Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.
Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.
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DOI：
10.1371/journal.pbio.1002557
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发表时间：
2016-09
期刊：
影响因子：
9.8
通讯作者：
Mishmar D
中科院分区：
文献类型：
--
作者：
Bar-Yaacov D;Frumkin I;Yashiro Y;Chujo T;Ishigami Y;Chemla Y;Blumberg A;Schlesinger O;Bieri P;Greber B;Ban N;Zarivach R;Alfonta L;Pilpel Y;Suzuki T;Mishmar D
翻译所有线粒体DNA（mtDNA）编码蛋白的线粒体核糖体应在转录前和转录后受到严格调控。最近，我们在人类线粒体16 S（大）rRNA位置947处发现了RNA-DNA差异（RDD），这表明转录后修饰。在这里，我们表明，这些16 S rRNA RDDs的结果从1-甲基腺苷（m1A）的修饰引入TRMT 61 B，因此是第一个脊椎动物甲基转移酶，修改tRNA和rRNA。m1 A947在人类和所有在相应mtDNA位置具有腺嘌呤的脊椎动物中是保守的（90%的脊椎动物）。然而，这个mtDNA碱基在10%的脊椎动物中是胸腺嘧啶，在95%的细菌中是鸟嘌呤，这表明了替代的进化解决方案。m1A、尿苷或鸟嘌呤可以稳定线粒体和细菌核糖体的局部结构。对基因组编辑的大肠杆菌的实验评估表明，未修饰的腺嘌呤会导致蛋白质合成和生长受损。我们的研究结果揭示了一种保守的rRNA修饰机制，该机制已被选择而不是DNA突变，以实现适当的线粒体核糖体功能。在进化过程中，选择了两种解决方案，以允许脊椎动物线粒体16 S核糖体RNA的适当功能，或者是通过tRNA甲基转移酶进行的RNA甲基化，或者是古老的进化突变。RNA修饰构成了一个重要的信息层，其功能含义并没有写在底层DNA序列中。最近，我们在人线粒体16 S核糖体RNA（rRNA）的947位上观察到一个明显的RNA-DNA差异（RDD），但其性质和机制尚不清楚。在这里，我们表明，这种差异反映了m1A修饰（腺嘌呤部分1位的甲基化），并通过细胞中的敲除实验和体外甲基化测定的组合证明，tRNA甲基转移酶TRMT 61 B是引入这种修饰的最佳候选酶。我们还表明，这种修饰存在于大多数的16 S rRNA分子在分离的线粒体核糖体，它发生在所有的脊椎动物与腺嘌呤（90%的脊椎动物），但不是在那些与胸苷在这个16 S rRNA的位置。最后，作为理解这种rRNA修饰的功能重要性的第一步，我们使用基因组编辑的细菌系统来证明，与野生型细菌和在相关位置具有胸苷的突变细菌相比，未修饰的腺嘌呤降低了细菌的生长和翻译速率。因此，在进化过程中选择了三种解决方案，以允许线粒体16 S rRNA的适当功能-RNA修饰或两种替代的古代进化DNA突变。
The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates). However, this mtDNA base is a thymine in 10% of the vertebrates and a guanine in the 23S rRNA of 95% of bacteria, suggesting alternative evolutionary solutions. m1A, uridine, or guanine may stabilize the local structure of mitochondrial and bacterial ribosomes. Experimental assessment of genome-edited Escherichia coli showed that unmodified adenine caused impaired protein synthesis and growth. Our findings revealed a conserved mechanism of rRNA modification that has been selected instead of DNA mutations to enable proper mitochondrial ribosome function. Two solutions were selected during evolution to allow proper function of the vertebrate mitochondrial 16S ribosomal RNAeither RNA methylation by a tRNA methyltransferase or ancient evolutionary mutation. RNA modifications constitute an important layer of information, with functional implications that are not written in the underlying DNA sequence. Recently, we observed an apparent RNA-DNA difference (RDD) at position 947 of the human mitochondrial 16S ribosomal RNA (rRNA), but its nature and mechanism were unclear. Here we show that this disparity reflects an m1A modification (methylation at position 1 of the adenine moiety), and demonstrated by a combination of knock-down experiments in cells and in vitro methylation assays that the tRNA methyltransferase TRMT61B is the best candidate enzyme to introduce this modification. We also show that this modification is present in most of the 16S rRNA molecules in isolated mitochondrial ribosomes, and that it occurs in all vertebrates with an adenine (90% of the vertebrates), but not in those with a thymidine at this 16S rRNA position. Finally, as the first step towards understanding the functional importance of this rRNA modification, we used a genome-edited bacterial system to demonstrate that an unmodified adenine reduced the growth and translation rates of the bacteria as compared to both wild-type bacteria and mutant bacteria with a thymidine in the relevant position. Hence, three solutions were selected during evolution to allow proper function of the mitochondrial 16S rRNA—either RNA modification or two alternative ancient evolutionary DNA mutations.
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影响因子：
14.9
作者：
Hauenschild R;Tserovski L;Schmid K;Thüring K;Winz ML;Sharma S;Entian KD;Wacheul L;Lafontaine DL;Anderson J;Alfonzo J;Hildebrandt A;Jäschke A;Motorin Y;Helm M
通讯作者：
Helm M
DOI：
10.1126/science.aaa1193
发表时间：
2015-04-03
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Amunts A;Brown A;Toots J;Scheres SHW;Ramakrishnan V
通讯作者：
Ramakrishnan V
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
3.3
作者：
Blumberg, Amit;Sailaja, Badi Sri;Mishmar, Dan
通讯作者：
Mishmar, Dan
DOI：
10.1016/1044-0305(92)85019-g
发表时间：
1992-01-01
影响因子：
3.2
作者：
MCLUCKEY, SA;VANBERKEL, GJ;GLISH, GL
通讯作者：
GLISH, GL