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Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing

  • 1.

    Gallo RL, Hooper LV. Epithelial antimicrobial defence of the skin and intestine. Nat Rev Immunol. 2012;12:503–16.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 2.

    Erin Chen Y, Fischbach MA, Belkaid Y. Skin microbiota-host interactions. Nature. 2018;553:427–36.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 3.

    Toledo RC, Jared C. Cutaneous granular glands and amphibian venoms. Comp Biochem Physiol A Physiol. 1995;111:1–29.

  • 4.

    Walke JB, Becker MH, Loftus SC, House LL, Cormier G, Jensen RV, et al. Amphibian skin may select for rare environmental microbes. ISME J. 2014;8:2207–17.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 5.

    Jani AJ, Briggs CJ. Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable. Front Microbiol. 2018;9:487.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 6.

    Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE, Rakotoarison A, et al. Host ecology rather than host phylogeny drives amphibian skin microbial community structure in the biodiversity hotspot of Madagascar. Front Microbiol. 2017;8:1–14.

    Google Scholar 

  • 7.

    Becker MH, Walke JB, Murrill L, Woodhams DC, Reinert LK, Rollins‐Smith LA, et al. Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis. Mol Ecol. 2015;24:1628–41.

    PubMed 

    Google Scholar 

  • 8.

    Flechas SV, Acosta-González A, Escobar LA, Kueneman JG, Sánchez-Quitian ZA, Parra-Giraldo CM, et al. Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. ISME J. 2019;13:361–73.

    PubMed 
    CAS 

    Google Scholar 

  • 9.

    Brunetti AE, Lyra ML, Melo WGP, Andrade LE, Palacios-Rodríguez P, Prado BM, et al. Symbiotic skin bacteria as a source for sex-specific scents in frogs. Proc Natl Acad Sci USA. 2019;116:2124–9.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 10.

    Vaelli PM, Theis KR, Williams JE, O’Connell LA, Foster JA, Eisthen HL. The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Elife. 2020;9:e53898.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Pukala TL, Bowie JH, Maselli VM, Musgrave IF, Tyler MJ. Host-defence peptides from the glandular secretions of amphibians: Structure and activity. Nat Prod Rep. 2006;23:368–93.

    PubMed 
    CAS 

    Google Scholar 

  • 12.

    Bevins CL, Zasloff M. Peptides from frog skin. Annu Rev Biochem. 1990;59:395–414.

    PubMed 
    CAS 

    Google Scholar 

  • 13.

    Woodhams DC, Rollins-Smith LA, Reinert LK, Lam BA, Harris RN, Briggs CJ, et al. Probiotics modulate a novel amphibian skin defense peptide that is antifungal and facilitates growth of antifungal bacteria. Micro Ecol. 2020;79:192–202.

    CAS 

    Google Scholar 

  • 14.

    Mergaert P. Role of antimicrobial peptides in controlling symbiotic bacterial populations. Nat Prod Rep. 2018;35:336–56.

    PubMed 
    CAS 

    Google Scholar 

  • 15.

    Pontes MH, Smith KL, de Vooght L, van den Abbeele J, Dale C. Attenuation of the sensing capabilities of PhoQ in transition to obligate insect-bacterial association. PLoS Genet. 2011;7:e1002349.

  • 16.

    Bosch TCG. Cnidarian-microbe interactions and the origin of innate immunity in metazoans. Annu Rev Microbiol. 2013;67:499–518.

    PubMed 
    CAS 

    Google Scholar 

  • 17.

    Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S. The evolution of the host microbiome as an ecosystem on a leash. Nature. 2017;548:43–51.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 18.

    Joo H-S, Fu C-I, Otto M. Bacterial strategies of resistance to antimicrobial peptides. Philos Trans R Soc B Biol Sci. 2016;371:20150292.

    Google Scholar 

  • 19.

    Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction. Annu Rev Biochem. 2000;69:183–215.

    PubMed 
    CAS 

    Google Scholar 

  • 20.

    Jacob-Dubuisson F, Mechaly A, Betton J-M, Antoine R. Structural insights into the signalling mechanisms of two-component systems. Nat Rev Microbiol. 2018;16:585–93.

    PubMed 
    CAS 

    Google Scholar 

  • 21.

    Gao R, Stock AM. Biological insights from structures of two-component proteins. Annu Rev Microbiol. 2009;63:133–54.

  • 22.

    Piddock LJV. Multidrug-resistance efflux pumps? not just for resistance. Nat Rev Microbiol. 2006;4:629–36.

    PubMed 
    CAS 

    Google Scholar 

  • 23.

    Jeannot K, Bolard A, Plésiat P. Resistance to polymyxins in Gram-negative organisms. Int J Antimicrob Agents. 2017;49:526–35.

    PubMed 
    CAS 

    Google Scholar 

  • 24.

    Fernández L, Jenssen H, Bains M, Wiegand I, Gooderham WJ, Hancock REW. The two-component system CprRS senses cationic peptides and triggers adaptive resistance in Pseudomonas aeruginosa independently of ParRS. Antimicrob Agents Chemother. 2012;56:6212–22.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 25.

    Hong J, Jiang H, Hu J, Wang L, Liu R. Transcriptome analysis reveals the resistance mechanism of Pseudomonas aeruginosa to tachyplesin I. Infect Drug Resist. 2020;13:155.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 26.

    Brunetti AE, Neto FC, Vera MC, Taboada C, Pavarini DP, Bauermeister A, et al. An integrative omics perspective for the analysis of chemical signals in ecological interactions. Chem Soc Rev. 2018;47:1574–91.

    PubMed 
    CAS 

    Google Scholar 

  • 27.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS 

    Google Scholar 

  • 28.

    Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 29.

    Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 30.

    Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47:W81–W87.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 31.

    Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q, Shapiro N, et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol. 2018;20:2142–59.

    PubMed 
    CAS 

    Google Scholar 

  • 32.

    Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinforma. 2011;12:124.

    Google Scholar 

  • 33.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 34.

    Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–W245.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 35.

    Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10:1–10.

    CAS 

    Google Scholar 

  • 36.

    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High-throughput ANI analysis of 90k prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

  • 37.

    Goloboff PA, Catalano SA. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics. 2016;32:221–38.

    Google Scholar 

  • 38.

    Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011;8:469–77.

    PubMed 
    CAS 

    Google Scholar 

  • 39.

    Min XJ, Butler G, Storms R, Tsang A. OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. 2005;33:W677–W680.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 40.

    Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525–7.

    PubMed 
    CAS 

    Google Scholar 

  • 41.

    Nacif-Marçal L, Pereira GR, Abranches MV, Costa NCS, Cardoso SA, Honda ER, et al. Identification and characterization of an antimicrobial peptide of Hypsiboas semilineatus (Spix, 1824) (Amphibia, Hylidae). Toxicon. 2015;99:16–22.

    PubMed 

    Google Scholar 

  • 42.

    Magalhães BS, Melo JAT, Leite JRSA, Silva LP, Prates MV, Vinecky F, et al. Post-secretory events alter the peptide content of the skin secretion of Hypsiboas raniceps. Biochem Biophys Res Commun. 2008;377:1057–61.

    PubMed 

    Google Scholar 

  • 43.

    Brunetti AE, Marani MM, Soldi RA, Mendonça JN, Faivovich J, Cabrera GM, et al. Cleavage of peptides from amphibian skin revealed by combining analysis of gland secretion and in situ MALDI imaging mass spectrometry. ACS Omega. 2018;3:5426–34.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 44.

    Van Zundert GCP, Rodrigues J, Trellet M, Schmitz C, Kastritis PL, Karaca E, et al. The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol. 2016;428:720–5.

    PubMed 

    Google Scholar 

  • 45.

    Cheung J, Bingman CA, Reyngold M, Hendrickson WA, Waldburger CD. Crystal structure of a functional dimer of the PhoQ sensor domain. J Biol Chem. 2008;283:13762–70.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 46.

    Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME J. 2016;10:1682–95.

  • 47.

    Bletz MC, Bunk B, Spröer C, Biwer P, Reiter S, Rabemananjara FCE, et al. Amphibian skin-associated Pigmentiphaga: genome sequence and occurrence across geography and hosts. PLoS One. 2019;14:1–14.

    Google Scholar 

  • 48.

    Reimer LC, Vetcininova A, Carbasse JS, Söhngen C, Gleim D, Ebeling C, et al. Bac Dive in 2019: bacterial phenotypic data for high-throughput biodiversity analysis. Nucleic Acids Res. 2019;47:D631–D636.

    PubMed 
    CAS 

    Google Scholar 

  • 49.

    Ramette A, Frapolli M, Saux MF-L, Gruffaz C, Meyer JM, Défago G, et al. Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Syst Appl Microbiol. 2011;34:180–8.

    PubMed 
    CAS 

    Google Scholar 

  • 50.

    Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, et al. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME J. 2016;10:2527–42.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 51.

    Flury P, Vesga P, Dominguez-Ferreras A, Tinguely C, Ullrich CI, Kleespies RG, et al. Persistence of root-colonizing Pseudomonas protegens in herbivorous insects throughout different developmental stages and dispersal to new host plants. ISME J. 2019;13:860–72.

    PubMed 
    CAS 

    Google Scholar 

  • 52.

    Pupin M, Esmaeel Q, Flissi A, Dufresne Y, Jacques P, Leclère V. Norine: a powerful resource for novel nonribosomal peptide discovery. Synth Syst Biotechnol. 2016;1:89–94.

    PubMed 
    CAS 

    Google Scholar 

  • 53.

    Wilson DJ, Shi C, Teitelbaum AM, Gulick AM, Aldrich CC. Characterization of AusA: a dimodular nonribosomal peptide synthetase responsible for the production of aureusimine pyrazinones. Biochemistry. 2013;52:926–37.

    PubMed 
    CAS 

    Google Scholar 

  • 54.

    Ryona I, Leclerc S, Sacks GL. Correlation of 3-isobutyl-2-methoxypyrazine to 3-Isobutyl-2-hydroxypyrazine during maturation of bell pepper (Capsicum annuum) and wine grapes (Vitis vinifera). J Agric Food Chem. 2010;58:9723–30.

    PubMed 
    CAS 

    Google Scholar 

  • 55.

    Brucker RM, Baylor CM, Walters RL, Lauer A, Harris RN, Minbiole KPC. The identification of 2, 4-diacetylphloroglucinol as an antifungal metabolite produced by cutaneous bacteria of the salamander Plethodon cinereus. J Chem Ecol. 2008;34:39–43.

    PubMed 
    CAS 

    Google Scholar 

  • 56.

    König E, Bininda-Emonds ORP, Shaw C. The diversity and evolution of anuran skin peptides. Peptides. 2015;63:96–117.

    PubMed 

    Google Scholar 

  • 57.

    Yeaman MR, Yount NY. Mechanisms of antimicrobial peptide action and resistance. Pharm Rev. 2003;55:27–55.

    PubMed 
    CAS 

    Google Scholar 

  • 58.

    Kumar P, Kizhakkedathu JN, Straus SK. Antimicrobial peptides: diversity, mechanism of action and strategies to improve the activity and biocompatibility in vivo. Biomolecules. 2018;8:4.

    PubMed Central 

    Google Scholar 

  • 59.

    Castro MS, Ferreira TCG, Cilli EM, Crusca E, Mendes-Giannini MJS, Sebben A, et al. Hylin a1, the first cytolytic peptide isolated from the arboreal South American frog Hypsiboas albopunctatus (‘spotted treefrog’). Peptides. 2009;30:291–6.

    PubMed 
    CAS 

    Google Scholar 

  • 60.

    Resnick NM, Maloy WL, Guy HR, Zasloff M. A novel endopeptidase from Xenopus that recognizes α-helical secondary structure. Cell. 1991;66:541–54.

    PubMed 
    CAS 

    Google Scholar 

  • 61.

    Gutu AD, Sgambati N, Strasbourger P, Brannon MK, Jacobs MA, Haugen E, et al. Polymyxin resistance of Pseudomonas aeruginosa phoQ mutants is dependent on additional two-component regulatory systems. Antimicrob Agents Chemother. 2013;57:2204–15.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 62.

    Möglich A, Ayers RA, Moffat K. Structure and signaling mechanism of Per-ARNT-Sim domains. Structure. 2009;17:1282–94.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 63.

    Zschiedrich CP, Keidel V, Szurmant H. Molecular mechanisms of two-component signal transduction. J Mol Biol. 2016;428:3752–75.

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 

  • 64.

    Shah N, Gaupp R, Moriyama H, Eskridge KM, Moriyama EN, Somerville GA. Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus. BMC Genomics. 2013;14:524.

  • 65.

    Bader MW, Sanowar S, Daley ME, Schneider AR, Cho U, Xu W, et al. Recognition of antimicrobial peptides by a bacterial sensor kinase. Cell. 2005;122:461–72.

    PubMed 
    CAS 

    Google Scholar 

  • 66.

    Chang C, Tesar C, Gu M, Babnigg G, Joachimiak A, Raj Pokkuluri P, et al. Extracytoplasmic PAS-like domains are common in signal transduction proteins. J Bacteriol. 2010;192:1156–9.

    PubMed 
    CAS 

    Google Scholar 


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