Center for Ecological and Evolutionary Synthesis, Department of Biological Sciences, University of Oslo, Blindern, N-0316 Oslo, Norway.
Comput Biol Chem. 2012 Dec;41:18-34. doi: 10.1016/j.compbiolchem.2012.08.002. Epub 2012 Aug 14.
Mitochondrial genes code for additional proteins after +2 frameshifts by reassigning stops to code for amino acids, which defines overlapping genetic codes for overlapping genes. Turtles recode stops UAR → Trp and AGR → Lys (AGR → Gly in the marine Olive Ridley turtle, Lepidochelys olivacea). In Lepidochelys the +2 frameshifted mitochondrial Cytb gene lacks stops, open reading frames from other genes code for unknown proteins, and for regular mitochondrial proteins after frameshifts according to the overlapping genetic code. Lepidochelys' inversion between proteins coded by regular and overlapping genetic codes substantiates the existence of overlap coding. ND4 differs among Lepidochelys mitochondrial genomes: it is regular in DQ486893; in NC_011516, the open reading frame codes for another protein, the regular ND4 protein is coded by the frameshifted sequence reassigning stops as in other turtles. These systematic patterns are incompatible with Genbank/sequencing errors and DNA decay. Random mixing of synonymous codons, conserving main frame coding properties, shows optimization of natural sequences for overlap coding; Ka/Ks analyses show high positive (directional) selection on overlapping genes. Tests based on circular genetic codes confirm programmed frameshifts in ND3 and ND4l genes, and predicted frameshift sites for overlap coding in Lepidochelys. Chelonian mitochondria adapt for overlapping gene expression: cloverleaf formation by antisense tRNAs with predicted anticodons matching stops coevolves with overlap coding; antisense tRNAs with predicted expanded anticodons (frameshift suppressor tRNAs) associate with frameshift-coding in ND3 and ND4l, a potential regulation of frameshifted overlap coding. Anaeroby perhaps switched between regular and overlap coding genes in Lepidochelys.
线粒体基因在 +2 移码后通过重新分配终止密码子来编码氨基酸，从而定义了重叠基因的重叠遗传密码。海龟重新编码终止密码 UAR→Trp 和 AGR→Lys（海洋丽龟，Lepidochelys olivacea 中的 AGR→Gly）。在 Lepidochelys 中，+2 移码的线粒体 Cytb 基因没有终止密码子，来自其他基因的开放阅读框编码未知蛋白，并且根据重叠遗传密码在移码后编码常规线粒体蛋白。Lepidochelys 中常规和重叠遗传密码编码的蛋白质之间的倒位证实了重叠编码的存在。Lepidochelys 的 ND4 在不同的线粒体基因组中存在差异：在 DQ486893 中是常规的；在 NC_011516 中，开放阅读框编码另一种蛋白，常规的 ND4 蛋白由移码序列编码，重新分配终止密码子与其他海龟相同。这些系统模式与 Genbank/测序错误和 DNA 衰变不兼容。同义密码子的随机混合，保持主要框架编码特性，表明重叠编码的自然序列得到了优化；Ka/Ks 分析表明重叠基因存在高度正向（定向）选择。基于圆形遗传密码的测试证实了 ND3 和 ND4l 基因中的程序性移码，以及预测了 Lepidochelys 中重叠编码的移码位点。龟鳖类线粒体适应重叠基因表达：反义 tRNA 的双叶环形成，预测的反密码子与终止密码子匹配，与重叠编码共同进化；预测的扩展反密码子（移码抑制 tRNA）与 ND3 和 ND4l 中的移码编码相关，这可能是对移码重叠编码的调控。在 Lepidochelys 中，厌氧可能在常规和重叠编码基因之间切换。
