scholarly journals Characterization of a cis-acting regulatory element in the protein coding region of thymidylate synthase mRNA

2000 ◽  
Vol 28 (6) ◽  
pp. 1381-1389 ◽  
Author(s):  
X. Lin
Keyword(s):  
Thymidylate Synthase ◽  
Regulatory Element ◽  
Coding Region ◽  
Protein Coding ◽  
Cis Acting

scholarly journals Characterization of Tomato Necrotic Spot Virus, a Subgroup 1 Ilarvirus Causing Necrotic Foliar, Stem, and Fruit Symptoms in Tomatoes in the United States

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1391-1396 ◽  
Author(s):  
Sara A. Bratsch ◽  
Samuel Grinstead ◽  
Tom C. Creswell ◽  
Gail E. Ruhl ◽  
Dimitre Mollov
Keyword(s):  
Genomic Sequence ◽  
The United States ◽  
Amino Acid Identity ◽  
Necrotic Spot ◽  
Coding Region ◽  
Spot Virus ◽  
Protein Coding ◽  
Serological Characterization ◽  
Necrotic Spots

The genomic, biological, and serological characterization of tomato necrotic spot virus (ToNSV), a virus first described infecting tomato in California, was completed. The complete genomic sequence identified ToNSV as a new subgroup 1 ilarvirus distinct from the previously described tomato-infecting ilarviruses. We identified ToNSV in Indiana in 2017 and 2018 and in Ohio in 2018. The coat protein coding region of the isolates from California, Indiana, and Ohio have 94 to 98% identity, while the same isolates had 99% amino acid identity. ToNSV is serologically related to TSV, a subgroup 1 ilarvirus, and shows no serological relationship to ilarviruses in the other subgroups. In tomato, ToNSV caused symptoms of necrotic spots and flecks on leaves, necrotic streaking on stems, and necrotic spots and circular patterns on fruit resulting in a yield loss of 1 to 13%. These results indicate that ToNSV is a proposed new subgroup 1 ilarvirus causing a necrotic spotting disease of tomato observed in California, Indiana, and Ohio.

scholarly journals Functional mapping of the translation-dependent instability element of yeast MATalpha1 mRNA.

1996 ◽  
Vol 16 (7) ◽  
pp. 3833-3843 ◽  
Author(s):  
A N Hennigan ◽  
A Jacobson
Keyword(s):  
Stability Boundary ◽  
Mrna Translation ◽  
Rare Codon ◽  
Molecular Evidence ◽  
Wild Type ◽  
Coding Region ◽  
Sequence Element ◽  
Protein Coding ◽  
Cis Acting ◽  
Mrna Stabilization

The determinants of mRNA stability include specific cis-acting destabilizing sequences located within mRNA coding and noncoding regions. We have developed an approach for mapping coding-region instability sequences in unstable yeast mRNAs that exploits the link between mRNA translation and turnover and the dependence of nonsense-mediated mRNA decay on the activity of the UPF1 gene product. This approach, which involves the systematic insertion of in-frame translational termination codons into the coding sequence of a gene of interest in a upf1delta strain, differs significantly from conventional methods for mapping cis-acting elements in that it causes minimal perturbations to overall mRNA structure. Using the previously characterized MATalpha1 mRNA as a model, we have accurately localized its 65-nucleotide instability element (IE) within the protein coding region. Termination of translation 5' to this element stabilized the MATalpha1 mRNA two- to threefold relative to wild-type transcripts. Translation through the element was sufficient to restore an unstable decay phenotype, while internal termination resulted in different extents of mRNA stabilization dependent on the precise location of ribosome stalling. Detailed mutagenesis of the element's rare-codon/AU-rich sequence boundary revealed that the destabilizing activity of the MATalpha1 IE is observed when the terminal codon of the element's rare-codon interval is translated. This region of stability transition corresponds precisely to a MATalpha1 IE sequence previously shown to be complementary to 18S rRNA. Deletion of three nucleotides 3' to this sequence shifted the stability boundary one codon 5' to its wild-type location. Conversely, constructs containing an additional three nucleotides at this same location shifted the transition downstream by an equivalent sequence distance. Our results suggest a model in which the triggering of MATalpha1 mRNA destabilization results from establishment of an interaction between translating ribosomes and a downstream sequence element. Furthermore, our data provide direct molecular evidence for a relationship between mRNA turnover and mRNA translation.

scholarly journals The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7031 ◽  
Author(s):  
Thanh Hoa Le ◽  
Khue Thi Nguyen ◽  
Nga Thi Bich Nguyen ◽  
Huong Thi Thanh Doan ◽  
Takeshi Agatsuma ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Lung Fluke ◽  
Short Tandem

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5′ end of nad4 overlapped with the 3′ end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

Regulation of Hoxc-8 during mouse embryonic development: identification and characterization of critical elements involved in early neural tube expression

Development ◽  
1995 ◽  
Vol 121 (12) ◽  
pp. 4339-4347 ◽  
Author(s):  
C.S. Shashikant ◽  
C.J. Bieberich ◽  
H.G. Belting ◽  
J.C. Wang ◽  
M.A. Borbely ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Neural Tube ◽  
Small Region ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Cis Acting ◽  
Critical Elements ◽  
Reporter Gene Analysis ◽  
Combinatorial Interactions

We have characterized cis-acting elements that direct the early phase of Hoxc-8 expression using reporter gene analysis in transgenic mice. By deletion we show that a 135 bp DNA fragment, located approximately 3 kb upstream of the coding region of Hoxc-8, is capable of directing posterior neural tube expression. This early neural tube (ENT) enhancer consists of four separate elements, designated A, B, C and D, whose nucleotide sequences are similar to binding sites of known transcription factors. Nucleotide substitutions suggest that element A is an essential component of the ENT enhancer. However element A by itself is incapable of directing neural tube expression. This element requires interactions at any two of the other three elements, B, C or D. Thus, the components of the ENT enhancer direct neural tube expression in an interdependent manner. We propose that Hoxc-8 is activated in the neural tube by combinatorial interactions among several proteins acting within a small region. Our transgenic analyses provide a means to identify transcription factors that regulate Hoxc-8 expression during embryogenesis.

Transcription control region within the protein-coding portion of adenovirus E1A genes

1984 ◽  
Vol 4 (7) ◽  
pp. 1293-1305
Author(s):  
T F Osborne ◽  
D N Arvidson ◽  
E S Tyau ◽  
M Dunsworth-Browne ◽  
A J Berk
Keyword(s):  
Control Region ◽  
Adenovirus Type ◽  
Coding Region ◽  
Transcription Control ◽  
Protein Coding ◽  
Single Base ◽  
Cis Acting ◽  
Single Base Deletion ◽  
Adenovirus Type 5 ◽  
E1a Protein

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

scholarly journals Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover.

1995 ◽  
Vol 15 (2) ◽  
pp. 809-823 ◽  
Author(s):  
K W Hagan ◽  
M J Ruiz-Echevarria ◽  
Y Quan ◽  
S W Peltz
Keyword(s):  
Mrna Decay ◽  
General Characteristic ◽  
Mrna Turnover ◽  
Coding Region ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nonsense Mutations ◽  
Cis Acting ◽  
Nonsense Mediated Mrna Decay ◽  
Translational Termination

Several lines of evidence indicate that the processes of mRNA turnover and translation are intimately linked and that understanding this relationship is critical to elucidating the mechanism of mRNA decay. One clear example of this relationship is the observation that nonsense mutations can accelerate the decay of mRNAs in a process that we term nonsense-mediated mRNA decay. The experiments described here demonstrate that in the yeast Saccharomyces cerevisiae premature translational termination within the initial two-thirds of the PGK1 coding region accelerates decay of that transcript regardless of which of the stop codons is used. Nonsense mutations within the last quarter of the coding region have no effect on PGK1 mRNA decay. The sequences required for nonsense-mediated mRNA decay include a termination codon and specific sequences 3' to the nonsense mutation. Translation of two-thirds of the PGK1 coding region inactivates the nonsense-mediated mRNA decay pathway. This observation explains why carboxyl-terminal nonsense mutations are resistant to accelerated decay. Characterization of the decay of nonsense-containing HIS4 transcripts yielded results mirroring those described above, suggesting that the sequence requirements described for the PGK1 transcript are likely to be a general characteristic of this decay pathway. In addition, an analysis of the decay intermediates of nonsense-containing mRNAs indicates that nonsense-mediated mRNA decay flows through a pathway similar to that described for a class of wild-type transcripts. The initial cleavage event occurs near the 5' terminus of the nonsense-containing transcript and is followed by 5'-->3' exonucleolytic digestion. A model for nonsense-mediated mRNA decay based on these results is discussed.

scholarly journals Transcription control region within the protein-coding portion of adenovirus E1A genes.

1984 ◽  
Vol 4 (7) ◽  
pp. 1293-1305 ◽  
Author(s):  
T F Osborne ◽  
D N Arvidson ◽  
E S Tyau ◽  
M Dunsworth-Browne ◽  
A J Berk
Keyword(s):  
Control Region ◽  
Adenovirus Type ◽  
Coding Region ◽  
Transcription Control ◽  
Protein Coding ◽  
Single Base ◽  
Cis Acting ◽  
Single Base Deletion ◽  
Adenovirus Type 5 ◽  
E1a Protein

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

scholarly journals Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (Insecta: Diptera: Calliphoridae)

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Luis Carvalho ◽  
Paul Maclean
Keyword(s):  
New Zealand ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Calliphora Vicina ◽  
Coding Region ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Next Generation Sequencing Technology ◽  
Monophyletic Cluster

ABSTRACTIn the present study, the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mitochondrial genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1,689 bp non-coding region, similar to most metazoan mitochondrial genomes. Phylogenetic analysis showed that C. vicina NZ_CalVic_NP does not form a monophyletic cluster with the remaining three Calliphorinae species. The complete mitochondrial genome sequence of C. vicina NZ_CalVic_NP is a resource to facilitate future species identification research within the Calliphoridae.

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