Data_Sheet_2_Pangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology.PDF

Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes. Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.

移动遗传元件（Mobile genetic elements, MGEs）是介导细菌适应与进化分化的关键因子。这类DNA元件的稳定定植依赖宿主因子，其中便包括类核关联蛋白（nucleoid-associated proteins, NAPs）。NAPs是一类丰度极高的DNA结合蛋白，可通过弯折DNA改变其拓扑结构与折叠状态，进而影响从复制到表达的所有已知细胞DNA代谢过程。尽管编码NAPs的基因在大多数原核基因组中均有分布，但目前仅对少数NAP家族在宿主染色体生物学及异源沉默中的功能有所认知。而关于由MGEs编码的NAPs在外源元件定植与迁移过程中的存在情况、丰度及功能，目前的研究仍较为匮乏。本研究结合比较基因组学与系统发育分析策略，对嗜酸杆菌纲（Acidithiobacillia）内NAPs的多样性、分布模式及功能角色展开探究，并重点关注其在MGE生物学中的作用。该纲的成员均为好氧化能自养嗜酸硫氧化菌，其丰富的基因型多样性可归因于MGEs的存在。我们对该纲90余个不同物种的基因组开展类核关联蛋白家族（protein families, PFs）检索，共鉴定得到1197个蛋白，隶属于12个不同的NAP家族，且各家族在不同物种中的存在情况与保守性存在显著差异。泛基因组水平分析显示，该纲内存在6个高度保守的核心NAP蛋白家族（PFs），其中部分家族还存在散在分布的变异形式；此外还发现了类群限制性分布的NAPs。基于基因组上下文的保守性与系统发育信号，本次鉴定得到的核心NAPs被认为是不可或缺的。与此同时，隶属于该纲灵活基因组分的多种高度多样化NAPs，要么被编码于已知质粒或大型整合型MGEs中，要么存在于带有MGE标志性基因的基因组位点中，这表明它们在大基因组菌株与物种中可稳定这些元件并维持其存续。本次鉴定得到的核心NAPs与灵活NAPs均具备作为分子标记的应用价值：前者可精准还原该纲的系统发育关系，后者则可作为生物信息学鉴定新型游离型与整合型移动元件的种子序列。