Tyrosine Phosphorylation-Dependent Localization of Tmar That Controls Activity of a Major Bacterial Sugar Regulator by Polar Sequestration

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Tyrosine Phosphorylation-Dependent Localization of Tmar That Controls Activity of a Major Bacterial Sugar Regulator by Polar Sequestration Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration Tamar Szokea, Nitsan Albochera,1, Sutharsan Govindarajana,b,1, Anat Nussbaum-Shochata, and Orna Amster-Chodera,2 aDepartment of Microbiology and Molecular Genetics, The Institute for Medical Research Israel–Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel; and bDepartment of Biology, SRM University - AP, Amaravati, Andhra Pradesh, 522 502, India Edited by Susan Gottesman, NIH, Bethesda, MD, and approved November 18, 2020 (received for review August 1, 2020) The poles of Escherichia coli cells are emerging as hubs for major via polar cluster formation. Execution of the PTS functions de- sensory systems, but the polar determinants that allocate their pends on a phosphorylation cascade that initiates with EI and components to the pole are largely unknown. Here, we describe HPr—the general PTS proteins—that deliver the phosphate to the discovery of a previously unannotated protein, TmaR, which the PTS sugar permeases, which import and phosphorylate the localizes to the E. coli cell pole when phosphorylated on a tyrosine incoming sugars (10). The PTS proteins also exert different ef- residue. TmaR is shown here to control the subcellular localization fects on non-PTS proteins depending on their phosphorylation and activity of the general PTS protein Enzyme I (EI) by binding on histidine residues, thus modulating the hierarchy in sugar and polar sequestration of EI, thus regulating sugar uptake and utilization (10). The PTS-imported sugars enter glycolysis, whose metabolism. Depletion or overexpression of TmaR results in EI re- product, phosphoenolpyruvate (PEP), phosphorylates EI, mak- lease from the pole or enhanced recruitment to the pole, which ing EI an important link between glycolysis and sugar uptake leads to increasing or decreasing the rate of sugar consumption, (11). We have previously shown that the general PTS proteins respectively. Notably, phosphorylation of TmaR is required to re- localize to the E. coli cell poles (12), although their localization lease EI and enable its activity. Like TmaR, the ability of EI to be depends on yet-unknown factors (13), that during growth EI recruited to the pole depends on phosphorylation of one of its polar clusters form stochastically from preexisting dispersed MICROBIOLOGY tyrosines. In addition to hyperactivity in sugar consumption, the molecules, and that EI clustering negatively correlates with EI absence of TmaR also leads to detrimental effects on the ability of function (14). Still, conclusive proof for polar localization as an cells to survive in mild acidic conditions. Our results suggest that inhibitory mechanism of EI function is lacking and the identity of this survival defect, which is sugar- and EI-dependent, reflects the the factor that captures EI at the pole remained unknown. difficulty of cells lacking TmaR to enter stationary phase. Our Polar clusters offer additional benefits, such as communication study identifies TmaR as the first, to our knowledge, E. coli protein between signal transduction systems in order to generate an reported to localize in a tyrosine-dependent manner and to control optimal response, e.g., the chemotaxis and the PTS system (15), the activity of other proteins by their polar sequestration and or the establishment of cellular asymmetry to coordinate devel- release. opmental programs with cell cycle progression (7). Polar proteins bacterial polarity | tyrosine phosphorylation | PTS system | Significance protein localization | cell pole In recent years, we have learned that bacterial cells have in- he central dogma describes the flow of genetic information tricate spatial organization despite the lack of membrane- Tfrom DNA to RNA to protein. However, for this process to bounded organelles. The endcaps of rod-shaped bacteria, — — be successful, the final product the protein needs to be in the termed poles, are emerging as hubs for sensing and respond- right place and at the right time. The consequences of mis- ing, but the processes involved in positioning macromolecules localization can be harmful to any cell type, let alone to the there are largely unknown. We discovered a protein, TmaR, unicellular bacterial cell, whose survival depends on fast and whose polar localization depends on a phospho-tyrosine efficient response to environmental changes. Hence, protein modification. We show that TmaR controls the activity of EI, localization is an important posttranslational regulatory step. the major regulator of sugar metabolism in most bacteria, by Thus far, most examples of protein targeting were reported in polar sequestration and release. Notably, TmaR is essential for eukaryotic cells, usually in the context of transport from one survival in conditions that Escherichia coli often encounters in organelle to another (1). In recent years, it became evident that nature. Hence, TmaR is a key regulator that connects tyrosine localization of proteins and RNAs to specific subcellular do- phosphorylation, spatial regulation, sugar metabolism, and mains occurs also in prokaryotic cells and is vital for many cel- survival in bacteria. lular processes (2–5). However, the mechanisms underlying macromolecules targeting to specific subcellular domains in Author contributions: T.S., S.G., A.N.-S., and O.A.-C. designed research; T.S., N.A., and bacterial cells, with the exception of membrane and cell division A.N.-S. performed research; T.S. contributed new reagents/analytic tools; T.S. and N.A. proteins, remain largely unknown. analyzed data; T.S., S.G., and O.A.-C. wrote the paper; and O.A.-C. provided advice and The bacterial cell poles are emerging as important domains supervised the research. that accommodate protein and RNA assemblies (5, 6). Pole-lo- The authors declare no competing interest. calized proteins are involved in a wide range of cellular func- This article is a PNAS Direct Submission. tions, including motility, regulation of cell cycle, metabolism, Published under the PNAS license. differentiation, pathogenesis, and secretion (7). Several proteins 1N.A. and S.G. contributed equally to this work. were reported to be kept as inactive at the Escherichia coli cell 2To whom correspondence may be addressed. Email: [email protected]. pole until needed, e.g., MurG (8), and FtsZ (9). The phospho- This article contains supporting information online at https://www.pnas.org/lookup/suppl/ transferase system (PTS), which controls sugar utilization and doi:10.1073/pnas.2016017118/-/DCSupplemental. metabolism in most bacteria, provides an example for regulation Published December 29, 2020. PNAS 2021 Vol. 118 No. 2 e2016017118 https://doi.org/10.1073/pnas.2016017118 | 1of12 Downloaded by guest on October 2, 2021 that recruit other proteins to the poles, thus regulating cell cycle A Phase YFP B Phase mYFP progression, were discovered in some bacteria, e.g., DivIVA in Bacillus subtilis, PopZ and TipN in Caulobacter crescentus, and HubP in Vibrio cholerae (7). In E. coli, the three Min proteins, MinCDE, cooperate to position the cell division site through TmaR-YFP pole-to-pole oscillation (16). mYFP-TmaR In some bacteria, e.g., C. crescentus, specific localization of proteins is linked to their phosphorylation or to the phosphory- C D lation of factors regulating them (17, 18). In most cases, these proteins are members of the two-component systems, which mediate sensing and regulation by phosphorylation on histidine and aspartic acid residues (19), events considered most prevalent Percent of detectable cluster detectable in bacteria. Only in recent years, improved methodologies E OD600 OD600 revealed numerous previously unknown Ser/Thr/Tyr phosphor- (AU) YFP intensity 0.2 0.4 0.6 0.8 1 1.3 1.7 ON TmaR-YFP 55 ylation sites, once thought to be hallmarks of eukaryotes, in 40 The normalized cell length bacterial and archaeal proteins. The degree to which these pu- GroEL 70 55 tative sites are phosphorylated is still unclear and proofs for their F WY72FT Y79 F15Y importance in vivo are just beginning to emerge. Also, the linkage between phosphorylation on Ser/Thr/TyR and localiza- tion of the phosphorylated bacterial proteins remained unknown. In this study, we show that a previously uncharacterized E. coli protein, YeeX, which is prevalent among Gram-negative bacte- ria, clusters at the pole in a tyrosine phosphorylation-dependent manner and recruits the major sugar utilization regulator EI. Y79F,Y72F Y79F,Y72F,Y51F G Fracon of cells with clusters We, therefore, renamed this protein TmaR for targeting of sugar WT metabolism-associated regulator. TmaR and EI are shown to Y79F physically interact and to colocalize. TmaR is necessary for EI Y72F polar clustering, but the opposite is not true. Only phosphory- Y51F lated, TmaR can release EI from the poles, since the diffuse Y79F, Y72F Y79F, Y72F, Y51F nonphosphorylated TmaR binds to EI quite irreversibly. Nota- Y79F bly, tyrosine phosphorylation of EI is also required for its polar Y79F Y79F Y72F H Y79F Y72F I WT Y79FY72F Y51F Y72F Y51F NC localization. We further show that TmaR-mediated EI clustering WT Y79F Y72F Y51F Y72F Y51F 17 inversely correlates with EI-mediated sugar uptake, implying that 40 the polar clusters serve as a reservoir for ready-to-act EI mole- 35 11 cules. Cells lacking TmaR have detrimental effects on cell sur- vival, which is affected by EI and sugar concentration, when Fig. 1. TmaR forms clusters that localize to the pole of E. coli cells in a ty- challenged with mildly acidic conditions that are typical to vari- rosine phosphorylation-dependent manner. (A) Images of cells expressing ous E. coli habitats. Taken together, our study identifies TmaR TmaR-YFP (yellow) from its native promoter and locus in the chromosome. as a spatial regulator of sugar metabolism and bacterial survival. (B) Images of cells expressing TmaR tagged at its N terminus with monomeric YFP (mYFP-TmaR, yellow) from its native promoter and locus in the chro- Results mosome. (C) The fluorescence intensity profile of 50 cells expressing a cluster of TmaR-YFP along the normalized long cell axis.
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