Bradyrhizobium are abundant soil bacteria and the major symbiont of legumes. The recent availability of Bradyrhizobium genome sequences provides a large source of information for analysis of symbiotic traits. In this study, we investigated the evolutionary dynamics of the nodulation genes (nod) and their relationship with the genes encoding type III secretion systems (T3SS) and their effectors among bradyrhizobia. Based on the comparative analysis of 146 Bradyrhizobium genome sequences, we identified six different types of T3SS gene clusters. The two predominant cluster types are designated RhcIa and RhcIb and both belong to the RhcI-T3SS family previously described in other rhizobia. They are found in 92/146 strains, most of them also containing nod genes. RhcIa and RhcIb gene clusters differ in the genes they carry: while the translocon-encoding gene nopX is systematically found in strains containing RhcIb, the nopE and nopH genes are specifically conserved in strains containing RhcIa, suggesting that these last two genes might functionally substitute nopX and play a role related to effector translocation. Phylogenetic analysis suggests that bradyrhizobia simultaneously gained nod and RhcI-T3SS gene clusters via horizontal transfer or subsequent vertical inheritance of a symbiotic island containing both. Sequence similarity searches for known Nop effector proteins in bradyrhizobial proteomes revealed the absence of a so-called core effectome, i.e. that no effector is conserved among all Bradyrhizobium strains. However, NopM and SUMO proteases were found to be the main effector families, being represented in the majority of the genus. This study indicates that bradyrhizobial T3SSs might play a more significant symbiotic role than previously thought and provides new candidates among T3SS structural proteins and effectors for future functional investigations.

中文翻译：

---

慢生根瘤菌属中 nod 和 T3SS 基因的系统发育分布和进化动力学。

Bradyrhizobium 是丰富的土壤细菌和豆类的主要共生体。Bradyrhizobium基因组序列的最新可用性为共生性状分析提供了大量信息来源。在这项研究中，我们研究了根瘤菌中结瘤基因 ( nod )的进化动力学及其与编码 III 型分泌系统 (T3SS) 的基因及其效应子的关系。基于146慢生根瘤菌的比较分析 基因组序列，我们确定了六种不同类型的 T3SS 基因簇。两种主要的簇类型被指定为 RhcIa 和 RhcIb，都属于先前在其他根瘤菌中描述的 RhcI-T3SS 家族。它们存在于 92/146 菌株中，其中大多数还含有nod基因。RhcIa 和 RhcIb 基因簇携带的基因不同：虽然编码转位子的基因nopX在含有 RhcIb 的菌株中系统地发现，但nopE和nopH基因在含有 RhcIa 的菌株中特别保守，这表明最后两个基因可能在功能上替代nopX并发挥与效应器易位相关的作用。系统发育分析表明，缓慢根瘤菌通过水平转移或随后垂直遗传的共生岛同时获得了nod和 RhcI-T3SS 基因簇。在慢根瘤菌蛋白质组中对已知 Nop 效应蛋白的序列相似性搜索揭示了所谓的核心效应组的缺失，即在所有慢生根瘤菌中没有保守的效应蛋白 菌株。然而，发现 NopM 和 SUMO 蛋白酶是主要的效应家族，在大多数属中都有代表。这项研究表明，慢根瘤菌 T3SS 可能发挥比以前认为的更重要的共生作用，并为未来的功能研究提供了 T3SS 结构蛋白和效应物的新候选者。