scholarly journals DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1

2018 ◽  
Vol 46 (11) ◽  
pp. 5470-5486 ◽  
Author(s):  
Xuecong Wang ◽  
Yogesh Srivastava ◽  
Aleksander Jankowski ◽  
Vikas Malik ◽  
Yuanjie Wei ◽  
...  
Keyword(s):  
Sequence Signature

scholarly journals Novel Victorivirus from a Pakistani Isolate of Alternaria alternata Lacking a Typical Translational Stop/Restart Sequence Signature

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 577 ◽  
Author(s):  
Atif Jamal ◽  
Yukiyo Sato ◽  
Sabitree Shahi ◽  
Wajeeha Shamsi ◽  
Hideki Kondo ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Rna Silencing ◽  
Polyacrylamide Gel Electrophoresis ◽  
Peptide Mass Fingerprinting ◽  
Cryphonectria Parasitica ◽  
Fungal Species ◽  
Open Reading Frames ◽  
Fusion Product ◽  
Peptide Mass ◽  
Sequence Signature

The family Totiviridae currently contains five genera Totivirus, Victorivirus, Leishmavirus, Trichomonasvirus, and Giardiavirus. Members in this family generally have a set of two-open reading frame (ORF) elements in their genome with the 5′-proximal ORF (ORF1) encoding a capsid protein (CP) and the 3′-proximal one (ORF2) for RNA-dependent RNA polymerase (RdRp). How the downstream open reading frames (ORFs) are expressed is genus-specific. All victoriviruses characterized thus far appear to use the stop/restart translation mechanism, allowing for the expression of two separate protein products from bicitronic genome-sized viral mRNA, while the totiviruses use a −1 ribosomal frame-shifting that leads to a fusion product of CP and RdRp. We report the biological and molecular characterization of a novel victorivirus termed Alternaria alternata victorivirus 1 (AalVV1) isolated from Alternaria alternata in Pakistan. The phylogenetic and molecular analyses showed AalVV1 to be distinct from previously reported victoriviruses. AalVV1 appears to have a sequence signature required for the −1 frame-shifting at the ORF1/2 junction region, rather than a stop/restart key mediator. By contrast, SDS–polyacrylamide gel electrophoresis and peptide mass fingerprinting analyses of purified virion preparations suggested the expression of two protein products, not a CP-RdRp fusion product. How these proteins are expressed is discussed in this study. Possible effects of infection by this virus were tested in two fungal species: A. alternata and RNA silencing proficient and deficient strains of Cryphonectria parasitica, a model filamentous fungus. AalVV1 showed symptomless infection in all of these fungal strains, even in the RNA silencing deficient C. parasitica strain.

scholarly journals Members of the Galectin Network with Deviations from the Canonical Sequence Signature. 1. Galectin-Related Inter-Fiber Protein (GRIFIN)

2018 ◽  
Vol 30 (172) ◽  
pp. SE1-SE9 ◽  
Author(s):  
Gabriel García Caballero ◽  
Joachim C. Manning ◽  
Anna-Kristin Ludwig ◽  
Federico M. Ruiz ◽  
Antonio Romero ◽  
...  
Keyword(s):  
Sequence Signature

A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish

2010 ◽  
Vol 433 (2) ◽  
pp. 345-355 ◽  
Author(s):  
Elio Pizzo ◽  
Antonello Merlino ◽  
Mimmo Turano ◽  
Irene Russo Krauss ◽  
Francesca Coscia ◽  
...  
Keyword(s):  
Functional Properties ◽  
Danio Rerio ◽  
Three Dimensional ◽  
Biological Properties ◽  
Rnase A ◽  
Dimensional Structure ◽  
Structural And Functional Properties ◽  
Sequence Signature ◽  
Bactericidal Activities ◽  
Rnase A Superfamily

Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.

scholarly journals Sequence Signature of Voltage Sensing Detected via Dimensionality Reduction Techniques

2015 ◽  
Vol 108 (2) ◽  
pp. 426a
Author(s):  
Daniele Granata ◽  
Matteo Marsili ◽  
Michael L. Klein ◽  
Vincenzo Carnevale
Keyword(s):  
Dimensionality Reduction ◽  
Voltage Sensing ◽  
Reduction Techniques ◽  
Sequence Signature ◽  
Dimensionality Reduction Techniques

scholarly journals Sll0254 (CrtLdiox) Is a Bifunctional Lycopene Cyclase/Dioxygenase in Cyanobacteria Producing Myxoxanthophyll

2006 ◽  
Vol 188 (9) ◽  
pp. 3337-3344 ◽  
Author(s):  
Hatem E. Mohamed ◽  
Wim F. J. Vermaas
Keyword(s):  
Normal Cell ◽  
The Other ◽  
Dual Function ◽  
Hydroxyl Groups ◽  
Biosynthesis Pathway ◽  
The Family ◽  
Lycopene Cyclase ◽  
N Terminus ◽  
Sequence Signature ◽  
Dioxygenase Activity

ABSTRACT Upon depletion of Sll0254 in Synechocystis sp. strain PCC 6803, cyclized carotenoids were replaced by linear, relatively hydrophilic carotenoids, and the amount of the two photosystems decreased greatly. Full segregants of the sll0254 deletion in Synechocystis were not obtained, implying that this gene is essential for survival, most likely to allow normal cell division. The N-terminal half of Sll0254 has limited similarity to the family of lycopene cyclases, has an additional dehydrogenase motif near the N terminus, and is followed by a Rieske 2Fe-2S center sequence signature. To test whether Sll0254 serves as a lycopene cyclase in Synechocystis, the corresponding gene was expressed in Escherichia coli strains that can produce lycopene or neurosporene. In the presence of Sll0254 these linear carotenoids were converted into cyclized, relatively hydrophilic pigments, with masses consistent with the introduction of two hydroxyl groups and with spectra indicative of only small changes in the number of conjugated double bonds. This suggests that Sll0254 catalyzes formation of oxygenated, cyclized carotenoids. We interpret the appearance of the hydroxyl groups in the carotenoids to be due to dioxygenase activity involving the Rieske 2Fe-2S center and the additional dehydrogenase domain. This dioxygenase activity is required in the myxoxanthophyll biosynthesis pathway, after or concomitant with cyclization on the other end of the molecule. We interpret Sll0254 to be a dual-function enzyme with both lycopene cyclase and dioxygenase activity and have named it CrtLdiox.

Application traffic classification using payload size sequence signature

2017 ◽  
Vol 27 (5) ◽  
pp. e1981 ◽  
Author(s):  
Kyu-Seok Shim ◽  
Jae-Hyun Ham ◽  
Baraka D. Sija ◽  
Myung-Sup Kim
Keyword(s):  
Traffic Classification ◽  
Sequence Signature

scholarly journals Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Science ◽  
2020 ◽  
Vol 371 (6525) ◽  
pp. 172-177 ◽  
Author(s):  
Bas B. Oude Munnink ◽  
Reina S. Sikkema ◽  
David F. Nieuwenhuijse ◽  
Robert Jan Molenaar ◽  
Emmanuelle Munger ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nonhuman Primates ◽  
Animal Experiments ◽  
Whole Genome ◽  
Infection Period ◽  
Modes Of Transmission ◽  
Whole Genomes ◽  
Sequence Signature ◽  
In The Beginning ◽  
Farm Residents

Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.

Requirement for asparagine in the aquaporin NPA sequence signature motifs for cation exclusion

FEBS Journal ◽  
2011 ◽  
Vol 278 (5) ◽  
pp. 740-748 ◽  
Author(s):  
Dorothea Wree ◽  
Binghua Wu ◽  
Thomas Zeuthen ◽  
Eric Beitz
Keyword(s):  
Sequence Signature

Phylogenetic analysis reveals Stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Phylogenetic Analysis ◽  
Inverted Repeat ◽  
Evolutionary Relationship ◽  
Open Reading Frames ◽  
Published Data ◽  
Terminal Inverted Repeat ◽  
Predominant Type ◽  
Sequence Signature ◽  
Eukaryotic Organisms ◽  
Reading Frames

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630–Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630–Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.Key words: Stowaway, Emigrant, MITE, mariner, transposon.

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