ADAR-mediated messenger RNA editing: analysis at the proteome level

2016 ◽  
Vol 62 (5) ◽  
pp. 510-519 ◽  
Author(s):  
A.A. Kliuchnikova ◽  
K.G. Kuznetsova ◽  
S.A. Moshkovskii
Keyword(s):  
Rna Editing ◽  
Protein Level ◽  
Messenger Rna ◽  
Nervous Tissue ◽  
Shotgun Proteomics ◽  
Amino Acid Substitutions ◽  
Qualitative And Quantitative Analysis ◽  
Adenosine Deaminases ◽  
Qualitative And Quantitative ◽  
Proteome Level

Post-transcriptional RNA editing by RNA specific adenosine deaminases (ADAR) was discovered more than two decades ago. It provides additional regulation of animal and human transcriptome. In most cases, it occurs in nervous tissue, where, as a result of the reaction, adenosine is converted to inosine in particular sites of RNA. In case of messenger RNA, during translation, inosine is recognized as guanine leading to amino acid substitutions. Those substitutions are shown to affect substantially the function of proteins, e.g. subunits of the glutamate receptor. Nevertheless, most of the works on RNA editing use analysis of nucleic acids, even those which deal with a coding RNA. In this review, we propose the use of shotgun proteomics based on high resolution liquid chromatography and mass spectrometry for investigation of the effects of RNA editing at the protein level. Recently developed methods of big data processing allow combining the results of various omics techniques, being referred to as proteogenomics. The proposed proteogenomic approach for the analysis of RNA editing at the protein level will directly conduct a qualitative and quantitative analysis of protein edited sequences in the scale of whole proteome.

ADAR-mediated messenger RNA Editing: Analysis at the proteome level

2017 ◽  
Vol 11 (1) ◽  
pp. 32-42
Author(s):  
A. A. Kliuchnikova ◽  
K. G. Kuznetsova ◽  
S. A. Moshkovskii
Keyword(s):  
Rna Editing ◽  
Messenger Rna ◽  
Proteome Level

scholarly journals Proteogenomics of adenosine-to-inosine RNA editing in the fruit fly

2017 ◽  
Author(s):  
Ksenia G Kuznetsova ◽  
Anna A Kliuchnikova ◽  
Irina Y Ilina ◽  
Alexey L Chernobrovkin ◽  
Svetlana E Novikova ◽  
...  
Keyword(s):  
Rna Editing ◽  
Membrane Trafficking ◽  
Multiple Reaction Monitoring ◽  
Shotgun Proteomics ◽  
Fruit Fly ◽  
Data Sets ◽  
Protein Database ◽  
Editing Event ◽  
Proteome Level ◽  
Proteomic Study

Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in the study: two taken from public repository and the third one obtained here. A customized protein sequence database was generated using results of genome-wide adenosine-to-inosine RNA studies and applied for identifying the edited proteins. The total number of 68 edited peptides belonging to 59 proteins was identified in all data sets. Eight of them being shared between the whole insect, head and brain proteomes. Seven edited sites belonging to synaptic vesicle and membrane trafficking proteins were selected for validation by orthogonal analysis by Multiple Reaction Monitoring. Five editing events in cpx, Syx1A, Cadps, CG4587 and EndoA were validated in fruit fly brain tissue at the proteome level using isotopically labeled standards. Ratios of unedited-to-edited proteoforms varied from 35:1 (Syx1A) to 1:2 (EndoA). Lys-137 to Glu editing of endophilin A may have functional consequences for its interaction to membrane. The work demonstrates the feasibility to identify the RNA editing event at the proteome level using shotgun proteomics and customized edited protein database.

scholarly journals Identification and Spatiotemporal Expression of Adenosine Deaminases Acting on RNA (ADAR) during Earthworm Regeneration: Its Possible Implication in Muscle Redifferentiation

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 448
Author(s):  
Yoo Bin Yoon ◽  
Yun-Sang Yu ◽  
Beom Jun Park ◽  
Sung-Jin Cho ◽  
Soon Cheol Park
Keyword(s):  
Rna Editing ◽  
Messenger Rna ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Binding Domain ◽  
Sequencing Analysis ◽  
Temporal Expression ◽  
Perionyx Excavatus ◽  
Double Stranded Rna ◽  
Adenosine Deaminases

Adenosine deaminases acting on RNA (ADAR) catalyze the hydrolytic deamination of adenosine (A) to produce inosine (I) in double-stranded RNA substrates. A-to-I RNA editing has increasingly broad physiological significance in development, carcinogenesis, and environmental adaptation. Perionyx excavatus is an earthworm with potent regenerative potential; it can regenerate the head and tail and is an advantageous model system to investigate the molecular mechanisms of regeneration. During RNA sequencing analysis of P. excavatus regenerates, we identified an ADAR homolog (Pex-ADAR), which led us to examine its spatial and temporal expression to comprehend how Pex-ADAR is linked to regeneration. At first, in domain analysis, we discovered that Pex-ADAR only has one double-stranded RNA-binding domain (dsRBD) and a deaminase domain without a Z-DNA-binding domain (ZBD). In addition, a comparison of the core deaminase domains of Pex-ADAR with those of other ADAR family members indicated that Pex-ADAR comprises the conserved three active-site motifs and a glutamate residue for catalytic activity. Pex-ADAR also shares 11 conserved residues, a characteristic of ADAR1, supporting that Pex-ADAR is a member of ADAR1 class. Its temporal expression was remarkably low in the early stages of regeneration before suddenly increasing at 10 days post amputation (dpa) when diverse cell types and tissues were being regenerated. In situ hybridization of Pex-ADAR messenger RNA (mRNA) indicated that the main expression was observed in regenerating muscle layers and related connective tissues. Taken together, the present results demonstrate that an RNA-editing enzyme, Pex-ADAR, is implicated in muscle redifferentiation during earthworm regeneration.

Designing a business unit and creating the first ever responsive kitchen

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Paolo FESTA ◽  
Tommaso CORA ◽  
Lucilla FAZIO
Keyword(s):  
Value Creation ◽  
Product Innovation ◽  
Research Laboratory ◽  
Direct Relationship ◽  
Multidisciplinary Approach ◽  
Design Thinking ◽  
Business Unit ◽  
Qualitative And Quantitative Analysis ◽  
Qualitative And Quantitative ◽  
The Relationship

Is it possible to transform stone into a technological and innovative device? The meeting with one of the main stone transformers in Europe produced the intention of a disruptive operation that could affect the strategy of the whole company. A contagious singularity. By intertwining LEAN methodologies and the human-centric approach of design thinking, we mapped the value creation in the company activating a dialogue with the workers and the management, listening to people, asking for ambitions, discovering problems and the potential of production. This qualitative and quantitative analysis conducted with a multidisciplinary approach by designers, architects and marketing strategists allowed us to define a new method. We used it to design a platform that could let all the players express their potential to the maximum. This is how the group's research laboratory was born, with the aim of promoting the relationship between humans and stone through product innovation. With this goal, we coordinated the new team, developing technologies that would allow creating a more direct relationship between man and surface, making the stone reactive. The result was the first responsive kitchen ever.

ANALISIS FAKTOR TINGKAT PENDIDIKAN DAN KOMPETENSI SUMBER DAYA MANUSIA TERHADAP PRODUKTIVITAS KERJA KARYAWAN PADA PT. TRAKTOR NUSANTARA CABANG LAMPUNG

2017 ◽  
Vol 2 (1) ◽  
pp. 46-63
Author(s):  
Raditee Sanusi Husin
Keyword(s):  
Work Productivity ◽  
Positive Influence ◽  
Education Level ◽  
Observation Data ◽  
Employee Productivity ◽  
Qualitative And Quantitative Analysis ◽  
Employee Education ◽  
Level Of Education ◽  
Qualitative And Quantitative ◽  
Level Variable

Achievement of company goals, PT. Traktor Nusantara often faces problems, where from within and from outside the company. One of the problems that comes from within the company in relation to human resources is the level of work productivity of employees who are still far from expectation. This is allegedly caused by the level of employee education that has not been in accordance with the function of office, in addition to the competence of employees who have not been in accordance with the field of work. This study aims to determine the influence of education level and competence on employee productivity. The sample used is 22 employees. Data collection techniques with questionnaires, documentation and observation. Data analysis with qualitative and quantitative analysis methods with the help of statistical tools SPSS application for linear regression model calculation. The results showed that the level of education has a positive influence on the productivity of employees of PT. Traktor Nusantara. The amount of influence of education level variable to productivity based on test of determination is equal to 38,1%. Competence influence on work productivity of employees of PT. Traktor Nusantara with contribution of 19.1%. The level of education and competence together have a positive influence and able to explain 38.2% of the changes in work productivity, while the remaining 4.7% sebesat is another variable outside the study.

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