Zymomonas mobilis is an ethanologenic alphaproteobacterium with promise for the industrial conversion of renewable plant biomass into fuels and chemical bioproducts. Limited functional annotation of the Z. mobilis genome is a current barrier to both fundamental studies of Z. mobilis and its development as a synthetic biology chassis. To gain insight, we collected sample-matched multiomics data, including RNA sequencing (RNA-seq), transcription start site (TSS) sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry, across different growth conditions and used these data to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5′ and 3′ ends, enabling the identification of 3,940 TSSs and their corresponding promoters and 2,091 transcription termination sites, which were distinguished from RNA processing sites by the lack of an adjacent RNA 5′ end. Our results revealed that Z. mobilis σ^A −35 and −10 promoter elements closely resemble canonical Escherichia coli −35 and −10 elements, with one notable exception: the Z. mobilis −10 element lacks the highly conserved −7 thymine observed in E. coli and other previously characterized σ^A promoters. The σ^A promoters of another alphaproteobacterium, Caulobacter crescentus, similarly lack the conservation of −7 thymine in their −10 elements. Our results anchor the development of Z. mobilis as a platform for synthetic biology and establish strategies for empirical genome annotation that can complement purely computational methods.

中文翻译：

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基因组规模的转录-翻译作图揭示了运动发酵单胞菌转录单位和启动子的特征。

运动发酵单胞菌（Zymomonas mobilis）是产乙醇的α变形杆菌，有望将可再生植物生物质工业转化为燃料和化学生物产品。的限制功能注释运动发酵单胞基因组是一个电流阻挡层的两个基础研究运动发酵单胞及其作为合成生物学底盘开发。为了获得洞察力，我们收集了与样品匹配的多组学数据，包括RNA测序（RNA-seq），转录起始位点（TSS）测序（TSS-seq），终止测序（term-seq），核糖体谱和无标记shot弹枪蛋白质组质谱，跨越不同的生长条件，并使用这些数据来改善注释和运动发酵单胞菌中的功能位点基因组。蛋白质组学和核糖体分析为蛋白质编码基因的修订提供了信息，其中包括44个起始密码子变化和42个添加的蛋白质。我们开发了用于注释转录本5'和3'末端的统计方法，从而能够鉴定3,940个TSS及其相应的启动子和2,091个转录终止位点，这些位点与RNA处理位点的区别在于缺少相邻的RNA 5'末端。我们的研究结果表明，运动发酵单胞σ^甲-35和-10启动子元件接近地类似规范大肠杆菌-35和-10的元件，有一个明显的例外：运动发酵单胞-10元件缺乏高度保守-7胸腺嘧啶中观察到ë大肠杆菌和其他先前表征的σ^一个发起人。所述σ^甲另一α-变形菌，的启动子柄杆菌新月，同样缺乏-7胸腺嘧啶在其-10元件保护。我们的结果锚定了运动发酵单胞菌作为合成生物学平台的发展，并建立了经验基因组注释策略，可以补充纯粹的计算方法。