School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
Universal Biology Institute, University of Tokyo, Tokyo 113-0033, Japan.
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae011.
Duplication is a major route for the emergence of new gene functions. However, the emergence of new gene functions via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because, under an emerging Black Queen dynamic, there is high gene redundancy spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede the fixation of new functions. Our results expand the mechanisms by which new gene functions can emerge in prokaryotic systems.
复制是新基因功能出现的主要途径。然而，由于冗余基因经常被快速清除，该途径在原核生物中产生新基因功能的可能性可能会降低。在基因组紧凑、流线型的谱系中，通过重复和分歧产生新功能似乎具有挑战性。在黑皇后动态下，另一种导致基因丢失的压力也会发生，因为失去产生公共利益能力的骗子可以从邻近的生产者那里获得这种能力。我们提出，黑皇后动态可以有利于新功能的出现，因为在新出现的黑皇后动态下，有大量的基因冗余分布在相互作用的细胞群落中。通过计算建模，我们证明了新的基因功能可以在黑皇后动态下出现。即使由于低复制率导致的删除偏差以及由于与携带基因座相关的高成本而导致的冗余基因副本的选择，从而导致冗余基因副本的选择，这一结果仍然成立。然而，当公共利益生产成本较高时，黑皇后动态会阻碍新功能的固定。我们的研究结果扩展了新基因功能在原核系统中出现的机制。
