scholarly journals Genome-Wide Identification and Characterization of bZIP Transcription Factors inBrassica oleraceaunder Cold Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Indeok Hwang ◽  
Ranjith Kumar Manoharan ◽  
Jong-Goo Kang ◽  
Mi-Young Chung ◽  
Young-Wook Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Cold Stress ◽  
Stress Responses ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Sequencing Data ◽  
Cold Response ◽  
Bzip Transcription Factors

Cabbages (Brassica oleraceaL.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsiveBolbZIPgenes were screened in inbred lines,BN106andBN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes,Bol008071,Bol033132, andBol042729, was significantly increased inBN107under cold conditions and was unchanged inBN106. The upregulation of these genes inBN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes,Bol033132has 97% sequence similarity toBra020735, which was identified in a screen for cold-related genes inB. rapaand a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses.

History, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19)

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Amaresh Mishra ◽  
Nisha Nair ◽  
Vishwas Tripathi ◽  
Yamini Pathak ◽  
Jaseela Majeed
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Sequence Similarity ◽  
Neurological Complications ◽  
Amino Acid Sequences ◽  
World Health ◽  
Amino Acid Sequence Similarity ◽  
Effective Prevention ◽  
Short Period ◽  
The World

: The Coronavirus Disease 2019 (COVID-19), also known as a novel coronavirus (2019-nCoV), reportedly originated from Wuhan City, Hubei Province, China. Coronavirus Disease 2019 rapidly spread all over the world within a short period. On January 30th, 2020, the World Health Organization (WHO) declared it a global epidemic. COVID-19 is a severe acute respiratory syndrome coronavirus (SARS-CoV) virus that evolves to respiratory, hepatic, gastrointestinal, and neurological complications, and eventually death. SARS-CoV and the Middle East Respiratory Syndrome coronavirus (MERS-CoV) genome sequences similar identity with 2019-nCoV or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, few amino acid sequences of 2019-nCoV differ from SARS-CoV and MERS-CoV. COVID-19 shares about 90% amino acid sequence similarity with SARS-CoV. Effective prevention methods should be taken in order to control this pandemic situation. Till now, there are no effective treatments available to treat COVID-19. This review provides information regarding COVID-19 history, epidemiology, pathogenesis, and molecular diagnosis. Also, we focus on the development of vaccines in the management of this COVID-19 pandemic and limiting the spread of the virus.

scholarly journals The 13C4 Monoclonal Antibody That Neutralizes Shiga Toxin Type 1 (Stx1) Recognizes Three Regions on the Stx1 B Subunit and Prevents Stx1 from Binding to Its Eukaryotic Receptor Globotriaosylceramide

2006 ◽  
Vol 74 (12) ◽  
pp. 6992-6998 ◽  
Author(s):  
Michael J. Smith ◽  
Humberto M. Carvalho ◽  
Angela R. Melton-Celsa ◽  
Alison D. O'Brien
Keyword(s):  
Monoclonal Antibody ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Single Amino Acid ◽  
Amino Acid Sequence Similarity ◽  
Lethal Challenge ◽  
B Subunit ◽  
Receptor Recognition

ABSTRACT The 13C4 monoclonal antibody (MAb) recognizes the B subunit of Stx1 (StxB1) and neutralizes the cytotoxic and lethal activities of Stx1. However, this MAb does not bind to the B polypeptide of Stx2, despite the 73% amino acid sequence similarity between StxB1 and StxB2. When we compared the amino acid sequences of StxB1 and StxB2, we noted three regions of dissimilarity (amino acids 1 to 6, 25 to 32, and 54 to 61) located near each other on the crystal structure of StxB1. To identify the 13C4 epitope, we generated seven Stx1/Stx2 B chimeric polypeptides that contained one, two, or three of the dissimilar StxB1 regions. The 13C4 MAb reacted strongly with StxB1 and the triple-chimeric B subunit but not with the other chimeras. Mice immunized with the triple-chimeric B subunit survived a lethal challenge with Stx1 but not Stx2, substantiating the identified regions as the 13C4 MAb epitope and suggesting that the incorporation of this epitope into StxB2 altered sites necessary for anti-Stx2-neutralizing Ab production. Next, single amino acid substitutions were made in StxB1 to mimic Stx1d, a variant not recognized by the 13C4 MAb. The 13C4 MAb reacted strongly to StxB1 with the T1A or G25A mutations but not with the N55T change. Finally, we found that the 13C4 MAb blocked the binding of Stx1 to its receptor, globotriaosyl ceramide. Taken together, these results indicate that the 13C4 MAb prevents the interaction of Stx1 with its receptor by binding three nonlinear regions of the molecule that span receptor recognition sites on StxB1, one of which includes the essential residue 55N.

Computer Analysis of Phytochrome Sequences from Five Species: Implications for the Mechanism of Action

1990 ◽  
Vol 45 (9-10) ◽  
pp. 987-998 ◽  
Author(s):  
Michael D. Partis ◽  
Rudolf Grimm
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Lipid Bilayers ◽  
Protein Interactions ◽  
Avena Sativa ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Post Translational Modification ◽  
C Terminus

Abstract The amino acid sequences of phytochrome from Avena sativa, Oryza sativa, Curcurbita pepo, Pisum sativum and Arabidopsis thaliana have been analyzed with a variety of computer programs, with a view to identifying areas of the protein which contribute to the properties of this photoreceptor. A region at the C-terminus has been shown to be amphiphilic, and by ana­logy with surface-seeking peptides, may be responsible for interaction of phytochrome with lipid bilayers. Possible targeting sequences in phytochromes have been identified, including a series of four basic residues which correspond to those responsible for transport of nuclear-located proteins. Sites capable of post-translational modification have been found in monocot sequences, but not in dicot sequences. Areas of the phytochrome molecule which are exposed on the surface of the portein, and which are therefore capable of interaction with other cellular macromolecules, have been identified. Analogies with other biliproteins have been used to define minimum chromophore-protein interactions. Possible enzymic activities associated with phytochromes have been discussed with respect to local amino acid sequence similarity with enzymes.

scholarly journals Φm46.1, the Main Streptococcus pyogenes Element Carrying mef(A) and tet(O) Genes

2009 ◽  
Vol 54 (1) ◽  
pp. 221-229 ◽  
Author(s):  
Andrea Brenciani ◽  
Alessandro Bacciaglia ◽  
Carla Vignaroli ◽  
Armanda Pugnaloni ◽  
Pietro E. Varaldo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Streptococcus Pyogenes ◽  
Integration Site ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
23S Rrna ◽  
Amino Acid Sequence Similarity ◽  
Modular Organization ◽  
Electron Microscopic ◽  
Phage Dna

ABSTRACT Φm46.1, the recognized representative of the most common variant of mobile, prophage-associated genetic elements carrying resistance genes mef(A) (which confers efflux-mediated erythromycin resistance) and tet(O) (which confers tetracycline resistance) in Streptococcus pyogenes, was fully characterized. Sequencing of the Φm46.1 genome (55,172 bp) demonstrated a modular organization typical of tailed bacteriophages. Electron microscopic analysis of mitomycin-induced Φm46.1 revealed phage particles with the distinctive icosahedral head and tail morphology of the Siphoviridae family. The chromosome integration site was within a 23S rRNA uracil methyltransferase gene. BLASTP analysis revealed that the proteins of Φm46.1 had high levels of amino acid sequence similarity to the amino acid sequences of proteins from other prophages, especially Φ10394.4 of S. pyogenes and λSa04 of S. agalactiae. Phage DNA was present in the host cell both as a prophage and as free circular DNA. The lysogeny module appears to have been split due to the insertion of a segment containing tet(O) (from integrated conjugative element 2096-RD.2) and mef(A) (from a Tn1207.1-like transposon) into the unintegrated phage DNA. The phage attachment sequence lies in the region between tet(O) and mef(A) in the unintegrated form. Thus, whereas in this form tet(O) is ∼5.5 kb upstream of mef(A), in the integrated form, tet(O), which lies close to the right end of the prophage, is ∼46.3 kb downstream of mef(A), which lies close to the left end of the prophage.

scholarly journals Site-directed mutagenesis at aspartate and glutamate residues of xylanase from Bacillus pumilus

1992 ◽  
Vol 288 (1) ◽  
pp. 117-121 ◽  
Author(s):  
E P Ko ◽  
H Akatsuka ◽  
H Moriyama ◽  
A Shinmyo ◽  
Y Hata ◽  
...  
Keyword(s):  
Amino Acids ◽  
Reaction Mechanism ◽  
Amino Acid ◽  
Bacillus Pumilus ◽  
Specific Activity ◽  
Sequence Similarity ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Amino Acid Sequence Similarity ◽  
Directed Mutagenesis

To elucidate the reaction mechanism of xylanase, the identification of amino acids essential for its catalysis is of importance. Studies have indicated the possibility that the reaction mechanism of xylanase is similar to that of hen's egg lysozyme, which involves acidic amino acid residues. On the basis of this assumption, together with the three-dimensional structure of Bacillus pumilus xylanase and its amino acid sequence similarity to other xylanases of different origins, three acidic amino acids, namely Asp-21, Glu-93 and Glu-182, were selected for site-directed mutagenesis. The Asp residue was altered to either Ser or Glu, and the Glu residues to Ser or Asp. The purified mutant xylanases D21E, D21S, E93D, E93S, E182D and E182S showed single protein bands of about 26 kDa on SDS/PAGE. C.d. spectra of these mutant enzymes show no effect on the secondary structure of xylanase, except that of D21E, which shows a little variation. Furthermore, mutations of Glu-93 and Glu-182 resulted in a drastic decrease in the specific activity of xylanase as compared with mutation of Asp-21. On the basis of these results we propose that Glu-93 and Glu-182 are the best candidates for the essential catalytic residues of xylanase.

scholarly journals Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L

2018 ◽  
Author(s):  
Sona. S Dev ◽  
P. Poornima ◽  
Akhil Venu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Interleukin 1 ◽  
Preliminary Investigation ◽  
Solanum Melongena ◽  
Wild Relatives ◽  
Amino Acid Sequences ◽  
R Genes ◽  
Multiple Sequence

Eggplantor brinjal (Solanum melongena L.), is highly susceptible to various soil-borne diseases. The extensive use of chemical fungicides to combat these diseases can be minimized by identification of resistance gene analogs (RGAs) in wild species of cultivated plants.In the present study, degenerate PCR primers for the conserved regions ofnucleotide binding site-leucine rich repeat (NBS-LRR) were used to amplify RGAs from wild relatives of eggplant (Black nightshade (Solanum nigrum), Indian nightshade (Solanumviolaceum)and Solanu mincanum) which showed resistance to the bacterial wilt pathogen, Ralstonia solanacearumin the preliminary investigation. The amino acid sequence of the amplicons when compared to each other and to the amino acid sequences of known RGAs deposited in Gen Bank revealed significant sequence similarity. The phylogenetic analysis indicated that they belonged to the toll interleukin-1 receptors (TIR)-NBS-LRR type R-genes. Multiple sequence alignment with other known R genes showed significant homology with P-loop, Kinase 2 and GLPL domains of NBS-LRR class genes. There has been no report on R genes from these wild eggplants and hence the diversity analysis of these novel RGAs can lead to the identification of other novel R genes within the germplasm of different brinjal plants as well as other species of Solanum.

Na(+)-independent transport (uniport) of amino acids and glucose in mammalian cells.

1994 ◽  
Vol 196 (1) ◽  
pp. 93-108
Author(s):  
D K Kakuda ◽  
C L MacLeod
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mammalian Cells ◽  
Glucose Transporter ◽  
Sequence Similarity ◽  
Amino Acid Sequence Similarity ◽  
Amino Acid Transporters ◽  
Cationic Amino Acid ◽  
Transporter Family ◽  
Share Amino Acid Sequence

Recent advances have made possible the isolation of the genes and their cDNAs encoding Na(+)-independent amino acid transporters. Two classes of amino acid 'uniporters' have been isolated. One class contains the mCAT (murine cationic amino acid transporter) gene family that encodes proteins predicted to span the membrane 12-14 times and exhibits structural properties similar to the GLUT (glucose transporter) family and to other well-known transporters. The other class consists of two known genes, rBAT (related to B system amino acid transporters) and 4F2hc, that share amino acid sequence similarity with alpha-amylases and alpha-glucosidases. They are type II glycoproteins predicted to span the membrane only once, yet they mediate the Na(+)-independent transport of cationic and zwitterionic amino acids in Xenopus oocytes. Mutations in the human rBAT gene have been identified by Palacín and his co-workers in several families suffering from a heritable form of cystinuria. This important finding clearly establishes a key role for rBAT in cystine transport. The two classes of amino acid transporters are compared with the well-studied GLUT family of Na(+)-independent glucose transporters.

The gene encoding a major component of the lateral elements of synaptonemal complexes of the rat is related to X-linked lymphocyte-regulated genes

1994 ◽  
Vol 14 (2) ◽  
pp. 1137-1146
Author(s):  
J H Lammers ◽  
H H Offenberg ◽  
M van Aalderen ◽  
A C Vink ◽  
A J Dietrich ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Sodium Dodecyl ◽  
Coiled Coil ◽  
Amino Acid Identity ◽  
Male Rat ◽  
Amino Acid Sequence Similarity ◽  
Gene Encoding ◽  
Synaptonemal Complexes ◽  
Complex Protein

The lateral elements of synaptonemal complexes (SCs) of the rat contain major components with relative electrophoretic mobilities (M(r)S) of 30,000 and 33,000. After one-dimensional separation of SC proteins on polyacrylamide-sodium dodecyl sulfate gels, these components show up as two broad bands. These bands contain closely related proteins, as judged from their peptide maps and immunological reactivity. Using affinity-purified polyclonal anti-30,000- and anti-33,000-M(r) component antibodies, we isolated a cDNA encoding at least one of the 30,000- or 33,000-M(r) SC components. The protein predicted from the nucleotide sequence of the cDNA, called SCP3 (for synaptonemal complex protein 3), has a molecular mass of 29.7 kDa and a pI value of 9.4. It has a potential nucleotide binding site and contains stretches that are predicted to be capable of forming coiled-coil structures. In the male rat, the gene encoding SCP3 is transcribed exclusively in the testis. SCP3 has significant amino acid similarity to the pM1 protein, which is one of the predicted products of an X-linked lymphocyte-regulated gene family of the mouse: there are 63% amino acid sequence similarity and 35% amino acid identity between the SCP3 and pM1 proteins. However, SCP3 differs from pM1 in several respects, and whether the proteins fulfill related functions is still an open question.

scholarly journals Engineered Resistance Against Papaya ringspot virus in Venezuelan Transgenic Papayas

Plant Disease ◽  
2004 ◽  
Vol 88 (5) ◽  
pp. 516-522 ◽  
Author(s):  
Gustavo Fermin ◽  
Valentina Inglessis ◽  
Cesar Garboza ◽  
Sairo Rangel ◽  
Manuel Dagert ◽  
...  
Keyword(s):  
Amino Acid ◽  
Agrobacterium Tumefaciens ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
Ringspot Virus ◽  
Amino Acid Sequence Similarity ◽  
Papaya Ringspot Virus ◽  
Local Varieties ◽  
Cp Gene

Local varieties of papaya grown in the Andean foothills of Mérida, Venezuela, were transformed independently with the coat protein (CP) gene from two different geographical Papaya ringspot virus (PRSV) isolates, designated VE and LA, via Agrobacterium tumefaciens. The CP genes of both PRSV isolates show 92 and 96% nucleotide and amino acid sequence similarity, respectively. Four PRSV-resistant R0 plants were intercrossed or selfed, and the progenies were tested for resistance against the homologous isolates VE and LA, and the heterologous isolates HA (Hawaii) and TH (Thailand) in greenhouse conditions. Resistance was affected by sequence similarity between the transgenes and the challenge viruses: resistance values were higher for plants challenged with the homologous isolates (92 to 100% similarity) than with the Hawaiian (94% similarity) and, lastly, Thailand isolates (88 to 89% similarity). Our results show that PRSV CP gene effectively protects local varieties of papaya against homologous and heterologous isolates of PRSV.

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