Cloning and nucleotide sequence of the cDNA encoding a β-1,3-glucanase-like protein secreted from growing pollen tubes of Japanese pear (Pyrus pyrifolia)

2005 ◽  
Vol 2 (1) ◽  
pp. 53-58
Author(s):  
Zhou Yue-Gang ◽  
Naoko Norioka ◽  
Li Shao-Liang ◽  
Shigemi Norioka
Keyword(s):  
Amino Acid ◽  
Untranslated Region ◽  
Three Dimensional ◽  
Pollen Tubes ◽  
Amino Acid Identity ◽  
Japanese Pear ◽  
Dimensional Structure ◽  
Pyrus Pyrifolia ◽  
Reading Frame ◽  
Hydrophobic Cluster Analysis

AbstractA pollen cDNA library of Japanese pear (Pyrus pyrifolia) from the family Rosaceae was constructed and a cDNA (bgn-1) of 1408 bp, which encodes a protein (BGN-1) secreted from growing pollen tubes, was cloned and sequenced. bgn-1 cDNA is composed of a 5′-untranslated region of 47 bp, an open reading frame of 1194 bp encoding 397 amino acid residues and a complete 3′-untranslated region of 167 bp. Alignment of the deduced amino acid sequence of bgn-1 with that of barley (Hordeum vulgare) β-1,3-glucanase (GII) showed 39.7% amino acid identity. Several residues that were critical for the function of GII were conserved in the deduced BGN-1 polypeptide. Moreover, hydrophobic cluster analysis (HCA) showed an overall HCA homology score of 87.1% and analysis of BGN-1 with the 3D-PSSM program predicted a three-dimensional structure of BGN-1 highly homologous to that of barley GII with ≥95% certainty. These results suggest that the cloned bgn-1 cDNA encodes a β-1,3-glucanase-like protein in Japanese pear. The predicted mature protein (375 amino acids) has a theoretical molecular mass of 40 723 Da, a basic pI of 9.59 and a diagnostic amino acid residue mode of D, L, S and L, which is very similar to that of growth-related subfamily D (D, L, S and Q) in cereals. A ProXXPro repeat is also found between positions 352 and 367 in the C-extension region.

Cloning and sequence analysis of complete cDNA of chitin deacetylase from Mucor racemosus

2007 ◽  
Vol 4 (2) ◽  
pp. 167-172 ◽  
Author(s):  
Jiang Xia-Yun ◽  
Zou Shu-Ming ◽  
Zhou Pei-Gen
Keyword(s):  
Amino Acid ◽  
Untranslated Region ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Functional Domain ◽  
Mucor Racemosus ◽  
Chitin Deacetylase ◽  
Reading Frame ◽  
Rapid Amplification

AbstractA complete chitin deacetylase (CDA) complementary DNA (cDNA) from Mucor racemosus was cloned and sequenced by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification cDNA end (RACE) with gene special conserved primers. The cDNA sequence was submitted to GenBank (DQ538514). The complete cDNA with full-length of 1506 bp contained a 67 bp 5′-untranslated region, an open reading frame of 1344 bp and 95 bp 3′-untranslated region including tailing site AATAAA. The gene encoded a sequence of 448 amino acid residues and consisted of core nucleotides encoding a polysaccharide deacetylase domain covering 32% of the entire sequence. The CDA gene shared sequence homology with those of several fungi. The corresponding homology of the deduced amino acid sequences varied from 21 to 69%. Phylogenetic analysis according to the deduced amino acid sequences matched the classical fungi taxonomy. The three-dimensional structure of this protein was predicted. The protein had a whole CDA functional domain and a polysaccharide deacetylase domain.

scholarly journals Identification of a positive regulator of the cell cycle ubiquitin-conjugating enzyme Cdc34 (Ubc3).

1996 ◽  
Vol 16 (2) ◽  
pp. 677-684 ◽  
Author(s):  
J A Prendergast ◽  
C Ptak ◽  
D Kornitzer ◽  
C N Steussy ◽  
R Hodgins ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Temperature Sensitive ◽  
Reading Frame ◽  
Positive Regulator ◽  
Morphological Defects ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

The Cdc34 (Ubc3) ubiquitin-conjugating enzyme from Saccharomyces cerevisiae plays an essential role in the progression of cells from the G1 to S phase of the cell division cycle. Using a high-copy suppression strategy, we have identified a yeast gene (UBS1) whose elevated expression suppresses the conditional cell cycle defects associated with cdc34 mutations. The UBS1 gene encodes a 32.2-kDa protein of previously unknown function and is identical in sequence to a genomic open reading frame on chromosome II (GenBank accession number Z36034). Several lines of evidence described here indicate that Ubs1 functions as a general positive regulator of Cdc34 activity. First, overexpression of UBS1 suppresses not only the cell proliferation and morphological defects associated with cdc34 mutants but also the inability of cdc34 mutant cells to degrade the general amino acid biosynthesis transcriptional regulator, Gcn4. Second, deletion of the UBS1 gene profoundly accentuates the cell cycle defect when placed in combination with a cdc34 temperature-sensitive allele. Finally, a comparison of the Ubs1 and Cdc34 polypeptide sequences reveals two noncontiguous regions of similarity, which, when projected onto the three-dimensional structure of a ubiquitin-conjugating enzyme, define a single region situated on its surface. While cdc34 mutations corresponding to substitutions outside this region are suppressed by UBS1 overexpression, Ubs1 fails to suppress amino acid substitutions made within this region. Taken together with other findings, the allele specificity exhibited by UBS1 expression suggests that Ubs1 regulates Cdc34 by interaction or modification.

scholarly journals Amino-acid sequence and predicted three-dimensional structure of pea seed (Pisum sativum) ferritin

1992 ◽  
Vol 288 (3) ◽  
pp. 931-939 ◽  
Author(s):  
S Lobreaux ◽  
S J Yewdall ◽  
J F Briat ◽  
P M Harrison
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Transit Peptide ◽  
Amino Acid Identity ◽  
Dimensional Structure ◽  
Three Dimensional Model ◽  
Iron Storage ◽  
Liver Ferritin ◽  
Pea Seed

The iron storage protein, ferritin, is widely distributed in the living kingdom. Here the complete cDNA and derived amino-acid sequence of pea seed ferritin are described, together with its predicted secondary structure, namely a four-helix-bundle fold similar to those of mammalian ferritins, with a fifth short helix at the C-terminus. An N-terminal extension of 71 residues contains a transit peptide (first 47 residues) responsible for plastid targetting as in other plant ferritins, and this is cleaved before assembly. The second part of the extension (24 residues) belongs to the mature subunit; it is cleaved during germination. The amino-acid sequence of pea seed ferritin is aligned with those of other ferritins (49% amino-acid identity with H-chains and 40% with L-chains of human liver ferritin in the aligned region). A three-dimensional model has been constructed by fitting the aligned sequence to the coordinates of human H-chains, with appropriate modifications. A folded conformation with an 11-residue helix is predicted for the N-terminal extension. As in mammalian ferritins, 24 subunits assemble into a hollow shell. In pea seed ferritin, its N-terminal extension is exposed on the outside surface of the shell. Within each pea subunit is a ferroxidase centre resembling those of human ferritin H-chains except for a replacement of Glu-62 by His. The channel at the 4-fold-symmetry axes defined by E-helices, is predicted to be hydrophilic in plant ferritins, whereas it is hydrophobic in mammalian ferritins.

scholarly journals AatA Is a Novel Autotransporter and Virulence Factor of Avian Pathogenic Escherichia coli

2009 ◽  
Vol 78 (3) ◽  
pp. 898-906 ◽  
Author(s):  
Ganwu Li ◽  
Yaping Feng ◽  
Subhashinie Kariyawasam ◽  
Kelly A. Tivendale ◽  
Yvonne Wannemuehler ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Chicken Embryo Fibroblast ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Virulence Plasmid ◽  
Passenger Domain ◽  
Reading Frame ◽  
E Coli ◽  
Amino Acid Signal Peptide

ABSTRACT Autotransporters (AT) are widespread in Gram-negative bacteria, and many of them are involved in virulence. An open reading frame (APECO1_O1CoBM96) encoding a novel AT was located in the pathogenicity island of avian pathogenic Escherichia coli (APEC) O1's virulence plasmid, pAPEC-O1-ColBM. This 3.5-kb APEC autotransporter gene (aatA) is predicted to encode a 123.7-kDa protein with a 25-amino-acid signal peptide, an 857-amino-acid passenger domain, and a 284-amino-acid β domain. The three-dimensional structure of AatA was also predicted by the threading method using the I-TASSER online server and then was refined using four-body contact potentials. Molecular analysis of AatA revealed that it is translocated to the cell surface, where it elicits antibody production in infected chickens. Gene prevalence analysis indicated that aatA is strongly associated with E. coli from avian sources but not with E. coli isolated from human hosts. Also, AatA was shown to enhance adhesion of APEC to chicken embryo fibroblast cells and to contribute to APEC virulence.

Identification and Characterization of Aminopeptidase N 1 Gene of the Indian Malaria Vector Anopheles culicifacies (Diptera: Culicidae)

2021 ◽  
Author(s):  
Renu Jakhar ◽  
Surendra Kumar Gakhar
Keyword(s):  
Amino Acid ◽  
Malaria Vector ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Anopheles Culicifacies ◽  
Reading Frame ◽  
Blood Digestion ◽  
Zinc Metalloprotease

Abstract Aminopeptidase N1 (APN) is one of the important enzymes involved in blood digestion and is up-regulated along with several other enzymes in response to bloodmeal ingestion. APN is a zinc metalloprotease that cleaves one amino acid residue at a time from the amino terminus of the protein. The APN1 gene of the Indian malaria vector Anopheles culicifacies Giles was cloned and characterized. The An. culicifacies APN1 (AcAPN1) gene has an Open Reading Frame of 3084 basepairs which encodes a putative protein of 1027 amino acids. The coding region of the gene shares 81% and 78% similarity to the APN1 genes found in An. stephensi (Diptera: Culicidae) and An. gambiae (Diptera: Culicidae), respectively. The organization of the APN1 gene was studied in available mosquito genomes and a three-dimensional structure of AcAPN1 modeled using homology structure modeling. The enzymatic active site was predicted to consist of HEYAH and GAMEN amino acid residues, and a comparison of the protein sequences among different genera revealed the conservation of zinc-binding residues. The expression pattern of AcAPN1 showed that the gene was expressed rapidly in response to the ingestion of the bloodmeal and therefore this gene may be used to exploit its promoter region as an antiparasite candidate molecule.

scholarly journals Structural analysis of mutations in the Drosophila beta 2-tubulin isoform reveals regions in the beta-tubulin molecular required for general and for tissue-specific microtubule functions.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 267-286 ◽  
Author(s):  
J D Fackenthal ◽  
J A Hutchens ◽  
F R Turner ◽  
E C Raff
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Variable Region ◽  
Internal Variable ◽  
Microtubule Assembly ◽  
Dimensional Structure ◽  
Wild Type ◽  
Beta Tubulin ◽  
Assembly Kinetics ◽  
Beta 2

Abstract We have determined the lesions in a number of mutant alleles of beta Tub85D, the gene that encodes the testis-specific beta 2-tubulin isoform in Drosophila melanogaster. Mutations responsible for different classes of functional phenotypes are distributed throughout the beta 2-tubulin molecule. There is a telling correlation between the degree of phylogenetic conservation of the altered residues and the number of different microtubule categories disrupted by the lesions. The majority of lesions occur at positions that are evolutionarily highly conserved in all beta-tubulins; these lesions disrupt general functions common to multiple classes of microtubules. However, a single allele B2t6 contains an amino acid substitution within an internal cluster of variable amino acids that has been identified as an isotype-defining domain in vertebrate beta-tubulins. Correspondingly, B2t6 disrupts only a subset of microtubule functions, resulting in misspecification of the morphology of the doublet microtubules of the sperm tail axoneme. We previously demonstrated that beta 3, a developmentally regulated Drosophila beta-tubulin isoform, confers the same restricted morphological phenotype in a dominant way when it is coexpressed in the testis with wild-type beta 2-tubulin. We show here by complementation analysis that beta 3 and the B2t6 product disrupt a common aspect of microtubule assembly. We therefore conclude that the amino acid sequence of the beta 2-tubulin internal variable region is required for generation of correct axoneme morphology but not for general microtubule functions. As we have previously reported, the beta 2-tubulin carboxy terminal isotype-defining domain is required for suprastructural organization of the axoneme. We demonstrate here that the beta 2 variant lacking the carboxy terminus and the B2t6 variant complement each other for mild-to-moderate meiotic defects but do not complement for proper axonemal morphology. Our results are consistent with the hypothesis drawn from comparisons of vertebrate beta-tubulins that the two isotype-defining domains interact in a three-dimensional structure in wild-type beta-tubulins. We propose that the integrity of this structure in the Drosophila testis beta 2-tubulin isoform is required for proper axoneme assembly but not necessarily for general microtubule functions. On the basis of our observations we present a model for regulation of axoneme microtubule morphology as a function of tubulin assembly kinetics.

scholarly journals Selection of sequence motifs and generative Hopfield-Potts models for protein families

2019 ◽  
Author(s):  
Kai Shimagaki ◽  
Martin Weigt
Keyword(s):  
Amino Acid ◽  
Ad Hoc ◽  
Three Dimensional ◽  
Generative Models ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Restricted Boltzmann Machines ◽  
Potts Models ◽  
Maximum Entropy Models

Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the three-dimensional structure of folded proteins, and about the effect of amino-acid substitutions in proteins. These models are typically requested to reproduce the one- and two-point statistics of the amino-acid usage in a protein family, i.e. to capture the so-called residue conservation and covariation statistics of proteins of common evolutionary origin. Pairwise Potts models are the maximum-entropy models achieving this. While being successful, these models depend on huge numbers of ad hoc introduced parameters, which have to be estimated from finite amount of data and whose biophysical interpretation remains unclear. Here we propose an approach to parameter reduction, which is based on selecting collective sequence motifs. It naturally leads to the formulation of statistical sequence models in terms of Hopfield-Potts models. These models can be accurately inferred using a mapping to restricted Boltzmann machines and persistent contrastive divergence. We show that, when applied to protein data, even 20-40 patterns are sufficient to obtain statistically close-to-generative models. The Hopfield patterns form interpretable sequence motifs and may be used to clusterize amino-acid sequences into functional sub-families. However, the distributed collective nature of these motifs intrinsically limits the ability of Hopfield-Potts models in predicting contact maps, showing the necessity of developing models going beyond the Hopfield-Potts models discussed here.

The Three-Dimensional Structure of the Herbicide Binding Niche on the Reaction Center Polypeptides of Photosystem II

1987 ◽  
Vol 42 (6) ◽  
pp. 742-750 ◽  
Author(s):  
Achim Trebst
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Reaction Center ◽  
Three Dimensional ◽  
Chemical Compounds ◽  
Dimensional Structure ◽  
Bacterial Reaction Center ◽  
Protein Subunits ◽  
Herbicide Binding ◽  
Hydropathy Analysis

The folding through the membrane of the plastoquinone and herbicide binding protein subunits of photosystem II and the topology of the binding niche for plastoquinone and herbicides is described. The model is based on the homology in amino acid sequence and folding prediction from the hydropathy analysis of the D-1 and D-2 subunits of photosystem II to the reaction center polypeptides L and M of the bacterial reaction center. It incorporates the amino acid changes in the D-1 polypeptide in herbicide tolerant plants and those indicated by chemical tagging to be involved in Qв binding. It proposes homologous amino acids in the D-1/D-2 polypeptides to those indicated by the X-ray structure of the bacterial reaction center to be involved in Fe-, quinone- and reaction center chlorophyll-binding. The different chemical compounds known to interfere with Qв function are grouped into two families depending on their orientation in the Qв binding niche.

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