Polina NAVIKOVA

Overview of archaeal functions within the human gut microbiome using sequence- and structure-
informed strategy for protein functional assignment

Roughly 40 years ago a separate and previously unknown branch of the Tree of Life – the Domain of
Archaea – was established. Archaea are remarkable not only in their ability to thrive in harsh
environments, but also in their capacity to profoundly interact with the surrounding environments
and organisms.
Nowadays archaea are of particularly high interest in the context of human gut. Knowledge on the
abundance and diversity of human-associated archaea is very limited, and little is known about their
functions and their overall role in the human health. Archaeal metabolism in the human gut has not
been proven to be pathogenic yet, however archaea are known to strongly impact human health and
well-being.
Archaea are extremely challenging to be studied in laboratory conditions, therefore metagenomic
sequencing of environmental samples benefits studying the microbes. Uncultured archaea can be
characterised via protein prediction, annotation, and comparison with other proteins. However,
conventional methods for protein prediction and functional assignment, i.e., sequence comparison-
based, do not prove to be particularly effective. However, when methods based on sequence

comparison report vague annotations, examination of protein tertiary structure can reveal remote
phylogenetic relationships and suggest functional roles.
In this work we propose an integrated sequence- and structure-informed strategy for the annotation
of “dark matter” archaeal gut proteins. We seek to identify roles of archaeal gut-specific proteins and
emphasise the most enriched functions performed by M.smithii, a common and important
methanogenic archaeon in the human microbiota. We propose a strategy for protein functional
annotation employing the most recent protein structure-based approaches, such as AlphaFold2,
trRosetta, ProFunc and DeepFri. We highlight the importance of structure-based function assignment
for cases when conventional sequence-based approaches do not prove competent. As a result, we
identify the major processes performed by the archaeal fraction of human gut microbiota and show
that M.smithii species possess a number of advantages allowing them to thrive in the human gut and
benefit from their neighborhood with surrounding species and environment.
Keywords: protein structure, archaea, methanogens, gut microbiome

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