MycoWiki: Functional annotation of the minimal model organism Mycoplasma pneumoniae

Abstract

The human pathogen Mycoplasma pneumoniae is viable independently from host cells or organisms, despite its strongly reduced genome with only about 700 protein-coding genes. The investigation of M. pneumoniae can therefore help to obtain general insights concerning the basic requirements for cellular life. Accordingly, M. pneumoniae has become a model organism for systems biology in the past decade. To support the investigation of the components of this minimal bacterium, we have generated the database MycoWiki. (http://mycowiki.uni-goettingen.de) MycoWiki organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae. Interestingly, M. pneumoniae has undergone an evolution that resulted in the limited similarity of many proteins to proteins of model organisms. To facilitate the analysis of the functions of M. pneumoniae proteins, we have integrated structure predictions from the AlphaFold Protein Structure Database for most proteins, structural information resulting from in vivo cross-linking, and protein-protein interactions based on a global in vivo study. MycoWiki is an important tool for the systems and synthetic biology community that will support the comprehensive understanding of a minimal organism and the functional annotation of so far uncharacterized proteins.

Understudied proteins and understudied functions in the model bacterium Bacillus subtilis—A major challenge in current research

“…Interaction studies might provide more insights into the function of unknown proteins—based on the principle “guilty by association.” Indeed, a large‐scale, global interactome analysis with the minimal organism Mycoplasma pneumoniae provided important clues for the function of many proteins. As an example, the completely unknown protein MPN530 interacts with multiple subunits of the RNA polymerase, including the house‐keeping sigma factor, suggesting that this protein plays a role in transcription (Elfmann et al, 2022; O'Reilly et al, 2020). A similar attempt has recently also been performed for B. subtilis , and many so far unknown proteins were found interacting with well‐characterized proteins or protein complexes, such as the ribosome (O'Reilly et al, 2023).…”

Understudied Proteins and Understudied Functions in the Model Bacterium Bacillus subtilis -- a Major Challenge in Current Research

“…Indeed, a large scale, global interactome analysis with the minimal organism Mycoplasma pneumoniae provided important clues for the function of many proteins. As an example, the completely unknown protein MPN530 interacts with multiple subunits of the RNA polymerase, including the house-keeping sigma factor, suggesting that this protein plays a role in transcription (O'Reilly et al, 2020;Elfmann et al, 2022). A similar attempt has recently also been performed for B. subtilis , and many so far unknown proteins were found interacting with well-characterized proteins or protein complexes, such as the ribosome (O'Reilly et al, 2023).…”

“…Such an integration of all available information on the genes and proteins is provided in the database Subti Wiki which is the major reference tool of the B. subtilis research community (Fig. 1; Pedreira et al, 2022). Other important online tools that help developing hypotheses are the protein interaction and association database STRING (Sklarczyk et al, 2023), the FlaGs webserver that allows to interrogate conserved gene organization which is often an indication of functional association between proteins (Saha et al 2021), as well as the UniProt and COG databases that provide information on protein functions that may have been identified in other, otherwise potentially overlooked (Galperin et al, 2021;UniProt Consortium, 2023).…”

“…With only 452 protein-coding genes, this organism currently defines the lower limit of the protein complement for an independently viable bacterium (Hutchison et al, 2016;Breuer et al, 2019). Yet, about one third of these proteins still have no known function, indicating major gaps in our knowledge even for the most simple cells (Hutchison et al, 2016;Pedreira et al, 2022 a). These gaps are caused by a focus on a limited set of intensively studied proteins for which more and more knowledge accumulates.…”

“…As a model organism for differentiation and workhorse in biotechnology, B. subtilis is one of the most intensively studied organisms. However, the function of about 25% of the proteins (about 1,000 proteins) encoded by the B. subtilis genome is still unknown or only very poorly understood (Pedreira et al, 2022). In this review, we give an overview on the strategies used to get initial minimal annotation for so far unknown proteins, we present a set of highly expressed unknown proteins that should be studied with highest priority, and we define and discuss fields of research that still have many open questions, i.e ., RNA-binding proteins, amino acid transport, and the control of metabolic homeostasis.…”