Cloning and characterization of MdGST1 from red apple leaves

2018 ◽  
Vol 98 (5) ◽  
pp. 1150-1158
Author(s):  
Xiaolei Han ◽  
Caixia Zhang ◽  
Yi Tian ◽  
Hera Gul ◽  
Peihua Cong ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Transcript Level ◽  
Glutathione S Transferase ◽  
Gene Encoding ◽  
Protein Coding ◽  
Apple Variety ◽  
Coding Regions ◽  
Qrt Pcr ◽  
Rapid Amplification

Glutathione S-transferase (GST) is involved in the downstream steps of the anthocyanin biosynthesis pathway in plants. However, the gene(s) encoding this enzyme have not been isolated from apple (Malus × domestica Borkh.) yet. We isolated a gene encoding GST from leaves of the red-fleshed apple variety ‘Royalty’ by full cDNA library sequencing and the 3′ rapid-amplification of cDNA ends method, and designated it MdGST1. In total, seven different MdGST1 transcripts were found. These had three different untranslated but identical protein-coding regions. Phylogenetic analysis showed that MdGST1 is a TT19-type GST, which is involved in anthocyanin transport. qRT-PCR analyses showed that the transcript level of MdGST1 was much higher in red leaves than in bagged or green leaves. When MdGST1 was introduced into a non-pigmented mutant of Arabidopsis, the transformants showed a visible purple phenotype in leaves and stems. Our results suggest that MdGST1 plays a role in anthocyanin biosynthesis. This information will help to improve the understanding of the mechanism of apple coloration.

scholarly journals Characterization of the gene for mp20: a Drosophila muscle protein that is not found in asynchronous oscillatory flight muscle.

1989 ◽  
Vol 108 (2) ◽  
pp. 521-531 ◽  
Author(s):  
A Ayme-Southgate ◽  
P Lasko ◽  
C French ◽  
M L Pardue
Keyword(s):  
Calcium Binding ◽  
Muscle Protein ◽  
Primary Cultures ◽  
Specific Protein ◽  
Gene Encoding ◽  
Significant Similarity ◽  
Coding Regions ◽  
Flight Muscles ◽  
Calcium Binding Sites

A Drosophila melanogaster gene encoding a muscle specific protein was isolated by differential screening with RNA from primary cultures of myotubes. The gene encodes a 20-kD protein, muscle protein 20 (mp20), that is not detected in the asynchronous oscillatory flight muscles, but is found in most, if not all, other muscles (the synchronous muscles). The sequence of the protein, deduced from the DNA, contains two regions of 12 amino acids with significant similarity to high-affinity calcium-binding sites of other proteins. This protein is easily extracted from the contractile apparatus and thus does not seem to be a tightly bound structural component. The gene (located in polytene region 49F 9-13) is unique in the D. melanogaster genome and yields two transcripts, 1.0 and 0.9 kb long. The levels of the two transcripts are regulated differently during development, yet the coding regions of the two transcripts are identical.

scholarly journals Building the vertebrate codex using the gene breaking protein trap library

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Noriko Ichino ◽  
MaKayla R Serres ◽  
Rhianna M Urban ◽  
Mark D Urban ◽  
Anthony J Treichel ◽  
...  
Keyword(s):  
Human Disease ◽  
Molecular Mechanisms ◽  
Genetic Diseases ◽  
Transgenic Zebrafish ◽  
Protein Coding ◽  
Coding Regions ◽  
Disease Associated Genes ◽  
Functional Genome Annotation ◽  
Specific Mrna

One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.

scholarly journals GENETIC ANALYSIS OF STAPHYLOCOCCAL NUCLEASE: IDENTIFICATION OF THREE INTRAGENIC "GLOBAL" SUPPRESSORS OF NUCLEASE-MINUS MUTATIONS

Genetics ◽  
1985 ◽  
Vol 110 (4) ◽  
pp. 539-555 ◽  
Author(s):  
David Shortle ◽  
Beth Lin
Keyword(s):  
Nuclease Activity ◽  
Staphylococcal Nuclease ◽  
Missense Mutations ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Protein Coding ◽  
E Coli ◽  
Suppressor Mutations ◽  
Cloned Gene

ABSTRACT A collection of 77 unique missense mutations distributed across the gene encoding staphylococcal nuclease (nuc) has been assembled. These mutations were induced by random gap misrepair mutagenesis of the cloned gene and were identified in E. coli transformants expressing reduced levels of nuclease activity. Four nuc  - mutations which alter amino acid residues at positions outside of the active site region of the enzyme were submitted to a second round of mutagenesis, and characterization of several independent NUC+ isolates lead to the identification of three second-site suppressor mutations within the protein-coding sequence of the nuc gene. On separation from the mutation originally suppressed and recombination with a number of other nuc  - mutations, all three suppressors displayed the property of "global" suppression, i.e., phenotypic suppression of the nuclease-minus character of multiple different alleles. A simple and generally applicable strategy was used to obtain efficient homologous recombination between plasmids for purposes of mapping nuc  - mutations, mapping second-site suppressors and constructing double mutant combinations from pairs of single mutations.

scholarly journals Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Sondos Samandi ◽  
Annie V Roy ◽  
Vivian Delcourt ◽  
Jean-François Lucier ◽  
Jules Gagnon ◽  
...  
Keyword(s):  
Mitochondrial Fission ◽  
Functional Characterization ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Protein Coding ◽  
Small Proteins ◽  
Conservation Patterns ◽  
Extreme Conservation

Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many genes are multicoding genes and code for a large protein and one or several small proteins.

scholarly journals How to find genomic regions relevant for gene regulation

2021 ◽  
Vol 33 (2) ◽  
pp. 157-165
Author(s):  
Xuanzong Guo ◽  
Uwe Ohler ◽  
Ferah Yildirim
Keyword(s):  
Functional Characterization ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
High Throughput Analysis ◽  
Protein Coding ◽  
Coding Regions ◽  
The Past ◽  
Genomic Regions ◽  
Regulatory Functions

Abstract Genetic variants associated with human diseases are often located outside the protein coding regions of the genome. Identification and functional characterization of the regulatory elements in the non-coding genome is therefore of crucial importance for understanding the consequences of genetic variation and the mechanisms of disease. The past decade has seen rapid progress in high-throughput analysis and mapping of chromatin accessibility, looping, structure, and occupancy by transcription factors, as well as epigenetic modifications, all of which contribute to the proper execution of regulatory functions in the non-coding genome. Here, we review the current technologies for the definition and functional validation of non-coding regulatory regions in the genome.

scholarly journals Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Qiuyue Ma ◽  
Yanan Wang ◽  
Lu Zhu ◽  
Changwei Bi ◽  
Shuxian Li ◽  
...  
Keyword(s):  
Tree Species ◽  
Tandem Repeats ◽  
Single Copy ◽  
Nervonic Acid ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Molecular Barcoding ◽  
Coding Regions ◽  
Cp Genome

Acer truncatum, which is a new woody oil tree species, is an important ornamental and medicinal plant in China. To assess the genetic diversity and relationships of A. truncatum, we analyzed its complete chloroplast (cp) genome sequence. The A. truncatum cp genome comprises 156,492 bp, with the large single-copy, small single-copy, and inverted repeat (IR) regions consisting of 86,010, 18,050, and 26,216 bp, respectively. The A. truncatum cp genome contains 112 unique functional genes (i.e., 4 rRNA, 30 tRNA, and 78 protein-coding genes) as well as 78 simple sequence repeats, 9 forward repeats, 1 reverse repeat, 5 palindromic repeats, and 7 tandem repeats. We analyzed the expansion/contraction of the IR regions in the cp genomes of six Acer species. A comparison of these cp genomes indicated the noncoding regions were more diverse than the coding regions. A phylogenetic analysis revealed that A. truncatum is closely related to A. miaotaiense. Moreover, a novel ycf4-cemA indel marker was developed for distinguishing several Acer species (i.e., A. buergerianum, A. truncatum, A. henryi, A. negundo, A. ginnala, and A. tonkinense). The results of the current study provide valuable information for future evolutionary studies and the molecular barcoding of Acer species.

scholarly journals Isolation and characterization of two mouse Pi-class glutathione S-transferase genes

1994 ◽  
Vol 298 (2) ◽  
pp. 385-390 ◽  
Author(s):  
T K Bammler ◽  
C A D Smith ◽  
C R Wolf
Keyword(s):  
Mouse Liver ◽  
Peptide Sequence ◽  
Tata Box ◽  
Sequence Motif ◽  
Glutathione S Transferase ◽  
Coding Regions ◽  
Isolation And Characterization ◽  
Glutathione S Transferases ◽  
Responsive Element

Pi-class glutathione S-transferases (GSTs) play an important role in the detoxification of chemical toxins and mutagens and are implicated in neoplastic development and drug resistance. In all species characterized to date, only one functional Pi-class GST gene has been described. In this report we have identified two actively transcribed murine Pi-class GST genes, Gst p-1 and Gst p-2. The coding regions of Gst p-1 and the mouse Pi-class GST cDNA (GST-II) reported by Hatayama, Satoh and Satoh (1990) (Nucleic Acids Res. 18, 4606) are identical, whereas Gst p-2 encodes a protein that has not been described previously. The two genes are approximately 3 kb long and contain seven exons interrupted by six introns. In addition to a TATA box and a sequence motif matching the phorbol-ester-responsive element, the promoters of Gst p-1 and Gst p-2 exhibit one and two G+C boxes (GGGCGG) respectively. The cDNAs of the two genes were isolated from total liver RNA using reverse PCR. The peptide sequence deduced from the cDNAs share 97% identity and differ in six amino acids. Both genes are transcribed at significantly higher levels in male mouse liver than in female, and Gst p-1 mRNA is more abundant in both sexes than Gst p-2.

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