Molecular insight into viral infection of Methanoarchaea and their respective viruses

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The proposal in general addresses viral infection of Methanoarchaea. The first and main part aims to study and understand the interaction between Methanosarcina mazei and its recent isolated lytic virus Methanosarcina Spherical Virus (MetSV) on a molecular level. MetSV contains double-stranded linear DNA with a genome size of 10,567bp containing 22 open reading frames (ORFs) including nine small ORFs encoding proteins with less than 50 amino acids in length. Aiming to gain insight into the virus - M. mazei interaction on the molecular level, we will generally apply a combination of biochemical and genetic approaches in the three goals proposed: (i) Elucidate the function of the small proteins within the infection cycle particularly focusing on those predicted to have anti-CRISPR or anti-defence function. This will include studying and imaging the infection process by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) in close collaboration with Dr. Urska Repnik and modeling the infection process in collaboration with Dr. Christel Kamp. (ii) Illuminate the predicted regulatory function(s) of viral DNA/RNA binding proteins in the infection process. Potential regulated host genes will be identified by RNAseq analysis of respective viral mutants in comparison with the wild type, as well as by localizing binding sites of the host genome by chromatin immunoprecipitation sequencing (ChIP-SEq) in collaboration with Dr. Julia Frunzke. (iii) Identify and characterize the virus encoded sRNAs and study their potential functions during the infection cycle by computational target prediction tools and genetic approaches. In the second and minor part we aim to initiate studying methanoarchaeal viruses present in human gastrointestinal tracts to predict and in future also evaluate impacts of methanoarchaeal viruses on the human gut microbiome. The vast majority of identified yet uncharacterized (methoano)archaeal viral species we identified by bioinformatics approaches in metagenomes of human gut microbiomes suggests a novel unrecognized diversity and importance of archaeal viruses. Consequently, we will characterize the identified novel viruses using bioinformatics approaches in collaboration with Dr. Cynthia M. Chibani and the Z-project. In parallel we aim to isolate identified methanoarchaeal viruses from different samples using targeted approaches. In the long run and in collaboration with Dr. Li Deng, Dr. Micheal Zimmermann, and Dr. Bärbel Stecher-Letsch this will allow to study the impact of methanoarchaeal viruses on (human) gut microbiomes.