Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

BMC Genomics

Dragana Gagic²  Jasna Rakonjac³  Graeme T Attwood²  Eric Altermann²  Christopher J Creevey¹  Sinead C Leahy²  Christina D Moon²  Milica Ciric³ 

[1] Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK;Animal Nutrition and Health, AgResearch Ltd, Palmerston North 4442, New Zealand;Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

关键词: Surface and secreted proteins;    Cellulosome;    Rumen;    Metagenomics;    Nxt generation sequencing;    Phage display;   

Others  :  1217242
DOI  :  10.1186/1471-2164-15-356

 received in 2013-11-05, accepted in 2014-04-29,  发布年份 2014

【 摘 要 】

Background

In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects.

Results

By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre.

Conclusions

As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.

【 授权许可】

   
2014 Ciric et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Cowan DA: Microbial genomes - the untapped resource. Trends Biotechnol 2000, 18(1):14-16.
• [2]Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P: Metagenomic gene discovery: past, present and future. Trends Biotechnol 2005, 23(6):321-329.
• [3]Amann RI, Ludwig W, Schleifer KH: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59(1):143-169.
• [4]Handelsman J: Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004, 68(4):669-685.
• [5]Streit WR, Daniel R, Jaeger KE: Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Curr Opin Biotechnol 2004, 15(4):285-290.
• [6]Xing MN, Zhang XZ, Huang H: Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis. Biotech Adv 2012, 30(4):920-929.
• [7]Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN: Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol 2005, 7(12):1996-2010.
• [8]Morgavi DP, Kelly WJ, Janssen PH, Attwood GT: Rumen microbial (meta)genomics and its application to ruminant production. Animal 2012, 7(s1):184-201.
• [9]Williams AG, Withers SE: Hemicellulose-degrading enzymes synthesized by rumen bacteria. J Appl Bacteriol 1981, 51(2):375-385.
• [10]Cotta MA: Amylolytic activity of selected species of ruminal bacteria. Appl Environ Microbiol 1988, 54(3):772-776.
• [11]Whitehead TR, Hespell RB: Cloning and expression in Escherichia coli of a xylanase gene from Bacteroides ruminicola 23. Appl Environ Microbiol 1989, 55(4):893-896.
• [12]Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, Alexander LJ, Nelson KE: Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One 2012, 7(11):e48289.
• [13]Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA: Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 2009, 106(6):1948-1953.
• [14]Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM: Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011, 331(6016):463-467.
• [15]Kim M, Morrison M, Yu Z: Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol 2011, 76(1):49-63.
• [16]Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW, Foust TD: Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 2007, 315(5813):804-807.
• [17]Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B: The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 2009, 37(Database issue):D233-D238.
• [18]Cuskin F, Flint JE, Gloster TM, Morland C, Basle A, Henrissat B, Coutinho PM, Strazzulli A, Solovyova AS, Davies GJ, Gilbert HJ: How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity. Proc Natl Acad Sci U S A 2012, 109(51):20889-20894.
• [19]Blake AW, McCartney L, Flint JE, Bolam DN, Boraston AB, Gilbert HJ, Knox JP: Understanding the biological rationale for the diversity of cellulose-directed carbohydrate-binding modules in prokaryotic enzymes. J Biol Chem 2006, 281(39):29321-29329.
• [20]Boraston AB, Bolam DN, Gilbert HJ, Davies GJ: Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 2004, 382(Pt 3):769-781.
• [21]Doi RH, Kosugi A: Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Microbiol 2004, 2(7):541-551.
• [22]Bayer EA, Lamed R, White BA, Flints HJ: From cellulosomes to cellulosomics. Chem Rec 2008, 8(6):364-377.
• [23]Bayer EA, Setter E, Lamed R: Organization and distribution of the cellulosome in Clostridium thermocellum. J Bacteriol 1985, 163(2):552-559.
• [24]Lamed R, Setter E, Bayer EA: Characterization of a cellulose-binding, cellulase-containing complex in Clostridium thermocellum. J Bacteriol 1983, 156(2):828-836.
• [25]Fierobe HP, Bayer EA, Tardif C, Czjzek M, Mechaly A, Belaich A, Lamed R, Shoham Y, Belaich JP: Degradation of cellulose substrates by cellulosome chimeras. Substrate targeting versus proximity of enzyme components. J Biol Chem 2002, 277(51):49621-49630.
• [26]Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Dore J, Monsan P, Remaud-Simeon M, Potocki-Veronese G: Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010, 20(11):1605-1612.
• [27]Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R, D’Agostino N, Mirion L, Buccato S, Mariani M, Galli G, Nogarotto R, Dei VN, Vegni F, Fraser C, Mancuso G, Teti G, Madoff LC, Paoletti LC, Rappuoli R, Kasper DL, Telford JL, Grandi G: Immunology: Identification of a universal group B Streptococcus vaccine by multiple genome screen. Science 2005, 309(5731):148-150.
• [28]Boekhorst J, Wels M, Kleeberezem M, Siezen RJ: The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology 2006, 152(11):3175-3183.
• [29]Hammerschmidt S: Adherence molecules of pathogenic pneumococci. Curr Opin Biotechnol 2006, 9(1):12-20.
• [30]Leary DH, Hervey WJ, Deschamps JR, Kusterbeck AW, Vora GJ: Which metaproteome? The impact of protein extraction bias on metaproteomic analyses. Mol Cell Probe 2013, 27:193-199.
• [31]Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B: Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PLoS One 2012, 7(11):e49138.
• [32]Economou A: Bacterial secretome: the assembly manual and operating instructions (review). Molec Membr Biol 2002, 19(3):159-169.
• [33]Petersen TN, Brunak S, Von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8(10):785-786.
• [34]Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S: Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel 2004, 17(4):349-356.
• [35]Krogh A, Larsson B, Von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580.
• [36]Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ: Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res 2008, 7(12):5082-5093.
• [37]Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, et al.: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5(3):e77.
• [38]Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE: Metagenomic analysis of the human distal gut microbiome. Science 2006, 312(5778):1355-1359.
• [39]Prakash T, Taylor TD: Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 2012, 13(6):711-727.
• [40]Jankovic D, Collett MA, Lubbers MW, Rakonjac J: Direct selection and phage display of a Gram-positive secretome. Genome Biol 2007, 8(12):R266. BioMed Central Full Text
• [41]Liu S, Han W, Sun C, Lei L, Feng X, Yan S, Diao Y, Gao Y, Zhao H, Liu Q, Yao C, Li M: Subtractive screening with the Mycobacterium tuberculosis surface protein phage display library. Tuberculosis (Edinb) 2011, 91(6):579-586.
• [42]Gagic D, Wen W, Collett MA, Rakonjac J: Unique secreted-surface protein complex of Lactobacillus rhamnosus, identified by phage display. Microbiol Open 2012, 2:1-17.
• [43]Liu SS, Han WY, Sun CJ, Lei LC, Feng X, Zu S, Zai ZD, Gao Y, Zhao HL, Yao CM: Identification of two new virulence factors of Mycobacterium tuberculosis that induce multifunctional CD4 T cell responses. J Mycobac Dis 2013, 3(1):S6.
• [44]Rakonjac J, Bennett NJ, Spagnuolo J, Gagic D, Russel M: Filamentous bacteriophage: biology, phage display and nanotechnology applications. Curr Issues Mol Biol 2011, 13(2):51-76.
• [45]Zwick MB, Shen J, Scott JK: Phage-displayed peptide libraries. Curr Opin Biotechnol 1998, 9(4):427-436.
• [46]Barbas CF III, Burton DR, Scott JK, Silverman GJ: Phage Display: A Laboratory Manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2001.
• [47]Paschke M, Höhne W: A twin-arginine translocation (Tat)-mediated phage display system. Gene 2005, 350(1):79-88.
• [48]Paschke M: Phage display systems and their applications. Appl Microbiol Biotechnol 2006, 70(1):2-11.
• [49]Jami E, Mizrahi I: Composition and similarity of bovine rumen microbiota across individual animals. PLoS One 2012, 7(3):e33306.
• [50]Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC: IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 2012, 40(Database issue):D123-D129.
• [51]Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD: The Pfam protein families database. Nucleic Acids Res 2012, 40(Database issue):D290-D301.
• [52]Antelmann H, Tjalsma H, Voigt B, Ohlmeier S, Bron S, Dijl J, Hecker M: A proteomic view on genome-based signal peptide predictions. Genome Res 2001, 11:1484-1502.
• [53]Lichanska AM: Secreted bacterial proteins. Genome Biol 2001, 2(12):reports0047.
• [54]Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y: dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012, 40(Web Server issue):W445-W451.
• [55]Dell A, Galadari A, Sastre F, Hitchen P: Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes. Int J Microbiol 2010, 2010:148-178.
• [56]Yutin N, Galperin MY: A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 2013, 10(15):2631-2641.
• [57]Whitman WB, Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Ludwig W, Suzuki K-i, Parte A: Bergey’s Manual® of Systematic Bacteriology. Volume 5. 2nd edition. New York: Springer; 2012.
• [58]Woodward R, Yi W, Li L, Zhao G, Eguchi H, Sridhar PR, Guo H, Song JK, Motari E, Cai L, Kelleher P, Liu X, Han W, Zhang W, Ding Y, Li M, Wang PG: In vitro bacterial polysaccharide biosynthesis: defining the functions of Wzy and Wzz. Nat Chem Biol 2010, 6(6):418-423.
• [59]Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, Berg ME, White BA, Bayer EA, Lamed R: Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens. J Bacteriol 2006, 188(22):7971-7976.
• [60]Rincon MT, Ding SY, McCrae SI, Martin JC, Aurilia V, Lamed R, Shoham Y, Bayer EA, Flint HJ: Novel organization and divergent dockerin specificities in the cellulosome system of Ruminococcus flavefaciens. J Bacteriol 2003, 185(3):703-713.
• [61]Dai X, Zhu Y, Luo Y, Song L, Liu D, Liu L, Chen F, Wang M, Li J, Zeng X, Dong Z, Hu S, Li L, Xu J, Huang L, Dong X: Metagenomic insights into the fibrolytic microbiome in yak rumen. PloS ONE 2012, 7(7):e40430.
• [62]Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG: Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS One 2012, 7(6):e38571.
• [63]Lamed R, Morag E, Mor-Yosef O, Bayer E: Cellulosome-like entities in Bacteroides cellulosolvens. Curr Microbiol 1991, 22:27-33.
• [64]Peer A, Smith SP, Bayer EA, Lamed R, Borovok I: Noncellulosomal cohesin- and dockerin-like modules in the three domains of life. FEMS Microbiol Lett 2009, 291(1):1-16.
• [65]Forrer P, Jung S, Plückthun A: Beyond binding: using phage display to select for structure, folding and enzymatic activity in proteins. Curr Opin Struc Biol 1999, 9(4):514-520.
• [66]Demartis S, Huber A, Viti F, Lozzi L, Giovannoni L, Neri P, Winter G, Neri D: A strategy for the isolation of catalytic activities from repertoires of enzymes displayed on phage. J Mol Biol 1999, 286(2):617-633.
• [67]Rakonjac J, Jovanovic G, Model P: Filamentous phage infection-mediated gene expression: construction and propagation of the gIII deletion mutant helper phage R408d3. Gene 1997, 198(1–2):99-103.
• [68]Stein J, Marsh T, Wu K, Shizuya H, DeLong E: Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 1996, 178(3):591.
• [69]Russel M: Protein-protein interactions during filamentous phage assembly. J Mol Biol 1993, 231(3):689-697.
• [70]Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A: Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 2003, 12(8):1652-1662.
• [71]Bendtsen JD, Kiemer L, Fausbøll A, Brunak S: Non-classical protein secretion in bacteria. BMC Microbiol 2005, 5(1):58. BioMed Central Full Text
• [72]Imam S, Chen Z, Roos DS, Pohlschröder M: Identification of surprisingly diverse type IV pili, across a broad range of Gram-positive bacteria. PLoS One 2011, 6(12):e28919.
• [73]Bagos PG, Nikolaou EP, Liakopoulos TD, Tsirigos KD: Combined prediction of Tat and Sec signal peptides with hidden Markov models. Bioinformatics 2010, 26(22):2811-2817.
• [74]SeqClean [http://seqclean.sourceforge.net/ webcite]
• [75]The Integrated Microbial Genomes and Metagenomes (IMG/M) system [https://img.jgi.doe.gov/cgi-bin/m/main.cgi webcite]
• [76]Huang Y, Niu B, Gao Y, Fu L, Li W: CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26(5):680-682.
• [77]Carlier JP, Bedora-Faure M, K’Ouas G, Alauzet C, Mory F: Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. Int J Syst Evol Microbiol 2010, 60(Pt 3):585-590.
• [78]Downes J, Dewhirst FE, Tanner AC, Wade WG: Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. Int J Syst Evol Microbiol 2013, 63(Pt 4):1214-1218.
• [79]Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013, 41(Database issue):D590-D596.
• [80]Krieg N, Ludwig W, Euzéby J, Whitman W: Phylum XIV. Bacteroidetes phyl. nov. In Bergey’s Manual® of Systematic Bacteriology. Edited by Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W. New York: Springer; 2010:25-469.
• [81]Schleifer K-H: Phylum XIII.Firmicutes Gibbons and Murray 1978, 5. In Bergey’s Manual® of Systematic Bacteriology. Edited by Vos P, Garrity G, Jones D, Krieg N, Ludwig W, Rainey F, Schleifer K-H, Whitman W. New York: Springer; 2009:19-1317.