Abstract
Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.
Highlights
The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates
Multiple alignments and the building of 3D models of YheA proteins allowed for the identification of two new aspects of this protein, a highly conserved 3D structure with respect to YmcA and YlbF, and the presence of a putative conserved motif located in the central region of com_ylbF domain, which could be involved in its function
We found a wider distribution of YheA ortholog proteins in the phylum Firmicutes than for YlbF and YmcA because it was identified in all species included in the study (e.g. Pediococcus pentosaceus, Lactobacillus acidophilus, Leuconostoc mesenteroides, Streptococcus pneumoniae, Listeria monocytogenes, and Geobacillus kaustophilus), except for in Clostridia, with identities between 26% (Streptococcus pneumoniae) and 83% (Staphylococcus saprophyticus) (Table 1)
Summary
There are two hypotheses about the function and participation of this tripartite complex (YlbF-YmcA-Yaat) in the processes of B. subtilis sporulation, competence, and biofilm formation; the first suggests that this complex stimulates the activity of the master response regulator Spo0A, increasing its phosphorylation [5, 6]. When Spo0A is phosphorylated (Spo0A~P), this regulator activates the transcription of genes needed to form biofilm, mature spores, and competence. YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established
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