scholarly journals The medaka fish Tol2 transposable element is in an early stage of decay: identification of a nonautonomous copy

Genome ◽  
2021 ◽  
Author(s):  
Sakura Hayashi ◽  
Takuji Tsukiyama ◽  
Atsuo Iida ◽  
Masato Kinoshita ◽  
Akihiko Koga
Keyword(s):  
Amino Acid ◽  
Stop Codon ◽  
Early Stage ◽  
Single Amino Acid ◽  
Base Substitution ◽  
Unique Element ◽  
Medaka Fish ◽  
Medaka Genome ◽  
Single Amino Acid Change ◽  
Local Sequence

The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The <i>Tol2</i> element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Here we report the presence of a nonautonomous <i>Tol2</i> copy that was identified by surveying the medaka genome sequence database. This copy contained 3 local sequence alterations that affected the deduced amino acid sequence of the transposase: a deletion of 15 nucleotides resulting in a deletion of 5 amino acids, a base substitution causing a single amino acid change, and another base substitution giving rise to a stop codon. Transposition assays using cultured human cells revealed that the transposase activity was reduced by the 15-nucleotide deletion and abolished by the nonsense mutation. This is the first example of a nonautonomous <i>Tol2</i> copy. Thus, <i>Tol2</i> is in an early stage of decay in the medaka genome, and is therefore a unique element to observe an almost whole decay process that progresses in natural populations.

scholarly journals A Single Amino Acid Change In Histone Methyltransferase CURLY LEAF Results In Premature Bolting In Chinese Cabbage (Brassica Rapa L. Ssp. Pekinensis)

2021 ◽  
Author(s):  
Chong Tan ◽  
Jie Ren ◽  
Lin Wang ◽  
Xueling Ye ◽  
Wei Fu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chinese Cabbage ◽  
Amino Acid Change ◽  
Nuclear Gene ◽  
Histone Methyltransferase ◽  
Single Amino Acid ◽  
Base Substitution ◽  
Nonsynonymous Mutation ◽  
Single Amino Acid Change ◽  
Curly Leaf

Abstract Background: Flowering is an important inflection point in the transformation from vegetative to reproductive growth, and premature bolting severely decreases crop yield and quality. Results: In this study, a stable early-bolting mutant, ebm3, was identified in an ethyl methanesulfonate (EMS)-mutagenized population of a Chinese cabbage doubled haploid (DH) line ‘FT’. Compared with ‘FT’, ebm3 showed early bolting under natural cultivation in autumn, and curled leaves. Genetic analysis showed that the early-bolting phenotype was controlled by a single recessive nuclear gene. Modified MutMap and genotyping analyses revealed that Brebm3 (BraA04g017190.3C), encoding the histone methyltransferase CURLY LEAF (CLF), was the causal gene of the emb3. A C to T base substitution in the 14th exon of Brebm3 resulted in an amino acid change (S to F) and the early-bolting phenotype of emb3. The mutation occurred in the SET domain (Suppressor of protein-effect variegation 3-9, Enhancer-of-zeste, Trithorax), which catalyzes site- and state-specific lysine methylation in histones. Tissue-specific expression analysis showed that Brebm3 was highly expressed in the flower and bud. Promoter activity assay confirmed that Brebm3 promoter was active in inflorescences. Subcellular localization analysis revealed that Brebm3 localized in the nucleus. Transcriptomic studies supported that Brebm3 mutation might repress H3K27me3 deposition and activate expression of the AGAMOUS (AG) and AGAMOUS-like (AGL) loci, resulting in early flowering.Conclusions: Our study revealed that an EMS-induced early-bolting mutant ebm3 in Chinese cabbage was caused by a nonsynonymous mutation in BraA04g017190.3C, encoding the histone methyltransferase CLF.These results improve our knowledge of the genetic and genomic resources of bolting and flowering, and may be beneficial to the genetic improvement of Chinese cabbage.

scholarly journals Evolution of DMY, a Newly Emergent Male Sex-Determination Gene of Medaka Fish

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1887-1895
Author(s):  
Jianzhi Zhang
Keyword(s):  
Amino Acid ◽  
Sex Determination ◽  
Synonymous Substitution ◽  
Single Amino Acid ◽  
Medaka Fish ◽  
Single Amino Acid Change ◽  
Dm Domain ◽  
Determination System ◽  
Male Sex ◽  
Sex Determination System

Abstract The Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (dN) to that of synonymous substitution (dS) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the dN/dS ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.

scholarly journals Single amino acid changes in the mumps virus haemagglutinin–neuraminidase and polymerase proteins are associated with neuroattenuation

2009 ◽  
Vol 90 (7) ◽  
pp. 1741-1747 ◽  
Author(s):  
Tahir H. Malik ◽  
Candie Wolbert ◽  
Laura Nerret ◽  
Christian Sauder ◽  
Steven Rubin
Keyword(s):  
Amino Acid ◽  
Clinical Isolate ◽  
Amino Acid Change ◽  
Mumps Virus ◽  
Site Directed Mutagenesis ◽  
Single Amino Acid ◽  
Supporting Evidence ◽  
L Protein ◽  
Single Amino Acid Change

It has previously been shown that three amino acid changes, one each in the fusion (F; Ala/Thr-91→Thr), haemagglutinin–neuraminidase (HN; Ser-466→Asn) and polymerase (L; Ile-736→Val) proteins, are associated with attenuation of a neurovirulent clinical isolate of mumps virus (88-1961) following serial passage in vitro. Here, using full-length cDNA plasmid clones and site-directed mutagenesis, it was shown that the single amino acid change in the HN protein and to a lesser extent, the change in the L protein, resulted in neuroattenuation, as assessed in rats. The combination of both amino acid changes caused neuroattenuation of the virus to levels previously reported for the clinical isolate following attenuation in vitro. The amino acid change in the F protein, despite having a dramatic effect on protein function in vitro, was previously shown to not be involved in the observed neuroattenuation, highlighting the importance of conducting confirmatory in vivo studies. This report provides additional supporting evidence for the role of the HN protein as a virulence factor and, as far as is known, is the first report to associate an amino acid change in the L protein with mumps virus neuroattenuation.

A single amino acid change makes a rat neuronal sodium channel highly sensitive to pyrethroid insecticides

FEBS Letters ◽  
2000 ◽  
Vol 470 (2) ◽  
pp. 135-138 ◽  
Author(s):  
H. Vais ◽  
S. Atkinson ◽  
N. Eldursi ◽  
A.L. Devonshire ◽  
M.S. Williamson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sodium Channel ◽  
Amino Acid Change ◽  
Single Amino Acid ◽  
Pyrethroid Insecticides ◽  
Highly Sensitive ◽  
Single Amino Acid Change

Further characterization and determination of the single amino acid change in thetsI138reovirus thermosensitive mutant

2012 ◽  
Vol 58 (5) ◽  
pp. 589-595
Author(s):  
Guy Lemay ◽  
Martin Bisaillon
Keyword(s):  
Amino Acid ◽  
Amino Acid Change ◽  
Genetic Alterations ◽  
Biological Properties ◽  
Single Amino Acid ◽  
Temperature Sensitive ◽  
Nonpermissive Temperature ◽  
Gene Encoding ◽  
Viral Particles ◽  
Single Amino Acid Change

Many temperature-sensitive mutants have been isolated in early studies of mammalian reovirus. However, the biological properties and nature of the genetic alterations remain incompletely explored for most of these mutants. The mutation harbored by the tsI138 mutant was already assigned to the L3 gene encoding the λ1 protein. In the present study, this mutant was further studied as a possible tool to establish the role of the putative λ1 enzymatic activities in viral multiplication. It was observed that synthesis of viral proteins is only marginally reduced, while it was difficult to recover viral particles at the nonpermissive temperature. A single nucleotide substitution resulting in an amino acid change was found; the position of this amino acid is consistent with a probable defect in assembly of the inner capsid at the nonpermissive temperature.

scholarly journals Pathogenic alleles in microtubule, secretory granule and extracellular matrix-related genes in familial keratoconus

2021 ◽  
Author(s):  
Vishal Shinde ◽  
Nara Sobreira ◽  
Elizabeth S Wohler ◽  
George Maiti ◽  
Nan Hu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Cultures ◽  
Cell Biology ◽  
Stromal Cell ◽  
Primary Cilia ◽  
Single Amino Acid ◽  
European Ancestry ◽  
Base Substitution ◽  
Amino Acid Substitutions ◽  
Functional Link

Abstract Keratoconus is a common corneal defect with a complex genetic basis. By whole exome sequencing of affected members from 11 multiplex families of European ancestry, we identified 23 rare, heterozygous, potentially pathogenic variants in 8 genes. These include nonsynonymous single amino acid substitutions in HSPG2, EML6 and CENPF in two families each, and in NBEAL2, LRP1B, PIK3CG and MRGPRD in three families each; ITGAX had nonsynonymous single amino acid substitutions in two families and an indel with a base substitution producing a nonsense allele in the third family. Only HSPG2, EML6 and CENPF have been associated with ocular phenotypes previously. With the exception of MRGPRD and ITGAX, we detected the transcript and encoded protein of the remaining genes in the cornea and corneal cell cultures. Cultured stromal cells showed cytoplasmic punctate staining of NBEAL2, staining of the fibrillar cytoskeletal network by EML6, while CENPF localized to the basal body of primary cilia. We inhibited the expression of HSPG2, EML6, NBEAL2 and CENPF in stromal cell cultures and assayed for the expression of COL1A1 as a readout of corneal matrix production. An upregulation in COL1A1 after siRNA inhibition indicated their functional link to stromal cell biology. For ITGAX, encoding a leukocyte integrin, we assayed its level in the sera of 3 affected families compared with 10 unrelated controls to detect an increase in all affecteds. Our study identified genes that regulate the cytoskeleton, protein trafficking and secretion, barrier tissue function and response to injury and inflammation, as being relevant to keratoconus.

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