1987. Proc. Natl. Acad. Sci. 84:779-783) families of gene products. The similarities to ras proteins (approximately 40% identical or related amino acids overall) were most pronounced in the regions that have been implicated in GTP binding and hydrolysis and in the COOH-terminal modifications leading to membrane association, suggesting that CDC42 function also involves these biochemical properties. The similarities to the rho proteins (approximately 60% identical or related amino acids overall) were more widely distributed through the coding region, suggesting more extensive similarities in as yet undefined biochemical properties and functions.

scholarly journals Molecular Cloning and Bioinformatics Analysis of DQA Gene from Mink (Neovison vison)

2019 ◽  
Vol 20 (5) ◽  
pp. 1037
Author(s):  
Zhaobin Fan ◽  
Houfeng Zhang ◽  
Min Rong ◽  
Dongmei Meng ◽  
Zhenxing Yu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Signal Sequence ◽  
Amino Acid Sequences ◽  
Neovison Vison ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Full Length Sequence

In the present study, we cloned, sequenced, and explored the structural and functional characteristics of the major histocompatibility complex (MHC)-DQA gene from mink (Neovison vison) for the first time. The full-length sequence of DQA gene was 1147-bp-long, contained a coding region of 768-bp, which was predicted to encoding 255 amino acid residues. The comparison between DQA from mink (Neovison vison) and other MHC-DQA molecules from different animal species showed that nucleotide and encoded amino acid sequences of the mink DQA gene exhibited high similarity with the ferret (Mustela pulourius furo). Phylogenetic analysis revealed that mink (Neovison vison) DQA is grouped with that of ferret (Mustela pulourius furo). The cloned sequence contained a 23-amino acid NH2-terminal signal sequence with the signal peptide cutting site located in amino acids 23–24, and had three Asn-Xaa-Ser/Thr sequons. Three cysteine residues were also identified (Cys-85, Cys-121, and Cys-138). The 218 to 240 amino acids were predicted to be the transmembrane domains. The prediction of the secondary structure revealed three α-helixes and fourteen β-sheets in Neovison vison DQA protein, while random coil was a major pattern. In this study, the whole CDS sequence of Neovison vison DQA gene was successfully cloned, which was valuable for exploring the function and antiviral molecular mechanisms underlying the molecule. The findings of the present study have laid the foundation for the disease resistance and breeding of mink.

scholarly journals Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17

2000 ◽  
Vol 182 (17) ◽  
pp. 4677-4687 ◽  
Author(s):  
Cornelius G. Friedrich ◽  
Armin Quentmeier ◽  
Frank Bardischewsky ◽  
Dagmar Rother ◽  
Regine Kraft ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Signal Peptide ◽  
Sulfur Oxidation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Putative Signal Peptide ◽  
Molecular Masses ◽  
Paracoccus Pantotrophus

ABSTRACT The gene region coding for lithotrophic sulfur oxidation ofParacoccus pantotrophus GB17 is located on a 13-kb insert of plasmid pEG12. Upstream of the previously described six open reading frames (ORFs) soxABCDEF with a partial sequence ofsoxA and soxF (C. Wodara, F. Bardischewsky, and C. G. Friedrich, J. Bacteriol. 179:5014–5023, 1997), 4,350 bp were sequenced. The sequence completed soxA, and uncovered six new ORFs upstream of soxA, designated ORF1, ORF2, and ORF3, and soxXYZ. ORF1 could encode a 275-amino-acid polypeptide of 29,332 Da with a 61 to 63% similarity to LysR transcriptional regulators. ORF2 could encode a 245-amino-acid polypeptide of 26,022 Da with the potential to form six transmembrane helices and with a 48 to 51% similarity to proteins involved in redox transport in cytochrome c biogenesis. ORF3 could encode a periplasmic polypeptide of 186 amino acids of 20,638 Da with a similarity to thioredoxin-like proteins and with a putative signal peptide of 21 amino acids. Purified SoxXA, SoxYZ, and SoxB are essential for thiosulfate or sulfite-dependent cytochrome creduction in vitro. N-terminal and internal amino acid sequences identified SoxX, SoxY, SoxZ, and SoxA to be coded by the respective genes. The molecular masses of the mature proteins determined by electrospray ionization spectroscopy (SoxX, 14,834 Da; SoxY, 11,094 Da; SoxZ, 11,717 Da; and SoxA, 30,452 Da) were identical or close to those deduced from the nucleotide sequence with differences for the covalent heme moieties. SoxXA represents a novel type of periplasmicc-type cytochromes, with SoxX as a monoheme and SoxA as a hybrid diheme cytochrome c. SoxYZ is an as-yet-unprecedented soluble protein. SoxY has a putative signal peptide with a twin arginine motif and possibly cotransports SoxZ to the periplasm. SoxYZ neither contains a metal nor a complex redox center, as proposed for proteins likely to be transported via the Tat system.

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

scholarly journals Murine erythropoietin gene: cloning, expression, and human gene homology.

1986 ◽  
Vol 6 (3) ◽  
pp. 849-858 ◽  
Author(s):  
C B Shoemaker ◽  
L D Mitsock
Keyword(s):  
Amino Acid ◽  
Genomic Library ◽  
Cdna Probe ◽  
Amino Acid Sequences ◽  
Nucleotide Sequence Analysis ◽  
Coding Region ◽  
Transcription Control ◽  
Erythroid Progenitor ◽  
Human Genes ◽  
Cell Expression

The gene for murine erythropoietin (EPO) was isolated from a mouse genomic library with a human EPO cDNA probe. Nucleotide sequence analysis permitted the identification of the murine EPO coding sequence and the prediction of the encoded amino acid sequence based on sequence conservation between the mouse and human EPO genes. Both the coding DNA and the amino acid sequences were 80% conserved between the two species. Transformation of COS-1 cells with a mammalian cell expression vector containing the murine EPO coding region resulted in secretion of murine EPO with biological activity on both murine and human erythroid progenitor cells. The transcription start site for the murine EPO gene in kidneys was determined. This permitted tentative identification of the transcription control region. The region included 140 base pairs upstream of the cap site which was over 90% conserved between the murine and human genes. Surprisingly, the first intron and much of the 5'- and 3'-untranslated sequences were also substantially conserved between the genes of the two species.

scholarly journals The amino acid sequence of cytochromes c-551 from three species of Pseudomonas

1973 ◽  
Vol 131 (3) ◽  
pp. 485-498 ◽  
Author(s):  
R. P. Ambler ◽  
Margaret Wynn
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Cytochrome C ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Mitochondrial Cytochrome ◽  
Cytochromes C ◽  
Lending Library ◽  
Single Peptide

The amino acid sequences of the cytochromes c-551 from three species of Pseudomonas have been determined. Each resembles the protein from Pseudomonas strain P6009 (now known to be Pseudomonas aeruginosa, not Pseudomonas fluorescens) in containing 82 amino acids in a single peptide chain, with a haem group covalently attached to cysteine residues 12 and 15. In all four sequences 43 residues are identical. Although by bacteriological criteria the organisms are closely related, the differences between pairs of sequences range from 22% to 39%. These values should be compared with the differences in the sequence of mitochondrial cytochrome c between mammals and amphibians (about 18%) or between mammals and insects (about 33%). Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50015 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.

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