Kasalo Niko, Domazet-Lošo Mirjana, Domazet-Lošo Tomislav
Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia.
Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000 Zagreb, Croatia.
Int J Mol Sci. 2025 Mar 26;26(7):3024. doi: 10.3390/ijms26073024.
All animals have outsourced about half of the 20 proteinogenic amino acids (AAs). We recently demonstrated that the loss of biosynthetic pathways for these outsourced AAs is driven by energy-saving selection. Paradoxically, these metabolic simplifications enabled animals to use costly AAs more frequently in their proteomes, allowing them to explore sequence space more freely. Based on these findings, we proposed that environmental AA availability and cellular respiration mode are the two primary factors determining the evolution of AA auxotrophies in animals. Remarkably, our recent analysis showed that bacterial AA auxotrophies are also governed by energy-related selection, thereby roughly converging with animals. However, bacterial AA auxotrophies are highly heterogeneous and scattered across the bacterial phylogeny, making direct ecological and physiological comparisons with the animal AA outsourcing model challenging. To better test the universality of our model, we focused on Bdellovibrionota and Myxococcota-two closely related bacterial phyla that, through aerobic respiration and a predatory lifestyle, best parallel animals. Here, we show that Bdellovibrionota, driven by energy-related selection, outsourced a highly similar set of AAs to those in animals. This sharply contrasts with Myxococcota, which exhibit far fewer AA auxotrophies and rarely show signatures of energy-driven selection. These differences are also reflected in Bdellovibrionota proteomes, which are substantially more expensive than those of Myxococcota. Finally, we found evidence that the expression of costly proteins plays a crucial role in the predatory phase of the Bdellovibrio life cycle. Together, our findings suggest that Bdellovibrionota, through their obligate predatory lifestyle, exhibit the closest analogy to the AA auxotrophy phenotype observed in animals. In contrast, facultative predation, as seen in Myxococcota, appears to substantially limit the evolution of AA auxotrophies. These cross-domain convergences strongly support the general validity of our AA outsourcing model.
所有动物都外包了20种蛋白质氨基酸（AA）中的约一半。我们最近证明，这些外包氨基酸生物合成途径的丧失是由节能选择驱动的。矛盾的是，这些代谢简化使动物能够在其蛋白质组中更频繁地使用昂贵的氨基酸，从而使它们能够更自由地探索序列空间。基于这些发现，我们提出环境氨基酸可用性和细胞呼吸模式是决定动物氨基酸营养缺陷型进化的两个主要因素。值得注意的是，我们最近的分析表明，细菌的氨基酸营养缺陷型也受能量相关选择的支配，从而与动物大致趋同。然而，细菌的氨基酸营养缺陷型高度异质，分散在细菌系统发育中，使得与动物氨基酸外包模型进行直接的生态和生理比较具有挑战性。为了更好地检验我们模型的普遍性，我们聚焦于蛭弧菌门和黏球菌门——两个密切相关的细菌门，它们通过有氧呼吸和捕食性生活方式，与动物最为相似。在这里，我们表明，蛭弧菌门在能量相关选择的驱动下，外包了一组与动物高度相似的氨基酸。这与黏球菌门形成鲜明对比，黏球菌门的氨基酸营养缺陷型要少得多，很少表现出能量驱动选择的特征。这些差异也反映在蛭弧菌门的蛋白质组中，其蛋白质组比黏球菌门的蛋白质组昂贵得多。最后，我们发现有证据表明，昂贵蛋白质的表达在蛭弧菌生命周期的捕食阶段起着关键作用。总之，我们的研究结果表明，蛭弧菌门通过其专性捕食性生活方式，与在动物中观察到的氨基酸营养缺陷型表型最为相似。相比之下，黏球菌门中所见的兼性捕食似乎在很大程度上限制了氨基酸营养缺陷型的进化。这些跨域趋同有力地支持了我们的氨基酸外包模型的普遍有效性。
