Characterization and comparative analysis of three low molecular weight glutenin C-subunit genes isolated from Aegilops tauschii

2007 ◽  
Vol 87 (2) ◽  
pp. 273-280 ◽  
Author(s):  
Yu-He Pei ◽  
Ai-Li Wang ◽  
Xue-Li An ◽  
Xiao-Hui Li ◽  
Yan-Zhen Zhang ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Aegilops Tauschii ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Low Molecular Weight ◽  
Primitive Form ◽  
Reading Frame ◽  
Specific Pcr

Three low molecular weight glutenin subunit (LMW-GS) genes from T121, T128 and T132 accessions of Aegilops tauschii (DD, 2n = 2x = 14) were amplified using allelic-specific PCR primers. The amplified products with a size of about 900 bp were cloned and sequenced. Three complete coding sequences of LMW-GS with 918 bp, 921 bp and 918 bp were obtained and named as LMW-T121, LMW-T128, LMW-T132, respectively. Each gene contained a complete open reading frame and had no introns. The deduced amino acid sequences showed that all belonged to LMW-m type subunit with a predicted molecular weight of about 32 kDa, corresponding to the size of LMW C-subunits. All three subunits possessed eight cysteine residues and had greater homology with previously characterized LMW-m subunits from bread wheat and related species than LMW-s or LMW-i sequences. Some amino acid substitutions and insertion/deletion variations among the sequences were detected. The corresponding three C-subunits in seed endosperm encoded by LMW-T121, LMW-T128, LMW-T132, respectively, were identified and confirmed by SDS-PAGE, MALDI-TOF-MS and direct N-terminal amino acid sequencing. Phylogenetic analysis demonstrated that LMW-m and LMW-s type subunit genes possessed higher identity and they were obviously separated from LMW-i type subunit genes. The LMW-m type might be the primitive form while the LMW-s and LMW-i types are variant forms. Key words: Aegilops tauschii, LMW-GS, AS-PCR, phylogenetic analysis

Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)

2006 ◽  
Vol 138 (2) ◽  
pp. 138-146 ◽  
Author(s):  
O. Mittapalli ◽  
R.H. Shukle ◽  
I.L. Wise
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Blot Analysis ◽  
Copy Number ◽  
Southern Blot Analysis ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Degenerate Pcr ◽  
Sitodiplosis Mosellana ◽  
Wheat Midge

AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

scholarly journals Genes for low-molecular-weight heat shock proteins of soybeans: sequence analysis of a multigene family.

1985 ◽  
Vol 5 (12) ◽  
pp. 3417-3428 ◽  
Author(s):  
R T Nagao ◽  
E Czarnecka ◽  
W B Gurley ◽  
F Schöffl ◽  
J L Key
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Heat Shock ◽  
Dna Sequences ◽  
Regulatory Element ◽  
Amino Acid Sequences ◽  
Striking Similarity ◽  
Low Molecular Weight ◽  
Genes Encoding ◽  
Flanking Regions

Soybeans, Glycine max, synthesize a family of low-molecular-weight heat shock (HS) proteins in response to HS. The DNA sequences of two genes encoding 17.5- and 17.6-kilodalton HS proteins were determined. Nuclease S1 mapping of the corresponding mRNA indicated multiple start termini at the 5' end and multiple stop termini at the 3' end. These two genes were compared with two other soybean HS genes of similar size. A comparison among the 5' flanking regions encompassing the presumptive HS promoter of the soybean HS-protein genes demonstrated this region to be extremely homologous. Analysis of the DNA sequences in the 5' flanking regions of the soybean genes with the corresponding regions of Drosophila melanogaster HS-protein genes revealed striking similarity between plants and animals in the presumptive promoter structure of thermoinducible genes. Sequences related to the Drosophila HS consensus regulatory element were found 57 to 62 base pairs 5' to the start of transcription in addition to secondary HS consensus elements located further upstream. Comparative analysis of the deduced amino acid sequences of four soybean HS proteins illustrated that these proteins were greater than 90% homologous. Comparison of the amino acid sequence for soybean HS proteins with other organisms showed much lower homology (less than 20%). Hydropathy profiles for Drosophila, Xenopus, Caenorhabditis elegans, and G. max HS proteins showed a similarity of major hydrophilic and hydrophobic regions, which suggests conservation of functional domains for these proteins among widely dispersed organisms.

A member of the HSP90 family from ovineBabesiain China: molecular characterization, phylogenetic analysis and antigenicity

Parasitology ◽  
2015 ◽  
Vol 142 (11) ◽  
pp. 1387-1397 ◽  
Author(s):  
GUIQUAN GUAN ◽  
JUNLONG LIU ◽  
AIHONG LIU ◽  
YOUQUAN LI ◽  
QINGLI NIU ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Structural Characteristics ◽  
Heat Shock Protein 90 ◽  
Cellular Transformation ◽  
Amino Acid Sequences ◽  
Enzyme Linked Immunosorbent Assay ◽  
Cdna Expression Library ◽  
Expression Library ◽  
Reading Frame

SUMMARYHeat shock protein 90 (HSP90) is a key component of the molecular chaperone complex essential for activating many signalling proteins involved in the development and progression of pathogenic cellular transformation. AHsp90gene (BQHsp90) was cloned and characterized fromBabesiasp. BQ1 (Lintan), an ovineBabesiaisolate belonging toBabesia motasi-like group, by screening a cDNA expression library and performing rapid amplification of cDNA ends. The full-length cDNA ofBQHsp90is 2399 bp with an open reading frame of 2154 bp encoding a predicted 83 kDa polypeptide with 717 amino acid residues. It shows significant homology and similar structural characteristics toHsp90of other apicomplex organisms. Phylogenetic analysis, based on the HSP90 amino acid sequences, showed that theBabesiagenus is clearly separated from other apicomplexa genera. Five Chinese ovineBabesiaisolates were divided into 2 phylogenetic clusters, namelyBabesiasp. Xinjiang (previously designated a new species) cluster andB. motasi-like cluster which could be further divided into 2 subclusters (Babesiasp. BQ1 (Lintan)/Babesiasp. Tianzhu andBabesiasp. BQ1 (Ningxian)/Babesiasp. Hebei). Finally, the antigenicity of rBQHSP90 protein from prokaryotic expression was also evaluated using western blot and enzyme-linked immunosorbent assay (ELISA).

scholarly journals Cloning and Characterization of a Cryptic Haloacid Dehalogenase from Burkholderia cepacia MBA4

1999 ◽  
Vol 181 (19) ◽  
pp. 6003-6009 ◽  
Author(s):  
Jimmy S. H. Tsang ◽  
Laiju Sam
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Burkholderia Cepacia ◽  
Amino Acid Sequences ◽  
Predicted Amino Acid Sequence ◽  
Haloacid Dehalogenase ◽  
Reading Frame ◽  
Relative Molecular Weight

ABSTRACT Burkholderia cepacia MBA4 has been shown to produce a single dehalogenase batch culture. Moreover, other cryptic dehalogenases were also detected when the cells were grown in continuous culture. In this paper, we report the cloning and characterization of one of the cryptic dehalogenases in MBA4. This cryptic haloacid dehalogenase, designated Chd1, was expressed constitutively in Escherichia coli. This recombinant Chd1 had a relative molecular weight of 58,000 and existed predominantly as a dimer. The subunits had a relative molecular weight of 27,000. Chd1 exhibited isomer specificity, being active towards thel-isomer of 2-monochloropropionic acid only. The structural gene, chd1, was isolated on a 1.7-kb PstI fragment. This fragment contains a functional promoter, because expression of chd1 in E. coli is orientation independent. The nucleotide sequence of this fragment was determined and characterized. An open reading frame of 840 bp encoding a putative peptide of 280 amino acids was identified. This corresponds closely with the size of the subunit. The nucleotide sequence of chd1 did not show any homology with those of other dehalogenase genes. Comparison of the predicted amino acid sequence, however, shows significant homology, ranging from 42 to 50%, with the amino acid sequences of many other dehalogenases. Chd1 is unusual in having a long leader sequence, a property of periplasmic enzymes.

Genetic and biochemical characterization of novel low molecular weight glutenin subunits in wheat (Triticum aestivum L.)

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Guttapadu Sreeramulu ◽  
Nagendra K. Singh
Keyword(s):  
Molecular Weight ◽  
Triticum Aestivum ◽  
Amino Acid ◽  
Biochemical Characterization ◽  
Amino Acid Sequences ◽  
Gene Location ◽  
Relative Molecular Mass ◽  
Low Molecular Weight ◽  
Glutenin Subunits ◽  
Moving Band

Two novel low molecular weight subunits of glutenin with relative molecular mass (Mr values) of 30 and 32 kDa were isolated from the seeds of hexaploid wheat and characterized at genetic and biochemical levels. Among 115 Indian bread wheat cultivars analysed, 40 had a narrow doublet of the new protein bands, 69 had a wide doublet, 3 had only the faster moving band of the doublet, and the remaining 3 cultivars had only the slower moving band. These subunits could be seen in the alkylated glutenin preparations only and the genes for the faster (designated Glu-D4) and slower (designated Glu-D5) moving protein bands of the doublet were located on chromosomes 1D and 7D, respectively. Amino acid composition of the two new subunits was quite different from those of the other well-characterized gluten proteins, as the new subunits have lower amounts of proline and relatively higher amounts of glycine, aspartic acid – asparagine, cysteine, and lysine. Polyclonal antibodies raised against these polypeptides cross-reacted strongly with the major low molecular weight subunits of wheat glutenin (Glu-3 subunits), but did not cross-react with the high molecular weight glutenin subunits or monomeric gliadins. Furthermore, preliminary results on the N-terminal amino acid sequences of the new subunits show homology with the major low molecular weight glutenin subunits, suggesting an evolutionary link between the two.Key words: Triticum aestivum, glutenin subunits, gene location, immunoblotting.

Molecular characterization and phylogenetic analysis of a novel glutenin gene (Dy10.1t) fromAegilops tauschii

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 735-745 ◽  
Author(s):  
Yanzhen Zhang ◽  
Qiaoyun Li ◽  
Yueming Yan ◽  
Jigang Zheng ◽  
Xueli An ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Aegilops Tauschii ◽  
Pcr Primers ◽  
Duplication Event ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

A novel y-type high molecular mass glutenin subunit (HMM-GS) possessing a mobility that is slightly slower than that of the subunit Dy10 obtained by SDS–PAGE, named Dy10.1t, in the wild wheat Aegilops tauschii was identified by 1- and 2-dimensional gel electrophoresis, capillary electrophoresis, and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI–TOF–MS). The gene encoding the HMM subunit Dy10.1twas amplified with allele-specific PCR primers, and the amplified products were cloned and sequenced. The coding domain of the Dy10.1tsubunit gene consisted of 1980 bp encoding a protein of 658 residues with an Mrsof 68 611 Da, which was similar to the Mrsdetermined by MALDI–TOF–MS. The deduced amino acid sequence indicated that Dy10.1tsubunit displayed a greater similarity to the Dy12 subunit, differing by only 8 amino acid substitutions. Six coding region single-nucleotide polymorphisms were discovered in the Dy10.1tgene by multiple alignments (1 per 330 bp), 1 in the N-terminal domain and the others in the central repeats. Five of them resulted in residue substitutions, whereas 3 created enzyme site changes. The homology and neighbour-joining trees constructed from code domain sequences of 20 x- and y-type glutenin genes from different Triticum species separated into 2 halves, which corresponded to the x-type and y-type HMM glutenin alleles. Phylogenetic analysis revealed that the Glu-1 gene duplication event probably occurred at about 16.83 million years ago, whereas the divergence times of A, B, and D genomes within x-type and y-type halves were before 7.047 and 10.54 million years ago, respectively.Key words: HMW glutenin genes, MALDI-TOF-MS, AS-PCR, cSNP, phylogenetic analysis, Aegilops tauschii.

Genes for low-molecular-weight heat shock proteins of soybeans: sequence analysis of a multigene family

1985 ◽  
Vol 5 (12) ◽  
pp. 3417-3428
Author(s):  
R T Nagao ◽  
E Czarnecka ◽  
W B Gurley ◽  
F Schöffl ◽  
J L Key
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Heat Shock ◽  
Dna Sequences ◽  
Regulatory Element ◽  
Amino Acid Sequences ◽  
Striking Similarity ◽  
Low Molecular Weight ◽  
Genes Encoding ◽  
Flanking Regions

Soybeans, Glycine max, synthesize a family of low-molecular-weight heat shock (HS) proteins in response to HS. The DNA sequences of two genes encoding 17.5- and 17.6-kilodalton HS proteins were determined. Nuclease S1 mapping of the corresponding mRNA indicated multiple start termini at the 5' end and multiple stop termini at the 3' end. These two genes were compared with two other soybean HS genes of similar size. A comparison among the 5' flanking regions encompassing the presumptive HS promoter of the soybean HS-protein genes demonstrated this region to be extremely homologous. Analysis of the DNA sequences in the 5' flanking regions of the soybean genes with the corresponding regions of Drosophila melanogaster HS-protein genes revealed striking similarity between plants and animals in the presumptive promoter structure of thermoinducible genes. Sequences related to the Drosophila HS consensus regulatory element were found 57 to 62 base pairs 5' to the start of transcription in addition to secondary HS consensus elements located further upstream. Comparative analysis of the deduced amino acid sequences of four soybean HS proteins illustrated that these proteins were greater than 90% homologous. Comparison of the amino acid sequence for soybean HS proteins with other organisms showed much lower homology (less than 20%). Hydropathy profiles for Drosophila, Xenopus, Caenorhabditis elegans, and G. max HS proteins showed a similarity of major hydrophilic and hydrophobic regions, which suggests conservation of functional domains for these proteins among widely dispersed organisms.

scholarly journals Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences.

1987 ◽  
Vol 84 (22) ◽  
pp. 7915-7919 ◽  
Author(s):  
R. G. Warr ◽  
S. Hawgood ◽  
D. I. Buckley ◽  
T. M. Crisp ◽  
J. Schilling ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Pulmonary Surfactant ◽  
Surfactant Protein ◽  
Amino Acid Sequences ◽  
Low Molecular Weight ◽  
Pulmonary Surfactant Protein

scholarly journals The complete amino acid sequence of the low molecular weight cytosolic acid phosphatase

1989 ◽  
Vol 264 (5) ◽  
pp. 2560-2567
Author(s):  
G Camici ◽  
G Manao ◽  
G Cappugi ◽  
A Modesti ◽  
M Stefani ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Acid Phosphatase ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Low Molecular Weight ◽  
Complete Amino Acid Sequence

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

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