scholarly journals An Improved Transposon for the Halophilic ArchaeonHaloarcula hispanica

1999 ◽  
Vol 181 (22) ◽  
pp. 7140-7142 ◽  
Author(s):  
Wayne G. Woods ◽  
Katrina Ngui ◽  
Michael L. Dyall-Smith
Keyword(s):  
Insertion Sequence ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Haloarcula Hispanica

ABSTRACT An improved transposon (ThD73) for Haloarcula hispanica is described. Based on the halobacterial insertion sequence ISH28, it showed little target sequence specificity but was biased toward a lower G+C content. Twenty randomly selected ThD73 mutants were analyzed, and the DNA flanking their insertions revealed several recognizable sequences, including two (unrelated) ISH elements.

scholarly journals Benchmarking substrate-based kinase activity inference using phosphoproteomic data

2016 ◽  
Author(s):  
Claudia Hernandez-Armenta ◽  
David Ochoa ◽  
Emanuel Gonçalves ◽  
Julio Saez-Rodriguez ◽  
Pedro Beltrao
Keyword(s):  
Kinase Activity ◽  
Multiple Linear Regression Model ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Gold Standard Dataset ◽  
Kolmogorov Smirnov

AbstractMotivationPhosphoproteomic experiments are increasingly used to study the changes in signalling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.ResultsWe curated public phosphoproteomic experiments to identify a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur. A list of kinase substrates was compiled and used to estimate changes in kinase activities using the following methods: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model (MLR). We also tested weighted variants of the Z-test, and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence (in vivo, in vitro or in silico) supporting these influence the predictions.ConclusionsMost models performed well with the Z-test and the GSEA performing best as determined by the area under the ROc curve (Mean AUC=0.722). Weighting kinase targets by the kinase target sequence preference improves the results only marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions.

Host-induced gene silencing and spray-induced gene silencing for crop protection against viruses.

2021 ◽  
pp. 72-85
Author(s):  
Angela Ricci ◽  
Silvia Sabbadini ◽  
Laura Miozzi ◽  
Bruno Mezzetti ◽  
Emanuela Noris
Keyword(s):  
Gene Silencing ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Plant Defence ◽  
Transcriptional Gene Silencing ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Rna Molecules ◽  
Political Concern ◽  
Post Transcriptional Gene Silencing

Abstract Since the beginning of agriculture, plant virus diseases have been a strong challenge for farming. Following its discovery at the very beginning of the 1990s, the RNA interference (RNAi) mechanism has been widely studied and exploited as an integrative tool to obtain resistance to viruses in several plant species, with high target-sequence specificity. In this chapter, we describe and review the major aspects of host-induced gene silencing (HIGS), as one of the possible plant defence methods, using genetic engineering techniques. In particular, we focus our attention on the use of RNAi-based gene constructs to introduce stable resistance in host plants against viral diseases, by triggering post-transcriptional gene silencing (PTGS). Recently, spray-induced gene silencing (SIGS), consisting of the topical application of small RNA molecules to plants, has been explored as an alternative tool to the stable integration of RNAi-based gene constructs in plants. SIGS has great and innovative potential for crop defence against different plant pathogens and pests and is expected to raise less public and political concern, as it does not alter the genetic structure of the plant.

scholarly journals Sequence specificity in DNA binding is determined by association rather than dissociation

2021 ◽  
Author(s):  
Emil Marklund ◽  
Guanzhong Mao ◽  
Sebastian Deindl ◽  
Johan Elf
Keyword(s):  
Dna Binding ◽  
Genetic Information ◽  
Specific Binding ◽  
Theoretical Framework ◽  
Simple Equation ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Target Search ◽  
Target Binding ◽  
Site Recognition

AbstractSequence-specific binding of proteins to DNA is essential for accessing genetic information. Here, we derive a simple equation for target-site recognition, which uncovers a previously unrecognized coupling between the macroscopic association and dissociation rates of the searching protein. Importantly, this relationship makes it possible to recover the relevant microscopic rates from experimentally determined macroscopic ones. We directly test the equation by observing the binding and unbinding of individual lac repressor (LacI) molecules during target search. We find that LacI dissociates from different target sequences with essentially identical microscopic dissociation rates. Instead, sequence specificity is determined by the efficiency with which the protein recognizes different targets, effectively reducing its risk of being retained on a non-target sequence. Our theoretical framework also accounts for the coupling between off-target binding and unbinding of the catalytically inactive Cas9 (dCas9), showing that the binding pathway can be obtained from macroscopic data.One Sentence SummaryAssociation and dissociation rates are anti-correlated for reactions that include a nonspecific probing step.

scholarly journals Tumorigenesis by Meis1 overexpression is accompanied by a change of DNA target-sequence specificity which allows binding to the AP-1 element

Oncotarget ◽  
2015 ◽  
Vol 6 (28) ◽  
pp. 25175-25187 ◽  
Author(s):  
Leila Dardaei ◽  
Dmitry Penkov ◽  
Lisa Mathiasen ◽  
Pranami Bora ◽  
Marco J. Morelli ◽  
...  
Keyword(s):  
Target Sequence ◽  
Sequence Specificity

Sequence Specificity in the Higher-Order Interaction of the Rev Protein of HIV-1 with its Target Sequence, the RRE

1995 ◽  
Vol 10 (3) ◽  
pp. 317???323 ◽  
Author(s):  
Douglas M. Powell ◽  
Ming Jie Zhang ◽  
Danielle A. M. Konings ◽  
Paul T. Wingfield ◽  
Stephen J. Stahl ◽  
...  
Keyword(s):  
Higher Order ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Order Interaction ◽  
Hiv 1 ◽  
Rev Protein

scholarly journals Transposons Tn1696 and Tn21and Their Integrons In4 and In2 Have Independent Origins

2001 ◽  
Vol 45 (4) ◽  
pp. 1263-1270 ◽  
Author(s):  
Sally R. Partridge ◽  
Heidi J. Brown ◽  
H. W. Stokes ◽  
Ruth M. Hall
Keyword(s):  
Insertion Sequence ◽  
Antibiotic Resistance Genes ◽  
Distinct Group ◽  
Mercury Resistance ◽  
Inverted Repeats ◽  
Target Sequence ◽  
Class 1 Integron ◽  
Class 1 Integrons ◽  
Class 1 ◽  
Full Copy

ABSTRACT The first 13.6 kb of the mercury and multidrug resistance transposon Tn1696, which includes the class 1 integron In4, has been sequenced. In4 is 8.33 kb long and contains the 5′-conserved segment (5′-CS) and 2.24 kb of the 3′-conserved segment (3′-CS) flanking four integrated cassettes. The 3′-CS region is followed by one full copy and an adjacent partial copy of the insertion sequence IS6100 flanked, in inverse orientation, by two short segments (123 and 152 bp) from the outer right-hand end of class 1 integrons. This structure is representative of a distinct group of class 1 integrons that differs from In2, found in Tn21, and other related class 1 integrons. In4 does not include transposition genes but is bounded by characteristic 25-bp inverted repeats and flanked by a direct duplication of 5 bp of the target sequence, indicating that it was inserted by a transpositional mechanism. In4 lies between the resII and resIsites of a backbone mercury resistance transposon which is >99.5% identical to Tn5036. Although Tn21 and Tn1696 are both classified as members of the Tn21 subfamily of the Tn3 transposon family, the backbone mercury resistance transposons are only 79 to 96% identical. Tn21 also contains a region of about 0.7 kb not found in Tn1696. The integrons In2 and In4 carrying the antibiotic resistance genes have been inserted at different locations into distinct ancestral mercury resistance transposons. Thus, Tn21 and Tn1696 have independent histories and origins. Other transposons (Tn1403 and Tn1412) that include a class 1 integron also have independent origins. In all except Tn21, the integron is located within theres region of the backbone transposon.

scholarly journals IS103, a new insertion element in Escherichia coli: characterization and distribution in natural populations.

Genetics ◽  
1989 ◽  
Vol 121 (3) ◽  
pp. 423-431 ◽  
Author(s):  
B G Hall ◽  
L L Parker ◽  
P W Betts ◽  
R F DuBose ◽  
S A Sawyer ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Copy Number ◽  
Insertion Sequence ◽  
Natural Populations ◽  
Single Copy ◽  
Target Sequence ◽  
Wild Type ◽  
Insertion Element ◽  
E Coli ◽  
Natural Isolates

Abstract IS103 is a previously unknown insertion sequence found in Escherichia coli K12. We have sequenced IS103 and find that it is a 1441-bp element that consists of a 1395-bp core flanked by imperfect 23-bp inverted repeats. IS103 causes a 6-bp duplication of the target sequence into which it inserts. There is a single copy of IS103 present in wild-type E. coli K12 strain HfrC. In strain X342 and its descendents there are two additional copies, one of which is located within the bglF gene. IS103 is capable of excising from within bglF and restoring function of that gene. IS103 exhibits 44% sequence identity with IS3, suggesting that the two insertion sequences are probably derived from a common ancestor. We have examined the distribution of IS103 in the chromosomes and plasmids of the ECOR collection of natural isolates of E. coli. IS103 is found in 36 of the 71 strains examined, and it strongly tends to inhabit plasmids rather than chromosomes. Comparison of the observed distribution of IS103 with distributions predicted by nine different models for the regulation of transposition according to copy number and of the effects of copy number on fitness suggest that transposition of IS103 is strongly regulated and that it has only minor effects on fitness. The strong clustering of IS103 within one phylogenetic subgroup of the E. coli population despite its presence on plasmids suggests that plasmids tend to remain within closely related strains and that transfer to distantly related strains is inhibited.

MyoD and myogenin act on the chicken myosin light-chain 1 gene as distinct transcriptional factors

1993 ◽  
Vol 13 (11) ◽  
pp. 7153-7162
Author(s):  
A Asakura ◽  
A Fujisawa-Sehara ◽  
T Komiya ◽  
Y Nabeshima ◽  
Y Nabeshima
Keyword(s):  
Light Chain ◽  
Dna Sequences ◽  
Regulatory Region ◽  
Target Sequence ◽  
Sequence Specificity ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Nonmuscle Cells ◽  
Flanking Sequences ◽  
E Boxes

Expression of MyoD, myogenin, MRF4, and Myf-5 converts nonmuscle cells to muscle cells. In an attempt to analyze the roles of these factors, we have investigated their effects on transcription driven by the promoter of the chicken myosin alkaline light-chain (MLC1) gene. The activation by CMD1 or c-myogenin (chicken MyoD or myogenin, respectively) was dependent on the existence of a muscle-specific regulatory region located from positions -2096 to -1743. Its distal half, containing a pair of E boxes (CANNTG), had been previously characterized as an enhancer responsive to CMD1 but not to c-myogenin. In this study, we report the identification of another enhancer in the muscle-specific regulatory region which is preferentially responsive to c-myogenin. Deletion and mutation analyses indicated that this enhancer requires a single E box and its flanking sequences. Furthermore, analysis of chimeric proteins of CMD1 and c-myogenin indicated that regions outside the basic helix-loop-helix domain of c-myogenin are involved in the specificity of the enhancer. These results show that CMD1 and c-myogenin act on the MLC1 gene by recognizing different upstream DNA sequences and that direct or indirect interactions between the regions outside the basic helix-loop-helix domain and flanking sequences of E boxes are involved in the target sequence specificity.

scholarly journals The Identification and Differentiation between Burkholderia mallei and Burkholderia pseudomallei Using One Gene Pyrosequencing

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Damian H. Gilling ◽  
Vicki Ann Luna ◽  
Cori Pflugradt
Keyword(s):  
New Species ◽  
Burkholderia Pseudomallei ◽  
Insertion Sequence ◽  
Single Gene ◽  
Target Sequence ◽  
Burkholderia Mallei ◽  
Insertion Point ◽  
P Gene ◽  
Etiologic Agents ◽  
The Difference

The etiologic agents for melioidosis and glanders, Burkholderia mallei and Burkholderia pseudomallei respectively, are genetically similar making identification and differentiation from other Burkholderia species and each other challenging. We used pyrosequencing to determine the presence or absence of an insertion sequence IS407A within the flagellin P (fliP) gene and to exploit the difference in orientation of this gene in the two species. Oligonucleotide primers were designed to selectively target the IS407A-fliP interface in B. mallei and the fliP gene specifically at the insertion point in B. pseudomallei. We then examined DNA from ten B. mallei, ten B. pseudomallei, 14 B. cepacia, eight other Burkholderia spp., and 17 other bacteria. Resultant pyrograms encompassed the target sequence that contained either the fliP gene with the IS407A interruption or the fully intact fliP gene with 100% sensitivity and 100% specificity. These pyrosequencing assays based upon a single gene enable investigators to reliably identify the two species. The information obtained by these assays provides more knowledge of the genomic reduction that created the new species B. mallei from B. pseudomallei and may point to new targets that can be exploited in the future.

scholarly journals Transposition of IS4Family Insertion Sequences ISTeha3, ISTeha4, and ISTeha5into thearcOperon Disrupts Arginine Deiminase System inTetragenococcus halophilus

2019 ◽  
Vol 85 (10) ◽  
Author(s):  
Takura Wakinaka ◽  
Jun Watanabe
Keyword(s):  
Insertion Sequence ◽  
Starter Culture ◽  
Arginine Deiminase ◽  
Soy Sauce ◽  
Target Sequence ◽  
Insertion Sequences ◽  
Content Type ◽  
Reading Frame ◽  
Wild Strains ◽  
Potential Carcinogen

ABSTRACTTetragenococcus halophilus, a halophilic lactic acid bacterium, is often used as a starter culture in the manufacturing of soy sauce.T. halophiluspossesses an arginine deiminase system, which is responsible for the accumulation of citrulline, the main precursor of the potential carcinogen ethyl carbamate. In this study, we generated five derivatives lacking arginine deiminase activity fromT. halophilusNBRC 12172 by UV irradiation. Using these derivatives as a fermentation starter prevented arginine deimination in soy sauce. DNA sequence analysis of the derivatives revealed that novel IS4family insertion sequences, designated ISTeha3, ISTeha4, and ISTeha5, were transposed into the region around the arginine deiminase (arc) operon in the mutants. These insertion sequences contain a single open reading frame encoding a putative transposase and 13- to 15-bp inverted repeats at both termini, which are adjacent to 7- to 9-bp duplications of the target sequence. Investigation of wild strains isolated from soy sauce mash incapable of arginine deimination also indicated that insertion sequences are involved in the disruption of the arginine deiminase system inT. halophilus.IMPORTANCEInsertion sequences play important roles in bacterial evolution and are frequently utilized in mutagenesis systems. However, the intrinsic insertion sequences of tetragenococci are not well characterized. Here, we identified three active insertion sequences ofT. halophilusby transposition into the region around thearcoperon. This report provides an example of insertion sequence-mediated generation and evolution ofT. halophilusand primary information about their characteristics.

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