Impact of Non-canonical Decoding on the Proteome

非规范解码对蛋白质组的影响

• 批准号: 8129498
• 负责人: Joseph A Loo
• 金额: $ 30.19万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8129498
• 关键词: Amino Acid Sequence; Amino Acids; Bypass; Disease; Gene Expression; Genetic Polymorphism; Genetic Translation; Genome; Hereditary Disease; Life; Messenger RNA; Methods; Microbiology; Nucleotides; Pathway interactions; Post-Transcriptional Regulation; Process; Proteins; Proteome; Proteomics; Reading Frames; Research; Translations; abstracting; in vivo; therapy development

DESCRIPTION (provided by applicant): A. Project Summary/Abstract Recoding describes the local reprogramming of mRNA translation to discard standard translational rules and decode non-canonically. The products of this stimulated process, proteins incorporating shifts in reading frame, bypassed nucleotide segments, and/or unexpected amino acids have been observed in all 3 domains and are known to contribute importantly to post-transcriptional regulation of gene expression. Our hypothesis is that recoded and miscoded proteins are more important than previously anticipated, but that they are consistently overlooked by high-throughput proteomic methods that regard the proteome as a mirror of the genome. We believe that an altered proteomic workflow can reveal proteins recoded and miscoded in vivo, and that these methods can provide amino acid sequences for some of the recoded products. If successful, these efforts can potentially impact research in protein translation, microbiology, and proteomics. They can impact the development of therapies for genetic diseases, and can suggest explanations for the unusual activity differences observed for some gene products differing only by a synonymous polymorphism. They may also suggest a function for pseudo-messenger RNA. B. Project Narrative This proposal describes a method to examine the importance of an alternate pathway for synthesizing essential components of life. Should the pathway be found to be more important than previously anticipated, it will suggest causes and potential therapies for some disorders.

描述(由申请人提供)：A.项目摘要/摘要重新编码描述了信使核糖核酸翻译的局部重新编程，以丢弃标准翻译规则并以非规范的方式解码。在这三个结构域中都观察到了这种刺激过程的产物、含有阅读框架移位的蛋白质、绕过的核苷酸片段和/或意想不到的氨基酸，并被认为对基因表达的转录后调控具有重要作用。我们的假设是，重新编码和错误编码的蛋白质比之前预期的更重要，但它们一直被高通量蛋白质组学方法忽视，这些方法将蛋白质组视为基因组的镜子。我们认为，改变蛋白质组工作流程可以揭示体内蛋白质的重新编码和错误编码，这些方法可以为一些重新编码的产品提供氨基酸序列。如果成功，这些努力可能会影响蛋白质翻译、微生物学和蛋白质组学的研究。它们可以影响遗传病治疗方法的发展，并可以为观察到的某些基因产品不寻常的活性差异提供解释，这些基因产品只是通过同义多态而不同。他们还可能提出了假信使RNA的功能。B.项目叙述本提案描述了一种方法，用来检验合成生命基本成分的替代途径的重要性。如果发现这条途径比之前预期的更重要，它将提出一些疾病的原因和潜在的治疗方法。

项目成果

Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.

乙酰辅酶A中的焦磷酸依赖性ATP形成，在酸性营养性的酸性ATP形成上是一种新的扭曲。

• DOI: 10.1128/mbio.01208-16
• 发表时间: 2016-08-16
• 期刊: mBio
• 影响因子: 6.4
• 作者: James KL;Ríos-Hernández LA;Wofford NQ;Mouttaki H;Sieber JR;Sheik CS;Nguyen HH;Yang Y;Xie Y;Erde J;Rohlin L;Karr EA;Loo JA;Ogorzalek Loo RR;Hurst GB;Gunsalus RP;Szweda LI;McInerney MJ
• 通讯作者: McInerney MJ

Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1.

• DOI: 10.3389/fmicb.2015.00149
• 发表时间: 2015
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Leon DR;Ytterberg AJ;Boontheung P;Kim U;Loo JA;Gunsalus RP;Ogorzalek Loo RR
• 通讯作者: Ogorzalek Loo RR

Leveraging Immonium Ions for Targeting Acyl-Lysine Modifications in Proteomic Datasets.

• DOI: 10.1002/pmic.202000111
• 发表时间: 2021-03
• 期刊: Proteomics
• 影响因子: 3.4
• 作者: Muroski JM;Fu JY;Nguyen HH;Ogorzalek Loo RR;Loo JA
• 通讯作者: Loo JA