scholarly journals A ROLE OF ENVIRONMENTAL FACTORS ON CALCIUM SIGNALING GENES IN NEUROSPORA CRASSA

2015 ◽  
Vol 5 (3) ◽  
pp. 699-710
Author(s):  
Ravi Gedela
Keyword(s):  
Environmental Factors ◽  
Neurospora Crassa ◽  
Nadh Dehydrogenase ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Conserve Domain ◽  
Knockout Mutants

 Neurospora crassa possesses a complex of Ca2+_signaling system consisting of 48 Ca2+-signaling proteins.  The Ca+2-signalling  protein plays an important role in a range of processes such as a Ca2+ stress tolerance, hyphal tip branching growth, cytoskeletal organization, cell cycle progression, circadian clocks, sporulation, sexual development, and ultraviolet (uv) survival.  The environmental factors, broadly defined to include chemical, physical, nutritional, and behavioral factors...etc.  In this article, we are reporting here a role of physic-chemical environmental factors pH, glucose and ultraviolet (UV) affect on ∆NCU06366, and ∆NCU05225 Ca2+ -signaling knockout mutants in N. crassa.  The verified result showed that, ∆NCU06366 and ∆NCU05225 Ca2+ -signaling knockout mutants slower growth rate at pH (7.6), and glucose starvation against to the control wild type respectively.  In addition to that the found results showed, ultraviolet (UV) survival, there is no UV radiation affects on ∆NCU06366 and ∆NCU05225 Ca2+-signaling knockout mutants as evaluate to the positive and the negative controls in N.crassa.  Along with that, In-silico analysis Multiple sequence analysis and Phylogenetics tree for conserve domain of NCU05225 (NADH dehydrogenase) and NCU06366 (Ca2+/H+ anti-porter) Ca2+-signaling genes encodes proteins in N.crassa, showed high sequence similarity and 68-100% and 89% homology  to the other class of fungi respectively.  It indicates that, NCU05225 (Mitochondrial NADH dehydrogenase) and NCU06366 (Ca2+/H+ exchangers) Ca2+-signaling gene encoding conserve domain widespread in other class of fungi as well.   

Comparative mapping of a QTL controlling black point formation in barley

2008 ◽  
Vol 35 (5) ◽  
pp. 427 ◽  
Author(s):  
Timothy J. March ◽  
Jason A. Able ◽  
Kerrie Willsmore ◽  
Carolyn J. Schultz ◽  
Amanda J. Able
Keyword(s):  
Candidate Genes ◽  
Sequence Similarity ◽  
Rice Genome ◽  
In Silico Analysis ◽  
Barley Grain ◽  
Future Research ◽  
Rflp Markers ◽  
Physiological Disorder ◽  
High Sequence Similarity ◽  
Black Point

The dark discoloration of the embryo end of barley grain (known as black point) is a physiological disorder and the discovery of a quantitative trait locus (QTL) on 2H confirms this trait is controlled genetically. The mechanisms underlying black point tolerance can now be dissected through identification of candidate genes. Comparisons between the QTL identified on chromosomes 2H of barley and 2B of wheat suggest that they are in similar positions near the centromere. In silico analysis, using rice, identified genes residing on two comparative chromosomes (4 and 7) of the rice genome. Analysis of the 12.6 Mb region revealed 1928 unique annotations classified into 11 functional categories. Expressed sequence tags (ESTs) with high sequence similarity to enzymes proposed to be involved in black point formation were used to develop restriction fragment length polymorphisms (RFLPs). To ensure an even coverage of markers across the QTL, RFLP markers were also developed from other ESTs. Mapping of these markers has reduced the QTL region from 28 to 18 cM. This study has identified candidate genes for the control of black point formation and paves the way for future research to develop black point resistant barley cultivars.

scholarly journals Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1413-1418 ◽  
Author(s):  
Kanchan Nasare ◽  
Amit Yadav ◽  
Anil K. Singh ◽  
K. B. Shivasharanappa ◽  
Y. S. Nerkar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Saccharum Officinarum ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequence Alignments ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Very High

A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning and sequencing of the 16S rRNA and spacer regions were performed. Multiple sequence alignments of the 16S rRNA sequences revealed that they share very high sequence similarity with phytoplasmas of rice yellow dwarf, 16SrXI. However, the 16S-23S rRNA SR sequence analysis revealed that while the majority of phytoplasmas shared very high (>99%) sequence similarity with previously reported sugarcane phytoplasmas, two of them, namely BV2 (DQ380342) and VD7 (DQ380343), shared relatively low sequence similarity (79 and 84%, respectively). Therefore, these two phytoplasmas may be previously unreported ones that cause significant yield losses in sugarcane in India.

scholarly journals Isolation of Cysteine-Rich Peptides from Citrullus colocynthis

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1326
Author(s):  
Behzad Shahin-Kaleybar ◽  
Ali Niazi ◽  
Alireza Afsharifar ◽  
Ghorbanali Nematzadeh ◽  
Reza Yousefi ◽  
...  
Keyword(s):  
Trypsin Inhibitor ◽  
High Performance ◽  
De Novo ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
Reversed Phase ◽  
Amino Acid Sequences ◽  
Peptide Fragments ◽  
Citrullus Colocynthis ◽  
High Sequence Similarity

The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

scholarly journals A Carbohydrate Hydrolysis Enzymes encoding Genes in Neurospora crassa

2015 ◽  
Vol 5 (3) ◽  
pp. 711-727
Author(s):  
Ravi Gedela
Keyword(s):  
Neurospora Crassa ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
High Sequence Similarity ◽  
Physiochemical Properties ◽  
Carbohydrate Hydrolysis ◽  
Genes Encoding ◽  
Multiple Sequences ◽  
Encoding Genes ◽  
Sequences Alignment

Neurospora crassa, NCU05882.7 (423aa) and NCU09774.7 (303 aa) (NCU, Neurospora 7 crassa unit) genes encoding a Cellulase, which hydrolysis the Cellulose. In addition to that, 8 reporting here other 35 Carbohydrate hydrolysis enzymes encoding genes in N.crassa. A 9 metagenomic analysis for multiple sequences alignment and Phylogenetics analysis, the evaluated 10 result showed high sequence similarity and 99% homology to the other class of fungi; in the 11 bacterial species showed extremely very less sequence similarities and 100 % homology. 12 Where as in inter species between fungi and bacteria, the results showed extremely less sequence 13 similarities and 97 % homology. The studies on physiochemical properties of Cellulase using 14 GeneDoc, the evaluated results showed Cellulase was an amphoteric (polor), aromatic, aliphatic 15 and highly repeated amino acids of glycine and proline. These metagenomic studies could help 16 to straightforward isolation of Cellulase enzymes from NCU05882.7 (Chromosome/Linkage 17 Group-VII), NCU09774.7 (Chromosome Linkage Group- II) and other 35 Carbohydrate 18 hydrolysis enzymes encoding genes in N.crassa.

The Role of Gene Conversion in Determining Sequence Variation and Divergence in the Est-5 Gene Family in Drosophila pseudoobscura

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 305-315
Author(s):  
Lynn Mertens King
Keyword(s):  
Gene Family ◽  
Gene Conversion ◽  
Sequence Variation ◽  
Sequence Similarity ◽  
Drosophila Pseudoobscura ◽  
High Sequence Similarity ◽  
Tests Of Neutrality ◽  
Synonymous Sites ◽  
Interspecific Comparisons

Abstract Nucleotide sequences of eight Est-5A and Est-5C genes corresponding to previously sequenced Est-5B genes in Drosophila pseudoobscura were determined to compare patterns of polymorphism and divergence among members of this small gene family. The three esterase genes were also sequenced from D. persimilis and D. miranda for interspecific comparisons. The data provide evidence that gene conversion between loci contributes to polymorphism and to the homogenization of the Est-5 genes. For Est-5B, which encodes one of the most highly polymorphic proteins in Drosophila, 12% of the segregating amino acid variants appear to have been introduced via gene conversion from other members of the gene family. Interlocus gene conversion can also explain high sequence similarity, especially at synonymous sites, between Est-5B and Est-5A. Tests of neutrality using interspecific comparisons show that levels of polymorphism conform to neutral expectations at each Est-5 locus. However, McDonald-Kreitman tests based on intraspecific gene comparisons indicate that positive selection on amino acids has accompanied Est-5 gene duplication and divergence in D. pseudoobscura.

scholarly journals Structure and Function of Filamin C in the Muscle Z-Disc

2020 ◽  
Vol 21 (8) ◽  
pp. 2696 ◽  
Author(s):  
Zhenfeng Mao ◽  
Fumihiko Nakamura
Keyword(s):  
Sequence Similarity ◽  
Actin Binding ◽  
Amino Acid Residues ◽  
Filamin A ◽  
Dimerization Domain ◽  
High Sequence Similarity ◽  
Actin Binding Domain ◽  
And Function ◽  
Filamin C

Filamin C (FLNC) is one of three filamin proteins (Filamin A (FLNA), Filamin B (FLNB), and FLNC) that cross-link actin filaments and interact with numerous binding partners. FLNC consists of a N-terminal actin-binding domain followed by 24 immunoglobulin-like repeats with two intervening calpain-sensitive hinges separating R15 and R16 (hinge 1) and R23 and R24 (hinge-2). The FLNC subunit is dimerized through R24 and calpain cleaves off the dimerization domain to regulate mobility of the FLNC subunit. FLNC is localized in the Z-disc due to the unique insertion of 82 amino acid residues in repeat 20 and necessary for normal Z-disc formation that connect sarcomeres. Since phosphorylation of FLNC by PKC diminishes the calpain sensitivity, assembly, and disassembly of the Z-disc may be regulated by phosphorylation of FLNC. Mutations of FLNC result in cardiomyopathy and muscle weakness. Although this review will focus on the current understanding of FLNC structure and functions in muscle, we will also discuss other filamins because they share high sequence similarity and are better characterized. We will also discuss a possible role of FLNC as a mechanosensor during muscle contraction.

scholarly journals The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

2013 ◽  
Vol 12 (9) ◽  
pp. 1305-1314 ◽  
Author(s):  
Violeta Díaz-Sánchez ◽  
Alejandro F. Estrada ◽  
M. Carmen Limón ◽  
Salim Al-Babili ◽  
Javier Avalos
Keyword(s):  
Neurospora Crassa ◽  
Sequence Similarity ◽  
Hydroxyl Groups ◽  
Mrna Levels ◽  
Pronounced Increase ◽  
Content Type ◽  
Carotenoid Metabolism ◽  
Cleavage Enzyme ◽  
Β Carotene

ABSTRACT The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C 40 carotene torulene, a key step in the synthesis of the C 35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving β-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl Cα-Cβ double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted Δ cao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora . However, under partial sorbose toxicity, the Δ cao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products.

scholarly journals Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2

2020 ◽  
Vol 21 (19) ◽  
pp. 7375 ◽  
Author(s):  
Annika Rogstam ◽  
Maria Nyblom ◽  
Signe Christensen ◽  
Celeste Sele ◽  
Vladimir O. Talibov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Severe Acute Respiratory Syndrome ◽  
Sequence Similarity ◽  
Economic Consequences ◽  
Structural Protein ◽  
High Sequence Similarity ◽  
Biophysical Characterization ◽  
Global Pandemic ◽  
Rna Capping

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing Coronavirus Disease 19 (COVID-19), emerged at the end of 2019 and quickly spread to cause a global pandemic with severe socio-economic consequences. The early sequencing of its RNA genome revealed its high similarity to SARS, likely to have originated from bats. The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. Here, we report the biophysical characterization and 1.6 Å resolution structure of the unbound form of nsp10 from SARS-CoV-2 and compare it to the structures of its SARS homologue and the complex-bound form with nsp16 from SARS-CoV-2. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication.

scholarly journals Duplications and functional specialization force distinct evolution of isoflavonoid biosynthetic genes in legumes

2018 ◽  
Author(s):  
Yin Shan Jiao ◽  
Yu Zhao ◽  
Wen Feng Chen
Keyword(s):  
Sequence Similarity ◽  
Protein Structures ◽  
Phenylpropanoid Pathway ◽  
Functional Specialization ◽  
Plant Metabolites ◽  
High Sequence Similarity ◽  
Genome Wide ◽  
Isoflavone Synthase ◽  
Isoflavone Reductase

AbstractIsoflavonoids are specialized plant metabolites, almost exclusive to legumes, and synthesized by the phenylpropanoid pathway. Leguminous plants produce 5-deoxyflavonoids and 5-deoxyisoflavonoids that act in symbiosis with nitrogen-fixing bacteria and involved in plant pathogen and stress response. However, little is known about evolutional origin of legume-specific isoflavonoid biosynthesis pathway. Here, we explored the genome-wide analysis of key genes: chalcone synthase (CHS), chalcone reductase (CHR), isoflavone synthase (IFS) and isoflavone reductase (IFR), encoding enzymes involved in the biosynthesis of (iso) flavonoids in legumes and nonlegumes. Among them, CHS, CHR and IFR comprise multigene families, underling the significant role of gene duplication in the evolutionary. Most duplications of CHS were highly the conventional leguminous type, whereas some were grouped with nonleguminous CHS genes. We also found that CHR homologs in soybean and Sesbania rostrata previously reported were ambiguous and should be re-identified. Phylogenetic analysis and protein sequences alignment indicated that IFSs in legumes are highly conserved. Intriguingly, unlike other IFRs in legumes, IFR-like homologs in Sophora flavescens and Lupinus angustifolius shared high sequence similarity and protein structures with homologs in nonlegumes. Overall, these results offer reasonable gene annotations and comparative analysis and also provided a glimpse into evolutional route of legume-specific isoflavonoid biosynthesis.HighlightIsoflavonoids are specialized plant metabolites, almost exclusive to legumes. We firstly provide evidence that evolutional origin of legume-specific isoflavonoid biosynthesis may be driven by gene duplications and functional specialization.

scholarly journals S-Methylmethionine Metabolism in Escherichia coli

1999 ◽  
Vol 181 (2) ◽  
pp. 662-665 ◽  
Author(s):  
Martin Thanbichler ◽  
Bernhard Neuhierl ◽  
August Böck
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Physiological Role ◽  
High Sequence Similarity ◽  
Reading Frame ◽  
Amino Acid Permeases ◽  
Sequence Similarities ◽  
Homocysteine Methyltransferase

ABSTRACT Selenium-accumulating Astragalus spp. contain an enzyme which specifically transfers a methyl group fromS-methylmethionine to the selenol of selenocysteine, thus converting it to a nontoxic, since nonproteinogenic, amino acid. Analysis of the amino acid sequence of this enzyme revealed thatEscherichia coli possesses a protein (YagD) which shares high sequence similarity with the enzyme. The properties and physiological role of YagD were investigated. YagD is anS-methylmethionine: homocysteine methyltransferase which also accepts selenohomocysteine as a substrate. Mutants inyagD which also possess defects in metE andmetH are unable to utilize S-methylmethionine for growth, whereas a metE metH double mutant still grows on S-methylmethionine. Upstream of yagD and overlapping with its reading frame is a gene (ykfD) which, when inactivated, also blocks growth on methylmethionine in ametE metH genetic background. Since it displays sequence similarities with amino acid permeases it appears to be the transporter for S-methylmethionine. Methionine but notS-methylmethionine in the medium reduces the amount ofyagD protein. This and the existence of four MET box motifs upstream of yfkD indicate that the two genes are members of the methionine regulon. The physiological roles of the ykfDand yagD products appear to reside in the acquisition ofS-methylmethionine, which is an abundant plant product, and its utilization for methionine biosynthesis.

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