Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria.
antimicrobial proteins
apoplastic proteins
intrinsically disordered proteins
microbe-microbe interactions
microbial community structure
microbiome
phyllosphere microbes
plant pathogen
Journal
The New phytologist
ISSN: 1469-8137
Titre abrégé: New Phytol
Pays: England
ID NLM: 9882884
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
received:
23
03
2023
accepted:
11
04
2023
medline:
18
8
2023
pubmed:
24
5
2023
entrez:
24
5
2023
Statut:
ppublish
Résumé
Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo-colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram-positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.
Substances chimiques
Anti-Infective Agents
0
Banques de données
RefSeq
['CCI44519.1', 'CCI46028.1', 'CCI45607.1', 'CCI42480.1']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2320-2334Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.
Références
Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S-T, Weigel D, Kemen EM. 2016. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biology 14: e1002352.
Almario J, Mahmoudi M, Kroll S, Agler M, Placzek A, Mari A, Kemen E. 2022. The leaf microbiome of Arabidopsis displays reproducible dynamics and patterns throughout the growing season. mBio 13: e02825-21.
Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. 2018. Long-term warming shifts the composition of bacterial communities in the phyllosphere of Galium album in a permanent grassland field-experiment. Frontiers in Microbiology 9: 144.
Berlin JD, Bowen CC. 1964. The host-parasite interface of Albugo candida on Raphanus sativus. American Journal of Botany 51: 445-452.
Bleackley MR, Samuel M, Garcia-Ceron D, McKenna JA, Lowe RGT, Pathan M, Zhao K, Ang C-S, Mathivanan S, Anderson MA. 2020. Extracellular vesicles from the cotton pathogen Fusarium oxysporum f. sp. vasinfectum induce a phytotoxic response in plants. Frontiers in Plant Science 10: 1610.
Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJR. 2009. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nature Protocols 4: 484-494.
Bollenbach T. 2015. Antimicrobial interactions: mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology 27: 1-9.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using Qiime 2. Nature Biotechnology 37: 852-857.
Bruisson S, Zufferey M, L'Haridon F, Trutmann E, Anand A, Dutartre A, Vrieze MD, Weisskopf L. 2019. Endophytes and epiphytes from the grapevine leaf microbiome as potential biocontrol agents against phytopathogens. Frontiers in Microbiology 10: 2726.
Burdukiewicz M, Sidorczuk K, Rafacz D, Pietluch F, Chilimoniuk J, Rödiger S, Gagat P. 2020. Proteomic screening for prediction and design of antimicrobial peptides with AmpGram. International Journal of Molecular Sciences 21: 4310.
Burki F, Roger AJ, Brown MW, Simpson AGB. 2019. The new tree of eukaryotes. Trends in Ecology & Evolution 35: 43-55.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. Blast+: architecture and applications. BMC Bioinformatics 10: 421.
Carlos C, Fan H, Currie CR. 2018. Substrate shift reveals roles for members of bacterial consortia in degradation of plant cell wall polymers. Frontiers in Microbiology 9: 364.
Carlson RR, Vidaver AK. 1982. Taxonomy of Corynebacterium plant pathogens, including a new pathogen of wheat, based on polyacrylamide gel electrophoresis of cellular proteins. International Journal of Systematic and Evolutionary Microbiology 32: 315-326.
Chen L, Dodd IC, Theobald JC, Belimov AA, Davies WJ. 2013. The rhizobacterium Variovorax paradoxus 5C-2, containing ACC deaminase, promotes growth and development of Arabidopsis thaliana via an ethylene-dependent pathway. Journal of Experimental Botany 64: 1565-1573.
Cooper AJ, Latunde-Dada AO, Woods-Tör A, Lynn J, Lucas JA, Crute IR, Holub EB. 2008. Basic compatibility of Albugo candida in Arabidopsis thaliana and Brassica juncea causes broad-spectrum suppression of innate immunity. Molecular Plant-Microbe Interactions 21: 745-756.
Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 26: 1367-1372.
Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. 2011. Andromeda: a peptide search engine integrated into the MaxQuant environment. Journal of Proteome Research 10: 1794-1805.
Cutrona KJ, Kaufman BA, Figueroa DM, Elmore DE. 2015. Role of arginine and lysine in the antimicrobial mechanism of histone-derived antimicrobial peptides. FEBS Letters 589: 3915-3920.
Dhaouadi S, Mougou AH, Rhouma A. 2020. The plant pathogen Rhodococcus fascians. History, disease symptomatology, host range, pathogenesis and plant-pathogen interaction. The Annals of Applied Biology 177: 4-15.
Dubreuil B, Matalon O, Levy ED. 2019. Protein abundance biases the amino acid composition of disordered regions to minimize non-functional interactions. Journal of Molecular Biology 431: 4978-4992.
Eitzen K, Sengupta P, Kroll S, Kemen E, Doehlemann G. 2021. A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme. eLife 10: e65306.
Figueiredo J, Santos RB, Guerra-Guimarães L, Leclercq CC, Renaut J, Malhó R, Figueiredo A. 2022. An in-planta comparative study of Plasmopara viticola proteome reveals different infection strategies towards susceptible and Rpv3-mediated resistance hosts. Scientific Reports 12: 20794.
Finkel OM, Salas-González I, Castrillo G, Conway JM, Law TF, Teixeira PJPL, Wilson ED, Fitzpatrick CR, Jones CD, Dangl JL. 2020. A single bacterial genus maintains root growth in a complex microbiome. Nature 587: 103-108.
Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, Gophna U, Sharan R, Ruppin E. 2011. Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications 2: 589.
Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG. 2022. An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the “CCG” class of effectors. Molecular Plant-Microbe Interactions 35: 39-48.
Gómez-Pérez D, Kemen E. 2021. Predicting lifestyle from positive selection data and genome properties in oomycetes. Pathogens 10: 807.
Harrison PM. 2021. fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PeerJ 9: e12363.
Hassani MA, Durán P, Hacquard S. 2018. Microbial interactions within the plant holobiont. Microbiome 6: 58.
Hjerde E, Pierechod MM, Williamson AK, Bjerga GEK, Willassen NP, Smalås AO, Altermark B. 2013. Draft genome sequence of the actinomycete Rhodococcus sp. strain AW25M09, isolated from the Hadsel Fjord, Northern Norway. Genome Announcements 1: e00055-13.
Hu G, Katuwawala A, Wang K, Wu Z, Ghadermarzi S, Gao J, Kurgan L. 2021. flDPnn: accurate intrinsic disorder prediction with putative propensities of disorder functions. Nature Communications 12: 4438.
Jashni MK, Mehrabi R, Collemare J, Mesarich CH, de Wit PJGM. 2015. The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant-pathogen interactions. Frontiers in Plant Science 6: 584.
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30: 1236-1240.
Kemen E, Gardiner A, Schultz-Larsen T, Kemen AC, Balmuth AL, Robert-Seilaniantz A, Bailey K, Holub E, Studholme DJ, MacLean D et al. 2011. Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biology 9: e1001094.
Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Vesztrocy AW, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M et al. 2018. Goatools: a Python library for Gene Ontology analyses. Scientific Reports 8: 10872.
Latendorf T, Gerstel U, Wu Z, Bartels J, Becker A, Tholey A, Schröder J-M. 2019. Cationic intrinsically disordered antimicrobial peptides (CIDAMPs) represent a new paradigm of innate defense with a potential for novel anti-infectives. Scientific Reports 9: 3331.
Lawrence TJ, Carper DL, Spangler MK, Carrell AA, Rush TA, Minter SJ, Weston DJ, Labbé JL. 2020. amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool. Bioinformatics 37: btaa917.
Li XS, Yuan XK. 2017. Genome sequences for multiple clavibacter strains from different subspecies. Genome Announcements 5: e00721-17.
Liebana-Jordan M, Brotons B, Falcon-Perez JM, Gonzalez E. 2021. Extracellular vesicles in the fungi kingdom. International Journal of Molecular Sciences 22: 7221.
Links MG, Holub E, Jiang RH, Sharpe AG, Hegedus D, Beynon E, Sillito D, Clarke WE, Uzuhashi S, Borhan MH. 2011. De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes. BMC Genomics 12: 503.
Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. 2019. Arms race: diverse effector proteins with conserved motifs. Plant Signaling & Behavior 14: 1557008.
Malanovic N, Lohner K. 2016. Antimicrobial peptides targeting Gram-positive bacteria. Pharmaceuticals 9: 59.
Malik E, Dennison SR, Harris F, Phoenix DA. 2016. pH dependent antimicrobial peptides and proteins, their mechanisms of action and potential as therapeutic agents. Pharmaceuticals 9: 67.
Marín M, Uversky VN, Ott T. 2013. Intrinsic disorder in pathogen effectors: protein flexibility as an evolutionary hallmark in a molecular arms race. Plant Cell 25: 3153-3157.
Mayer T, Mari A, Almario J, Murillo-Roos M, Abdullah HSM, Dombrowski N, Hacquard S, Kemen EM, Agler MT. 2021. Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing. Molecular Ecology Resources 21: 1952-1965.
Micsonai A, Moussong É, Murvai N, Tantos Á, Tőke O, Réfrégiers M, Wien F, Kardos J. 2022. Disordered-ordered protein binary classification by circular dichroism spectroscopy. Frontiers in Molecular Biosciences 9: 863141.
Molloy EM, Hertweck C. 2017. Antimicrobial discovery inspired by ecological interactions. Current Opinion in Microbiology 39: 121-127.
Oh E-J, Bae C, Lee H-B, Hwang IS, Lee H-I, Yea MC, Yim K-O, Lee S, Heu S, Cha J-S et al. 2016. Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper. International Journal of Systematic and Evolutionary Microbiology 66: 4065-4070.
Oldfield CJ, Uversky VN, Dunker AK, Kurgan L. 2019. Intrinsically disordered proteins. Cambridge, MA, USA: Academic Press, 1-34. doi: 10.1016/b978-0-12-816348-1.00001-6.
Perazzolli M, Nesler A, Giovannini O, Antonielli L, Puopolo G, Pertot I. 2020. Ecological impact of a rare sugar on grapevine phyllosphere microbial communities. Microbiological Research 232: 126387.
Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M et al. 2021. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Research 50: D543-D552.
Plisson F, Ramírez-Sánchez O, Martínez-Hernández C. 2020. Machine learning-guided discovery and design of non-hemolytic peptides. Scientific Reports 10: 16581.
Ruhe J, Agler MT, Placzek A, Kramer K, Finkemeier I, Kemen EM. 2016. Obligate biotroph pathogens of the genus Albugo are better adapted to active host defense compared to niche competitors. Frontiers in Plant Science 7: 820.
Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, vol. 1, 3rd edn. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press.
Savojardo C, Martelli PL, Fariselli P, Casadio R. 2015. TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. Bioinformatics 31: 3269-3275.
Snelders NC, Kettles GJ, Rudd JJ, Thomma BPHJ. 2018. Plant pathogen effector proteins as manipulators of host microbiomes? Molecular Plant Pathology 19: 257-259.
Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ. 2021. An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proceedings of the National Academy of Sciences, USA 118: e2110968118.
Snelders NC, Rovenich H, Petti GC, Rocafort M, van den Berg GCM, Vorholt JA, Mesters JR, Seidl MF, Nijland R, Thomma BPHJ. 2020. Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nature Plants 6: 1365-1374.
Tackmann J, Rodrigues JFM, von Mering C. 2019. Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data. Cell Systems 9: 286-296.
Teufel F, Armenteros JJA, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H. 2022. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature Biotechnology 40: 1023-1025.
Uversky VN. 2013. The alphabet of intrinsic disorder. Intrinsically Disordered Proteins 1: e24684.
Veltri D, Kamath U, Shehu A. 2018. Deep learning improves antimicrobial peptide recognition. Bioinformatics 34: 2740-2747.
Wang Y, Wang Y, Wang Y. 2020. Apoplastic proteases: powerful weapons against pathogen infection in plants. Plant Communications 1: 100085.
Zhang J, Zhou J-M. 2010. Plant immunity triggered by microbial molecular signatures. Molecular Plant 3: 783-793.
Zittlau KI, Lechado-Terradas A, Nalpas N, Geisler S, Kahle PJ, Macek B. 2021. Temporal analysis of protein ubiquitylation and phosphorylation during Parkin-dependent mitophagy. Molecular & Cellular Proteomics 21: 100191.