1887

Abstract

The evolution of gene fusions that result in covalently linked protein domains is widespread in bacteria, where spatially coupling domain functionalities can have functional advantages in vivo. Fusions to integral membrane proteins are less widely studied but could provide routes to enhance membrane function in synthetic biology. We studied the major facilitator superfamily (MFS), as the largest family of transporter proteins in bacteria, to examine the extent and nature of fusions to these proteins. A remarkably diverse variety of fusions are identified and the 8 most abundant examples are described, including additional enzymatic domains and a range of sensory and regulatory domains, many not previously described. Significantly, these fusions are found almost exclusively as C-terminal fusions, revealing that the usually cytoplasmic C-terminal end of MFS protein would the permissive end for engineering synthetic fusions to other cytoplasmic proteins.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000771
2019-01-18
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/micro/165/4/419.html?itemId=/content/journal/micro/10.1099/mic.0.000771&mimeType=html&fmt=ahah

References

  1. Wheeldon I, Minteer SD, Banta S, Barton SC, Atanassov P et al. Substrate channelling as an approach to cascade reactions. Nat Chem 2016; 8:299–309 [View Article][PubMed]
    [Google Scholar]
  2. Laskowski RA, Gerick F, Thornton JM. The structural basis of allosteric regulation in proteins. FEBS Lett 2009; 583:1692–1698 [View Article][PubMed]
    [Google Scholar]
  3. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO et al. Detecting protein function and protein-protein interactions from genome sequences. Science 1999; 285:751–753 [View Article][PubMed]
    [Google Scholar]
  4. Liu C, Chin JX, Lee DY. SynLinker: an integrated system for designing linkers and synthetic fusion proteins. Bioinformatics 2015; 31:3700–3702 [View Article][PubMed]
    [Google Scholar]
  5. Alberts B, Johnson A, Lewis J. Carrier proteins and active membrane transport. Molecular Biology of the Cell Garland Science; pp. 1–8
    [Google Scholar]
  6. Barabote RD, Tamang DG, Abeywardena SN, Fallah NS, Fu JY, Jyc F et al. Extra domains in secondary transport carriers and channel proteins. Biochim Biophys Acta 2006; 1758:1557–1579 [View Article][PubMed]
    [Google Scholar]
  7. Harvat EM, Zhang YM, Tran CV, Zhang Z, Frank MW et al. Lysophospholipid flipping across the Escherichia coli inner membrane catalyzed by a transporter (LplT) belonging to the major facilitator superfamily. J Biol Chem 2005; 280:12028–12034 [View Article][PubMed]
    [Google Scholar]
  8. Yan N. Structural advances for the major facilitator superfamily (MFS) transporters. Trends Biochem Sci 2013; 38:151–159 [View Article][PubMed]
    [Google Scholar]
  9. Hinchliffe P, Greene NP, Paterson NG, Crow A, Hughes C et al. Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump. FEBS Lett 2014; 588:3147–3153 [View Article][PubMed]
    [Google Scholar]
  10. Pao SS, Paulsen IT, Saier MH. Major facilitator superfamily. Microbiol Mol Biol Rev 1998; 62:1–34[PubMed]
    [Google Scholar]
  11. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001; 29:37–40 [View Article][PubMed]
    [Google Scholar]
  12. Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 2017; 45:D190–D199 [View Article][PubMed]
    [Google Scholar]
  13. Bateman A, Martin MJ, O’Donovan C, Magrane M, Alpi E et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res 2017; 45:D158–D169 [View Article][PubMed]
    [Google Scholar]
  14. NCBI Resource Coordinators Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2016; 44:D7–D19 [View Article][PubMed]
    [Google Scholar]
  15. Wood NJ, Alizadeh T, Richardson DJ, Ferguson SJ, Moir JW. Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol Microbiol 2002; 44:157–170 [View Article][PubMed]
    [Google Scholar]
  16. Goddard AD, Moir JW, Richardson DJ, Ferguson SJ. Interdependence of two NarK domains in a fused nitrate/nitrite transporter. Mol Microbiol 2008; 70:667–681 [View Article][PubMed]
    [Google Scholar]
  17. MacMillan SV, Alexander DA, Culham DE, Kunte HJ, Marshall EV et al. The ion coupling and organic substrate specificities of osmoregulatory transporter ProP in Escherichia coli. Biochim Biophys Acta 1999; 1420:30–44 [View Article][PubMed]
    [Google Scholar]
  18. Gouesbet G, Trautwetter A, Bonnassie S, Wu LF, Blanco C. Characterization of the Erwinia chrysanthemi osmoprotectant transporter gene ousA. J Bacteriol 1996; 178:447–455 [View Article][PubMed]
    [Google Scholar]
  19. Culham DE, Tripet B, Racher KI, Voegele RT, Hodges RS et al. The role of the carboxyl terminal alpha-helical coiled-coil domain in osmosensing by transporter ProP of Escherichia coli. J Mol Recognit 2000; 13:309–322 [View Article][PubMed]
    [Google Scholar]
  20. Tsatskis Y, Khambati J, Dobson M, Bogdanov M, Dowhan W et al. The osmotic activation of transporter ProP is tuned by both its C-terminal coiled-coil and osmotically induced changes in phospholipid composition. J Biol Chem 2005; 280:41387–41394 [View Article][PubMed]
    [Google Scholar]
  21. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580 [View Article][PubMed]
    [Google Scholar]
  22. Saier MH, Reddy VS, Tsu BV, Ahmed MS, Li C et al. The transporter classification database (TCDB): recent advances. Nucleic Acids Res 2016; 44:D372–D379 [View Article][PubMed]
    [Google Scholar]
  23. Chu AJ. Characterising Two Genomic Islands Involved in Metabolism in Neisseria meningitidis University of York: 2017
    [Google Scholar]
  24. Zen KH, McKenna E, Bibi E, Hardy D, Kaback HR. Expression of lactose permease in contiguous fragments as a probe for membrane-spanning domains. Biochemistry 1994; 33:8198–8206 [View Article][PubMed]
    [Google Scholar]
  25. Zomot E, Yardeni EH, Vargiu AV, Tam HK, Malloci G et al. A new critical conformational determinant of multidrug efflux by an MFS transporter. J Mol Biol 2018; 430:1368–1385 [View Article][PubMed]
    [Google Scholar]
  26. Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH. The major facilitator superfamily (MFS) revisited. FEBS J 2012; 279:2022–2035 [View Article][PubMed]
    [Google Scholar]
  27. Minguet EG, vera-Sirera F, Marina A, Carbonell J, Blázquez MA. Evolutionary diversification in polyamine biosynthesis. Mol Biol Evol 2008; 25:2119–2128 [View Article][PubMed]
    [Google Scholar]
  28. Major P, Embley TM, Williams TA. Phylogenetic diversity of NTT nucleotide transport proteins in free-living and parasitic bacteria and eukaryotes. Genome Biol Evol 2017; 9:480–487 [View Article][PubMed]
    [Google Scholar]
  29. Banerji S, Flieger A. Patatin-like proteins: a new family of lipolytic enzymes present in bacteria?. Microbiology 2004; 150:522–525 [View Article][PubMed]
    [Google Scholar]
  30. Hoffmann T, Frankenberg N, Marino M, Jahn D. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J Bacteriol 1998; 180:186–189[PubMed]
    [Google Scholar]
  31. Cruz Ramos H, Boursier L, Moszer I, Kunst F, Danchin A et al. Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms. EMBO J 1995; 14:5984–5994 [View Article][PubMed]
    [Google Scholar]
  32. Verbaendert I, de Vos P, Boon N, Heylen K. Denitrification in Gram-positive bacteria: an underexplored trait. Biochem Soc Trans 2011; 39:254–258 [View Article][PubMed]
    [Google Scholar]
  33. Taylor BL, Zhulin IB. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 1999; 63:479–506[PubMed]
    [Google Scholar]
  34. Martinez-Argudo I, Little R, Shearer N, Johnson P, Dixon R. The NifL-NifA System: a multidomain transcriptional regulatory complex that integrates environmental signals. J Bacteriol 2004; 186:601–610 [View Article][PubMed]
    [Google Scholar]
  35. Baykov AA, Tuominen HK, Lahti R. The CBS domain: a protein module with an emerging prominent role in regulation. ACS Chem Biol 2011; 6:1156–1163 [View Article][PubMed]
    [Google Scholar]
  36. Anashkin VA, Baykov AA, Lahti R. Enzymes regulated via cystathionine β-synthase domains. Biochem 2017; 82:1079–1087 [View Article]
    [Google Scholar]
  37. Ruiz L, O'Connell-Motherway M, Zomer A, de Los Reyes-Gavilán CG, Margolles A et al. A bile-inducible membrane protein mediates bifidobacterial bile resistance. Microb Biotechnol 2012; 5:523–535 [View Article][PubMed]
    [Google Scholar]
  38. Gueimonde M, Garrigues C, van Sinderen D, de Los Reyes-Gavilán CG, Margolles A. Bile-inducible efflux transporter from Bifidobacterium longum NCC2705, conferring bile resistance. Appl Environ Microbiol 2009; 75:3153–3160 [View Article][PubMed]
    [Google Scholar]
  39. Chen C, Beattie GA. Characterization of the osmoprotectant transporter OpuC from Pseudomonas syringae and demonstration that cystathionine-beta-synthase domains are required for its osmoregulatory function. J Bacteriol 2007; 189:6901–6912 [View Article][PubMed]
    [Google Scholar]
  40. Tomita A, Zhang M, Jin F, Zhuang W, Takeda H et al. ATP-dependent modulation of MgtE in Mg2+ homeostasis. Nat Commun 2017; 8:148 [View Article][PubMed]
    [Google Scholar]
  41. Hirata Y, Funato Y, Takano Y, Miki H. Mg2+-dependent interactions of ATP with the cystathionine-β-synthase (CBS) domains of a magnesium transporter. J Biol Chem 2014; 289:14731–14739 [View Article][PubMed]
    [Google Scholar]
  42. Kvint K, Nachin L, Diez A, Nyström T. The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 2003; 6:140–145 [View Article][PubMed]
    [Google Scholar]
  43. Wang C, Huang W, Ying Y, Li S, Secco D et al. Functional characterization of the rice SPX-MFS family reveals a key role of OsSPX-MFS1 in controlling phosphate homeostasis in leaves. New Phytol 2012; 196:139–148 [View Article][PubMed]
    [Google Scholar]
  44. Liu TY, Huang TK, Yang SY, Hong YT, Huang SM et al. Identification of plant vacuolar transporters mediating phosphate storage. Nat Commun 2016; 7:11095 [View Article][PubMed]
    [Google Scholar]
  45. Fu C, Tanaka A, Free SJ. Neurospora crassa 1,3-α-glucan synthase, AGS-1, is required for cell wall biosynthesis during macroconidia development. Microbiology 2014; 160:1618–1627 [View Article][PubMed]
    [Google Scholar]
  46. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article][PubMed]
    [Google Scholar]
  47. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN et al. The protein data bank. Nucleic Acids Res 2000; 28:235–242 [View Article][PubMed]
    [Google Scholar]
  48. Jiang D, Zhao Y, Wang X, Fan J, Heng J et al. Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A. Proc Natl Acad Sci USA 2013; 110:14664–14669 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000771
Loading
/content/journal/micro/10.1099/mic.0.000771
Loading

Data & Media loading...

Supplements

Supplementary File 1

Supplementary File 2

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error