In-silico functional analysis of hypothetical proteins from Lactiplantibacillus plantarum plasmids reveals enrichment of cell envelope proteins

Lactiplantibacillus plantarum is one of the important species of lactic acid bacterium (LAB) found in diverse en-vironments, with many strains exhibiting probiotic properties. In our previous study, 41.6% of protein families (PFs) encoded by 395 plasmids from several L. plantarum strains were found to be hypothetical proteins with no predicted function. This study aimed at predicting the functions of these 647 hypothetical proteins using 21 different bioinformatics methods. As a result, 160 PFs could be newly annotated. A lower proportion of plasmid-specific functions was annotated as compared to the functions shared between plasmids and chromosomes. Also, hypothetical proteins were less conserved than the annotated proteins across L. plantarum plasmids. Based on the subcellular localization, cell envelope proteins represented the biggest category in the newly annotated proteins. Transporters (112 PFs) which was a part of cell envelop proteins represented the largest functional group. Additionally, 40 and 25 other PFs were predicted to contain signal peptides and transmembrane helices, respectively. We speculate that such hypothetical proteins might be involved in the transport of various chem-icals and environmental interactions in L. plantarum. In the future, functional characterization of these proteins through wet-lab experimental approach can provide novel insights into their contribution to the physiology, probiotic properties, and industrial utility of these bacteria.

Automated summary

This study aimed to predict the functions of 647 hypothetical proteins in Lactiplantibacillus plantarum using 21 different bioinformatics methods, resulting in the annotation of 160 new protein families. Plasmid-specific functions had a lower proportion compared to those shared between plasmids and chromosomes. Hypothetical proteins were less conserved than annotated proteins in L. plantarum plasmids. Among the newly annotated proteins, cell envelope proteins, particularly transporters, represented the largest functional group. Additionally, some proteins were predicted to contain signal peptides or transmembrane helices. These hypothetical proteins may be involved in the transport of chemicals and environmental interactions in L. plantarum. Further functional characterization through wet-lab experiments could provide novel insights into their physiological contributions, probiotic properties, and industrial utility in these bacteria.