Toward the Complete Functional Characterization of a Minimal Bacterial Proteome

Recently, we presented a whole-cell kinetic model of
the genetically
minimal bacterium JCVI-syn3A that described the coupled metabolic
and genetic information processes and predicted behaviors emerging
from the interactions among these networks. JCVI-syn3A is a genetically
reduced bacterial cell that has the fewest number and smallest fraction
of genes of unclear function, with approximately 90 of its 452 protein-coding
genes (that is less than 20%) unannotated. Further characterization
of unclear JCVI-syn3A genes strengthens the robustness and predictive
power of cell modeling efforts and can lead to a deeper understanding
of biophysical processes and pathways at the cell scale. Here, we
apply computational analyses to elucidate the functions of the products
of several essential but previously uncharacterized genes involved
in integral cellular processes, particularly those directly affecting
cell growth, division, and morphology. We also suggest directed wet-lab
experiments informed by our analyses to further understand these “missing
puzzle pieces” that are an essential part of the mosaic of
biological interactions present in JCVI-syn3A. Our workflow leverages
evolutionary sequence analysis, protein structure prediction, interactomics,
and genome architecture to determine upgraded annotations. Additionally,
we apply the structure prediction analysis component of our work to
all 452 protein coding genes in JCVI-syn3A to expedite future functional
annotation studies as well as the inverse mapping of the cell state
to more physical models requiring all-atom or coarse-grained representations
for all JCVI-syn3A proteins.