来自美国西南部的六种裂解性噬菌体的比较基因组学
Comparative Genomics of Six Lytic Phages from the Southwest United States.
作者信息
Vill Albert C, Delesalle Véronique A, Tomko Brianne E, Lichty Katherine B, Strine Madison S, Guffey Alexandra A, Burton Elizabeth A, Tanke Natalie T, Krukonis Greg P
机构信息
Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA.
出版信息
Phage (New Rochelle). 2022 Sep 1;3(3):171-178. doi: 10.1089/phage.2022.0030. Epub 2022 Sep 19.
BACKGROUND
Despite their importance to microbial dynamics involving , we have a limited understanding of the diversity of phages that can lyse this model organism.
MATERIALS AND METHODS
Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild strain. Their genomes were assembled, characterized, and bioinformatically compared.
RESULTS
Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.
CONCLUSIONS
A comparative approach provides insights into phage evolution, including the role of indels in protein folding.
背景
尽管噬菌体对于涉及的微生物动态具有重要意义，但我们对能够裂解这种模式生物的噬菌体多样性了解有限。
材料与方法
从美国西南部沙漠不同地点采集的土壤样本中，在一株野生菌株上分离噬菌体。对其基因组进行组装、表征，并进行生物信息学比较。
结果
分离出六种彼此具有高核苷酸和氨基酸相似性（>80%）但与GenBank中目前的噬菌体相似性非常有限的长尾噬菌体科噬菌体。这些噬菌体具有双链DNA基因组（55,312至56,127 bp），带有86 - 91个推定的蛋白质编码基因，且GC含量较低。比较基因组学揭示了编码推定参与细菌吸附的蛋白质的基因座差异，有基因组镶嵌现象的证据以及小基因可能发挥的作用。
结论
一种比较方法为噬菌体进化提供了见解，包括插入缺失在蛋白质折叠中的作用。
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