Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
ISME J. 2022 Apr;16(4):1065-1073. doi: 10.1038/s41396-021-01154-y. Epub 2021 Nov 25.
Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here, we focus on di-prolyl motifs (XXPPX) and ask whether their prevalence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 35 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.
快速的细菌生长取决于核糖体将 mRNA 翻译成蛋白质的速度。编码连续脯氨酸的 mRNAs 会导致核糖体停滞，从而大大降低翻译速度。这种停滞对必须快速生长和分裂的物种尤其不利。在这里，我们专注于二脯氨酸基序 (XXPPX)，并询问它们的普遍性是否随生长速率而变化。为了找出答案，我们对超过 35 个门的 3000 多个细菌基因组中的此类基序进行了广泛调查。事实上，快速生长的物种比慢速生长的物种编码的基序更少，尤其是在高表达蛋白中。我们还在嗜热菌中发现了许多二脯氨酸基序，脯氨酸可以帮助维持蛋白质组的稳定性。此外，具有复杂多细胞生命周期的细菌也编码许多二脯氨酸基序。在生长缓慢的粘球菌门中尤其明显。该门中的细菌编码许多丝氨酸苏氨酸激酶，以及这些激酶中潜在磷酸化位点的许多二脯氨酸基序。丝氨酸苏氨酸激酶参与细胞信号转导，并有助于调节与粘球菌门多细胞性相关的发育过程。总之，我们的观察结果表明，无论是由于生长缓慢还是嗜热，翻译速率的选择减弱可能会允许二脯氨酸基序在与翻译速率无关的新的生物过程中发挥作用。
