遗传密码和基因组域的能量映射:密码进化和分子达尔文主义的含义。

IF 7.2 2区 生物学 Q1 BIOPHYSICS Quarterly Reviews of Biophysics Pub Date : 2020-11-04 DOI:10.1017/S0033583520000098
Horst H Klump, Jens Völker, Kenneth J Breslauer
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引用次数: 8

摘要

当标志性的DNA遗传密码以能量差异的形式表达时,人们观察到嵌入在化学序列中的信息,包括一些生物结果,与独特的自由能谱相关。具体来说,我们发现密码子使用和密码子自由能之间存在相关性,这表明密码子使用存在热力学选择。我们还发现被认为是古老氨基酸和高密码子自由能值之间的相关性。这种相关性可能反映了基于序列的遗传密码从根本上映射为能量密码。从这个角度来看,我们可以想象遗传密码是由连锁的热力学循环组成的,这些循环允许密码子通过一系列连续的转换和翻转而相互“进化”,这些转换和翻转受到热力学和动力学因素调节的能量景观的影响。因此,遗传密码的早期进化可能部分是由不同的能量学驱动的,而不是完全由任何基因产物的功能驱动的。在这种情况下,进化压力可以部分地来自生物物理特性的优化(例如,相对稳定性和相对速率),以及由表型适应优势(自然选择)驱动的经典观点。遗传密码的这种差异能量图谱,以及更大的基因组域,可能反映了一种能量分解和进化的基因组景观,与一种差异的、能量驱动的“分子达尔文主义”相一致。密码的进化受到微分能量学的影响,这并不奇怪,因为热力学是在所有时间和长度尺度上运作的最普遍、最普遍的科学分支。
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Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism.

When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to 'evolve' from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven 'molecular Darwinism'. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.

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来源期刊
Quarterly Reviews of Biophysics
Quarterly Reviews of Biophysics 生物-生物物理
CiteScore
12.90
自引率
1.60%
发文量
16
期刊介绍: Quarterly Reviews of Biophysics covers the field of experimental and computational biophysics. Experimental biophysics span across different physics-based measurements such as optical microscopy, super-resolution imaging, electron microscopy, X-ray and neutron diffraction, spectroscopy, calorimetry, thermodynamics and their integrated uses. Computational biophysics includes theory, simulations, bioinformatics and system analysis. These biophysical methodologies are used to discover the structure, function and physiology of biological systems in varying complexities from cells, organelles, membranes, protein-nucleic acid complexes, molecular machines to molecules. The majority of reviews published are invited from authors who have made significant contributions to the field, who give critical, readable and sometimes controversial accounts of recent progress and problems in their specialty. The journal has long-standing, worldwide reputation, demonstrated by its high ranking in the ISI Science Citation Index, as a forum for general and specialized communication between biophysicists working in different areas. Thematic issues are occasionally published.
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