RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells.
RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells.
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RNA-Seq 和微阵列分析揭示类杆菌和自由生活细胞之间 Mesorhizobium huakuii 7653R 的整体差异转录组
DOI：
10.1371/journal.pone.0093626
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Li Y
中科院分区：
文献类型：
--
作者：
Peng J;Hao B;Liu L;Wang S;Ma B;Yang Y;Xie F;Li Y
华癸中生根瘤菌7653 R既可与寄主紫云英共生固氮，也可在土壤中自由生长。分枝华癸7653 R基因组已完成测序。为了更好地了解7653 R在类菌体发育过程中发生的复杂生化和发育变化，使用RNA-Seq和微阵列研究了7653 R类菌体和自由生活细胞的差异转录组。这两种方法鉴定了几千个差异表达的基因。在共生质粒中基因表达上调最为显著，同时类菌体中基因表达集中在一组基因（簇）上，以满足相应的功能需求。结果表明，类杆菌主要的能量代谢活跃，脂肪酸代谢不活跃，与细胞周期相关的基因表达下调。为了进行全局分析，我们重建了7653 R的蛋白质-蛋白质相互作用（PPI）网络，并使用Cytoscape将基因表达数据整合到网络中。一个高度互连的子网络，功能富集固氮，被发现，并确定了一组枢纽和以前未知的基因参与固氮。这里描述的结果提供了一个更广泛的生物景观和新的见解，阐明根瘤菌类细菌分化，固氮和相关的新基因功能。
Mesorhizobium huakuii 7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii 7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in 7653R during bacteroid development, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of 7653R bacteroids and free-living cells. The two approaches identified several thousand differentially expressed genes. The most prominent up-regulation occurred in the symbiosis plasmids, meanwhile gene expression is concentrated to a set of genes (clusters) in bacteroids to fulfill corresponding functional requirements. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly. For a global analysis, we reconstructed a protein-protein interaction (PPI) network for 7653R and integrated gene expression data into the network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.
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在共生期间米洛洛氏菌的转录组分析。
影响因子：
12.3
作者：
Ampe, Frederic;Kiss, Erno;Sabourdy, Frederique;Batut, Jacques
通讯作者：
Batut, Jacques
影响因子：
14.9
作者：
BECKERANDRE, M;HAHLBROCK, K
通讯作者：
HAHLBROCK, K
影响因子：
6.2
作者：
Chen, Da-Song;Li, You-Guo;Zhou, Jun-Chu
通讯作者：
Zhou, Jun-Chu
影响因子：
14.9
作者：
Barnes M;Freudenberg J;Thompson S;Aronow B;Pavlidis P
通讯作者：
Pavlidis P
DOI：
10.1073/pnas.0407269101
发表时间：
2004-11-23
影响因子：
11.1
作者：
Barnett, MJ;Tolman, CJ;Long, SR
通讯作者：
Long, SR