PreprintCited by 14Bacterial Genetics and BiotechnologyEscherichia coli research studiesEnterobacteriaceae and Cronobacter Research

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Conserved Metabolic Regulator ArcA Responds to Oxygen Availability, Iron Limitation, and Cell Envelope Perturbations during Bacteremia

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Preprint — published as 10.1128/mbio.01448-23 · Paper page

Abstract

Bacteremia, a systemic infection associated with severe clinical outcomes, is often caused by Gram-negative facultative anaerobes. ArcAB, a two-component regulatory system that represses aerobic respiration, is a key mediator of metabolic adaptation for such bacteria. Using targeted mutational analysis informed by global genetic screens, we identified the arcA gene as promoting fitness of Klebsiella pneumoniae , Citrobacter freundii , and Serratia marcescens but not Escherichia coli in a murine model of bacteremia. Engineered mutants lacking arcA exhibit a dysregulated response to changes in oxygen availability, iron limitation, and membrane perturbations, all of which bacterial cells experience during infection. The genetic response of the arcA mutants relative to wild-type strains to the cationic antimicrobial peptide polymyxin B demonstrates an expanded role for ArcA as an activator in response to membrane damage in addition to metabolic adaptation. ArcA function is furthermore linked to electron transport chain activity based on its response to uncoupling of proton motive force by carbonyl cyanide- m -chlorophenylhydrazone (CCCP). Differences in lactate and acetate levels as well as lactate dehydrogenase activity between arcA mutant and wild-type cells following CCCP treatment establish an ArcA-mediated shift to fermentation independent of oxygen availability. This study highlights the semi-conserved role of ArcA during bacteremia and consolidates infection phenotypes into a comprehensive model based on respiratory activity. AUTHOR SUMMARY: Infections of the bloodstream are life-threatening and can result in sepsis, an overreaction of the host immune system that ultimately damages the body. Gram-negative bacteria are responsible for causing many cases of bloodstream infections, also referred to as bacteremia. The long-term goal of our work is to understand how these bacteria establish and maintain infection during bacteremia. We have previously identified the transcription factor ArcA, which promotes fermentation in bacteria, as a likely contributor to the growth and survival of bacteria in this environment. Here, we study ArcA in the Gram-negative species Citrobacter freundii , Klebsiella pneumoniae, and Serratia marcescens. Our findings aid in determining how these bacteria sense their environment, utilize nutrients, and generate energy while also countering attacks from the host immune system. This information is critical for developing better models of infection to inform future therapeutic development.

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Research works printed but not linked: 84

  1. 2021, The selective advantage of facultative anaerobes relies on their unique ability to cope with changing oxygen levels during infection, Cell Microbiol, 23, e13338
  2. Thaden JT , Li Y , Ruffin F , Maskarinec SA , Hill-Rorie JM , Wanda LC , et al. Increased Costs Associated with Bloodstream Infections Caused by Multidrug-Resistant Gram-Negative Bacteria Are Due Primarily to Patients with Hospital-Acquired Infections. Antimicrob Agents Chemother. 2017;61(3). · DOI
  3. Holmes CL , Anderson MT , Mobley HLT , Bachman MA . Pathogenesis of Gram-Negative Bacteremia. Clin Microbiol Rev [Internet]. 2021 Jun 16 [cited 2021 Apr 5];34(2). Available from: https://cmr.asm.org/content/34/2/e00234-20 · DOI
  4. 2019 15, and Preventability of Sepsis-Associated Mortality in US Acute Care Hospitals, JAMA Netw Open, 2, e187571, 10.1001/jamanetworkopen.2018.7571 · DOI
  5. 2021 1, Current spectrum of causative pathogens in sepsis: A prospective nationwide cohort study in Japan, Int J Infect Dis, 103, 343, 10.1016/j.ijid.2020.11.168 · DOI
  6. 2020 16, Prevalence of Antibiotic-Resistant Pathogens in Culture-Proven Sepsis and Outcomes Associated With Inadequate and Broad-Spectrum Empiric Antibiotic Use, JAMA Netw Open, 3, e202899, 10.1001/jamanetworkopen.2020.2899 · DOI · Paper page
  7. 2018, Epidemiology of Carbapenem-Resistant Enterobacteriaceae Infections: Report from the China CRE Network, Antimicrob Agents Chemother, 62, e01882
  8. 2019 1, Antimicrobial-resistant pathogens in Canadian ICUs: results of the CANWARD 2007 to 2016 study, J Antimicrob Chemother, 74, 645, 10.1093/jac/dky477 · DOI
  9. Subashchandrabose S , Smith SN , Spurbeck RR , Kole MM , Mobley HLT . Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic Infection. PLoS Pathog. 2013 Dec 5;9(12). · DOI
  10. 2017 23, Capsule Production and Glucose Metabolism Dictate Fitness during Serratia marcescens Bacteremia, mBio, 8, e00740
  11. 10.1038/s41598-018-30196-0 · DOI
  12. 10.1101/2023.02.23.529827 · DOI
  13. 10.1016/j.mib.2020.05.009 · DOI
  14. 2022 20, The ArcAB Two-Component System: Function in Metabolism, Redox Control, and Infection, Microbiol Mol Biol Rev, 86, e00110
  15. 10.1039/c6mb00721j · DOI
  16. 10.1128/IAI.71.1.163-172.2003 · DOI
  17. Pardo-Esté C , Hidalgo AA , Aguirre C , Briones AC , Cabezas CE , Castro-Severyn J , et al. The ArcAB two-component regulatory system promotes resistance to reactive oxygen species and systemic infection by Salmonella Typhimurium. PLoS ONE. 2018 Sept 4;13(9). · DOI
  18. Park DM , Akhtar MdS , Ansari AZ , Landick R , Kiley PJ . The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally. PLoS Genet. 2013 Oct 17;9(10). · DOI
  19. Iyer MS , Pal A , Srinivasan S , Somvanshi PR , Venkatesh KV . Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli . mSystems. 2021 Mar 30;6(2). · DOI
  20. 10.1371/journal.pgen.1004264 · DOI
  21. Loui C , Chang AC , Lu S . Role of the ArcAB two-component system in the resistance of Escherichia coli to reactive oxygen stress. BMC Microbiol. 2009 Aug 28;9:183. · DOI
  22. Iyer MS , Pal A , Venkatesh KV . A Systems Biology Approach To Disentangle the Direct and Indirect Effects of Global Transcription Factors on Gene Expression in Escherichia coli . Microbiol Spectr. 2023 Feb 7;e0210122. · DOI
  23. 10.1093/NAR/GKAB1061 · DOI · Paper page
  24. 10.1016/j.jmb.2005.03.059 · DOI
  25. 10.1128/JB.182.13.3858-3862.2000 · DOI
  26. 10.1139/cjm-2015-0345 · DOI
  27. 10.1006/jmbi.1997.1065 · DOI
  28. Sievers F , Wilm A , Dineen D , Gibson TJ , Karplus K , Li W , et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. · DOI
  29. 2021 31, Replication Dynamics for Six Gram-Negative Bacterial Species during Bloodstream Infection, mBio, 12, e0111421, 10.1128/mBio.01114-21 · DOI
  30. Hullahalli K , Waldor MK . Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection. eLife. 10:e70910. · DOI
  31. 10.1073/pnas.252529799 · DOI
  32. 10.1128/IAI.58.5.1281-1289.1990 · DOI
  33. Broberg CA , Wu W , Cavalcoli JD , Miller VL , Bachman MA . Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology Studies. Genome Announc. 2014 Sep 25;2(5). · DOI
  34. 2020, Transcription Factor ArcA is a Flux Sensor for the Oxygen Consumption Rate in Escherichia coli, Biotechnol J, 15, 1900353, 10.1002/biot.201900353 · DOI
  35. 10.1371/journal.pgen.1008078 · DOI
  36. Gao G , Li J , Zhang Y , Chang YZ . Cellular Iron Metabolism and Regulation. In: Chang YZ , editor. Brain Iron Metabolism and CNS Diseases [Internet]. Singapore: Springer; 2019 [cited 2022 Sep 23]. p. 21–32. (Advances in Experimental Medicine and Biology). Available from: https://doi.org/10.1007/978-981-13-9589-5_2 · DOI
  37. 2020, Iron in infection and immunity, Mol Aspects Med, 75, 100864, 10.1016/j.mam.2020.100864 · DOI · Paper page
  38. 10.1126/science.1059361 · DOI
  39. 10.1073/pnas.0403064101 · DOI
  40. 2021, Mutual interplay between ArcA and σE orchestrates envelope stress response in Shewanella oneidensis, Environ Microbiol, 23, 652, 10.1111/1462-2920.15060 · DOI
  41. Xie P , Liang H , Wang J , Huang Y , Gao H . Lipopolysaccharide Transport System Links Physiological Roles of σE and ArcA in the Cell Envelope Biogenesis in Shewanella oneidensis . Microbiol Spectr. 2021 Aug 18;e0069021. · DOI
  42. Ramos PIP , Custódio MGF , Quispe Saji G del R , Cardoso T , da Silva GL , Braun G , et al. The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets . BMC Genomics. 2016 Oct 25;17(Suppl 8). · DOI
  43. 10.1111/1574-6968.12419 · DOI
  44. Huan Y , Kong Q , Mou H , Yi H . Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields. Front Microbiol. 2020;11. · DOI
  45. 2021, The Potential of Human Peptide LL-37 as an Antimicrobial and Anti-Biofilm Agent, Antibiotics, 10, 650, 10.3390/antibiotics10060650 · DOI
  46. Napier BA , Burd EM , Satola SW , Cagle SM , Ray SM , McGann P , et al. Clinical Use of Colistin Induces Cross-Resistance to Host Antimicrobials in Acinetobacter baumannii. mBio. 2013 May 21;4(3). · DOI
  47. 1997, Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors, Biochim Biophys Acta BBA - Bioenerg, 3, 217
  48. Förster AH , Gescher J . Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products. Front Bioeng Biotechnol. 2014 May 23;2. · DOI
  49. 10.1099/00221287-113-1-83 · DOI
  50. Grimont PAD , Grimont F. Klebsiella . In: Bergey’s Manual of Systematics of Archaea and Bacteria [Internet]. John Wiley & Sons, Ltd; 2015 [cited 2023 Mar 7]. p. 1–26. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118960608.gbm01150 · DOI
  51. 1928, THE FERMENTATION OF GLUCOSE BY ORGANISMS OF THE GENUS SERRATIA, J Bacteriol, 16, 163, 10.1128/jb.16.3.163-185.1928 · DOI
  52. 10.1111/j.1574-6968.1989.tb03398.x · DOI
  53. 10.1128/AEM.02558-12 · DOI
  54. 2018, Microbial Cell Factories à la Carte: Elimination of Global Regulators Cra and ArcA Generates Metabolic Backgrounds Suitable for the Synthesis of Bioproducts in Escherichia coli, Appl Environ Microbiol, 84, e01337
  55. 10.1021/bi00357a004 · DOI
  56. 10.1111/j.1582-4934.2011.01258.x · DOI · Paper page
  57. Pittman RN . Oxygen Transport [Internet]. Morgan & Claypool Life Sciences; 2011 [cited 2018 Jun 1]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK54103/
  58. Alteri CJ , Smith SN , Mobley HLT . Fitness of Escherichia coli during Urinary Tract Infection Requires Gluconeogenesis and the TCA Cycle. PLoS Pathog. 2009 May 29;5(5). · DOI
  59. 10.1016/j.mib.2011.12.004 · DOI
  60. 10.1073/pnas.1707189114 · DOI
  61. 2022, Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures while upregulating anaerobic respiratory chains, New Biotechnol, 71, 11, 10.1016/j.nbt.2022.06.004 · DOI
  62. 10.1073/pnas.90.9.4304 · DOI · Paper page
  63. 10.1053/j.gastro.2013.12.031 · DOI · Paper page
  64. 10.1128/MCB.23.24.9361-9374.2003 · DOI · Paper page
  65. Morales EH , Collao B , Desai PT , Calderón IL , Gil F , Luraschi R , et al. Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium. BMC Genomics. 2013 Sep 17;14:626. · DOI
  66. 10.1128/IAI.00312-15 · DOI
  67. 69. Sabnis A , Hagart KL , Klöckner A , Becce M , Evans LE , Furniss RCD , et al. Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane. Cole PA, Gao L, van Schaik W, editors. eLife. 2021 Apr 6;10:e65836. · DOI
  68. 10.1038/ja.2013.111 · DOI
  69. Waegeman H , Beauprez J , Moens H , Maertens J , De Mey M , Foulquié-Moreno MR , et al. Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3). BMC Microbiol. 2011 Apr 11;11:70. · DOI
  70. 2021, Thiol-based functional mimicry of phosphorylation of the two-component system response regulator ArcA promotes pathogenesis in enteric pathogens, Cell Rep, 37, 110147, 10.1016/j.celrep.2021.110147 · DOI
  71. 1951, Studies on Lysogenesis I: The Mode of Phage Liberation by Lysogenic Escherichia coli, J Bacteriol, 62, 293, 10.1128/jb.62.3.293-300.1951 · DOI
  72. 10.1073/pnas.100127597 · DOI
  73. 2014, Recombineering: genetic engineering in bacteria using homologous recombination, Curr Protoc Mol Biol, 1, 16.1
  74. 10.1016/0378-1119(95)00584-1 · DOI
  75. Smith SN , Hagan EC , Lane MC , Mobley HLT . Dissemination and Systemic Colonization of Uropathogenic Escherichia coli in a Murine Model of Bacteremia. mBio. 2010 Dec 30;1(5). · DOI
  76. 10.1038/nprot.2008.73 · DOI · Paper page
  77. 2020, Measurement of Short-Chain Fatty Acids in Respiratory Samples: Keep Your Assay above the Water Line, Am J Respir Crit Care Med, 202, 610, 10.1164/rccm.201909-1840LE · DOI
  78. 2023, Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR, Nucleic Acids Res, 51, D678, 10.1093/nar/gkac1003 · DOI
  79. Edgar RC . MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004 Aug 19;5:113. · DOI
  80. 2022 12, Search and sequence analysis tools services from EMBL-EBI in 2022, Nucleic Acids Res, 50, W276, 10.1093/nar/gkac240 · DOI
  81. 10.1093/nar/gkaa1100 · DOI · Paper page
  82. 10.1093/nar/gkw408 · DOI · Paper page
  83. 2011, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinforma Oxf Engl, 27, 1164, 10.1093/bioinformatics/btr088 · DOI
  84. 2011, FIMO: scanning for occurrences of a given motif, Bioinforma Oxf Engl, 27, 1017

Metadata

Authors
Brown, A. N., Anderson, M. T., Smith, S. N., Bachman, M. A., & Mobley, H. L. T.
Affiliations
University of Michigan (US)
Corresponding author
Mobley, Harry L. T.
Venue
mBio
Publisher
openRxiv
Published
2023-04-18
Volume
14
Issue
5
Pages
e0144823-e0144823
ISSN
2150-7511 (ISSN-L)
OpenAlex
W4386529760
Cited by
14
References
1
Citations by year
2026: 7 · 2025: 3 · 2024: 4
FWCI
2.32
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • mBio (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • American Heart Association (828854)
  • University of Michigan
  • National Institutes of Health
  • National Institute of Allergy and Infectious Diseases (R01AI134731)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Immunology and Microbiology › Microbiology › Escherichia coli research studies
  • Life Sciences › Immunology and Microbiology › Microbiology › Enterobacteriaceae and Cronobacter Research
Keywords
Arca, bacteremia, oxygen availability, iron limitation, polymyxin B, membrane damage, electron transport chain, fermentation, lactate dehydrogenase, Citrobacter freundii, Klebsiella pneumoniae, Serratia marcescens, bacterial metabolism, sepsis
MeSH terms
Gram-Negative Bacteria, Humans, Iron, Klebsiella pneumoniae, Bacteremia, Sepsis

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