Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Abstract

Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; $30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

Are Antisense Proteins in Prokaryotes Functional?

“…Signalling or interactions between cells will be a significant area to investigate regarding possible functions of antisense proteins. This suggestion is based on both the evidence gained so far for small proteins (Sberro et al, 2019) and the potential importance of any such genes. Any antisense proteins which are involved in signalling or inter-cell interactions may be of particular practical importance.…”

“…As an example, the NCBI prokaryotic genome annotation standards include among the minimum standards that there can be "[n]o gene completely contained in another gene on the same or opposite strand" (NCBI, 2020). For instance, a recent study investigated small proteins in the human microbiome (Sberro et al, 2019), finding hundreds of previously unknown small proteins with evidence from evolutionary sequence constraint, and many also with evidence of transcription and/or translation. Two key steps were the use of MetaProdigal for gene prediction and RNAcode for inference of conservation.…”

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

“…Similar is the case of small protein members of toxinantitoxin (TA) systems, particularly type-II, where both the toxin and the antitoxin are proteins (Harms et al, 2018). However, starting with the discovery almost two decades ago of previously overlooked conserved small open reading frames (sORFs) in the Escherichia coli chromosome (Wassarman et al, 2001), interest in other potential roles of bacterial small proteins has been increasing (Miravet-Verde et al, 2019;Sberro et al, 2019;Storz et al, 2014). In-depth characterization of individual small proteins has since revealed an unexpected diversity of functions in several different species.…”

A proteogenomics workflow to uncover the world of small proteins inStaphylococcus aureus

“…Over the last years, various attempts have been made that address one or both of these issues. This includes experimental approaches such as ribosomal profiling and proteogenomics to identify these group of proteins as well as bioinformatic approaches for a more reliable prediction and comprehensive annotation of sORFs (14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26). For instance, different computational approaches have been developed for sORF prediction which have in common that the coding potential of a putative sORF is scored based on at least one or more features such as nucleotide composition, synonymous and non-synonymous substitution rates, phylogenetic conservation or protein domain detection (13,16).…”