背景:细菌RNA聚合酶全酶需要sigma70因子来通过鉴定启动子元件启动转录。蓝藻具有多个sigma70因子以适应各种各样的生态位。这些因子分为两类:初级sigma因子在正常生长条件下启动管家基因的转录,而替代sigma因子在特定条件下启动特定基因的转录。然而,目前的分类没有考虑其结构域的模块化组织,因此引入了多种功能和结构偏见。需要对蓝细菌中的这种蛋白质家族进行全面分析以解决这些限制。
结果:我们研究了蓝藻中sigma70因子的结构和演化,分析它们的模块化架构和单细胞之间的变化,丝状的,和异形形成形态型。发现了4,193个sigma70同源物,具有59种不同的模块化模式,包括六个基本域名和29个附属域名,例如DUF6596。90%的蓝细菌通常具有5至17个sigma70同源物,这个数字可能取决于菌株形态类型,分类顺序和基因组大小。我们将sigma70因子分为12个氏族和36个家庭。根据分类顺序和表型性状,14个主要家庭中的同源物数量是可变的,A.1家族包括主要的sigma因子,因为该家族在所有蓝细菌物种中都被发现。发现A.1,A.5,C.1,E.1,J.1和K.1家族是区分异形形成菌株的关键sigma家族。为了解释sigma70的多样化和进化,我们提出了一种源于A1家族共同祖先多样化的进化情景。这种情况的特征是进化事件,包括域丢失,gains,插入,和修改。DUF6596结构域在细菌sigma70蛋白中的高出现,以及它与放线菌中观察到的最高患病率的关联,表明该域可能对sigma70功能很重要。这也意味着该结构域可能已经出现在放线菌中,并通过水平基因转移进行了转移。
结论:我们的分析提供了对sigma70模块化领域架构的详细见解,引入了一种新颖的稳健分类。它还提出了一个进化场景,解释了它们在不同分类顺序之间的多样性。
BACKGROUND: Bacterial RNA polymerase holoenzyme requires sigma70 factors to start transcription by identifying promoter elements. Cyanobacteria possess multiple sigma70 factors to adapt to a wide variety of ecological niches. These factors are grouped into two categories: primary sigma factor initiates transcription of housekeeping genes during normal growth conditions, while alternative sigma factors initiate transcription of specific genes under particular conditions. However, the present classification does not consider the modular organization of their structural domains, introducing therefore multiple functional and structural biases. A comprehensive analysis of this protein family in cyanobacteria is needed to address these limitations.
RESULTS: We investigated the structure and evolution of sigma70 factors in cyanobacteria, analyzing their modular architecture and variation among unicellular, filamentous, and heterocyst-forming morphotypes. 4,193 sigma70 homologs were found with 59 distinct modular patterns, including six essential and 29 accessory domains, such as DUF6596. 90% of cyanobacteria typically have 5 to 17 sigma70 homologs and this number likely depends on the strain morphotype, the taxonomic order and the genome size. We classified sigma70 factors into 12 clans and 36 families. According to taxonomic orders and phenotypic traits, the number of homologs within the 14 main families was variable, with the A.1 family including the primary sigma factor since this family was found in all cyanobacterial species. The A.1, A.5, C.1, E.1, J.1, and K.1 families were found to be key sigma families that distinguish heterocyst-forming strains. To explain the diversification and evolution of sigma70, we propose an evolutionary scenario rooted in the diversification of a common ancestor of the A1 family. This scenario is characterized by evolutionary events including domain losses, gains, insertions, and modifications. The high occurrence of the DUF6596 domain in bacterial sigma70 proteins, and its association with the highest prevalence observed in Actinobacteria, suggests that this domain might be important for sigma70 function. It also implies that the domain could have emerged in Actinobacteria and been transferred through horizontal gene transfer.
CONCLUSIONS: Our analysis provides detailed insights into the modular domain architecture of sigma70, introducing a novel robust classification. It also proposes an evolutionary scenario explaining their diversity across different taxonomical orders.