scholarly journals Genetic Variability of Acetolactate Synthase (ALS) Sequence in Centaurea Cyanus Plants Resistant and Susceptible to Tribenuron-methyl

2021 ◽  
Author(s):  
Barbara Wrzesinska ◽  
Tadeusz Praczyk ◽  
Aleksandra Obrępalska-Stęplowska
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Amino Acid Sequence ◽  
Herbicide Resistance ◽  
Resistance Mechanism ◽  
Sequence Information ◽  
Sequence Variability ◽  
Centaurea Cyanus ◽  
Arable Weed ◽  
Tribenuron Methyl

Abstract Centaurea cyanus, belonging to the Asteraceae family, is an arable weed species being encountered mainly in the fields with cereals, sugar beet, and corn. C. cyanus high genetic variability has recently been reported, however, little is known about sequence variability in the context of herbicide resistance. C. cyanus resistance was found mainly against acetolactate inhibitors (ALS) inhibitors, but no ALS sequence information concerning herbicide resistance mechanism has been published yet. Therefore, the aim of this study was to determine ALS sequences for biotypes susceptible and resistant to tribenuron-methyl in order to identify possible mutations conferring the resistance. DNA isolation from susceptible and resistant plants was followed by PCR amplification and sequencing of ALS sequence. As a result different lengths of DNA products were obtained. Moreover, both nucleotide and amino acid sequence analysis revealed high sequence variability within one plant as well as between plants from the same biotype. In a few resistant plants, six changes in amino acid sequence were identified in comparison to susceptible ones. However, these preliminary studies require further investigation toward confirming the significance of these mutations in herbicide resistance development. This study provides the first attempt in the research on C. cyanus target-site resistance mechanism.

scholarly journals Genetic Variability of Acetolactate Synthase (ALS) Sequence in Centaurea cyanus Plants Resistant and Susceptible to Tribenuron-Methyl

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2311
Author(s):  
Barbara Wrzesińska ◽  
Tadeusz Praczyk
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Amino Acid Sequence ◽  
Herbicide Resistance ◽  
Resistance Mechanism ◽  
Acetolactate Synthase ◽  
Sequence Information ◽  
Sequence Variability ◽  
Centaurea Cyanus ◽  
Tribenuron Methyl

Centaurea cyanus, belonging to the Asteraceae family, is an arable weed species encountered mainly in fields with cereals, sugar beet, and maize. The high genetic variability of C. cyanus has been recently reported; however, little is known about its sequence variability in the context of its herbicide resistance. C. cyanus resistance was found mainly against acetolactate synthase (ALS) inhibitors, but no ALS sequence information concerning the herbicide resistance mechanism has been published yet. The aim of this study was to determine the ALS sequences for biotypes susceptible and resistant to tribenuron-methyl in order to identify mutations that may be associated with the resistance emergence. DNA isolation from susceptible and resistant plants was followed by PCR amplification and ALS sequencing. As a result, different lengths of DNA products were obtained. Moreover, both nucleotide and amino acid sequence analysis revealed high sequence variability within one plant as well as between plants from the same biotype. In a few resistant plants, four changes in the amino acid sequence were identified in comparison to those in the susceptible ones. However, these preliminary studies require further investigation toward confirming the significance of these mutations in herbicide resistance development. This study provides preliminary information contributing to the research on the C. cyanus target-site resistance mechanism.

scholarly journals Genetic variability in cysteine protease genes ofHaemonchus contortus

Parasitology ◽  
2004 ◽  
Vol 128 (5) ◽  
pp. 549-559 ◽  
Author(s):  
A. RUIZ ◽  
J. M. MOLINA ◽  
A. NJUE ◽  
R. K. PRICHARD
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Genetic Variability ◽  
Amino Acid Sequence ◽  
Cysteine Protease ◽  
Haemonchus Contortus ◽  
Significant Variation ◽  
Nucleotide Diversity ◽  
Cysteine Proteases ◽  
Different Strains

To increase the existent genetic variability in cysteine proteases, a polymorphism study was performed inHaemonchus contortusby comparing 2 different strains of the parasite: North American (NA) and Spanish (SP) strains. For this purpose, the polymorphism of 5 previously reported genes (AC-1,AC-3,AC-4,AC-5andGCP-7) were analysed by PCR–SSCP and sequencing procedures. Based on the SSCP results, a total of 20 different alleles were identified for the 5lociassessed. Exceptlocus AC-5, all thelociwere polymorphic.Loci AC-1,AC-3,AC-4andGCP-7showed 5, 8, 2 and 4 alleles, respectively. The allelic frequencies ranged from 0·0070 to 0·8560 and were significantly different between strains. In addition, nucleotide diversity analyses showed a significant variation within and between strains. The variations in the nucleotide sequence of the different alleles were translated in some cases into changes in the amino acid sequence. Evidence of genetic variability in cysteine proteases from two different strains ofH. contortusfor the same set of genes had not been previously reported.

scholarly journals Molecular Identification of Family 38 α-Mannosidase of Bacillus sp. Strain GL1, Responsible for Complete Depolymerization of Xanthan

2002 ◽  
Vol 68 (6) ◽  
pp. 2731-2736 ◽  
Author(s):  
Hirokazu Nankai ◽  
Wataru Hashimoto ◽  
Kousaku Murata
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Cell Extract ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolase Family ◽  
Sequence Information ◽  
Reading Frame ◽  
A Cell ◽  
Terminal Amino ◽  
Amino Acid Sequence Information

ABSTRACT When cells of Bacillus sp. strain GL1 were grown in a medium containing xanthan as a carbon source, α-mannosidase exhibiting activity toward p-nitrophenyl-α-d-mannopyranoside (pNP-α-d-Man) was produced intracellularly. The 350-kDa α-mannosidase purified from a cell extract of the bacterium was a trimer comprising three identical subunits, each with a molecular mass of 110 kDa. The enzyme hydrolyzed pNP-α-d-Man (Km = 0.49 mM) and d-mannosyl-(α-1,3)-d-glucose most efficiently at pH 7.5 to 9.0, indicating that the enzyme catalyzes the last step of the xanthan depolymerization pathway of Bacillus sp. strain GL1. The gene for α-mannosidase cloned most by using N-terminal amino acid sequence information contained an open reading frame (3,144 bp) capable of coding for a polypeptide with a molecular weight of 119,239. The deduced amino acid sequence showed homology with the amino acid sequences of α-mannosidases belonging to glycoside hydrolase family 38.

scholarly journals The gdhB Gene of Pseudomonas aeruginosaEncodes an Arginine-Inducible NAD+-Dependent Glutamate Dehydrogenase Which Is Subject to Allosteric Regulation

2001 ◽  
Vol 183 (2) ◽  
pp. 490-499 ◽  
Author(s):  
Chung-Dar Lu ◽  
Ahmed T. Abdelal
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Glutamate Dehydrogenase ◽  
Legionella Pneumophila ◽  
Caulobacter Crescentus ◽  
Sodium Dodecyl ◽  
Sequence Information ◽  
Saturation Curve ◽  
Moderate Degree ◽  
Amino Terminal

ABSTRACT The NAD+-dependent glutamate dehydrogenase (NAD-GDH) from Pseudomonas aeruginosa PAO1 was purified, and its amino-terminal amino acid sequence was determined. This sequence information was used in identifying and cloning the encodinggdhB gene and its flanking regions. The molecular mass predicted from the derived sequence for the encoded NAD-GDH was 182.6 kDa, in close agreement with that determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme (180 kDa). Cross-linking studies established that the native NAD-GDH is a tetramer of equal subunits. Comparison of the derived amino acid sequence of NAD-GDH from P. aeruginosa with the GenBank database showed the highest homology with hypothetical polypeptides from Pseudomonas putida, Mycobacterium tuberculosis, Rickettsia prowazakii, Legionella pneumophila, Vibrio cholerae, Shewanella putrefaciens, Sinorhizobium meliloti, andCaulobacter crescentus. A moderate degree of homology, primarily in the central domain, was observed with the smaller tetrameric NAD-GDH (protomeric mass of 110 kDa) fromSaccharomyces cerevisiae or Neurospora crassa. Comparison with the yet smaller hexameric GDH (protomeric mass of 48 to 55 kDa) of other prokaryotes yielded a low degree of homology that was limited to residues important for binding of substrates and for catalytic function. NAD-GDH was induced 27-fold by exogenous arginine and only 3-fold by exogenous glutamate. Primer extension experiments established that transcription of gdhB is initiated from an arginine-inducible promoter and that this induction is dependent on the arginine regulatory protein, ArgR, a member of the AraC/XyIS family of regulatory proteins. NAD-GDH was purified to homogeneity from a recombinant strain of P. aeruginosa and characterized. The glutamate saturation curve was sigmoid, indicating positive cooperativity in the binding of glutamate. NAD-GDH activity was subject to allosteric control by arginine and citrate, which function as positive and negative effectors, respectively. Both effectors act by influencing the affinity of the enzyme for glutamate. NAD-GDH from this organism differs from previously characterized enzymes with respect to structure, protomer mass, and allosteric properties indicate that this enzyme represents a novel class of microbial glutamate dehydrogenases.

Acetolactate Synthase Gene Proline (197) Mutations Confer Tribenuron-Methyl Resistance in Flixweed (Descurainia sophia) Populations from China

Weed Science ◽  
2011 ◽  
Vol 59 (3) ◽  
pp. 376-379 ◽  
Author(s):  
Hai Lan Cui ◽  
Chao Xian Zhang ◽  
Shou Hui Wei ◽  
Hong Jun Zhang ◽  
Xiang Ju Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Basis ◽  
Resistance Mechanism ◽  
Point Mutations ◽  
Acetolactate Synthase ◽  
Amino Acid Position ◽  
Resistance Level ◽  
Coding Sequence ◽  
Whole Plant ◽  
Tribenuron Methyl

The molecular basis of resistance to tribenuron-methyl, an acetolactate synthase (ALS)–inhibiting herbicide was investigated in four resistant (R) and three susceptible (S) flixweed populations. The resistance level in the R populations was assessed in whole-plant pot experiments in a greenhouse, and resistance indices ranged from 723 to 1422. The ALS genes of the three S populations and four R populations were cloned and sequenced, and the full coding sequence of the ALS gene of flixweed was 2,004 bp. The sequences of the ALS genes of the three S populations collected from Shaanxi, Gansu, and Tianjin were identical. Comparison of the ALS gene sequences of the S and R populations withArabidopsisrevealed that proline at position 197 of the ALS gene was substituted by leucine in R population SSX-2, by alanine in R population SSX-3, and by serine in R populations TJ-2 and GS-2. In another study of two R flixweed populations from Hebei and Shaanxi, resistance was also related to mutation at position 197 of the ALS gene. Both studies confirmed tribenuron-methyl resistance in flixweed in China, with the resistance mechanism being conferred by specific ALS point mutations at amino acid position 197.

scholarly journals The amino acid sequence of the cytochrome c2 from the phototrophic bacterium Rhodopseudomonas globiformis

1987 ◽  
Vol 246 (1) ◽  
pp. 115-120 ◽  
Author(s):  
R P Ambler ◽  
T E Meyer ◽  
M A Cusanovich ◽  
M D Kamen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
British Library ◽  
Sequence Information ◽  
Cytochrome C2 ◽  
Percentage Sequence Identity ◽  
Acidophilic Bacterium ◽  
High Degree ◽  
Rhodopseudomonas Globiformis

The amino acid sequence of the principal soluble cytochrome c from the phototrophic acidophilic bacterium Rhodopseudomonas (or Rhodopila) globiformis was determined. By the criteria of percentage sequence identity and fewness of internal insertions and deletions it is more similar in sequence to some mitochondrial cytochromes c than to any known bacterial cytochrome. The organism does not have any properties that commend it as being particularly similar to postulated prokaryotic precursors of the mitochondrion. We consider that the relatively high degree of sequence similarity is an instance of convergence, and is an example of the limitations that are imposed on attempts to deduce distant evolutionary relationships from sequence information. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50136 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment [see Biochem. J. (1987) 241, 5].

scholarly journals A model of k-mer surprisal to quantify local sequence information content surrounding splice regions

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10063
Author(s):  
Sam Humphrey ◽  
Alastair Kerr ◽  
Magnus Rattray ◽  
Caroline Dive ◽  
Crispin J. Miller
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Information Content ◽  
Sequence Information ◽  
Optimal Size ◽  
Multiple Sequence ◽  
Molecular Sequences ◽  
Donor And Acceptor ◽  
Exon Junctions ◽  
Cg Dinucleotide

Molecular sequences carry information. Analysis of sequence conservation between homologous loci is a proven approach with which to explore the information content of molecular sequences. This is often done using multiple sequence alignments to support comparisons between homologous loci. These methods therefore rely on sufficient underlying sequence similarity with which to construct a representative alignment. Here we describe a method using a formal metric of information, surprisal, to analyse biological sub-sequences without alignment constraints. We applied our model to the genomes of five different species to reveal similar patterns across a panel of eukaryotes. As the surprisal of a sub-sequence is inversely proportional to its occurrence within the genome, the optimal size of the sub-sequences was selected for each species under consideration. With the model optimized, we found a strong correlation between surprisal and CG dinucleotide usage. The utility of our model was tested by examining the sequences of genes known to undergo splicing. We demonstrate that our model can identify biological features of interest such as known donor and acceptor sites. Analysis across all annotated coding exon junctions in Homo sapiens reveals the information content of coding exons to be greater than the surrounding intron regions, a consequence of increased suppression of the CG dinucleotide in intronic space. Sequences within coding regions proximal to exon junctions exhibited novel patterns within DNA and coding mRNA that are not a function of the encoded amino acid sequence. Our findings are consistent with the presence of secondary information encoding features such as DNA and RNA binding sites, multiplexed through the coding sequence and independent of the information required to define the corresponding amino-acid sequence. We conclude that surprisal provides a complementary methodology with which to locate regions of interest in the genome, particularly in situations that lack an appropriate multiple sequence alignment.

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