Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation

Abstract

Moonlighting proteins are proteins with more than one function. During the past 25 years, they have been found to be rather widespread in bacteria. In Bacillus subtilis, moonlighting has been disclosed to occur via DNA, protein or RNA binding or protein phosphorylation. In addition, two metabolic enzymes, enolase and phosphofructokinase, were localized in the degradosome-like network (DLN) where they were thought to be scaffolding components. The DLN comprises the major endoribonuclease RNase Y, 3′-5′ exoribonuclease PnpA, endo/5′-3′ exoribonucleases J1/J2 and helicase CshA. We have ascertained that the metabolic enzyme GapA is an additional component of the DLN. In addition, we identified two small proteins that bind scaffolding components of the degradosome: SR1P encoded by the dual-function sRNA SR1 binds GapA, promotes the GapA-RNase J1 interaction and increases the RNase J1 activity. SR7P encoded by the dual-function antisense RNA SR7 binds to enolase thereby enhancing the enzymatic activity of enolase bound RNase Y. We discuss the role of small proteins in modulating the activity of two moonlighting proteins.

A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation

“…To substantiate the importance of complementary region D for the SR1- kinA mRNA interaction in vivo , we constructed pGKSR1 mD S carrying the same 7 nt exchange in region D which was shown in the EMSAs (Figure 3C ) to be important for kinA mRNA binding. This mutation does not affect the previously demonstrated ability of SR1P to interact with GapA for modulating the B. subtilis degradosome-like network ( 20 , 21 ). The β-galactosidase activities in the Δ sr1 strain with and without pGKSR1 mD S were comparable (Figure 4A ), indicating that SR1 mD cannot downregulate translation of wild-type kinA mRNA.…”

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

“…Secondly, there was a reduced level of a key enzyme in the glycolytic pathway of glucose utilization: glyceraldehyde-3-phosphate dehydrogenase (EP10_12960), which produces NADH and leads to the synthesis of pyruvate. It should be mentioned here that glyceraldehyde-3-phosphate dehydrogenase has multiple functions in the cell, and its downregulation under THz irradiation can affect not only the glycolytic pathway activity, but also the efficiency of such processes as DNA repair, translation elongation, and the degradation of RNA and proteins through interactions with various factors, as shown for the translation elongation factor EF-Tu and the molecular chaperone DnaK in E. coli and B. subtilis [ 27 , 28 , 29 ].…”

Cis- and Trans-Encoded Small Regulatory RNAs in Bacillus subtilis

“…Microorganisms 2021, 9, x FOR PEER REVIEW 8 of 14 degradation [36,54] (see Figure 3). An experimental analysis of 9 of the 23 SR1 homologues detected in 2012 demonstrated that both the base-pairing and the protein-encoding functions of SR1 are highly conserved over one billion years of evolution [55].…”

“…This small protein interacts with the glycolytic enzyme enolase, thereby promoting its recruitment to RNase Y to enhance the RNase Y activity on at least two substrate RNAs, rpsO mRNA, and the 5′ UTR of yitJ mRNA [ 35 ]. Consequently, SR7P plays a role in RNA degradation [ 35 , 36 ]. SR7 only acts in cis to reduce the amount of rpsD mRNA, most likely by transcriptional interference [ 37 ].…”

“…The SR1P/GapA interaction surface has been elucidated [ 53 ]. So far, SR1 is the only dual-function sRNA with functions in different physiological pathways, arginine metabolism, and RNA degradation [ 36 , 54 ] (see Figure 3 ). An experimental analysis of 9 of the 23 SR1 homologues detected in 2012 demonstrated that both the base-pairing and the protein-encoding functions of SR1 are highly conserved over one billion years of evolution [ 55 ].…”