“Candidatus Accumulibacter” is a unique and pivotal genus of polyphosphate-accumulating organisms prevalent in wastewater treatment plants and plays mainstay roles in the global phosphorus cycle. However, the efforts to fully understand their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods. Here, we reported an integrated approach combining pangenome analysis, protein structure prediction and clustering, and meta-omic characterization, to uncover genetic and metabolic traits previously unexplored for Ca. Accumulibacter. The identification of a previously overlooked pyrophosphate-fructose 6-phosphate 1-phosphotransferase gene (pfp) suggested that all Ca. Accumulibacter encoded a complete Embden–Meyerhof–Parnas pathway. A homologue of the phosphate-specific transport system accessory protein (PhoU) was suggested to be an inorganic phosphate transport (Pit) accessory protein (Pap) conferring effective and efficient phosphate transport. Additional lineage members were found to encode complete denitrification pathways. A pipeline was built, generating a pan-Ca. Accumulibacter annotation reference database, covering >200,000 proteins and their encoding genes. Benchmarking on 27 Ca. Accumulibacter genomes showed major improvement in the average annotation coverage from 51% to 82%. This pipeline is readily applicable to diverse cultured and uncultured bacteria to establish high-coverage annotation reference databases, facilitating the exploration of genomic dark matter in the bacterial domain.

中文翻译：

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从基因到结构：解开 Ca. Accumulibacter 中的基因组暗物质


“Candidatus Accumulibacter” 是污水处理厂中普遍存在的多磷酸盐积累生物的一个独特而关键的属，在全球磷循环中起着主要作用。然而，充分理解它们的遗传和代谢特征的努力在很大程度上受到现有基于序列的注释方法的主要局限性的阻碍。在这里，我们报道了一种结合泛基因组分析、蛋白质结构预测和聚类以及宏组学表征的综合方法，以揭示以前未探索的 Ca的遗传和代谢特征。Accumulibacter 的以前被忽视的焦磷酸-果糖 6-磷酸 1-磷酸转移酶基因 （pfp） 的鉴定表明，所有 Ca. Accumulibacter 都编码完整的 Embden-Meyerhof-Parnas 通路。磷酸盐特异性转运系统辅助蛋白 （PhoU） 的同源物被认为是一种无机磷酸盐转运 （Pit） 辅助蛋白 （Pap），可赋予有效和高效的磷酸盐转运。发现其他谱系成员编码完整的反硝化途径。构建了一个管道，生成了 pan-Ca。Accumulibacter 注释参考数据库，涵盖 >200,000 个蛋白质及其编码基因。27 Ca.Accumulibacter 基因组显示平均注释覆盖率从 51% 大幅提高到 82%。该管道适用于各种培养和未培养的细菌，以建立高覆盖率的注释参考数据库，促进细菌领域中基因组暗物质的探索。