Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont
Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont
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兼性细菌内共生体 Sodalis glsinidius 中假基因的大规模和显着表达
DOI：
10.1101/124388
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Goodhead I
中科院分区：
文献类型：
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作者：
Goodhead I
大多数细菌基因组具有较高的编码效率，但也有一些胞内细菌基因组的基因密度较低。内共生体 Sodalis Glossinidius 的基因组包含几乎 50% 的假基因，这些假基因含有突变，这些突变可能在基因组水平上使它们沉默。我们应用了多种“组学”策略，结合 Illumina 和 Pacific Biosciences 的单分子实时 DNA 测序和注释、链 RNA 测序和蛋白质组分析，以更好地了解 Sodalispseudogenes 的转录和翻译景观及其控制的潜在机制。 53% 至 74% 的 Sodalist 转录组在无细胞培养物中仍保持活性。编码域序列 (CDS) 的平均有义转录是假基因的四倍。对来自不同宿主舌藻属物种的六种 Illumina 测序的 Sodalis 分离株进行的比较基因组分析显示，核心基因组中 2729 个基因中的 40% 为假基因，表明它们是稳定的和/或 Sodalis 是最近引入舌藻属的兼性共生体。这些数据进一步阐明了转录和翻译控制在破译宿主-微生物相互作用中的重要性。基因组学、转录组学和蛋白质组学的结合为研究原核基因组提供了多维视角，以阐明对新环境生态位的进化适应。
The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiontSodalis glossinidiuscontains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape ofSodalispseudogenes, and potential mechanisms for their control. Between 53 and 74 % of theSodalistranscriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequencedSodalisisolates from different hostGlossinaspecies shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or thatSodalisis a recent introduction across the genusGlossinaas a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.