Translation (Austin, Tex.)最新文献_第6页

Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system. 利用重组元件(PURE)系统分析蛋白质合成的限制因素。

Translation (Austin, Tex.) Pub Date : 2017-05-09 eCollection Date: 2017-01-01 DOI: 10.1080/21690731.2017.1327006

Jun Li, Chi Zhang, Poyi Huang, Erkin Kuru, Eliot T C Forster-Benson, Taibo Li, George M Church

{"title":"Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system.","authors":"Jun Li, Chi Zhang, Poyi Huang, Erkin Kuru, Eliot T C Forster-Benson, Taibo Li, George M Church","doi":"10.1080/21690731.2017.1327006","DOIUrl":"10.1080/21690731.2017.1327006","url":null,"abstract":"Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batch systems suffer from low ribosome recycling efficiency when translating proteins from 82 kD to 224 kD. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ∼1.5 to ∼2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"5 1","pages":"e1327006"},"PeriodicalIF":0.0,"publicationDate":"2017-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21690731.2017.1327006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35163467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 27

The utilization of selenocysteine-tRNA^[Ser]Sec isoforms is regulated in part at the level of translation in vitro. 硒代半胱氨酸- trna [Ser]Sec亚型的利用在体外翻译水平上受到部分调控。

Translation (Austin, Tex.) Pub Date : 2017-04-03 eCollection Date: 2017-01-01 DOI: 10.1080/21690731.2017.1314240

Bradley A Carlson, Nirupama Gupta, Mark H Pinkerton, Dolph L Hatfield, Paul R Copeland

{"title":"The utilization of selenocysteine-tRNA[Ser]Sec isoforms is regulated in part at the level of translation in vitro.","authors":"Bradley A Carlson, Nirupama Gupta, Mark H Pinkerton, Dolph L Hatfield, Paul R Copeland","doi":"10.1080/21690731.2017.1314240","DOIUrl":"https://doi.org/10.1080/21690731.2017.1314240","url":null,"abstract":"The tRNA for the 21st proteinogenic amino acid, selenocysteine, exists in mammalian cells as 2 isoforms differing by a single 2'-O-methylribosyl moiety at position 34 (Um34). These isoforms contain either 5-methoxycarbonylmethyluridine (mcm5U) or 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) at position 34. The accumulation of the mcm5Um isoform is tightly correlated with the expression of nonessential \"stress response\" selenoproteins such as glutathione peroxidase 1 (GPX1). The expression of essential selenoproteins, such as thioredoxin reductase 1 (TXNRD1), is not affected by changes in Sec-tRNA[Ser]Sec isoform accumulation. In this work we used purified mcm5U and mcm5Um Sec-tRNA[Ser]Sec isoforms to analyze possible differences in binding to the selenocysteine-specific elongation factor, EEFSEC, and the translation of GPX1 and TXNRD1in vitro. Our results indicate that no major distinction between mcm5U and mcm5Um isoforms is made by the translation machinery, but a small consistent increase in GPX1 translation is associated with the mcm5Um isoform. These results implicate fundamental differences in translation efficiency in playing a role in regulating selenoprotein expression as a function of isoform accumulation.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"5 1","pages":"e1314240"},"PeriodicalIF":0.0,"publicationDate":"2017-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21690731.2017.1314240","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35163465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. PRIMA:一种以基因为中心，rna到蛋白质的方法，用于绘制rna -蛋白质相互作用。

Translation (Austin, Tex.) Pub Date : 2017-02-28 eCollection Date: 2017-01-01 DOI: 10.1080/21690731.2017.1295130

Alex M Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D Holdorf, Sean P Ryder, Albertha J M Walhout

{"title":"PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions.","authors":"Alex M Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D Holdorf, Sean P Ryder, Albertha J M Walhout","doi":"10.1080/21690731.2017.1295130","DOIUrl":"https://doi.org/10.1080/21690731.2017.1295130","url":null,"abstract":"Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest-in a 'gene-centered' manner-yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA 'bait' can be tested versus multiple RBP 'preys' in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-length Caenorhabditis elegans 3' UTRs. PRIMA faithfully recapitulated numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmed in vivo. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"5 1","pages":"e1295130"},"PeriodicalIF":0.0,"publicationDate":"2017-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21690731.2017.1295130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35163466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Class II members of the poly(A) binding protein family exhibit distinct functions during Arabidopsis growth and development. 聚(A)结合蛋白家族II类成员在拟南芥生长发育过程中表现出不同的功能。

Translation (Austin, Tex.) Pub Date : 2017-02-17 eCollection Date: 2017-01-01 DOI: 10.1080/21690731.2017.1295129

Daniel R Gallie

{"title":"Class II members of the poly(A) binding protein family exhibit distinct functions during Arabidopsis growth and development.","authors":"Daniel R Gallie","doi":"10.1080/21690731.2017.1295129","DOIUrl":"https://doi.org/10.1080/21690731.2017.1295129","url":null,"abstract":"The poly(A)-binding protein (PABP) binds to the poly(A) tail of eukaryotic cellular mRNAs and contributes to their stability and translational efficiency. In plants, PABP is expressed from an unusually large gene family grouped into 3 classes that expanded during the evolution of land plants. Subsequent to expansion of the family, members diverged in their primary sequence and in expression. Further expansion of the family and divergence of its members in the Brassicaceae demonstrate the continued dynamic evolution of PABP in plants. In this study, the function of the widely-expressed class II PABP family members was examined to determine how individual class II members contribute to plant growth and development. Of the 3 class II PABP members, PAB2 and PAB4 contribute most to vegetative growth and vegetative-to-floral transition whereas PAB2, and the recently-evolved third class II member, PAB8, contribute to inflorescence and silique growth. Interestingly, although class I and class III PABP members are expressed specifically in reproductive organs, class II PABP members are also necessary for fertility in that the combinatorial loss of PAB2 and either PAB4 or PAB8 expression resulted in reduced fertility. Although all 3 class II members are required for protein expression, PAB4 contributes most to the steady-state level of a reporter mRNA and to protein expression. These findings suggest that class II PABP members are partially overlapping in function but also involved in distinct aspects of plant growth and development.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"5 1","pages":"e1295129"},"PeriodicalIF":0.0,"publicationDate":"2017-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21690731.2017.1295129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35163537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Radiation-induced translational control of gene expression. 辐射诱导的基因表达转化控制。

Translation (Austin, Tex.) Pub Date : 2016-12-01 eCollection Date: 2017-01-01 DOI: 10.1080/21690731.2016.1265703

Amy Wahba, Stacey L Lehman, Philip J Tofilon

引用次数: 0

The eukaryotic translation initiation factor eIF4E wears a “cap” for many occasions 真核翻译起始因子eIF4E在许多场合都戴着“帽子”

Translation (Austin, Tex.) Pub Date : 2016-07-02 DOI: 10.1080/21690731.2016.1220899

K. Borden

{"title":"The eukaryotic translation initiation factor eIF4E wears a “cap” for many occasions","authors":"K. Borden","doi":"10.1080/21690731.2016.1220899","DOIUrl":"https://doi.org/10.1080/21690731.2016.1220899","url":null,"abstract":"ABSTRACT The eukaryotic translation initiation factor eIF4E plays important roles in controlling the composition of the proteome. Indeed, dysregulation of eIF4E is associated with poor prognosis cancers. The traditional view has been that eIF4E acts solely in translation. However, over the last ∼25 years, eIF4E was found in the nucleus where it acts in mRNA export and in the last ∼10 years, eIF4E was found in cytoplasmic processing bodies (P-bodies) where it functions in mRNA sequestration and stability. The common biochemical thread for these activities is the ability of eIF4E to bind the 7-methylguanosine cap on the 5′ end of mRNAs. Recently, the possibility that eIF4E directly binds some mRNA elements independently of the cap has also been raised. Importantly, the effects of eIF4E are not genome-wide with a subset of transcripts targeted depending on the presence of specific mRNA elements and context-dependent regulatory factors. Indeed, eIF4E governs RNA regulons through co-regulating the expression of groups of transcripts acting in the same biochemical pathways. In addition, studies over the past ∼15 years indicate that there are multiple strategies that regulatory factors employ to modulate eIF4E activities in context-dependent manners. This perspective focuses on these new findings and incorporates them into a broader model for eIF4E function.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81278645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

RNA G-quadruplexes and their potential regulatory roles in translation RNA g -四联体及其在翻译中的潜在调控作用

Translation (Austin, Tex.) Pub Date : 2016-07-02 DOI: 10.1080/21690731.2016.1244031

Jingwen Song, J. Perreault, I. Topisirovic, S. Richard

引用次数: 110

Fusion proteins of Arabidopsis cap-binding proteins: Cautionary “tails” of woe 拟南芥帽结合蛋白的融合蛋白:灾难的警示“尾巴”

Translation (Austin, Tex.) Pub Date : 2016-07-02 DOI: 10.1080/21690731.2016.1257408

Elizabeth Levins, C. Tseng, R. M. Patrick, Laura K. Mayberry, Nicola A. Cole, K. Browning

{"title":"Fusion proteins of Arabidopsis cap-binding proteins: Cautionary “tails” of woe","authors":"Elizabeth Levins, C. Tseng, R. M. Patrick, Laura K. Mayberry, Nicola A. Cole, K. Browning","doi":"10.1080/21690731.2016.1257408","DOIUrl":"https://doi.org/10.1080/21690731.2016.1257408","url":null,"abstract":"ABSTRACT The use of fluorescent proteins fused to other proteins has been very useful in revealing the location and function of many proteins. However, it is very important to show that the fusion of these reporter proteins does not impact the function of the protein of interest. Plants have 2 forms of the cap-binding protein that function in initiation of translation, eIF4E and a plant specific form, eIFiso4E. In an attempt to determine the cellular localization of eIFiso4E, fusions to GFP were made, but were found to not be competent to rescue the lethal phenotype of plants lacking eIF4E and eIFiso4E. This suggested that the GFP fusions at either the N- or C-terminus of eIFiso4E were not functional. Biochemical analysis of the fusions revealed that eIFiso4E•GFP fusions were not able to bind to m7GTP Sepharose indicating that they were not functional as cap-binding proteins. Analysis of eIF4E•GFP fusions, both in yeast and in vitro, showed that the N-terminal fusion may be functional, whereas the C-terminal fusion bound m7GTP Sepharose very poorly and functioned poorly in yeast. These results highlight the importance of verification both biochemically and in vivo that reporter fusions of proteins maintain activity and are stable in order to prevent observations that may result in artifacts.","PeriodicalId":90376,"journal":{"name":"Translation (Austin, Tex.)","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88374643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma 高水平的核糖体蛋白eL36和eL42控制横纹肌肉瘤Hsp90的表达

Translation (Austin, Tex.) Pub Date : 2016-07-02 DOI: 10.1080/21690731.2016.1244395

Sarah Shaikho, C. Dobson, Thet Naing, Bahram Samanfar, H. Moteshareie, Maryam Hajikarimloo, A. Golshani, M. Holcik

引用次数: 5

The “periodic table” of the genetic code: A new way to look at the code and the decoding process 遗传密码的“元素周期表”:一种看待密码和解码过程的新方法

Translation (Austin, Tex.) Pub Date : 2016-07-02 DOI: 10.1080/21690731.2016.1234431

A. Komar

引用次数: 5