Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence
Evolutionary conservation and structural localizations suggest a physical trace of metabolism’s progressive geochronological emergence
复制标题
进化保守和结构定位表明新陈代谢的物理痕迹——渐进的地质年代出现
DOI：
10.1080/07391102.2019.1679666
复制
发表时间：
2020
影响因子：
4.4
通讯作者：
Pearl, Dennis K.
中科院分区：
文献类型：
--
作者：
Pollack, J. Dennis;Gerard, David;Makhatadze, George I.;Pearl, Dennis K.
我们研究了多序列比对（MSA）的共识氨基酸分布模式在2844个氨基酸序列的八个酶的克雷布的氧化三羧酸途径（oTCA）在古细菌，细菌和真核生物和5545个序列的33种细菌作为地理年代学分离的酶与MSA共识网站模态身份。这33种细菌是地球上最早出现的20种酶（Hadean-Escherean）（“第一纪元”）或13种最新出现的酶（“第三纪元”）。该酶的MSA共有位点通过它们的模态同一性、在九个等级的进化保守区（CZ）之一中的%占据和从它们的每个共有MSA C区到它们报告的功能中心中的相同原子（锚定原子）的欧几里得距离（Euclidean distance）来鉴定。这些MSA共有位点是称为回收氨基酸（RAA）的四元数据点。跨域，八个占主导地位的RAAs的克雷布氏循环和33种细菌的%占有率被发现是类似的排名。与Trifonov的“地球上氨基酸出现的假定排序时间顺序”（TOAE）相比，跨结构域的四元RAA的最大统计一致性是那些被表征为在最进化保守的保守区（CZ 9）内的那些，通常最接近它们的酶的催化/活性中心。地质年代学特征的早期最古老的Hadean-Escherean细菌'时代I'的酶相比，最新的细菌酶，有更大的氨基酸残基/序列的平均数和统计学显着较大的变化，在其RAA组成-Escher 3-卷。最新的“Epoch III”酶具有统计学上显著较低的体积值，具体地，它们的天然体积、空隙体积和展开时的体积变化。我们的酶数据表明了“新陈代谢的逐步出现”的地质年代学痕迹。Sarma
We studied multiple sequence alignment (MSA) consensus amino acid distributional patterns in 2844 amino acid sequences of the eight enzymes of the Kreb’s oxidative tricarboxylic acid pathway (oTCA) in Archaea, Bacteria and Eukarya and 5545 sequences of 33 bacteria as geochronologically separated enzymes with MSA consensus site modal identities. The 33 bacteria were 20 presumptive examples of early-oldest (Hadean-Archaean) (‘Epoch I’) or 13 late-newest (contemporary) (‘Epoch III’) appearing enzymes on Earth. The enzyme’s MSA consensus sites were identified by their modal identity, % Occupancy in one of nine-graded evolutionary-conservation zones (CZs) and the Euclidean distance (Å) from each of their consensus MSA Cɑs to the same atom (Anchor-atom) in their reported functional center. These MSA consensus sites are tetrad-data points called recovered-amino acids (RAA). Across Domains, the % Occupancies of the eight-dominant RAAs of the Kreb’s cycle and the 33 bacteria were found to be similarly ranked. Compared to Trifonov’s ‘putative ranked temporal order of the appearance of amino acids on Earth’ (TOAE), the greatest statistical concordance with tetrad-RAAs across Domains were those characterized as within the most-evolutionary conserved conservation zone (CZ9), typically nearest (Å) their enzyme’s catalytic/active center. The geochronologically characterized early-oldest Hadean-Archaean Bacteria ‘Epoch I’ enzymes, compared to late-newest Bacteria enzymes, had greater average numbers of amino acid residues/sequence and a statistically significant larger variability in their RAA compositional-Å3-volumes. The late-newest ‘Epoch III’ enzymes had statistically significant lower volumetric values, specifically, their native Å3-volume, void-volume and volume change on unfolding. Our enzyme data suggest a geochronological trace of ‘metabolism’s progressive emergence’.Communicated by Ramaswamy H. Sarma
登录
查看更多内容
影响因子：
3
作者：
Chen CR;Makhatadze GI
通讯作者：
Makhatadze GI
合成生物学的强大工具包：超过 38 亿年的进化
影响因子：
4
作者：
L. Rothschild
通讯作者：
L. Rothschild
影响因子：
5.7
作者：
Ingles-Prieto, Alvaro;Ibarra-Molero, Beatriz;Delgado-Delgado, Asuncion;Perez-Jimenez, Raul;Fernandez, Julio M.;Gaucher, Eric A.;Sanchez-Ruiz, Jose M.;Gavira, Jose A.
通讯作者：
Gavira, Jose A.
关于益生元肽和现存酶之间缺乏进化连续性。
DOI：
10.1039/c6cp00793g
发表时间：
2016
期刊：
Physical chemistry chemical physics : PCCP
影响因子：
--
作者：
L. Raggi;J. Bada;A. Lazcano
通讯作者：
A. Lazcano
DOI：
--
发表时间：
1997
期刊：
影响因子：
--
作者：
J. Peretó;R. Fani;J. Leguina;Antonio Reyes
通讯作者：
Antonio Reyes