Iron–sulfur (Fe–S) clusters are ubiquitous cofactors essential for life. It is largely thought that the emergence of oxygenic photosynthesis and progressive oxygenation of the atmosphere led to the origin of multiprotein machineries (ISC, NIF and SUF) assisting Fe–S cluster synthesis in the presence of oxidative stress and shortage of bioavailable iron. However, previous analyses have left unclear the origin and evolution of these systems. Here, we combine exhaustive homology searches with genomic context analysis and phylogeny to precisely identify Fe–S cluster biogenesis systems in over 10,000 archaeal and bacterial genomes. We highlight the existence of two additional and clearly distinct ‘minimal’ Fe–S cluster assembly machineries, MIS (minimal iron–sulfur) and SMS (SUF-like minimal system), which we infer in the last universal common ancestor (LUCA) and we experimentally validate SMS as a bona fide Fe–S cluster biogenesis system. These ancestral systems were kept in archaea whereas they went through stepwise complexification in bacteria to incorporate additional functions for higher Fe–S cluster synthesis efficiency leading to SUF, ISC and NIF. Horizontal gene transfers and losses then shaped the current distribution of these systems, driving ecological adaptations such as the emergence of aerobic lifestyles in archaea. Our results show that dedicated machineries were in place early in evolution to assist Fe–S cluster biogenesis and that their origin is not directly linked to Earth oxygenation.

铁硫（Fe-S）簇是生命所必需的普遍存在的辅助因子。人们普遍认为，含氧光合作用的出现和大气的渐进氧化导致了多蛋白机制（ISC、NIF 和 SUF）的起源，在氧化应激和生物可利用铁短缺的情况下协助 Fe-S 簇的合成。然而，之前的分析并不清楚这些系统的起源和演化。在这里，我们将详尽的同源性搜索与基因组背景分析和系统发育相结合，以精确识别 10,000 多个古细菌和细菌基因组中的 Fe-S 簇生物发生系统。我们强调存在两种额外且明显不同的“最小”Fe-S簇组装机制，MIS（最小铁硫）和SMS（类似SUF的最小系统），我们在最后一个普遍共同祖先（LUCA）中推断出它们和我们通过实验验证了 SMS 是一个真正的 Fe-S 簇生物发生系统。这些祖先系统被保存在古细菌中，而它们在细菌中经历了逐步复杂化，以整合额外的功能，以实现更高的 Fe-S 簇合成效率，从而产生 SUF、ISC 和 NIF。随后，水平基因转移和损失塑造了这些系统目前的分布，推动了生态适应，例如古细菌中有氧生活方式的出现。我们的结果表明，在进化的早期就已经存在专门的机器来协助铁硫簇的生物发生，并且它们的起源与地球氧合没有直接关系。