Thermus Bacteria and the Viruses That Infect Them

Abstract

Thermus phages, much like Thermus bacteria, are of great interest in research due to their thermostability, in particular in regard to their enzymes and gene expression regulation. In this study, nine Icelandic thermophilic viruses that infect Thermus bacteria were investigated, as well as their relationship with selected strains isolated from Iceland and abroad. This was done by analysing the host-ranges of the phages, the genomes of the Thermus strains and phages, and the CRISPR/Cas systems. Viral lysates were prepared and quantified through the plaque assay method. The host ranges of the bacteriophages were analysed through cross-infection trials involving 27 Thermus strains from 11 different species. The results showed diversity in host ranges, as both unique and similar patterns were seen within and between Thermus species. Whole genome sequences of both bacteriophages and hosts were obtained using the Nanopore and Illumina sequencing methods. The sequence information was used to analyse the CRISPR/Cas systems of the Thermus strains. Five systems, Type IB, Type IC, Type IE, Type IIIA, and Type IIIB, were found in the Thermus genomes. Also, 1269 Thermus CRISPR spacers were identified. Immunity and infection seen through the cross-infection trials were cross-referenced to the CRISPR spacers and 30 protospacers were found in seven of the Thermus phages. The morphology of the viruses was analysed using transmission electron microscopy, which aided in their characterization and classification. The phages were classified into the families Myoviridae, Siphoviridae, Inoviridae, and Tectiviridae. This study was a part of the Virus-X (H2020) project and ultimately facilitated its aim, which was to expand the knowledge of the world‘s virosphere and develop novel viral enzymes for use in genetic engineering.

Thermus veirur, líkt og Thermus bakteríur, eru mjög áhugaverðar vegna hitastöðugleika þeirra, einkum hvað varðar ensím þeirra og stjórnun gentjáningar. Markmið verkefnisins var að rannsaka níu íslenskar veirur sem sýkja hitakærar bakteríur af ættkvíslinni Thermus. Samband veiranna og valinna Thermus stofna frá Íslandi og öðrum löndum var rannsakað. Þetta var gert með því að greina hýsilsvið veiranna, skoða erfðamengi Thermus stofnanna og veiranna, og finna CRISPR/Cas kerfin. Lýsöt voru útbúin af veirunum og styrkur þeirra áætlaður með raðþynningum og sýkingum. Ennfremur voru þau notuð í sýkingum til að áætla hýsilsvið veirann meðal 27 stofna af 11 mismunandi Thermus tegundum. Niðurstöður sýkinganna sýndu fram á fjölbreytni í hýsilsviðs veiranna, en bæði sáust einstök og sameiginleg mynstur bæði milli og innan Thermus tegunda. Erfðamengi Thermus stofnanna og veiranna voru raðgreind með Illumina og Nanopore tækni. Leitað var að CRISPR/Cas kerfum í erfðamengjum Thermus stofnanna sem og CRISPR bilum. Niðurstöðurnar voru svo bornar saman við sýkingamynstrin sem sáust. Fimm kerfi fundust í Thermus erfðamengjunum, gerðir IB, IC, IE, IIIA og IIIB. Ennfremur fundust 1269 CRISPR bil. Af CRISPR bilunum pössuð 30 við sjö af veirunum. Allar veirurnar voru skoðaðar í smásjá og í kjölfarið flokkaðar eftir formgerð. Þær voru flokkaðar til fjölskyldnanna, Myoviridae, Siphoviridae, Inoviridae and Tectiviridae. Rannsóknin var hluti af Virus-X verkefninu (H2020) og vann jafnframt að markmiði þeirra, en það var að auka þekkingu á breytileika veira og þróa ný veiruensím til notkunar í erfðatækni.