CoChat
Sign Up
Cited by 5Plant Pathogenic Bacteria StudiesBacterial Genetics and BiotechnologyPlant-Microbe Interactions and Immunity

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate

Open access
Velando, Félix, Xing, Jiawei, Genova, Roberta, Cerna-Vargas, Jean Paul, Vázquez-Santiago, Raquel, Matilla, Miguel A., Zhulin, Igor B., Krell, Tino·2025·Genome Biology
DOI 10.1186/s13059-025-03703-6PMC PMC12395807

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Background: Chemotaxis to plant compounds is frequently the initial step for the colonization of plants by bacteria. Plant pathogens and plant-associated bacteria contain approximately twice as many chemoreceptors as the bacterial average does, indicating that chemotaxis is particularly important for bacteria–plant interactions. However, information on the corresponding chemoreceptors and their chemoeffectors is limited. Results: We identify the chemoreceptor PacP from the phytopathogen Pectobacterium atrosepticum , which exclusively recognizes phosphorylated C3 compounds at its sCache ligand binding domain, mediating chemoattraction. Using a motif of PacP amino acid residues involved in ligand binding, we identify a chemoreceptor family, termed sCache_PC3, that is specific for phosphorylated C3 compounds. Isothermal titration calorimetry studies reveal that family members preferentially bind glycerol 3-phosphate, a key plant signaling molecule. Family members recognize glycerol 2-phosphate and glycolysis intermediates glyceraldehyde 3-phosphate, dihydroxyacetone phosphate, and 3-phosphoglycerate. This study presents the first evidence of chemoreceptors that bind phosphorylated compounds. We show that the sCache_PC3 family has evolved from an ancestral sCache domain that responds primarily to Krebs cycle intermediates. Members of the sCache_PC3 family are predominantly found in plant-associated bacteria, including many important phytopathogens belonging to the genera Brenneria , Dickeya , Musicola , Pectobacterium , and Herbaspirillum . Consistently, glycerol 3-phosphate is a signal molecule that is excreted by plants in response to stress and infection. Conclusions: Chemotaxis toward glycerol 3-phosphate may be a means for bacteria to localize stressed plants and move to infection sites. This study lays the groundwork for investigating the role of chemotaxis to phosphorylated C3 compounds in plant–bacteria interactions and virulence.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13059-025-03703-6

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 99

  1. Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol. 2023;75: 102358. · DOI
  2. Zhang L, Li S, Liu X, Wang Z, Jiang M, Wang R, et al. Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes. Nat Commun. 2020;11:5371. · DOI
  3. Santamaría-Hernando S, López-Maroto Á, Galvez-Roldán C, Munar-Palmer M, Monteagudo-Cascales E, Rodríguez-Herva J-J, et al. Pseudomonas syringae pv. tomato infection of tomato plants is mediated by GABA and l-Pro chemoperception. Mol Plant Pathol. 2022;23:1433–45. · DOI
  4. Lopes JG, Sourjik V. Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut. ISME J. 2018;12:2736–47. · DOI
  5. Pasupuleti S, Sule N, Cohn WB, MacKenzie DS, Jayaraman A, Manson MD. Chemotaxis of Escherichia coli to norepinephrine (NE) requires conversion of NE to 3,4-dihydroxymandelic acid. J Bacteriol. 2014;196:3992–4000. · DOI
  6. Matilla MA, Krell T. The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol Rev. 2018;42: fux052. · DOI
  7. Feng H, Fu R, Hou X, Lv Y, Zhang N, Liu Y, et al. Chemotaxis of beneficial rhizobacteria to root exudates: the first step towards root-microbe rhizosphere interactions. Int J Mol Sci. 2021;22: 6655. · DOI
  8. Parkinson JS, Hazelbauer GL, Falke JJ. Signaling and sensory adaptation in Escherichia coli chemoreceptors: 2015 update. Trends Microbiol. 2015;23:257–66. · DOI
  9. Bi S, Sourjik V. Stimulus sensing and signal processing in bacterial chemotaxis. Curr Opin Microbiol. 2018;45:22–9. · DOI
  10. Gumerov VM, Andrianova EP, Zhulin IB. Diversity of bacterial chemosensory systems. Curr Opin Microbiol. 2021;61:42–50. · DOI
  11. Lacal J, García-Fontana C, Muñoz-Martínez F, Ramos JL, Krell T. Sensing of environmental signals: classification of chemoreceptors according to the size of their ligand binding regions. Environ Microbiol. 2010;12:2873–84. · DOI
  12. Alexandre G, Greer-Phillips S, Zhulin IB. Ecological role of energy taxis in microorganisms. FEMS Microbiol Rev. 2004;28:113–26. · DOI
  13. Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev. 2022;46: fuab043. · DOI
  14. Allard-Massicotte R, Tessier L, Lecuyer F, Lakshmanan V, Lucier JF, Garneau D, et al. Bacillus subtilis early colonization of Arabidopsis thaliana roots involves multiple chemotaxis receptors. mBio. 2016;7:e01664-16. · DOI
  15. de Weert S, Vermeiren H, Mulders IH, Kuiper I, Hendrickx N, Bloemberg GV, et al. Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant Microbe Interact. 2002;15:1173–80. · DOI
  16. Liu W, Bai X, Li Y, Min J, Kong Y, Hu X. CheY1 and CheY2 of Azorhizobium caulinodans ORS571 regulate chemotaxis and competitive colonization with the host plant. Appl Environ Microbiol. 2020;86:e00599–620. · DOI
  17. Miller LD, Yost CK, Hynes MF, Alexandre G. The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation. Mol Microbiol. 2007;63:348–62. · DOI
  18. Yao J, Allen C. Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen Ralstonia solanacearum. J Bacteriol. 2006;188:3697–708. · DOI
  19. Antunez-Lamas M, Cabrera-Ordonez E, Lopez-Solanilla E, Raposo R, Trelles-Salazar O, Rodriguez-Moreno A, et al. Role of motility and chemotaxis in the pathogenesis of Dickeya dadantii 3937 (ex Erwinia chrysanthemi 3937). Microbiology. 2009;155:434–42. · DOI
  20. Clarke CR, Hayes BW, Runde BJ, Markel E, Swingle BM, Vinatzer BA. Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity. PeerJ. 2016;4: e2570. · DOI
  21. Kroupitski Y, Golberg D, Belausov E, Pinto R, Swartzberg D, Granot D, et al. Internalization of Salmonella enterica in leaves is induced by light and involves chemotaxis and penetration through open stomata. Appl Environ Microbiol. 2009;75:6076–86. · DOI
  22. Gálvez-Roldán C, Cerna-Vargas JP, Rodriguez Herva JJ, Krell T, Santamaria-Hernando S, López-Solanilla E. A NIT sensor domain containing chemoreceptor is required for a successful entry and virulence of Dickeya dadantii 3937 in potato plants. Phytopathology. 2022. https://doi.org/10.1094/PHYTO-10-22-0367-R. · DOI
  23. Cerna-Vargas JP, Santamaría-Hernando S, Matilla MA, Rodríguez-Herva JJ, Daddaoua A, Rodríguez-Palenzuela P, et al. Chemoperception of specific amino acids controls phytopathogenicity in Pseudomonas syringae pv. tomato. mBio. 2019;10:e01868-19. · DOI
  24. Kumar Verma R, Samal B, Chatterjee S. Xanthomonas oryzae pv. oryzae chemotaxis components and chemoreceptor Mcp2 are involved in the sensing of constituents of xylem sap and contribute to the regulation of virulence-associated functions and entry into rice. Mol Plant Pathol. 2018;19:2397–415. · DOI
  25. Sanchis-López C, Cerna-Vargas JP, Santamaría-Hernando S, Ramos C, Krell T, Rodríguez-Palenzuela P, et al. Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria. mSystems. 2021;6:e0095121. · DOI
  26. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol. 2012;13:614–29. · DOI
  27. Gumerov VM, Ortega DR, Adebali O, Ulrich LE, Zhulin IB. MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. Nucleic Acids Res. 2020;48:D459-64. · DOI
  28. Monteagudo-Cascales E, Gavira JA, Xing J, Velando F, Matilla MA, Zhulin IB, et al. Bacterial sensor evolved by decreasing complexity. Proc Natl Acad Sci U S A. 2025;122: e2409881122. · DOI · Paper page
  29. Matilla MA, Velando F, Tajuelo A, Martin-Mora D, Xu W, Sourjik V, et al. Chemotaxis of the human pathogen Pseudomonas aeruginosa to the neurotransmitter acetylcholine. mBio. 2022;13:e0345821. · DOI
  30. Velando F, Matilla MA, Zhulin IB, Krell T. Three unrelated chemoreceptors provide Pectobacterium atrosepticum with a broad-spectrum amino acid sensing capability. Microb Biotechnol. 2023;16:1548–60. · DOI
  31. Monteagudo-Cascales E, Ortega Á, Velando F, Morel B, Matilla MA, Krell T. Study of NIT domain-containing chemoreceptors from two global phytopathogens and identification of NIT domains in eukaryotes. Mol Microbiol. 2023;119:739–51. · DOI
  32. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes. PLoS Computat Biol. 2016;12: e1004862. · DOI
  33. Martín-Mora D, Ortega Á, Pérez-Maldonado FJ, Krell T, Matilla MA. The activity of the C4-dicarboxylic acid chemoreceptor of Pseudomonas aeruginosa is controlled by chemoattractants and antagonists. Sci Rep. 2018;8:2102. · DOI
  34. García V, Reyes-Darias J-A, Martín-Mora D, Morel B, Matilla MA, Krell T. Identification of a chemoreceptor for C2 and C3 carboxylic acids. Appl Environ Microbiol. 2015;81:5449–57. · DOI
  35. Brewster JL, McKellar JL, Finn TJ, Newman J, Peat TS, Gerth ML. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Sci Rep. 2016;6:35198. · DOI
  36. Compton KK, Hildreth SB, Helm RF, Scharf BE. Sinorhizobium meliloti chemoreceptor McpV senses short-chain carboxylates via direct binding. J Bacteriol. 2018;200:pii : e00519-18. · DOI
  37. Pokkuluri PR, Dwulit-Smith J, Duke NE, Wilton R, Mack JC, Bearden J, et al. Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein. Microbiologyopen. 2013;2:766–77. · DOI
  38. Gasperotti AF, Karina Herrera Seitz M, Balmaceda RS, Prosa LM, Jung K, Studdert CA. Direct binding of benzoate derivatives to two chemoreceptors with Cache sensor domains in Halomonas titanicae KHS3. Mol Microbiol. 2020;115:672–83. · DOI
  39. Huang JY, Sweeney EG, Sigal M, Zhang HC, Remington SJ, Cantrell MA, et al. Chemodetection and destruction of host urea allows Helicobacter pylori to locate the epithelium. Cell Host Microbe. 2015;18:147–56. · DOI
  40. Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, et al. Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis. Nat Commun. 2022;13:5878. · DOI
  41. Hanyu H, Engevik KA, Matthis AL, Ottemann KM, Montrose MH, Aihara E. Helicobacter pylori uses the TlpB receptor to sense sites of gastric injury. Infect Immun. 2019;87:e00202–19. · DOI
  42. McKellar JL, Minnell JJ, Gerth ML. A high-throughput screen for ligand binding reveals the specificities of three amino acid chemoreceptors from Pseudomonas syringae pv. actinidiae. Mol Microbiol. 2015;96:694–707. · DOI
  43. Boyeldieu A, Poli J, Ali Chaouche A, Fierobe H, Giudici-Orticoni M, Méjean V, et al. Multiple detection of both attractants and repellents by the dCache-chemoreceptor SO_1056 of Shewanella oneidensis. FEBS J. 2022;289:6752–66. · DOI
  44. Baaziz H, Compton KK, Hildreth SB, Helm RF, Scharf BE. McpT, a broad-range carboxylate chemoreceptor in Sinorhizobium meliloti. J Bacteriol. 2021;203: e0021621. · DOI
  45. Corral-Lugo A, Matilla MA, Martín-Mora D, Silva Jiménez H, Mesa Torres N, Kato J, et al. High-affinity chemotaxis to histamine mediated by the TlpQ chemoreceptor of the human pathogen Pseudomonas aeruginosa. mBio. 2018;9:e01894-18. · DOI
  46. Gumerov VM, Andrianova EP, Matilla MA, Page KM, Monteagudo-Cascales E, Dolphin AC, et al. Amino acid sensor conserved from bacteria to humans. Proc Natl Acad Sci USA. 2022;119: e2110415119. · DOI
  47. Cerna-Vargas JP, Gumerov VM, Krell T, Zhulin IB. Amine-recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor. Proc Natl Acad Sci U S A. 2023;120: e2305837120. · DOI
  48. Monteagudo-Cascales E, Gumerov VM, Fernández M, Matilla MA, Gavira JA, Zhulin IB, et al. Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria. Nat Commun. 2024;15:5867. · DOI · Paper page
  49. Chanda B, Xia Y, Mandal MK, Yu K, Sekine K-T, Gao Q, et al. Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants. Nat Genet. 2011;43:421–7. · DOI
  50. Shine MB, Gao Q-M, Chowda-Reddy RV, Singh AK, Kachroo P, Kachroo A. Glycerol-3-phosphate mediates rhizobia-induced systemic signaling in soybean. Nat Commun. 2019;10:5303. · DOI
  51. Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc Natl Acad Sci U S A. 2018;115:E4284–93. · DOI
  52. Sun J, Cui H, Wu B, Wang W, Yang Q, Zhang Y, et al. Genome-wide identification of cotton (Gossypium spp.) glycerol-3-phosphate dehydrogenase (GPDH) family members and the role of GhGPDH5 in response to drought stress. Plants. 2022;11: 592. · DOI
  53. Zhang X, Hughes JG, Subuyuj GA, Ditty JL, Parales RE. Chemotaxis of Pseudomonas putida F1 to alcohols is mediated by the carboxylic acid receptor McfP. Appl Environ Microbiol. 2019;85:e01625–719. · DOI
  54. Nikel PI, Kim J, de Lorenzo V. Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440. Environ Microbiol. 2014;16:239–54. · DOI
  55. Cronan JE. Bacterial membrane lipids: where do we stand? Annu Rev Microbiol. 2003;57:203–24. · DOI
  56. Sharkey TD. The end game(s) of photosynthetic carbon metabolism. Plant Physiol. 2024;195:kiad601. · DOI
  57. Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev. 2021;45: fuab038. · DOI
  58. Gavira JA, Gumerov VM, Rico-Jiménez M, Petukh M, Upadhyay AA, Ortega A, et al. How bacterial chemoreceptors evolve novel ligand specificities. mBio. 2020;11:e03066-19. · DOI
  59. Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci U S A. 2004;101:11105–10. · DOI
  60. Toth IK. Microbe profile: Pectobacterium atrosepticum: an enemy at the door. Microbiology (Reading). 2022;168:168. · DOI
  61. Brady C, Hunter G, Kirk S, Arnold D, Denman S. Description of Brenneria roseae sp. nov. and two subspecies, Brenneria roseae subspecies roseae ssp. nov and Brenneria roseae subspecies americana ssp. nov. isolated from symptomatic oak. Syst Appl Microbiol. 2014;37:396–401. · DOI
  62. Hauben, L., Swings, J. Genus: Brenneria. DJ Brenner, NR Krieg, JT Staley (Eds), Bergey’s manual of systematic bacteriology, the proteobacteria, part B: the gammaproteobacteria, vol 2, Springer, New York. 2005;628–33.
  63. Rothballer M, Eckert B, Schmid M, Fekete A, Schloter M, Lehner A, et al. Endophytic root colonization of gramineous plants by Herbaspirillum frisingense. FEMS Microbiol Ecol. 2008;66:85–95. · DOI
  64. Sheu S-Y, Chen J-C, Young C-C, Chen W-M. Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river. Int J Syst Evol Microbiol. 2014;64:2009–16. · DOI
  65. Huang K, He Y, Wang W, Jiang R, Zhang Y, Li J, et al. Temporal differentiation in the adaptation of functional bacteria to low-temperature stress in partial denitrification and anammox system. Environ Res. 2024;244: 117933. · DOI
  66. Kim B-Y, Weon H-Y, Yoo S-H, Chen W-M, Kwon S-W, Go S-J, et al. Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol. 2006;56:1761–4. · DOI
  67. Bouzar H, Jones JB. Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina. Int J Syst Evol Microbiol. 2001;51:1023–6. · DOI
  68. Smalley NE, Taipale S, De Marco P, Doronina NV, Kyrpides N, Shapiro N, et al. Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol. 2015;65:2227–33. · DOI
  69. Kwon SW, Kim BY, Kim WG, Yoo KH, Yoo SH, Son JA, et al. Paludibacterium yongneupense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea. Int J Syst Evol Microbiol. 2008;58:190–4. · DOI
  70. Sheu S-Y, Chen Z-H, Young C-C, Chen W-M. Paludibacterium paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol. 2014;64:2497–502. · DOI
  71. Miyazaki M, Nogi Y, Fujiwara Y, Horikoshi K. Psychromonas japonica sp. nov., Psychromonas aquimarina sp. nov., Psychromonas macrocephali sp. nov. and Psychromonas ossibalaenae sp. nov., psychrotrophic bacteria isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan. Int J Syst Evol Microbiol. 2008;58:1709–14. · DOI
  72. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. · DOI · Paper page
  73. Matilla MA, Martín-Mora D, Krell T. The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms. Environ Microbiol. 2020;22:3005–19. · DOI
  74. Hugouvieux-Cotte-Pattat N, Jacot-des-Combes C, Briolay J. Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France. Int J Syst Evol Microbiol. 2019;69:721–6. · DOI
  75. Portier P, Pédron J, Taghouti G, Fischer-Le Saux M, Caullireau E, Bertrand C, et al. Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants. Int J Syst Evol Microbiol. 2019;69:3207–16. · DOI
  76. Bull CY, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, Saddler GS, et al. Comprehensive list of names of plant pathogenic bacteria, 1980–2007. J Plant Pathol. 2010;92:551–92.
  77. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, Saddler GS, et al. List of new names of plant pathogenic bacteria (2008–2010). J Plant Pathol. 2012;94:21–7.
  78. Chanda B, Venugopal SC, Kulshrestha S, Navarre DA, Downie B, Vaillancourt L, et al. Glycerol-3-phosphate levels are associated with basal resistance to the hemibiotrophic fungus Colletotrichum higginsianum in Arabidopsis. Plant Physiol. 2008;147:2017–29. · DOI
  79. Shine MB, Xiao X, Kachroo P, Kachroo A. Signaling mechanisms underlying systemic acquired resistance to microbial pathogens. Plant Sci. 2019;279:81–6. · DOI
  80. Tawaraya K, Horie R, Shinano T, Wagatsuma TT, Saito K, Oikawa A. Metabolite profiling of soybean root exudates under phosphorus deficiency. Soil Sci Plant Nutr. 2014;60:679–94. · DOI
  81. Tawaraya K, Horie R, Saito S, Wagatsuma T, Saito K, Oikawa A. Metabolite profiling of root exudates of common bean under phosphorus deficiency. Metabolites. 2014;4:599–611. · DOI
  82. Liu Y, Sun W, Ma L, Xu R, Yang C, Xu P, et al. Metabolic mechanism and physiological role of glycerol 3-phosphate in Pseudomonas aeruginosa PAO1. mBio. 2022;13:e0262422. · DOI
  83. Clerc EE, Raina J-B, Keegstra JM, Landry Z, Pontrelli S, Alcolombri U, et al. Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nat Commun. 2023;14:8080. · DOI
  84. Ordal GW, Villani DP, Rosendahl MS. Chemotaxis towards sugars by Bacillus subtilis. J Gen Microbiol. 1979;115:167–72. · DOI
  85. Straley SC, LaMarre AG, Lawrence LJ, Conti SF. Chemotaxis of Bdellovibrio bacteriovorus toward pure compounds. J Bacteriol. 1979;140:634–42. · DOI
  86. Woodcock DM, Crowther PJ, Doherty J, Jefferson S, DeCruz E, Noyer-Weidner M, et al. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 1989;17:3469–78. · DOI
  87. Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, et al. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol. 2009;394:644–52. · DOI
  88. Herrero M, de Lorenzo V, Timmis KN. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacteriol. 1990;172:6557–67. · DOI
  89. Demarre G, Guerout AM, Matsumoto-Mashimo C, Rowe-Magnus DA, Marliere P, Mazel D. A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPalpha) conjugative machineries and their cognate Escherichia coli host strains. Res Microbiol. 2005;156:245–55. · DOI
  90. Kaniga K, Delor I, Cornelis GR. A wide-host-range suicide vector for improving reverse genetics in gram-negative bacteria: inactivation of the blaA gene of Yersinia enterocolitica. Gene. 1991;109:137–41. · DOI
  91. Obranic S, Babic F, Maravic-Vlahovicek G. Improvement of pBBR1MCS plasmids, a very useful series of broad-host-range cloning vectors. Plasmid. 2013;70:263–7. · DOI
  92. Kelliher JL, Radin JN, Grim KP, Párraga Solórzano PK, Degnan PH, Kehl-Fie TE. Acquisition of the phosphate transporter NptA enhances Staphylococcus aureus pathogenesis by improving phosphate uptake in divergent environments. Infect Immun. 2018;86:e00631-e717. · DOI
  93. Corso G, Stärk H, Jing B, Barzilay R, Jaakkola T. DiffDock: diffusion steps, twists, and turns for molecular docking. https://doi.org/10.48550/arXiv221001776. · DOI
  94. O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733-745. · DOI · Paper page
  95. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings Bioinformat. 2019;20:1160–6. · DOI · Paper page
  96. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2. · DOI · Paper page
  97. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–91. · DOI
  98. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9. · DOI
  99. Straub D, Rothballer M, Hartmann A, Ludewig U. The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants. Front Microbiol. 2013;4:168. · DOI

Metadata

Authors
Velando, F., Xing, J., Genova, R., Cerna-Vargas, J. P., Vázquez-Santiago, R., Matilla, M. A., Zhulin, I. B., & Krell, T.
Affiliations
  • Consejo Superior de Investigaciones Científicas (ES)
  • The Ohio State University (US)
Corresponding author
  • Zhulin, Igor B.
  • Krell, Tino
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2025-08-29
Volume
26
Issue
1
Pages
260-260
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-025-03703-6
PMC
PMC12395807
OpenAlex
W4413804273
Cited by
5
References
1
Citations by year
2026: 4 · 2025: 1
FWCI
2.69
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Ministerio de Ciencia e Innovación (PID2020-112612GB-I00, PID2019-103972GA-I00)
  • National Institutes of Health (R35GM 131760)
  • European Union (EU RD 289/2021)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Pathogenic Bacteria Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
Keywords
chemoreceptors, glycerol-3-phosphate, chemotaxis, plant-associated bacteria, plant pathogens, plant signaling molecules, ligand binding, glycerol-2-phosphate, Krebs cycle intermediates, plant-bacteria interactions, bacterial virulence, Pectobacterium atrosepticum
MeSH terms
Bacterial Proteins, Chemotaxis, Glycerophosphates, Phosphorylation, Plants, Signal Transduction, Pectobacterium

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review