Sendker Franziska L, Schlotthauer Tabea, Mais Christopher-Nils, Lo Yat Kei, Girbig Mathias, Bohn Stefan, Heimerl Thomas, Schindler Daniel, Weinstein Arielle, Metzger Brian P H, Thornton Joseph W, Pillai Arvind, Bange Gert, Schuller Jan M, Hochberg Georg K A
Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35043, Marburg, Germany.
Nat Commun. 2024 Dec 3;15(1):10515. doi: 10.1038/s41467-024-54408-6.
Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assembly states and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
许多酶组装成同聚体蛋白复合物，由一种蛋白质的多个拷贝组成。由于在生物化学中通常认为结构形式遵循功能，这些组装体被认为是进化而来的，因为它们提供了一些功能优势。然而，在许多情况下，并不清楚具体的优势是什么，而且在某些情况下，直系同源物之间的四级结构也有所不同。这就导致了一种观点，即自组装在蛋白质家族中可能反而呈中性变化。由于直到最近四级结构都很难进行大规模测量，所以这种变化的程度一直难以确定。在这里，我们利用质量光度法、系统发育学和结构生物学来研究原核柠檬酸合酶整个系统发育过程中同寡聚体组装的进化——柠檬酸合酶是一种功能高度保守的酶。我们发现了一系列在进化过程中出现和消失的不同组装类型，包括平行进化的情况以及从复杂组装体到简单组装体的逆转。体外和体内的功能实验表明，不同组装体之间的进化转变不会强烈影响酶的催化作用。我们的工作表明，酶可以在一个由大量可能的组装状态构成的空间中相对自由地变化，并展示了在整个系统发育过程中表征结构 - 功能关系的强大作用。
