The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli.

Mn exporter Mn homeostasis MntP MntS manganese signal peptide small proteins

Journal

Molecular microbiology
ISSN: 1365-2958
Titre abrégé: Mol Microbiol
Pays: England
ID NLM: 8712028

Informations de publication

Date de publication:
17 Dec 2023
Historique:
revised: 17 11 2023
received: 15 09 2023
accepted: 24 11 2023
medline: 18 12 2023
pubmed: 18 12 2023
entrez: 17 12 2023
Statut: aheadofprint

Résumé

Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.

Identifiants

pubmed: 38104967
doi: 10.1111/mmi.15206
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NIH HHS
ID : R15GM137249
Pays : United States

Informations de copyright

© 2023 John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Références

Alix, E. & Blanc-Potard, A.B. (2008) Peptide-assisted degradation of the Salmonella MgtC virulence factor. The EMBO Journal, 27, 546-557.
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
Alva, V., Soding, J. & Lupas, A.N. (2015) A vocabulary of ancient peptides at the origin of folded proteins. eLife, 4, e09410.
Arnold, F.H. & Zhang, J.H. (1994) Metal-mediated protein stabilization. Trends in Biotechnology, 12, 189-192.
Bartsevich, V.V. & Pakrasi, H.B. (1995) Molecular identification of an ABC transporter complex for manganese: analysis of a cyanobacterial mutant strain impaired in the photosynthetic oxygen evolution process. The EMBO Journal, 14, 1845-1853.
Battesti, A. & Bouveret, E. (2012) The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli. Methods, 58, 325-334.
Bosma, E.F., Rau, M.H., van Gijtenbeek, L.A. & Siedler, S. (2021) Regulation and distinct physiological roles of manganese in bacteria. FEMS Microbiology Reviews, 45, fuab028. https://doi.org/10.1093/femsre/fuab028
Chan, D.W., Son, S.C., Block, W., Ye, R., Khanna, K.K., Wold, M.S. et al. (2000) Purification and characterization of ATM from human placenta. A manganese-dependent, wortmannin-sensitive serine/threonine protein kinase. The Journal of Biological Chemistry, 275, 7803-7810.
Chandrangsu, P., Rensing, C. & Helmann, J.D. (2017) Metal homeostasis and resistance in bacteria. Nature Reviews. Microbiology, 15, 338-350.
Cherepanov, P.P. & Wackernagel, W. (1995) Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene, 158, 9-14.
Couso, J.P. & Patraquim, P. (2017) Classification and function of small open reading frames. Nature Reviews. Molecular Cell Biology, 18, 575-589.
Dalbey, R.E., Wang, P. & van Dijl, J.M. (2012) Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiology and Molecular Biology Reviews, 76, 311-330.
Daly, M.J., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Venkateswaran, A. et al. (2004) Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science, 306, 1025-1028.
Dambach, M., Sandoval, M., Updegrove, T.B., Anantharaman, V., Aravind, L., Waters, L.S. et al. (2015) The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Molecular Cell, 57, 1099-1109.
Datsenko, K.A. & Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences of the United States of America, 97, 6640-6645.
Davies, B.W. & Walker, G.C. (2007) Disruption of sitA compromises Sinorhizobium meliloti for manganese uptake required for protection against oxidative stress. Journal of Bacteriology, 189, 2101-2109.
de Alvarenga, L.V., Hess, W.R. & Hagemann, M. (2020) AcnSP-a novel small protein regulator of aconitase activity in the cyanobacterium Synechocystis sp. PCC 6803. Frontiers in Microbiology, 11, 1445.
Deorowicz, S., Debudaj-Grabysz, A. & Gudys, A. (2016) FAMSA: fast and accurate multiple sequence alignment of huge protein families. Scientific Reports, 6, 33964.
DeWitt, M.A., Kliegman, J.I., Helmann, J.D., Brennan, R.G., Farrens, D.L. & Glasfeld, A. (2007) The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state. Journal of Molecular Biology, 365, 1257-1265.
Du, D., Neuberger, A., Orr, M.W., Newman, C.E., Hsu, P.C., Samsudin, F. et al. (2020) Interactions of a bacterial RND transporter with a transmembrane small protein in a lipid environment. Structure, 28, 625-634.e6.
Galperin, M.Y. & Chou, S.H. (2022) Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP Type c-di-GMP Phosphodiesterases. Journal of Bacteriology, 204, e0056121.
Garai, P. & Blanc-Potard, A. (2020) Uncovering small membrane proteins in pathogenic bacteria: regulatory functions and therapeutic potential. Molecular Microbiology, 114, 710-720.
Gralnick, J.A. & Newman, D.K. (2007) Extracellular respiration. Molecular Microbiology, 65, 1-11.
Gray, T., Storz, G. & Papenfort, K. (2022) Small proteins; Big questions. Journal of Bacteriology, 204, e0034121.
Guerra, A.J., Dann, C.E., 3rd & Giedroc, D.P. (2011) Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. Journal of the American Chemical Society, 133, 19614-19617.
Guzman, L.M., Belin, D., Carson, M.J. & Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. Journal of Bacteriology, 177, 4121-4130.
Hegde, R.S. & Bernstein, H.D. (2006) The surprising complexity of signal sequences. Trends in Biochemical Sciences, 31, 563-571.
Hemm, M.R., Weaver, J. & Storz, G. (2020) Escherichia coli Small Proteome. EcoSal Plus, 9. https://pubmed.ncbi.nlm.nih.gov/32385980/
Horsburgh, M.J., Wharton, S.J., Karavolos, M. & Foster, S.J. (2002) Manganese: elemental defence for a life with oxygen. Trends in Microbiology, 10, 496-501.
Humphreys, I.R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S. et al. (2021) Computed structures of core eukaryotic protein complexes. Science, 374, eabm4805.
Iyer, L.M. & Aravind, L. (2012) Insights from the architecture of the bacterial transcription apparatus. Journal of Structural Biology, 179, 299-319.
Jakubovics, N.S. & Jenkinson, H.F. (2001) Out of the iron age: new insights into the critical role of manganese homeostasis in bacteria. Microbiology, 147, 1709-1718.
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O. et al. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583-589.
Juttukonda, L.J. & Skaar, E.P. (2015) Manganese homeostasis and utilization in pathogenic bacteria. Molecular Microbiology, 97, 216-228.
Katoh, K., Rozewicki, J. & Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20, 1160-1166.
Kaur, G., Iyer, L.M., Subramanian, S. & Aravind, L. (2018) Evolutionary convergence and divergence in archaeal chromosomal proteins and chromo-like domains from bacteria and eukaryotes. Scientific Reports, 8, 6196.
Kehres, D.G., Janakiraman, A., Slauch, J.M. & Maguire, M.E. (2002) SitABCD is the alkaline Mn(2+) transporter of Salmonella enterica serovar typhimurium. Journal of Bacteriology, 184, 3159-3166.
Kehres, D.G. & Maguire, M.E. (2003) Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria. FEMS Microbiology Reviews, 27, 263-290.
Lee, Y. & Szymanski, D.B. (2021) Multimerization variants as potential drivers of neofunctionalization. Science Advances, 7, eabf0984.
Lisher, J.P. & Giedroc, D.P. (2013) Manganese acquisition and homeostasis at the host-pathogen interface. Frontiers in Cellular and Infection Microbiology, 3, 91.
Luo, Z., Neville, S.L., Campbell, R., Morey, J.R., Menon, S., Thomas, M. et al. (2019) Structure and metal binding properties of Chlamydia trachomatis YtgA. Journal of Bacteriology, 202, e00580-19.
Lupas, A.N. & Alva, V. (2017) Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins. Journal of Structural Biology, 198, 74-81.
Martin, J.E., Lisher, J.P., Winkler, M.E. & Giedroc, D.P. (2017) Perturbation of manganese metabolism disrupts cell division in Streptococcus pneumoniae. Molecular Microbiology, 104, 334-348.
Martin, J.E. & Waters, L.S. (2022) Regulation of bacterial manganese homeostasis and usage during stress responses and pathogenesis. Frontiers in Molecular Biosciences, 9, 945724.
Martin, J.E., Waters, L.S., Storz, G. & Imlay, J.A. (2015) The Escherichia coli small protein MntS and exporter MntP optimize the intracellular concentration of manganese. PLoS Genetics, 11, e1004977.
Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A. et al. (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530-1534.
Mirdita, M., Steinegger, M. & Soding, J. (2019) MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics, 35, 2856-2858.
Moncrief, M.B. & Hausinger, R.P. (1997) Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. Journal of Bacteriology, 179, 4081-4086.
Musik, J.E., Zalucki, Y.M., Beacham, I.R. & Jennings, M.P. (2022) The role of signal sequence proximal residues in the mature region of bacterial secreted proteins in E. coli. Biochimica et Biophysica Acta-Biomembranes, 1864, 184000.
Nader, S., Perard, J., Carpentier, P., Arnaud, L., Crouzy, S. & Michaud-Soret, I. (2019) New insights into the tetrameric family of the fur metalloregulators. Biometals, 32, 501-519.
Nicastro, R., Gaillard, H., Zarzuela, L., Peli-Gulli, M.P., Fernandez-Garcia, E., Tome, M. et al. (2022) Manganese is a physiologically relevant TORC1 activator in yeast and mammals. eLife, 11, e80497.
Nielsen, H. (2017) Predicting secretory proteins with SignalP. Methods in Molecular Biology, 1611, 59-73.
Olson, J.W., Fu, C. & Maier, R.J. (1997) The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase. Molecular Microbiology, 24, 119-128.
Orr, M.W., Mao, Y., Storz, G. & Qian, S.B. (2020) Alternative ORFs and small ORFs: shedding light on the dark proteome. Nucleic Acids Research, 48, 1029-1042.
Paetzel, M., Karla, A., Strynadka, N.C. & Dalbey, R.E. (2002) Signal peptidases. Chemical Reviews, 102, 4549-4580.
Papp-Wallace, K.M. & Maguire, M.E. (2006) Manganese transport and the role of manganese in virulence. Annual Review of Microbiology, 60, 187-209.
Perry, R.D., Bobrov, A.G. & Fetherston, J.D. (2015) The role of transition metal transporters for iron, zinc, manganese, and copper in the pathogenesis of Yersinia pestis. Metallomics, 7, 965-978.
Pi, H., Wendel, B.M. & Helmann, J.D. (2020) Dysregulation of magnesium transport protects Bacillus subtilis against manganese and cobalt intoxication. Journal of Bacteriology, 202, e00711-19. https://pubmed.ncbi.nlm.nih.gov/31964700/
Porter, L.L. & Rose, G.D. (2012) A thermodynamic definition of protein domains. Proceedings of the National Academy of Sciences of the United States of America, 109, 9420-9425.
Price, M.N., Dehal, P.S. & Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
Rostol, J.T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R. et al. (2021) The Card1 nuclease provides defence during type III CRISPR immunity. Nature, 590, 624-629.
Saghatelian, A. & Couso, J.P. (2015) Discovery and characterization of smORF-encoded bioactive polypeptides. Nature Chemical Biology, 11, 909-916.
Saito, A., Hizukuri, Y., Matsuo, E., Chiba, S., Mori, H., Nishimura, O. et al. (2011) Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108, 13740-13745.
Schreiter, E.R., Sintchak, M.D., Guo, Y., Chivers, P.T., Sauer, R.T. & Drennan, C.L. (2003) Crystal structure of the nickel-responsive transcription factor NikR. Nature Structural Biology, 10, 794-799.
Sehnal, D., Bittrich, S., Deshpande, M., Svobodova, R., Berka, K., Bazgier, V. et al. (2021) Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49, W431-W437.
Soding, J., Biegert, A. & Lupas, A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research, 33, W244-W248.
Steinberg, R. & Koch, H.G. (2021) The largely unexplored biology of small proteins in pro- and eukaryotes. The FEBS Journal, 288, 7002-7024.
Steinchen, W., Ahmad, S., Valentini, M., Eilers, K., Majkini, M., Altegoer, F. et al. (2021) Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism. Molecular Microbiology, 115, 1339-1356.
Tal, N., Morehouse, B.R., Millman, A., Stokar-Avihail, A., Avraham, C., Fedorenko, T. et al. (2021) Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell, 184, 5728-5739.e16.
Uppalapati, S.R. & Vazquez-Torres, A. (2022) Manganese utilization in salmonella pathogenesis: beyond the canonical antioxidant response. Frontiers in Cell and Development Biology, 10, 924925.
Vinyard, D.J., Ananyev, G.M. & Dismukes, G.C. (2013) Photosystem II: the reaction center of oxygenic photosynthesis. Annual Review of Biochemistry, 82, 577-606.
Wagih, O. (2017) ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics, 33, 3645-3647.
Wang, C., Guan, Y., Lv, M., Zhang, R., Guo, Z., Wei, X. et al. (2018) Manganese increases the sensitivity of the cGAS-STING pathway for double-stranded DNA and is required for the host defense against DNA viruses. Immunity, 48, 675-687.e7.
Waters, L.S. (2020) Bacterial manganese sensing and homeostasis. Current Opinion in Chemical Biology, 55, 96-102.
Waters, L.S., Sandoval, M. & Storz, G. (2011) The Escherichia coli MntR Miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. Journal of Bacteriology, 193, 5887-5897.
Weihofen, A. & Martoglio, B. (2003) Intramembrane-cleaving proteases: controlled liberation of proteins and bioactive peptides. Trends in Cell Biology, 13, 71-78.
Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S.M., Ma, W. & Doudna, J.A. (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure, 17, 904-912.
Yadavalli, S.S. & Yuan, J. (2022) Bacterial small membrane proteins: the swiss army knife of regulators at the lipid bilayer. Journal of Bacteriology, 204, e0034421.
Yan, X., Guo, W. & Yuan, Y.A. (2015) Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease. RNA Biology, 12, 749-760.
Yokoyama, T., Niinae, T., Tsumagari, K., Imami, K., Ishihama, Y., Hizukuri, Y. et al. (2021) The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. The Journal of Biological Chemistry, 296, 100673.
Yu, D., Ellis, H.M., Lee, E.C., Jenkins, N.A., Copeland, N.G. & Court, D.L. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 97, 5978-5983.
Zeinert, R., Martinez, E., Schmitz, J., Senn, K., Usman, B., Anantharaman, V. et al. (2018) Structure-function analysis of manganese exporter proteins across bacteria. The Journal of Biological Chemistry, 293, 5715-5730.

Auteurs

Zachary Wright (Z)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Mackenzie Seymour (M)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Kalista Paszczak (K)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Taylor Truttmann (T)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Katherine Senn (K)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Samuel Stilp (S)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Nickolas Jansen (N)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Magdalyn Gosz (M)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Lindsay Goeden (L)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Vivek Anantharaman (V)

National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA.

L Aravind (L)

National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA.

Lauren S Waters (LS)

Department of Chemistry, University of Wisconsin, Oshkosh, Wisconsin, USA.

Classifications MeSH