Characterization of guanidine carboxylases.

4区 生物学 Q3 Biochemistry, Genetics and Molecular Biology
Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-11-07 DOI:10.1016/bs.mie.2024.10.013
M Sinn, J Techel, A Joachimi, J S Hartig
{"title":"Characterization of guanidine carboxylases.","authors":"M Sinn, J Techel, A Joachimi, J S Hartig","doi":"10.1016/bs.mie.2024.10.013","DOIUrl":null,"url":null,"abstract":"<p><p>Guanidine metabolism has been an overlooked aspect of the global nitrogen cycle until RNA sensors (riboswitches) were discovered in bacteria that bind the nitrogen-rich compound. The associated genes were initially proposed to detoxify guanidine from the cells. We were intrigued by a genetic organization where the guanidine riboswitch is located upstream of an operon comprising a carboxylase, two putative hydrolases, and an assigned allophanate hydrolase. An ABC transporter is located on the same operon with a periplasmic binding domain that is indicative of an importer. Therefore, we hypothesized that certain bacteria actively import guanidine and assimilate the nitrogen. To test this hypothesis, we searched for bacteria that were able to assimilate guanidine. We isolated three enterobacteria (Raoultella terrigena str. JH01, Erwinia rhapontici str. JH02 and Klebsiella michiganensis str. JH07) that utilize guanidine efficiently as a nitrogen source. Proteome analyses demonstrate that the expression of the guanidine riboswitch-associated carboxylase, in conjunction with associated hydrolases and transport genes, is markedly elevated in the presence of guanidine. Subsequent analysis of the carboxylases that are homologous to urea carboxylase confirmed the substrate preference of guanidine over urea. This chapter outlines a procedure for the isolation of guanidine-assimilating bacteria and the analysis of their proteome to identify enzymes responsible for guanidine degradation. Finally, an assay for the characterization of the endogenous guanidine carboxylases in comparison with the endogenous urea carboxylase from E. rhapontici is described.</p>","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"708 ","pages":"105-123"},"PeriodicalIF":0.0000,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Methods in enzymology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/bs.mie.2024.10.013","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/11/7 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0

Abstract

Guanidine metabolism has been an overlooked aspect of the global nitrogen cycle until RNA sensors (riboswitches) were discovered in bacteria that bind the nitrogen-rich compound. The associated genes were initially proposed to detoxify guanidine from the cells. We were intrigued by a genetic organization where the guanidine riboswitch is located upstream of an operon comprising a carboxylase, two putative hydrolases, and an assigned allophanate hydrolase. An ABC transporter is located on the same operon with a periplasmic binding domain that is indicative of an importer. Therefore, we hypothesized that certain bacteria actively import guanidine and assimilate the nitrogen. To test this hypothesis, we searched for bacteria that were able to assimilate guanidine. We isolated three enterobacteria (Raoultella terrigena str. JH01, Erwinia rhapontici str. JH02 and Klebsiella michiganensis str. JH07) that utilize guanidine efficiently as a nitrogen source. Proteome analyses demonstrate that the expression of the guanidine riboswitch-associated carboxylase, in conjunction with associated hydrolases and transport genes, is markedly elevated in the presence of guanidine. Subsequent analysis of the carboxylases that are homologous to urea carboxylase confirmed the substrate preference of guanidine over urea. This chapter outlines a procedure for the isolation of guanidine-assimilating bacteria and the analysis of their proteome to identify enzymes responsible for guanidine degradation. Finally, an assay for the characterization of the endogenous guanidine carboxylases in comparison with the endogenous urea carboxylase from E. rhapontici is described.

胍基羧化酶的特征。
胍的代谢一直是全球氮循环中被忽视的一个方面,直到在细菌中发现了能与富氮化合物结合的 RNA 传感器(核糖开关)。相关基因最初被认为是为了从细胞中解毒胍。胍核糖开关位于一个操作子的上游,该操作子包括一个羧化酶、两个推测的水解酶和一个指定的异氨酸水解酶。一个 ABC 转运体位于同一操作子上,其外质结合域表明它是一个输入体。因此,我们假设某些细菌会主动导入胍并同化氮。为了验证这一假设,我们寻找了能够同化胍的细菌。我们分离了三种肠杆菌(Raoultella terrigena str.JH01, Erwinia rhapontici str.JH02 和密歇根克雷伯氏菌 str.JH07)有效利用胍作为氮源。蛋白质组分析表明,胍核糖开关相关羧化酶以及相关水解酶和转运基因的表达在有胍存在的情况下明显升高。随后对与脲羧化酶同源的羧化酶进行的分析证实,胍对底物的偏好高于脲。本章概述了分离胍同化细菌和分析其蛋白质组以确定负责胍降解的酶的程序。最后,本章还介绍了一种用于鉴定内源性胍羧化酶与来自 E. rhapontici 的内源性脲羧化酶的测定方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Methods in enzymology
Methods in enzymology 生物-生化研究方法
CiteScore
2.90
自引率
0.00%
发文量
308
审稿时长
3-6 weeks
期刊介绍: The critically acclaimed laboratory standard for almost 50 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 500 volumes the series contains much material still relevant today and is truly an essential publication for researchers in all fields of life sciences, including microbiology, biochemistry, cancer research and genetics-just to name a few. Five of the 2013 Nobel Laureates have edited or contributed to volumes of MIE.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信