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 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.   

scholarly journals Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance

2020 ◽  
Vol 21 (7) ◽  
pp. 504-511
Author(s):  
Milind Balkrishna Ratnaparkhe ◽  
Niharika Marmat ◽  
Giriraj Kumawat ◽  
Maranna Shivakumar ◽  
Viraj Gangadhar Kamble ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Sequence Variation ◽  
Sequence Similarity ◽  
Resistance Mechanism ◽  
Comparative Sequence Analysis ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
High Sequence Similarity ◽  
Soybean Genotype ◽  
Genomic Landscape

Background: In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods: A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results: Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred. by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion: The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.

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 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.

scholarly journals Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1944
Author(s):  
Shaoqi Shen ◽  
Yuxian Li ◽  
Jianyu Wang ◽  
Chendan Wei ◽  
Zhenyi Wang ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Sequence Similarity ◽  
Dna Recombination ◽  
Duplicate Gene ◽  
Duplicated Genes ◽  
Biological Functions ◽  
High Sequence Similarity ◽  
Arachis Hypogaea L ◽  
Peanut Genome ◽  
Chromosome Regions

The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid and three tetraploid peanut genomes, we identified the duplicated genes generated from legume common tetraploidy (LCT) and peanut recent allo-tetraploidy (PRT) within genomes. In each peanut genome (or subgenomes), we inferred that 6.8–13.1% of LCT-related and 11.3–16.5% of PRT-related duplicates were affected by gene conversion, in which the LCT-related duplicates were the most affected by partial gene conversion, whereas the PRT-related duplicates were the most affected by whole gene conversion. Notably, we observed the conversion between duplicates as the long-lasting contribution of polyploidizations accelerated the divergence of different Arachis genomes. Moreover, we found that the converted duplicates are unevenly distributed across the chromosomes and are more often near the ends of the chromosomes in each genome. We also confirmed that well-preserved homoeologous chromosome regions may facilitate duplicates’ conversion. In addition, we found that these biological functions contain a higher number of preferentially converted genes, such as catalytic activity-related genes. We identified specific domains that are involved in converted genes, implying that conversions are associated with important traits of peanut growth and development.

scholarly journals Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Mohamed Ramadan ◽  
Muna Alariqi ◽  
Yizan Ma ◽  
Yanlong Li ◽  
Zhenping Liu ◽  
...  
Keyword(s):  
Genetic Transformation ◽  
Sequence Similarity ◽  
High Specificity ◽  
Transformation Method ◽  
High Sequence Similarity ◽  
Single Experiment ◽  
Next Generation Sequencing Technology ◽  
Cotton Transformation ◽  
Assembly Method ◽  
Multiple Genes

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

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