1887

Abstract

can use C4-dicarboxylic acids to grow heterotrophically or photoheterotropically, and it was previously demonstrated in that the DctPQM transporter system is essential to support growth using these organic acids under heterotrophic but not under photoheterotrophic conditions. In this work we show that in this transporter system is essential for photoheterotrophic and heterotrophic growth, when C4-dicarboxylic acids are used as a carbon source. We also found that over-expression of is detrimental for photoheterotrophic growth in the presence of succinic acid in the culture medium. In agreement with this, we observed a reduction of the promoter activity in cells growing under these conditions, indicating that the amount of DctPQM needs to be reduced under photoheterotrophic growth. It has been reported that the two-component system DctS and DctR activates the expression of . Our results demonstrate that in the absence of DctR, is still expressed albeit at a low level. In this work, we have found that the periplasmic component of the transporter system, DctP, has a role in both transport and in signalling the DctS/DctR two-component system.

Funding
This study was supported by the:
  • GeorgesDreyfus , Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México , (Award IG200420)
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/content/journal/micro/10.1099/mic.0.001037
2021-02-23
2021-02-26
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References

  1. Unden G, Kleefeld A. C4-Dicarboxylate degradation in aerobic and anaerobic growth. EcoSal Plus American Society for Microbiology; 2016
    [Google Scholar]
  2. Imhoff JF. The Phototrophic Alpha Proteobacteria , 3 ed. Springer-Verlag New York; 2006
    [Google Scholar]
  3. Janausch IG, Zientz E, Tran QH, Kroger A, Unden G. C4-Dicarboxylate carriers and sensors in bacteria. Biochim Biophys Acta 2002; 1553: 39 56 [CrossRef] [PubMed]
    [Google Scholar]
  4. Unden G, Wörner S, Monzel C. Cooperation of secondary transporters and sensor kinases in transmembrane Signalling: the DctA/DcuS and DcuB/DcuS sensor complexes of Escherichia coli . Adv Microb Physiol 2016; 68: 139 167 [CrossRef] [PubMed]
    [Google Scholar]
  5. Davies SJ, Golby P, Omrani D, Broad SA, Harrington VL et al. Inactivation and regulation of the aerobic C(4)-dicarboxylate transport (dctA) gene of Escherichia coli . J Bacteriol 1999; 181: 5624 5635 [CrossRef] [PubMed]
    [Google Scholar]
  6. Janausch IG, Kim OB, Unden G. DctA- and Dcu-independent transport of succinate in Escherichia coli: contribution of diffusion and of alternative carriers. Arch Microbiol 2001; 176: 224 230 [CrossRef] [PubMed]
    [Google Scholar]
  7. Karinou E, Compton EL, Morel M, Javelle A. The Escherichia coli SLC26 homologue YchM (DauA) is a C(4)-dicarboxylic acid transporter. Mol Microbiol 2013; 87: 623 640 [CrossRef] [PubMed]
    [Google Scholar]
  8. Engel P, Kramer R, Unden G. Anaerobic fumarate transport in Escherichia coli by an fnr-dependent dicarboxylate uptake system which is different from the aerobic dicarboxylate uptake system. J Bacteriol 1992; 174: 5533 5539 [CrossRef] [PubMed]
    [Google Scholar]
  9. Six S, Andrews SC, Unden G, Guest JR. Escherichia coli possesses two homologous anaerobic C4-dicarboxylate membrane transporters (DcuA and DcuB) distinct from the aerobic dicarboxylate transport system (Dct). J Bacteriol 1994; 176: 6470 6478 [CrossRef] [PubMed]
    [Google Scholar]
  10. Mulligan C, Kelly DJ, Thomas GH. Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization. J Mol Microbiol Biotechnol 2007; 12: 218 226 [CrossRef] [PubMed]
    [Google Scholar]
  11. Mulligan C, Fischer M, Thomas GH. Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea. FEMS Microbiol Rev 2011; 35: 68 86 [CrossRef] [PubMed]
    [Google Scholar]
  12. Forward JA, Behrendt MC, Wyborn NR, Cross R, Kelly DJ. TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria. J Bacteriol 1997; 179: 5482 5493 [CrossRef] [PubMed]
    [Google Scholar]
  13. Zientz E, Bongaerts J, Unden G. Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR genes) two-component regulatory system. J Bacteriol 1998; 180: 5421 5425 [CrossRef] [PubMed]
    [Google Scholar]
  14. Golby P, Davies S, Kelly DJ, Guest JR, Andrews SC. Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli . J Bacteriol 1999; 181: 1238 1248 [CrossRef] [PubMed]
    [Google Scholar]
  15. Abo-Amer AE, Munn J, Jackson K, Aktas M, Golby P et al. DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli . J Bacteriol 2004; 186: 1879 1889 [CrossRef] [PubMed]
    [Google Scholar]
  16. Janausch IG, Garcia-Moreno I, Lehnen D, Zeuner Y, Unden G. Phosphorylation and DNA binding of the regulator DcuR of the fumarate-responsive two-component system DcuSR of Escherichia coli . Microbiology 2004; 150: 877 883 [CrossRef] [PubMed]
    [Google Scholar]
  17. Steinmetz PA, Worner S, Unden G. Differentiation of DctA and DcuS function in the DctA/DcuS sensor complex of Escherichia coli: function of DctA as an activity switch and of DcuS as the C4-dicarboxylate sensor. Mol Microbiol 2014; 94: 218 229 [CrossRef] [PubMed]
    [Google Scholar]
  18. Worner S, Strecker A, Monzel C, Zeltner M, Witan J et al. Conversion of the sensor kinase DcuS of Escherichia coli of the DcuB/DcuS sensor complex to the C4 -dicarboxylate responsive form by the transporter DcuB. Environ Microbiol 2016; 18: 4920 4930 [CrossRef] [PubMed]
    [Google Scholar]
  19. Witan J, Bauer J, Wittig I, Steinmetz PA, Erker W et al. Interaction of the Escherichia coli transporter DctA with the sensor kinase DcuS: presence of functional DctA/DcuS sensor units. Mol Microbiol 2012; 85: 846 861 [CrossRef] [PubMed]
    [Google Scholar]
  20. Valentini M, Lapouge K. Catabolite repression in Pseudomonas aeruginosa PAO1 regulates the uptake of C4 -dicarboxylates depending on succinate concentration. Environ Microbiol 2013; 15: 1707 1716 [CrossRef] [PubMed]
    [Google Scholar]
  21. Madigan MT, Jug DO. An overview of purple bacteria: systematics, physiology and habitats. In Hunter CND F, Thurnauer MC, Beatty JT. (editors) The Purple Phototrophic Bacteria Vol 28 from Advances in Photosythesis and Respiration Springer Science & Business Media; 2008; 2008
    [Google Scholar]
  22. Clayton RK, Clayton BJ. Relations between pigments and proteins in the photosynthetic membranes of Rhodopseudomonas spheroides . Biochim Biophys Acta 1972; 283: 492 504 [CrossRef] [PubMed]
    [Google Scholar]
  23. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49: 25 68 [CrossRef] [PubMed]
    [Google Scholar]
  24. Sistrom WR. The kinetics of the synthesis of photopigments in Rhodopseudomonas spheroides. J Gen Microbiol 1962; 28: 607 616 [CrossRef] [PubMed]
    [Google Scholar]
  25. Imam S, Noguera DR, Donohue TJ. Global insights into energetic and metabolic networks in Rhodobacter sphaeroides . BMC Syst Biol 2013; 7: 89 [CrossRef] [PubMed]
    [Google Scholar]
  26. Hamblin MJ, Shaw JG, Curson JP, Kelly DJ. Mutagenesis, cloning and complementation analysis of C 4 -dicarboxylate transport genes from Rhodobacter capsulatus . Mol Microbiol 1990; 4: 1567 1574 [CrossRef]
    [Google Scholar]
  27. Shaw JG, Hamblin MJ, Kelly DJ. Purification, characterization and nucleotide sequence of the periplasmic C4-dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus . Mol Microbiol 1991; 5: 3055 3062 [CrossRef] [PubMed]
    [Google Scholar]
  28. Wyborn NR, Alderson J, Andrews SC, Kelly DJ. Topological analysis of DctQ, the small integral membrane protein of the C4-dicarboxylate TRAP transporter of Rhodobacter capsulatus . FEMS Microbiol Lett 2001; 194: 13 17 [CrossRef] [PubMed]
    [Google Scholar]
  29. Hamblin MJ, Shaw JG, Kelly DJ. Sequence analysis and interposon mutagenesis of a sensor-kinase (DctS) and response-regulator (DctR) controlling synthesis of the high-affinity C4-dicarboxylate transport system in Rhodobacter capsulatus . Mol Gen Genet 1993; 237: 215 224 [CrossRef] [PubMed]
    [Google Scholar]
  30. del Campo AM, Ballado T, de la Mora J, Poggio S, Camarena L et al. Chemotactic control of the two flagellar systems of Rhodobacter sphaeroides is mediated by different sets of CheY and FliM proteins. J Bacteriol 2007; 189: 8397 8401 [CrossRef] [PubMed]
    [Google Scholar]
  31. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. Current Protocols in Molecular Biology New York: John Wiley; 1987
    [Google Scholar]
  32. Lanzer M, Bujard H. Promoters largely determine the efficiency of repressor action. Proc Natl Acad Sci U S A 1988; 85: 8973 8977 [CrossRef] [PubMed]
    [Google Scholar]
  33. Ind AC, Porter SL, Brown MT, Byles ED, de Beyer JA et al. Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans . Appl Environ Microbiol 2009; 75: 6613 6615 [CrossRef] [PubMed]
    [Google Scholar]
  34. Servín-Gonzalez L, Sampieri AI, Cabello J, Galván L, Juárez V et al. Sequence and functional analysis of the Streptomyces phaeochromogenes plasmid pJV1 reveals a modular organization of Streptomyces plasmids that replicate by rolling circle. Microbiology 1995; 141: 2499 2510 [CrossRef] [PubMed]
    [Google Scholar]
  35. Quandt J, Hynes MF. Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 1993; 127: 15 21 [CrossRef] [PubMed]
    [Google Scholar]
  36. Ballado T, Camarena L, Gonzalez-Pedrajo B, Silva-Herzog E, Dreyfus G. The hook gene (flgE) is expressed from the flgBCDEF operon in Rhodobacter sphaeroides: study of an flgE mutant. J Bacteriol 2001; 183: 1680 1687 [CrossRef] [PubMed]
    [Google Scholar]
  37. Davis J, Donohue TJ, Kaplan S. Construction, characterization, and complementation of a Puf- mutant of Rhodobacter sphaeroides . J Bacteriol 1988; 170: 320 329 [CrossRef] [PubMed]
    [Google Scholar]
  38. Keen NT, Tamaki S, Kobayashi D, Trollinger D. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene 1988; 70: 191 197 [CrossRef] [PubMed]
    [Google Scholar]
  39. Girard L, Brom S, Davalos A, Lopez O, Soberon M et al. Differential regulation of fixN-reiterated genes in Rhizobium etli by a novel fixL-fixK cascade. Mol Plant Microbe Interact 2000; 13: 1283 1292 [CrossRef] [PubMed]
    [Google Scholar]
  40. Jefferson RA, Burgess SM, Hirsh D. Beta-Glucuronidase from Escherichia coli as a gene-fusion marker. Proc Natl Acad Sci U S A 1986; 83: 8447 8451 [CrossRef] [PubMed]
    [Google Scholar]
  41. Bao K, Cohen SN. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces . Genes Dev 2001; 15: 1518 1527 [CrossRef] [PubMed]
    [Google Scholar]
  42. Harlow E, Lane D. Antibodies. A Laboratory Manual Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 1988
    [Google Scholar]
  43. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227: 680 685 [CrossRef] [PubMed]
    [Google Scholar]
  44. Towbin H, Staehelin T, Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A 1979; 76: 4350 4354 [CrossRef] [PubMed]
    [Google Scholar]
  45. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010; 5: 725 738 [CrossRef] [PubMed]
    [Google Scholar]
  46. Yang J, Roy A, Zhang Y. Protein-Ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics 2013; 29: 2588 2595 [CrossRef] [PubMed]
    [Google Scholar]
  47. Inui M, Nakata K, Roh JH, Vertes AA, Yukawa H. Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus. Appl Environ Microbiol 2003; 69: 725 733 [CrossRef] [PubMed]
    [Google Scholar]
  48. Richardson DJ, King GF, Kelly DJ, Mcewan AG, Ferguson SJ et al. The role of auxiliary oxidants in maintaining redox balance during phototrophic growth of Rhodobacter capsulatus on propionate or butyrate. Arch Microbiol 1988; 150: 131 137 [CrossRef]
    [Google Scholar]
  49. Spero MA, Brickner JR, Mollet JT, Pisithkul T, Amador-Noguez D et al. Different functions of phylogenetically distinct bacterial complex I isozymes. J Bacteriol 2016; 198: 1268 1280 [CrossRef] [PubMed]
    [Google Scholar]
  50. Gordon GC, McKinlay JB. Calvin cycle mutants of photoheterotrophic purple nonsulfur bacteria fail to grow due to an electron imbalance rather than toxic metabolite accumulation. J Bacteriol 2014; 196: 1231 1237 [CrossRef] [PubMed]
    [Google Scholar]
  51. Tichi MA, Tabita FR. Maintenance and control of redox poise in Rhodobacter capsulatus strains deficient in the Calvin-Benson-Bassham pathway. Arch Microbiol 2000; 174: 322 333 [CrossRef] [PubMed]
    [Google Scholar]
  52. Tichi MA, Meijer WG, Tabita FR. Complex I and its involvement in redox homeostasis and carbon and nitrogen metabolism in Rhodobacter capsulatus. J Bacteriol 2001; 183: 7285 7294 [CrossRef] [PubMed]
    [Google Scholar]
  53. Gibson J. Uptake of C4 dicarboxylates and pyruvate by Rhodopseudomonas spheroides . J Bacteriol 1975; 123: 471 480 [CrossRef] [PubMed]
    [Google Scholar]
  54. Gopel Y, Gorke B. Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli . PLoS Genet 2018; 14: e1007547 [CrossRef] [PubMed]
    [Google Scholar]
  55. Cangelosi GA, Ankenbauer RG, Nester EW. Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc Natl Acad Sci U S A 1990; 87: 6708 6712 [CrossRef] [PubMed]
    [Google Scholar]
  56. Shimoda N, Toyoda-Yamamoto A, Aoki S, Machida Y. Genetic evidence for an interaction between the VirA sensor protein and the ChvE sugar-binding protein of Agrobacterium . J Biol Chem 1993; 268: 26552 26558 [CrossRef] [PubMed]
    [Google Scholar]
  57. Antoine R, Huvent I, Chemlal K, Deray I, Raze D et al. The periplasmic binding protein of a tripartite tricarboxylate transporter is involved in signal transduction. J Mol Biol 2005; 351: 799 809 [CrossRef] [PubMed]
    [Google Scholar]
  58. Neiditch MB, Federle MJ, Pompeani AJ, Kelly RC, Swem DL et al. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 2006; 126: 1095 1108 [CrossRef] [PubMed]
    [Google Scholar]
  59. Cheung J, Hendrickson WA. Crystal structures of C4-dicarboxylate ligand complexes with sensor domains of histidine kinases DcuS and DctB. J Biol Chem 2008; 283: 30256 30265 [CrossRef] [PubMed]
    [Google Scholar]
  60. Zhou YF, Nan B, Nan J, Ma Q, Panjikar S et al. C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain. J Mol Biol 2008; 383: 49 61 [CrossRef] [PubMed]
    [Google Scholar]
  61. Piepenbreier H, Fritz G, Gebhard S. Transporters as information processors in bacterial signalling pathways. Mol Microbiol 2017; 104: 1 15 [CrossRef] [PubMed]
    [Google Scholar]
  62. Asai K, Baik SH, Kasahara Y, Moriya S, Ogasawara N. Regulation of the transport system for C4-dicarboxylic acids in Bacillus subtilis . Microbiology 2000; 146 (Pt 2: 263 271 [CrossRef] [PubMed]
    [Google Scholar]
  63. Graf S, Schmieden D, Tschauner K, Hunke S, Unden G. The sensor kinase DctS forms a tripartite sensor unit with DctB and DctA for sensing C4-dicarboxylates in Bacillus subtilis . J Bacteriol 2014; 196: 1084 1093 [CrossRef] [PubMed]
    [Google Scholar]
  64. Antoine R, Jacob-Dubuisson F, Drobecq H, Willery E, Lesjean S et al. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella . J Bacteriol 2003; 185: 1470 1474 [CrossRef] [PubMed]
    [Google Scholar]
  65. Rosa LT, Springthorpe V, Bianconi ME, Thomas GH, Kelly DJ. Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860. Microb Genom 2018; 4: [CrossRef] [PubMed]
    [Google Scholar]
  66. Wubbeler JH, Hiessl S, Schuldes J, Thurmer A, Daniel R et al. Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate. Microbiology 2014; 160: 1401 1416 [CrossRef] [PubMed]
    [Google Scholar]
  67. Arai H, Roh JH, Kaplan S. Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2008; 190: 286 299 [CrossRef] [PubMed]
    [Google Scholar]
  68. Adnan F, Weber L, Klug G. The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides . RNA Biol 2015; 12: 569 577 [CrossRef] [PubMed]
    [Google Scholar]
  69. Figurski DH, Helinski DR. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A 1979; 76: 1648 1652 [CrossRef] [PubMed]
    [Google Scholar]
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