Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
复制标题
cas1 的靶向组装表明 CRISPR-Cas 对土壤变暖的反应
DOI：
10.1038/s41396-020-0635-1
复制
发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Tiedje, James M.
中科院分区：
文献类型：
--
作者：
Wu, Ruonan;Chai, Benli;Cole, James R.;Gunturu, Santosh K.;Guo, Xue;Tian, Renmao;Gu, Ji-Dong;Zhou, Jizhong;Tiedje, James M.
人们越来越关注成簇的规则间隔短回文重复序列CRISPR相关蛋白（CRISPR-Cas）系统，以揭示潜在的病毒-宿主动力学。cas 1是一种通用的、最保守的Cas蛋白，是阐明CRISPR-Cas生态学的理想标记。我们通过靶向基因组装器Xander直接从宏基因组构建了八个隐马尔可夫模型（Himp）和Himp cas 1，以提高检测能力并解决不同的CRISPR-Cas系统。通过从11门91个原核基因组产生的模拟宏基因组中回收所有17个cas 1亚型，首次验证了8个HSPs。我们用来自俄克拉荷马州中部高草草原的48个宏基因组挑战了靶向方法，回收了3394个cas 1。其中，88个接近全长，比来自俄克拉荷马州宏基因组的从头组装多5倍。为了验证cas 1的宿主分配，将靶向扩增的cas 1定位到从头组装的重叠群。这些映射的重叠群的所有门分配独立于相同重叠群上的CRISPR-Cas基因进行分配，并且与mappedcas预测的宿主分类学一致1。然后，我们调查了8年的土壤变暖是否改变了社区内的患病率。在温差最大的年份（平均比环境温度高4.16 °C）观察到微生物丰度的变化。在接下来的3年中，cas 1流行率增加，甚至在微生物丰度减少的门中，这表明病毒-宿主相互作用增加，以应对土壤变暖。这种有针对性的方法提供了一种替代手段，有效地从宏基因组中挖掘cas 1，并揭示宿主社区。
There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein,cas1is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembledcas1directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17cas1subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment bycas1, the targeted-assembledcas1was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mappedcas1. We then investigated whether 8 years of soil warming alteredcas1prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient).cas1prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively minecas1from metagenomes and uncover the host communities.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
基于特征的轮廓隐马尔可夫模型的鲁棒远程同源检测
DOI：
10.2202/1544-6115.1159
发表时间：
2005
影响因子：
0.9
作者：
T. Plötz;G. Fink
通讯作者：
G. Fink
影响因子：
64.8
作者：
Burstein D;Harrington LB;Strutt SC;Probst AJ;Anantharaman K;Thomas BC;Doudna JA;Banfield JF
通讯作者：
Banfield JF