Comparative genome analysis provides novel insight into the interaction of Aquimarina sp. AD1, BL5 and AD10 with their macroalgal host
Tóm tắt
Từ khóa
Tài liệu tham khảo
Achenbach, 1978, Investigations of the pigments from Cytophaga johnsonae Cy j1, Arch. Microbiol., 117, 253, 10.1007/BF00738543
Bernardet, 2006, The genus Flavobacterium
Bernardet, 2002, Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family, Int. J. Syst. Evol. Microbiol., 52, 1049
Blin, 2017, antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res., 45, W36, 10.1093/nar/gkx319
Brameyer, 2015, Dialkylresorcinols as bacterial signaling molecules, Proc. Natl. Acad. Sci., 112, 572, 10.1073/pnas.1417685112
Brown, 2012, Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control, Trends Microbiol., 20, 336, 10.1016/j.tim.2012.04.005
Campbell, 2011, Climate change and disease: bleaching of a chemically defended seaweed, Glob. Chang. Biol., 17, 2958, 10.1111/j.1365-2486.2011.02456.x
Casadevall, 2003, ‘Ready made’ virulence and ‘dual use’ virulence factors in pathogenic environmental fungi—the Cryptococcus neoformans paradigm, Curr. Opin. Microbiol., 6, 332, 10.1016/S1369-5274(03)00082-1
Chen, 2012, Aquimarina salinaria sp. nov., a novel algicidal bacterium isolated from a saltpan, Arch. Microbiol., 194, 103, 10.1007/s00203-011-0730-9
Chin, 2013, Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nat. Methods, 10, 563, 10.1038/nmeth.2474
Chistoserdov, 2005, Culture-dependent characterization of the microbial community associated with epizootic shell disease lesions in American lobster, Homarus americanus, J. Shellfish Res., 24, 741, 10.2983/0730-8000(2005)24[741:CCOTMC]2.0.CO;2
Chistoserdov, 2012, Bacterial communities associated with lesions of shell disease in the American lobster, Homarus americanus Milne-Edwards, J. Shellfish Res., 31, 449, 10.2983/035.031.0205
Croft, 2005, Algae acquire vitamin B 12 through a symbiotic relationship with bacteria, Nature, 438, 90, 10.1038/nature04056
Domozych, 2011, Algal cell walls
Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340
Egan, 2013, The seaweed holobiont: understanding seaweed–bacteria interactions, FEMS Microbiol. Rev., 37, 462, 10.1111/1574-6976.12011
Gorasia, 2015, Porphyromonas gingivalis type IX secretion substrates are cleaved and modified by a sortase-like mechanism, PLoS Pathog., 11, 10.1371/journal.ppat.1005152
Guan, 2013, Identification of an iron acquisition machinery in Flavobacterium columnare, Dis. Aquat. Org., 106, 129, 10.3354/dao02635
Han, 2017, Aquimarina rubra sp. nov., isolated from sediment of a sea cucumber culture pond, Int. J. Syst. Evol. Microbiol., 67, 1932, 10.1099/ijsem.0.001889
Harms, 2018, Antimicrobial Dialkylresorcins from marine-derived microorganisms: insights into their mode of action and putative ecological relevance, Planta Med., 84, 1363, 10.1055/a-0653-7451
Kadowaki, 2016, A two-component system regulates gene expression of the type IX secretion component proteins via an ECF sigma factor, Sci. Rep., 6, 10.1038/srep23288
Kennedy, 2014, Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum, Int. J. Syst. Evol. Microbiol., 64, 501, 10.1099/ijs.0.049650-0
Kharade, 2013, The Flavobacterium johnsoniae chitinase ChiA is required for chitin utilization and is secreted by the type IX secretion system, J. Bacteriol., 196, 961, 10.1128/JB.01170-13
Kharade, 2015, Flavobacterium johnsoniae PorV is required for secretion of a subset of proteins targeted to the type IX secretion system, J. Bacteriol., 197, 147, 10.1128/JB.02085-14
Kumar, 2016, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 33, 1870, 10.1093/molbev/msw054
Kumar, 2016, Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra, Environ. Microbiol., 18, 3962, 10.1111/1462-2920.13403
Lasica, 2017, The type IX secretion system (T9SS): highlights and recent insights into its structure and function, Front. Cell. Infect. Microbiol., 7, 215, 10.3389/fcimb.2017.00215
Lee, 2017, Aquimarina versatilis sp. nov., isolated from seashore sand, and emended description of the genus Aquimarina, Int. J. Syst. Evol. Microbiol., 67, 411, 10.1099/ijsem.0.001645
Lewin, 1969, A classification of Flexibacteria, Microbiology, 58, 189
Li, 2014, Aquimarina atlantica sp. nov., isolated from surface seawater of the Atlantic Ocean, Antonie Van Leeuwenhoek, 106, 293, 10.1007/s10482-014-0196-2
Manefield, 2002, Halogenated furanones inhibit quorum sensing through accelerated LuxR turnover, Microbiology, 148, 1119, 10.1099/00221287-148-4-1119
McBride, 2009, Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis, Appl. Environ. Microbiol., 75, 6864, 10.1128/AEM.01495-09
Miyazaki, 2010, Aquimarina macrocephali sp. nov., isolated from sediment adjacent to sperm whale carcasses, Int. J. Syst. Evol. Microbiol., 60, 2298, 10.1099/ijs.0.018747-0
Nedashkovskaya, 2005, Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov, Int. J. Syst. Evol. Microbiol., 55, 225, 10.1099/ijs.0.63349-0
Nedashkovskaya, 2006, Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina, Int. J. Syst. Evol. Microbiol., 56, 2037, 10.1099/ijs.0.64155-0
Oh, 2010, Aquimarina litoralis sp. nov., isolated from a coastal seawater, J. Microbiol., 48, 433, 10.1007/s12275-010-0088-8
Park, 2012, Aquimarina mytili sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of Aquimarina macrocephali, Int. J. Syst. Evol. Microbiol., 62, 1974, 10.1099/ijs.0.032904-0
Park, 2013, Aquimarina gracilis sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of Aquimarina spongiae, Int. J. Syst. Evol. Microbiol., 63, 1782, 10.1099/ijs.0.044289-0
Pohanka, 2006, Antimicrobial dialkylresorcinols from Pseudomonas sp. Ki19, J. Nat. Prod., 69, 654, 10.1021/np0600595
Pumbwe, 2008, Presence of quorum-sensing systems associated with multidrug resistance and biofilm formation in Bacteroides fragilis, Microb. Ecol., 56, 412, 10.1007/s00248-007-9358-3
Quinn, 2012, Exposures of Homarus americanus shell to three bacteria isolated from naturally occurring epizootic shell disease lesions, J. Shellfish Res., 31, 485, 10.2983/035.031.0208
Quinn, 2017, Real-time PCR assay for Aquimarina macrocephali subsp. homaria and its distribution in shell disease lesions of Homarus americanus, Milne-Edwards, 1837, and environmental samples, J. Microbiol. Methods, 139, 61, 10.1016/j.mimet.2017.04.001
Ramanan, 2016, Algae–bacteria interactions: evolution, ecology and emerging applications, Biotechnol. Adv., 34, 14, 10.1016/j.biotechadv.2015.12.003
Ranson, 2018, Draft genome sequence of the putative marine pathogen Aquimarina sp. Strain I32. 4, Genome Announc., 6, e00313, 10.1128/genomeA.00313-18
Reichenbach, 1980, Flexirubin-type pigments in Flavobacterium, Arch. Microbiol., 126, 291, 10.1007/BF00409934
Rhodes, 2010, Flavobacterium johnsoniae gldN and gldO are partially redundant genes required for gliding motility and surface localization of SprB, J. Bacteriol., 192, 1201, 10.1128/JB.01495-09
Romero, 2010, Acylhomoserine lactone production and degradation by the fish pathogen Tenacibaculum maritimum, a member of the Cytophaga–Flavobacterium–Bacteroides (CFB) group, FEMS Microbiol. Lett., 304, 131, 10.1111/j.1574-6968.2009.01889.x
Saiki, 2014, Porphyromonas gingivalis C-terminal signal peptidase PG 0026 and HagA interact with outer membrane protein PG 27/LptO, Mol Oral Microbiol, 29, 32, 10.1111/omi.12043
Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406
Sato, 2010, A protein secretion system linked to Bacteroidete gliding motility and pathogenesis, Proc. Natl. Acad. Sci., 107, 276, 10.1073/pnas.0912010107
Shrivastava, 2013, Flavobacterium johnsoniae GldK, GldL, GldM, and SprA are required for secretion of the cell-surface gliding motility adhesins SprB and RemA, J. Bacteriol., 3201, 10.1128/JB.00333-13
Singh, 2014, Seaweed–microbial interactions: key functions of seaweed-associated bacteria, FEMS Microbiol. Ecol., 88, 213, 10.1111/1574-6941.12297
Walker, 2014, Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, 9, 10.1371/journal.pone.0112963
Wang, 2016, Aquimarina aggregata sp. nov., isolated from seawater, Int. J. Syst. Evol. Microbiol., 66, 3406, 10.1099/ijsem.0.001209
Xu, 2015, Genomic insight into Aquimarina longa SW024 T: its ultra-oligotrophic adapting mechanisms and biogeochemical functions, BMC Genomics, 16, 772, 10.1186/s12864-015-2005-3
Xue, 2001, Biosynthesis and combinatorial biosynthesis of pikromycin-related macrolides in Streptomyces venezuelae, Metab. Eng., 3, 15, 10.1006/mben.2000.0167
Yang, 2012, BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions, Nucleic Acids Res., 41, D1096, 10.1093/nar/gks966
Yang, 2013, Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29, 2588, 10.1093/bioinformatics/btt447
Yi, 2011, Aquimarina addita sp. nov., isolated from seawater, Int. J. Syst. Evol. Microbiol., 61, 2445, 10.1099/ijs.0.027433-0
Yoon, 2011, Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro, Int. J. Syst. Evol. Microbiol., 61, 417, 10.1099/ijs.0.022046-0
Yu, 2013, Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri, Int. J. Syst. Evol. Microbiol., 63, 1235, 10.1099/ijs.0.041509-0
Yu, 2014, Aquimarina megaterium sp. nov., isolated from seawater, Int. J. Syst. Evol. Microbiol., 64, 122, 10.1099/ijs.0.055517-0
Zhang, 2014, Aquimarina pacifica sp. nov., isolated from seawater, Int. J. Syst. Evol. Microbiol., 64, 1991, 10.1099/ijs.0.062695-0
Zhang, 2017, Complete genome sequence analysis of the fish pathogen Flavobacterium columnare provides insights into antibiotic resistance and pathogenicity related genes, Microb. Pathog., 111, 203, 10.1016/j.micpath.2017.08.035