Members of the Burkholderia family occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of available Burkholderia genomes has revealed a core set of 178 glycan-associated proteins shared by all Burkholderia of which 68 are homologous to known essential genes. The genome sequence comparisons revealed insights into species-specific gene acquisitions through gene transfers, identified an S-layer protein, and proposed that significantly reactive surface proteins are associated to sugar moieties as a potential means to circumvent host defense mechanisms. The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of the Burkholderia spp. The curated list of glycan-associated proteins used can also be directed to screen other genomes for glycan-associated homologs. 1. Introduction Members of the genus Burkholderia, with over 30 known species, have a unique ability to occupy diverse ecological niches, ranging from soil to the human respiratory tract [1]. Several strains are known to enhance disease resistance in plants [2] and improve nitrogen fixation [3, 4]. B. pseudomallei, B. mallei and B. cenocepacia are known to be involved in lung infections and are well recognized as pathogens of humans and animals. B. pseudomallei, a soil dwelling member of the Burkholderia genus is the causative agent for melioidosis and is capable of existing as a latent infection for decades with the longest period reported being 62 years [5]. The current use of antimicrobial therapy to treat melioidosis patients often fails due to intrinsic resistance of these bacteria. Prior to the discovery of an RNA helicase inhibitor toxin [6], the pathogenicity and virulence factors associated to B. pseudomallei have been elusive and many reports were inconclusive. Despite this significant progress, much remains to be discovered regarding the virulence of B. pseudomallei and the Burkholderia pathogens in general, including potential roles played by glycan-associated proteins in pathogenesis. The interactions and association between proteins and carbohydrates play important roles in numerous cellular functions, including processes which are associated with the pathogenicity of many bacterial species. Proteins can
References
[1]
T. Coenye and P. Vandamme, “Diversity and significance of Burkholderia species occupying diverse ecological niches,” Environmental Microbiology, vol. 5, no. 9, pp. 719–729, 2003.
[2]
S. Compant, B. Duffy, J. Nowak, C. Clément, and E. A. Barka, “Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects,” Applied and Environmental Microbiology, vol. 71, no. 9, pp. 4951–4959, 2005.
[3]
A. Sessitsch, T. Coenye, A. V. Sturz et al., “Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties,” International Journal of Systematic and Evolutionary Microbiology, vol. 55, no. 3, pp. 1187–1192, 2005.
[4]
E. Ait Barka, J. Nowak, and C. Clément, “Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN,” Applied and Environmental Microbiology, vol. 72, no. 11, pp. 7246–7252, 2006.
[5]
V. Ngauy, Y. Lemeshev, L. Sadkowski, and G. Crawford, “Cutaneous melioidosis in a man who was taken as a prisoner of war by the Japanese during World War II,” Journal of Clinical Microbiology, vol. 43, no. 2, pp. 970–972, 2005.
[6]
A. Cruz-Migoni, G. M. Hautbergue, P. J. Artymiuk, et al., “A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A,” Science, vol. 334, no. 6057, pp. 821–824, 2011.
[7]
C. Steichen, P. Chen, J. F. Kearney, and C. L. Turnbough, “Identification of the immunodominant protein and other proteins of the Bacillus anthracis exosporium,” Journal of Bacteriology, vol. 185, no. 6, pp. 1903–1910, 2003.
[8]
P. Doig, N. Kinsella, P. Guerry, and T. J. Trust, “Characterization of a post-translational modification of Campylobacter flagellin: identification of a sero-specific glycosyl moiety,” Molecular Microbiology, vol. 19, no. 2, pp. 379–387, 1996.
[9]
J. W. McBride, X. J. Yu, and D. H. Walker, “Glycosylation of homologous immunodominant proteins of Ehrlichia chaffeensis and Ehrlichia canis,” Infection and Immunity, vol. 68, no. 1, pp. 13–18, 2000.
[10]
I. Lerouge and J. Vanderleyden, “O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions,” FEMS Microbiology Reviews, vol. 26, no. 1, pp. 17–47, 2002.
[11]
C. Ryder, M. Byrd, and D. J. Wozniak, “Role of polysaccharides in Pseudomonas aeruginosa biofilm development,” Current Opinion in Microbiology, vol. 10, no. 6, pp. 644–648, 2007.
[12]
P. R. Crocker, “Siglecs: sialic-acid-binding immunoglobulin-like lectins in cell-cell interactions and signalling,” Current Opinion in Structural Biology, vol. 12, no. 5, pp. 609–615, 2002.
[13]
A. Weintraub, “Immunology of bacterial polysaccharide antigens,” Carbohydrate Research, vol. 338, no. 23, pp. 2539–2547, 2003.
[14]
J. Adam, M. Pokorná, C. Sabin, E. P. Mitchell, A. Imberty, and M. Wimmerová, “Engineering of PA-IIL lectin from Pseudomonas aeruginosa—unravelling the role of the specificity loop for sugar preference,” BMC Structural Biology, vol. 7, article 36, 2007.
[15]
V. C. Chu and G. R. Whittaker, “Influenza virus entry and infection require host cell N-linked glycoprotein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 52, pp. 18153–18158, 2004.
[16]
G. F. Audette, L. T. J. Delbaere, and J. Xiang, “Mapping protein: carbohydrate interactions,” Current Protein and Peptide Science, vol. 4, no. 1, pp. 11–20, 2003.
[17]
C. Shionyu-Mitsuyama, T. Shirai, H. Ishida, and T. Yamane, “An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins,” Protein Engineering, vol. 16, no. 7, pp. 467–478, 2003.
[18]
M. T. G. Holden, R. W. Titball, S. J. Peacock et al., “Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 39, pp. 14240–14245, 2004.
[19]
W. C. Nierman, D. DeShazer, H. S. Kim et al., “Structural flexibility in the Burkholderia mallei genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 39, pp. 14246–14251, 2004.
[20]
H. S. Kim, M. A. Schell, Y. Yu et al., “Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies,” BMC Genomics, vol. 6, article 174, 2005.
[21]
J. Goris, P. De Vos, J. Caballero-Mellado et al., “Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 5, pp. 1677–1681, 2004.
[22]
A. Copeland, S. Lucas, A. Lapidus, et al., “Complete sequence of chromosome 1 ofBurkholderiaphymatum STM815,” submitted to (APR-2008) to the EMBL/GenBank/DDBJ Database, http://www.ncbi.nlm.nih.gov/nuccore/NC_010622.1.
[23]
Y. Ohtsubo, A. Yamashita, K. Kurokawa, et al., “Complete genome sequence of Burkholderia multivorans ATCC 17616,” submitted to (APR-2007) to the EMBL/GenBank/DDBJ Databases, http://www.ncbi.nlm.nih.gov/nuccore/NC_010804.1.
[24]
A. Copeland, S. Lucas, A. Lapidus, et al., “Complete sequence of chromosome 1 of Burkholderia ambifaria MC40-6,” submitted to (APR-2008) to the EMBL/GenBank/DDBJ Databases, http://www.ncbi.nlm.nih.gov/nuccore/NC_010551.1. In press.
[25]
A. Copeland, S. Lucas, A. Lapidus, Barry, et al., “Complete sequence of chromosome 1 of Burkholderia vietnamiensis G4,” submitted to (MAR-2007) to the EMBL/GenBank/DDBJ Databases, http://www.ncbi.nlm.nih.gov/nuccore/NC_009256.1.
[26]
M. T. G. Holden, H. M. B. Seth-Smith, L. C. Crossman et al., “The Genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients,” Journal of Bacteriology, vol. 191, no. 8, p. 2907, 2009.
[27]
D. Kang, E. S. Ji, M. H. Moon, and J. S. Yoo, “Lectin-based enrichment method for glycoproteomics using hollow fiber flow field-flow fractionation: application to Streptococcus pyogenes,” Journal of Proteome Research, vol. 9, no. 6, pp. 2855–2862, 2010.
[28]
M. González-Zamorano, G. M. Hernández, W. Xolalpa et al., “Mycobacterium tuberculosis glycoproteomics based on ConA-lectin affinity capture of mannosylated proteins,” Journal of Proteome Research, vol. 8, no. 2, pp. 721–733, 2009.
[29]
A. E. Scott, S. M. Twine, K. M. Fulton et al., “Flagellar glycosylation in Burkholderia pseudomallei and Burkholderia thailandensis,” Journal of Bacteriology, vol. 193, no. 14, pp. 3577–3587, 2011.
[30]
B. Boeckmann, A. Bairoch, R. Apweiler et al., “The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003,” Nucleic Acids Research, vol. 31, no. 1, pp. 365–370, 2003.
[31]
H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000.
[32]
A. Malik and S. Ahmad, “Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network,” BMC Structural Biology, vol. 7, article 1, 2007.
[33]
M. Schirm, E. C. Soo, A. J. Aubry, J. Austin, P. Thibault, and S. M. Logan, “Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori,” Molecular Microbiology, vol. 48, no. 6, pp. 1579–1592, 2003.
[34]
M. F. Mescher, J. L. Strominger, and S. W. Watson, “Protein and carbohydrate composition of the cell envelope of Halobacterium salinarium,” Journal of Bacteriology, vol. 120, no. 2, pp. 945–954, 1974.
[35]
S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
[36]
K. Belov, C. E. Sanderson, J. E. Deakin et al., “Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system,” Genome Research, vol. 17, no. 7, pp. 982–991, 2007.
[37]
S. Gopal, M. Schroeder, U. Pieper et al., “Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome,” Nature Genetics, vol. 27, no. 3, pp. 337–340, 2001.
[38]
S. F. Altschul, T. L. Madden, A. A. Sch？ffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
[39]
M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genes and genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30, 2000.
[40]
A. Bateman, L. Coin, R. Durbin et al., “The Pfam protein families database,” Nucleic Acids Research, vol. 32, pp. D138–D141, 2004.
[41]
M. R. Remm, C. E. V. Storm, and E. L. L. Sonnhammer, “Automatic clustering of orthologs and in-paralogs from pairwise species comparisons,” Journal of Molecular Biology, vol. 314, no. 5, pp. 1041–1052, 2001.
[42]
A. Alexeyenko, I. Tamas, G. Liu, and E. L. L. Sonnhammer, “Automatic clustering of orthologs and inparalogs shared by multiple proteomes,” Bioinformatics, vol. 22, no. 14, pp. e9–e15, 2006.
[43]
P. L. Felgner, M. A. Kayala, A. Vigil et al., “A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 32, pp. 13499–13504, 2009.
[44]
R. Tiyawisutsri, M. T. G. Holden, S. Tumapa et al., “Burkholderia Hep_Hap autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis,” BMC Microbiology, vol. 7, article 19, 2007.
[45]
T. J. Carver, K. M. Rutherford, M. Berriman, M. A. Rajandream, B. G. Barrell, and J. Parkhill, “ACT: the Artemis comparison tool,” Bioinformatics, vol. 21, no. 16, pp. 3422–3423, 2005.
[46]
B. Petersen, T. N. Petersen, P. Andersen, M. Nielsen, and C. Lundegaard, “A generic method for assignment of reliability scores applied to solvent accessibility predictions,” BMC Structural Biology, vol. 9, article 51, 2009.
[47]
B. Rost, “Twilight zone of protein sequence alignments,” Protein Engineering, vol. 12, no. 2, pp. 85–94, 1999.
[48]
T. Schwede, “Protein structure modeling,” in Computational Structural Biology Methods and Applications, T. Schwede and M. C. Peitsch, Eds., chapter 1, 2008.
[49]
N. Y. Yu, J. R. Wagner, M. R. Laird et al., “PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes,” Bioinformatics, vol. 26, no. 13, pp. 1608–1615, 2010.
[50]
C. Caragea, J. Sinapov, A. Silvescu, D. Dobbs, and V. Honavar, “Glycosylation site prediction using ensembles of Support Vector Machine classifiers,” BMC Bioinformatics, vol. 8, article 438, 2007.
[51]
E. Gasteiger, A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, and A. Bairoch, “ExPASy: the proteomics server for in-depth protein knowledge and analysis,” Nucleic Acids Research, vol. 31, no. 13, pp. 3784–3788, 2003.
[52]
J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of Molecular Biology, vol. 157, no. 1, pp. 105–132, 1982.
[53]
B. Petersen, T. N. Petersen, P. Andersen, M. Nielsen, and C. Lundegaard, “A generic method for assignment of reliability scores applied to solvent accessibility predictions,” BMC Structural Biology, vol. 9, article 51, 2009.
[54]
J. Garnier, J. F. Gibrat, and B. Robson, “GOR method for predicting protein secondary structure from amino acid sequence,” Methods in Enzymology, vol. 266, pp. 540–553, 1996.
[55]
J. D. Bendtsen, H. Nielsen, G. von Heijne, and S. Brunak, “Improved prediction of signal peptides: signalP 3.0,” Journal of Molecular Biology, vol. 340, no. 4, pp. 783–795, 2004.
[56]
Z. H. Zhang, J. Li, X. Q. Zhao, J. Wang, G. K. S. Wong, and J. Yu, “KaKs_calculator: calculating Ka and Ks through model selection and model averaging,” Genomics, Proteomics and Bioinformatics, vol. 4, no. 4, pp. 259–263, 2006.
[57]
Z. Yang and R. Nielsen, “Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models,” Molecular Biology and Evolution, vol. 17, no. 1, pp. 32–43, 2000.
[58]
U. Dobrindt and J. Hacker, “Whole genome plasticity in pathogenic bacteria,” Current Opinion in Microbiology, vol. 4, no. 5, pp. 550–557, 2001.
[59]
H. Masoud, M. Ho, T. Schollaardt, and M. B. Perry, “Characterization of the capsular polysaccharide of Burkholderia (Pseudomonas) pseudomallei 304b,” Journal of Bacteriology, vol. 179, no. 18, pp. 5663–5669, 1997.
[60]
S. M. Prasad, Y. Yin, E. Rodzinski, E. I. Tuomanen, and H. R. Masure, “Identification of a carbohydrate recognition domain in filamentous hemagglutinin from Bordetella pertussis,” Infection and Immunity, vol. 61, no. 7, pp. 2780–2785, 1993.
[61]
B. M. Q. Sim, N. Chantratita, W. F. Ooi et al., “Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates,” Genome Biology, vol. 11, no. 8, article R89, 2010.
[62]
M. Kuroda, T. Ohta, I. Uchiyama et al., “Whole genome sequencing of meticillin-resistant Staphylococcus aureus,” The Lancet, vol. 357, no. 9264, pp. 1225–1240, 2001.
[63]
H. Ochman, J. G. Lawrence, and E. A. Grolsman, “Lateral gene transfer and the nature of bacterial innovation,” Nature, vol. 405, no. 6784, pp. 299–304, 2000.
[64]
J. G. Lawrence and H. Hendrickson, “Lateral gene transfer: when will adolescence end?” Molecular Microbiology, vol. 50, no. 3, pp. 739–749, 2003.
[65]
B. J. Currie, M. Mayo, N. M. Anstey, P. Donohoe, A. Haase, and D. J. Kemp, “A cluster of melioidosis cases from an endemic region is clonal and is linked to the water supply using molecular typing of Burkholderia pseudomallei isolates,” American Journal of Tropical Medicine and Hygiene, vol. 65, no. 3, pp. 177–179, 2001.
[66]
T. J. J. Inglis, S. C. Garrow, C. Adams, M. Henderson, M. Mayo, and B. J. Currie, “Acute melioidosis outbreak in Western Australia,” Epidemiology and Infection, vol. 123, no. 3, pp. 437–443, 1999.
[67]
T. J. J. Inglis, S. C. Garrow, M. Henderson et al., “Burkholderia pseudomallei traced to water treatment plant in Australia,” Emerging Infectious Diseases, vol. 6, no. 1, pp. 56–59, 2000.
[68]
W. L. Van Veen, E. G. Mulder, and M. H. Deinema, “The Sphaerotilus-Leptothrix group of bacteria,” Microbiological Reviews, vol. 42, no. 2, pp. 329–356, 1978.
[69]
D. D. Roberts, L. D. Olson, M. F. Barile, V. Ginsburg, and H. C. Krivan, “Sialic acid-dependent adhesion of Mycoplasma pneumoniae to purified glycoproteins,” Journal of Biological Chemistry, vol. 264, no. 16, pp. 9289–9293, 1989.
[70]
A. L. Mattos-Guaraldi, L. C. Duarte Formiga, and G. A. Pereira, “Cell surface components and adhesion in corynebacterium diphtheriae,” Microbes and Infection, vol. 2, no. 12, pp. 1507–1512, 2000.
[71]
N. K. Sauter, J. E. Hanson, G. D. Glick et al., “Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography,” Biochemistry, vol. 31, no. 40, pp. 9609–9621, 1992.
[72]
J. E. Peters and R. A. DiCapua, “Immunochemical characterization of Lymantria dispar NPV hemagglutinin: protein-carbohydrate interaction,” Intervirology, vol. 9, no. 4, pp. 231–242, 1978.
[73]
Y. Yu, H. S. Kim, H. C. Hui et al., “Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis,” BMC Microbiology, vol. 6, article 46, 2006.
[74]
H. J. Boot and P. H. Pouwels, “Expression, secretion and antigenic variation of bacterial S-layer proteins,” Molecular Microbiology, vol. 21, no. 6, pp. 1117–1123, 1996.
[75]
M. Sára and U. B. Sleytr, “S-layer proteins,” Journal of Bacteriology, vol. 182, no. 4, pp. 859–868, 2000.
[76]
J. Lannergard, M. C. U. Gustafsson, J. Waldemarsson, A. Norrby-Teglund, M. Stalhammar-Carlemalm, and G. Lindahl, “The hypervariable region of streptococcus pyogenes M protein escapes antibody attack by antigenic variation and weak immunogenicity,” Cell Host & Microbe, vol. 10, no. 2, pp. 147–157, 2011.
[77]
L. E. Comstock and D. L. Kasper, “Bacterial glycans: key mediators of diverse host immune responses,” Cell, vol. 126, no. 5, pp. 847–850, 2006.
[78]
L. Loza, Y. Fu, A. S. Ibrahim, D. C. Sheppard, S. G. Filler, and J. E. Edwards, “Functional analysis of the Candida albicans ALSI gene product,” Yeast, vol. 21, no. 6, pp. 473–482, 2004.
[79]
A. J. Sheets and J. W. S. Geme, “Adhesive activity of the haemophilus cryptic genospecies cha autotransporter is modulated by variation inn tandem peptide repeats,” Journal of Bacteriology, vol. 193, no. 2, pp. 329–339, 2011.
[80]
M. Hussain, A. Haggar, G. Peters et al., “More than one tandem repeat domain of the extracellular adherence protein of Staphylococcus aureus is required for aggregation, adherence, and host cell invasion but not for leukocyte activation,” Infection and Immunity, vol. 76, no. 12, pp. 5615–5623, 2008.
[81]
J. M. Rauceo, R. De Armond, H. Otoo et al., “Threonine-rich repeats increase fibronectin binding in the Candida albicans adhesin Als5p,” Eukaryotic Cell, vol. 5, no. 10, pp. 1664–1673, 2006.
[82]
L. E. Vinall, A. S. Hill, P. Pigny et al., “Variable number tandem repeat polymorphism of the mucin genes located in the complex on 11p15.5,” Human Genetics, vol. 102, no. 3, pp. 357–366, 1998.
[83]
K. Kyo, T. Muto, H. Nagawa, G. M. Lathrop, and Y. Nakamura, “Associations of distinct variants of the intestinal mucin gene MUC3A with ulcerative colitis and Crohn's disease,” Journal of Human Genetics, vol. 46, no. 1, pp. 5–20, 2001.
[84]
S. Kakizawa, K. Oshima, H. Y. Jung et al., “Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas,” Journal of Bacteriology, vol. 188, no. 9, pp. 3424–3428, 2006.
[85]
L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes under positive selection in Escherichia coli,” Genome Research, vol. 17, no. 9, pp. 1336–1343, 2007.
[86]
F. M. Jiggins, G. D. D. Hurst, and Z. Yang, “Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae,” Molecular Biology and Evolution, vol. 19, no. 8, pp. 1341–1349, 2002.
[87]
C. Darwin and A. R. Wallace, “On the tendency of species for form varieties; and on the perpetuation of varieties and species by natural means of selection,” Proceedings of the Linnean Society of London, vol. 3, pp. 45–62, 1858.
