Identification of spatial specifically expressed genes in rice (Oryza sativa) seedlings using cDNA microarray

2004 ◽  
Vol 1 (2) ◽  
pp. 133-139
Author(s):  
Sun Liang-Xian ◽  
Dong Hai-Tao ◽  
Zhuang Xiao-Feng ◽  
Zhang Feng ◽  
Li De-Bao
Keyword(s):  
Ribosomal Protein ◽  
Lipid Transfer Protein ◽  
Protein Biosynthesis ◽  
Critical Role ◽  
Phosphoglycerate Kinase ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Metabolic Reaction ◽  
Lipid Transfer ◽  
Molecular Physiology

AbstractMembranous cDNA microarrays containing 2200 unique rice transcripts were designed for screening the characteristics of spatially expressed genes in post-germination rice seedlings. By comparing the profiles obtained, 31 genes were identified as expressed specifically in the plumule, 36 in the mesocotyl and 73 in the radicle. Several genes, such as polyubiquitin, UDP-glucose pyrophosphorylase, sucrose synthase and phosphoglycerate kinase, which encode components of the carbohydrate or protein metabolic reaction cascades, were expressed specifically in the mesocotyl, indicating that degradation reactions of the endospermous reserve starch and proteins occur mainly in the mesocotyl during the post-germination stage. A number of genes involved in defence mechanisms or in the processes of replication, transcription and translation were identified as expressed specifically in the plumule or radicle. Among plumule specifically expressed genes, translation initiation factor 5a, 40s ribosomal protein s28 and ribosomal protein 136 are considered to have a critical role in protein biosynthesis; while allergenic protein, β-D-glucan exohydrolase and actin 11 are genes with defending functions. Among the catalogue of radicle specifically expressed genes, EF-1a, Tat binding protein, replication protein A2, histone h3.2, ribosomal protein s29a and 40s ribosomal protein s19 are genes that function in the process of replication, transcription or translation; whereas glycine-rich protein, wound-induced basic protein, Bowman-Birk proteinase inhibitor and lipid transfer protein-2 are genes involved in defence responses. Results of this experiment have provided insight into post-germination molecular physiology at the genomic level of gene expression.

scholarly journals Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms

2021 ◽  
Vol 9 (8) ◽  
pp. 1546
Author(s):  
Sarah Hendrickx ◽  
João Luís Reis-Cunha ◽  
Sarah Forrester ◽  
Daniel C. Jeffares ◽  
Guy Caljon
Keyword(s):  
Ribosomal Protein ◽  
Protein Tyrosine Phosphatase ◽  
Copy Number ◽  
Leishmania Donovani ◽  
Rna Binding ◽  
Tyrosine Phosphatase ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Gene Copy ◽  
Protein Tyrosine

The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug resistance challenge its broad application and urge for rational use and monitoring of resistance. However, no causal molecular mechanisms to Leishmania PMM resistance have been identified so far. To gain insights into potential resistance mechanisms, twelve experimentally selected Leishmania donovani clonal lines and the non-cloned preselection population, with variable degrees of PMM resistance, were subjected to whole genome sequencing. To identify genomic variations potentially associated with resistance, SNPs, Indels, chromosomal somy and gene copy number variations were compared between the different parasite lines. A total of 11 short nucleotide variations and the copy number alterations in 39 genes were correlated to PMM resistance. Some of the identified genes are involved in transcription, translation and protein turn-over (transcription elongation factor-like protein, RNA-binding protein, ribosomal protein L1a, 60S ribosomal protein L6, eukaryotic translation initiation factor 4E-1, proteasome regulatory non-ATP-ase subunit 3), virulence (major surface protease gp63, protein-tyrosine phosphatase 1-like protein), mitochondrial function (ADP/ATP mitochondrial carrier-like protein), signaling (phosphatidylinositol 3-related kinase, protein kinase putative and protein-tyrosine phosphatase 1-like protein) and vesicular trafficking (ras-related protein RAB1). These results indicate that, in Leishmania, the aminoglycoside PMM affects protein translational processes and underlines the complex and probably multifactorial origin of resistance.

scholarly journals OseIF3h Regulates Plant Growth and Pollen Development at Translational Level Presumably through Interaction with OsMTA2

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1101
Author(s):  
Yuqing Huang ◽  
Peng Zheng ◽  
Xuejiao Liu ◽  
Hao Chen ◽  
Jumin Tu
Keyword(s):  
Plant Growth ◽  
Translation Initiation ◽  
Pollen Development ◽  
Messenger Rna ◽  
Protein Biosynthesis ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Sequencing Data ◽  
Knock Out ◽  
Translational Level

The initiation stage of protein biosynthesis is a sophisticated process tightly regulated by numerous initiation factors and their associated components. However, the mechanism underlying translation initiation has not been completely understood in rice. Here, we showed knock-out mutation of the rice eukaryotic translation initiation factor 3 subunit h (OseIF3h) resulted in plant growth retardation and seed-setting rate reduction as compared to the wild type. Further investigation demonstrated an interaction between OseIF3h and OsMTA2 (mRNA adenosine methylase 2), a rice homolog of METTL3 (methyltransferase-like 3) in mammals, which provided new insight into how N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is engaged in the translation initiation process in monocot species. Moreover, the RIP-seq (RNA immunoprecipitation sequencing) data suggested that OseIF3h was involved in multiple biological processes, including photosynthesis, cellular metabolic process, precursor metabolites, and energy generation. Therefore, we infer that OseIF3h interacts with OsMTA2 to target a particular subset of genes at translational level, regulating plant growth and pollen development.

scholarly journals Development of Biochemical Assays for the Identification of eIF4E-Specific Inhibitors

2012 ◽  
Vol 17 (5) ◽  
pp. 581-592 ◽  
Author(s):  
Carlo Visco ◽  
Claudia Perrera ◽  
Sandrine Thieffine ◽  
Federico Riccardi Sirtori ◽  
Roberto D’Alessio ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Cell Cycle Progression ◽  
Critical Role ◽  
Mrna Translation ◽  
Binding Pocket ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Oncogenic Pathways ◽  
Biochemical Assays ◽  
Specific Inhibitors

Control of mRNA translation plays a critical role in cell growth, proliferation, and differentiation and is tightly regulated by AKT and RAS oncogenic pathways. A key player in the regulation of this process is the mRNA 5′ cap-binding protein, eukaryotic translation initiation factor 4E (eIF4E). eIF4E contributes to malignancy by selectively enabling the translation of a limited pool of mRNAs that generally encode key proteins involved in cell cycle progression, angiogenesis, and metastasis. Several data indicate that the inhibition of eIF4E in tumor cell lines and xenograft models impairs tumor growth and induces apoptosis; eIF4E, therefore, can be considered a valuable target for cancer therapy. Targeting the cap-binding pocket of eIF4E should represent a way to inhibit all the eIF4E cellular functions. We present here the development and validation of different biochemical assays based on fluorescence polarization and surface plasmon resonance techniques. These assays could support high-throughput screening, further refinement, and characterization of eIF4E inhibitors, as well as selectivity assessment against CBP80/CBP20, the other major cap-binding complex of eukaryotic cells, overall providing a robust roadmap for development of eIF4E-specific inhibitors.

scholarly journals Molecular Structure and Functional Elucidation of IF-3 Protein of Chloroflexus Aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

2021 ◽  
Author(s):  
Abu Saim Mohammad Saikat
Keyword(s):  
Translation Initiation ◽  
Protein Interactions ◽  
In Silico ◽  
Tertiary Structure ◽  
Protein Biosynthesis ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Chloroflexus Aurantiacus ◽  
Protein Protein Interactions ◽  
Functional Interpretation

<p><i>Chloroflexus aurantiacus</i> is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study aimed to allocate the structure and function through an in-silico approach required for bacterial protein biosynthesis. This in-silico viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The in-silico investigation documented the protein's hydrophilic nature with predominantly alpha (α) helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of <i>C. aurantiacus</i>. </p> <p> </p>

scholarly journals Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In-Silico Approach

2021 ◽  
Author(s):  
Abu Saim Mohammad Saikat ◽  
Md. Ekhlas Uddin ◽  
Tasnim Ahmad ◽  
Shahriar Mahmud ◽  
Md. Abu Sayeed Imran ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Protein Interactions ◽  
In Silico ◽  
Tertiary Structure ◽  
Protein Biosynthesis ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Chloroflexus Aurantiacus ◽  
Protein Protein Interactions ◽  
Functional Interpretation

<p>Chloroflexus aurantiacus is a thermophilic bacterium that produces a multitude of proteins<br>within its genome. Bioinformatics strategies can facilitate comprehending this organism through<br>functional and structural interpretation assessments.This study aimed to allocate the structure and<br>function through an in-silico approach required for bacterial protein biosynthesis. This in-silico<br>viewpoint provides copious properties, including the physicochemical properties, subcellular location,<br>three-dimensional structure, protein-protein interactions, and functional elucidation of the protein<br>(WP_012256288.1). The STRING program is utilized for the explication of protein-protein<br>interactions. The in-silico investigation documented the protein's hydrophilic nature with<br>predominantly alpha (α) helices in its secondary structure.The tertiary-structure model of the protein<br>has been shown to exhibit reasonably high consistency based on various quality assessment<br>methods.The functional interpretation suggested that the protein can act as a translation initiation<br>factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also<br>demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in<br>protein synthesis. This study is bioinformatically examined that the protein (WP_012256288.1) is<br>affiliated in protein biosynthesis as a translation initiation factor IF-3 of C. aurantiacus. <br><br></p>

scholarly journals Knockdown of EIF3H inhibits the development and progression of pancreatic cancer by regulating cell proliferation and apoptosis in vitro

2022 ◽  
Vol 67 (4) ◽  
pp. 83-90
Author(s):  
Yuqiang Shan ◽  
Wencheng Kong ◽  
Akao Zhu ◽  
Jiangtao Li ◽  
Huicheng Jin ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cancer Cells ◽  
Critical Role ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Loss Of Function ◽  
Eukaryotic Translation ◽  
Proliferation Capacity ◽  
Pancreatic Cancer Cells

Nowadays, pancreatic cancer has been recognized as one of the most fatal malignancies worldwide, the molecular mechanism of which is still not fully understood. In this study, we aimed to uncover the fundamental functions of the eukaryotic translation initiation factor 3H subunit (EIF3H) in the development and progression of pancreatic cancer. Firstly, the results of immunohistochemical (IHC) staining revealed that EIF3H was highly expressed in pancreatic cancer. Moreover, lentiviruses were used to deliver shRNAs into pancreatic cancer cells for silencing EIF3H. Furthermore, the loss-of-function assays demonstrated that knockdown of EIF3H could inhibit the progression of pancreatic cancer cells by reducing proliferation capacity, promoting apoptosis, arresting cell cycle in G2 and suppressing cell migration. In summary, EIF3H may play a critical role in the development and progression of pancreatic cancer, which possesses the potential to act as a therapeutic target for pancreatic cancer treatment.

GCD11, a negative regulator of GCN4 expression, encodes the gamma subunit of eIF-2 in Saccharomyces cerevisiae

1993 ◽  
Vol 13 (1) ◽  
pp. 506-520
Author(s):  
E M Hannig ◽  
A M Cigan ◽  
B A Freeman ◽  
T G Kinzy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Metal Binding ◽  
Critical Role ◽  
Cross Reactivity ◽  
Translation Initiation Factor ◽  
Negative Regulator ◽  
Initiation Factor ◽  
Translational Efficiency ◽  
Gamma Subunit

The eukaryotic translation initiation factor eIF-2 plays a critical role in regulating the expression of the yeast transcriptional activator GCN4. Mutations in genes encoding the alpha and beta subunits of eIF-2 alter translational efficiency at the GCN4 AUG codon and constitutively elevate GCN4 translation. Mutations in the yeast GCD11 gene have been shown to confer a similar phenotype. The nucleotide sequence of the cloned GCD11 gene predicts a 527-amino-acid polypeptide that is similar to the prokaryotic translation elongation factor EF-Tu. Relative to EF-Tu, the deduced GCD11 amino acid sequence contains a 90-amino-acid N-terminal extension and an internal cysteine-rich sequence that contains a potential metal-binding finger motif. We have identified the GCD11 gene product as the gamma subunit of eIF-2 by the following criteria: (i) sequence identities with mammalian eIF-2 gamma peptides; (ii) increased eIF-2 activity in extracts prepared from cells cooverexpressing GCD11, eIF-2 alpha, and eIF-2 beta; and (iii) cross-reactivity of antibodies directed against the GCD11 protein with the 58-kDa polypeptide present in purified yeast eIF-2. The predicted GCD11 polypeptide contains all of the consensus elements known to be required for guanine nucleotide binding, suggesting that, in Saccharomyces cerevisiae, the gamma subunit of eIF-2 is responsible for GDP-GTP binding.

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