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从哥伦比亚安第斯山脉超帕拉莫土壤样本中分离出的USBA-GBX 515菌株的基因组序列草图。

Draft genome sequence of strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes.

作者信息

López Gina, Diaz-Cárdenas Carolina, Shapiro Nicole, Woyke Tanja, Kyrpides Nikos C, David Alzate J, González Laura N, Restrepo Silvia, Baena Sandra

机构信息

Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia.

Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA.

出版信息

Stand Genomic Sci. 2017 Dec 15;12:78. doi: 10.1186/s40793-017-0292-9. eCollection 2017.

DOI:10.1186/s40793-017-0292-9
PMID:29255573
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5731063/
Abstract

Here we present the physiological features of strain USBA-GBX-515 (), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0-3.0 μm × 0.5-1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of genus and, the similarity of the 16S rDNA sequence was 100% with strain CT14-3. The draft genome of strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, and related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The and operons also appeared complete in the genome. strain USBA-GBX-515 conserves the same gene organization of the type strain CT14-3. We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.

摘要

在此，我们展示了从南美洲安第斯山脉北部海拔超过4000米的超帕拉莫生态系统土壤中分离出的USBA - GBX - 515菌株（ ）的生理特征，以及对其基因组草图的详尽分析。USBA - GBX - 515菌株是一种革兰氏阴性杆菌，大小为1.0 - 3.0μm×0.5 - 1μm，具有运动性且不能形成芽孢，它在有氧条件下生长，细胞有一根单一的鞭毛。多项遗传指标、16S rRNA基因序列的系统发育分析以及表型特征证实，USBA - GBX - 515是 属的一员，其16S rDNA序列与CT14 - 3菌株的相似度为100%。USBA - GBX - 515菌株的基因组草图由6,143,638 Mb组成，G + C含量为60.9 mol%。共预测到5665个基因，其中5544个为蛋白质编码基因，121个为RNA基因。基因在COG功能分类中的分布表明，大多数基因归类于氨基酸转运和代谢类别（10.5%），其次是转录（8.4%）和信号转导机制（7.3%）。我们对脂肪分解活性进行了实验分析，结果表明活性主要作用于短链脂肪酸。基因组分析表明存在两个基因，分别与三酰甘油脂肪酶和羧酸酯酶相关。还观察到氨化基因，主要是硝酸还原酶基因。检测到与聚羟基脂肪酸酯（PHA）合成相关的基因，尤其是聚羟基丁酸酯（PHB）。 和 操纵子在基因组中也显得完整。USBA - GBX - 515菌株保留了与模式菌株CT14 - 3相同的基因组织。我们还详尽分析了次级代谢产物的产生潜力，在参与其产生的32个生物合成基因簇中发现了近400个基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ac43f1b75437/40793_2017_292_Fig12_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/54319a05f2a5/40793_2017_292_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ec28793a4e8a/40793_2017_292_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/eaa3a31805a1/40793_2017_292_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/b07acaa43f52/40793_2017_292_Fig9_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/2f75512aed89/40793_2017_292_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ac43f1b75437/40793_2017_292_Fig12_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/54319a05f2a5/40793_2017_292_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/e73a5cf2a021/40793_2017_292_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ea0591d514d6/40793_2017_292_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/95793e08da51/40793_2017_292_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/32d7394cede2/40793_2017_292_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/f0885a2275c1/40793_2017_292_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ec28793a4e8a/40793_2017_292_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/eaa3a31805a1/40793_2017_292_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/b07acaa43f52/40793_2017_292_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/46419056027f/40793_2017_292_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/2f75512aed89/40793_2017_292_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4d7f/5731063/ac43f1b75437/40793_2017_292_Fig12_HTML.jpg

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