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Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding 具有不同特征的两个茎和RNA适体的内部环有助于精子结合

The Journal of Biochemistry Pub Date : 2016-10-25 DOI: 10.1093/jb/mvw062

A. Oguro, A. Yanagida, Y. Fujieda, Ryotaro Amano, M. Otsu, T. Sakamoto, G. Kawai, S. Matsufuji

{"title":"Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding","authors":"A. Oguro, A. Yanagida, Y. Fujieda, Ryotaro Amano, M. Otsu, T. Sakamoto, G. Kawai, S. Matsufuji","doi":"10.1093/jb/mvw062","DOIUrl":"https://doi.org/10.1093/jb/mvw062","url":null,"abstract":"Though polyamines (putrescine, spermidine, and spermine) bind to the specific position in RNA molecules, interaction mechanisms are poorly understood. SELEX procedure has been used to isolate high-affinity oligoribonucleotides (aptamers) from randomized RNA libraries. Selected aptamers are useful in exploring sequences and/or structures in RNAs for binding molecules. In this study, to analyze the interaction mechanism of polyamine to RNA, we selected RNA aptamers targeted for spermine. Two spermine-binding aptamers (#5 and #24) were obtained and both of them had two stem-loop structures. The 3′ stem-loop of #5 (SL_2) bound to spermine more effectively than the 5′ stem-loop of #5 did. A thermodynamic analysis by an isothermal titration calorimetry revealed that the dissociation constant of SL_2 for spermine was 27.2 μM and binding ratio was nearly 1:1. Binding assay with base-pair replaced variants showed that two stem regions and an internal loop in SL_2 were important for their spermine-binding activities. NMR analyses proposed that a terminal-side and a loop-side stem in SL_2 take a loose and a stable structure, respectively and a conformational change of SL_2 is induced by spermine. It is conclusive that two stems with different characteristics and an internal loop in SL_2 contribute to the specific spermine-binding.","PeriodicalId":22605,"journal":{"name":"The Journal of Biochemistry","volume":"78 1","pages":"197–206"},"PeriodicalIF":0.0,"publicationDate":"2016-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83642455","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: 11

Loop 5 region is important for the activity of the long-chain base transporter Rsb1 环5区对长链碱基转运体Rsb1的活性起重要作用

The Journal of Biochemistry Pub Date : 2016-10-22 DOI: 10.1093/jb/mvw059

H. Makuta, K. Obara, A. Kihara

{"title":"Loop 5 region is important for the activity of the long-chain base transporter Rsb1","authors":"H. Makuta, K. Obara, A. Kihara","doi":"10.1093/jb/mvw059","DOIUrl":"https://doi.org/10.1093/jb/mvw059","url":null,"abstract":"Intracellular lipid amounts are regulated not only by metabolism but also by efflux. Yeast Rsb1 is the only known transporter/floppase of the sphingolipid components long-chain bases (LCBs). However, even fundamental knowledge about Rsb1, such as important amino acid residues for activity and substrate recognition, still remains unclear. Rsb1 belongs to the Rta1-like family. To date, it has not been determined whether all family members share a common ability to export LCBs. Here, we revealed that within the Rta1-like family, only Rsb1 suppressed the hypersensitivity of the mutant cells lacking LCB 1-phoshate-degrading enzymes, suggesting that LCB-exporting activity is specific to Rsb1. Rsb1 contains a characteristic region (loop 5), which does not exist in other proteins of the Rta1-like family. We found that deletion of this region caused loss of Rsb1 function. Further mutational analysis of loop 5 revealed that the charged amino acid residues E223, D225 and R236 were important for Rsb1 activity. In addition to LCBs, Rsb1 facilitated the export of 1-hexadecanol, but not palmitic acid, which suggests that Rsb1 recognizes the C1 hydroxyl group. Thus, our findings provide an important clue for understanding the molecular mechanism of LCB export.","PeriodicalId":22605,"journal":{"name":"The Journal of Biochemistry","volume":"58 1","pages":"207–213"},"PeriodicalIF":0.0,"publicationDate":"2016-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78166614","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: 4

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