Insights into the evolution of sialic acid catabolism among bacteria

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Almagro Moreno, Salvador ^a,b   Boyd, E Fidelma ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

EPIMERASE; LYASE; N ACETYLNEURAMINE EPIMERASE; N ACETYLNEURAMINE KINASE; N ACETYLNEURAMINE LYASE; PHOSPHOTRANSFERASE; RNA 16S; SIALIC ACID; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; COTRANSPORTER; N ACETYLNEURAMINIC ACID; ORGANIC ANION TRANSPORTER; SIALIC ACID TRANSPORT PROTEINS;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL COLONIZATION; BACTEROIDETES; CATABOLISM; GENE CLUSTER; GENE TRANSFER; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; INTESTINE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; SALMONELLA ENTERICA; VIBRIO CHOLERAE; VIBRIO VULNIFICUS; YERSINIA; YERSINIA ENTEROCOLITICA; YERSINIA PESTIS; BACTERIUM; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; MULTIGENE FAMILY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); BACTEROIDETES; EUKARYOTA; MAMMALIA; NEGIBACTERIA; POSIBACTERIA; SALMONELLA ENTERICA; VERRUCOMICROBIA; VIBRIO; VIBRIO CHOLERAE; VIBRIO VULNIFICUS; YERSINIA; YERSINIA ENTEROCOLITICA; YERSINIA PESTIS;

BACTERIA; BACTERIAL PROTEINS; BASE COMPOSITION; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; MULTIGENE FAMILY; N-ACETYLNEURAMINIC ACID; ORGANIC ANION TRANSPORTERS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYMPORTERS;

EID: 67449122992     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-118     Document Type: Article

References (60)

1. Diversity of microbial sialic acid metabolism. ER Vimr KA Kalivoda EL Deszo SM Steenbergen, Microbiol Mol Biol Rev 2004 68 1 132 153 15007099 10.1128/MMBR.68.1.132-153.2004
2. Chemical diversity in the sialic acids and related alpha-keto acids: an evolutionary perspective. T Angata A Varki, Chem Rev 2002 102 2 439 469 10.1021/cr000407m 11841250
3. Sialic acid utilization by bacterial pathogens. E Severi DW Hood GH Thomas, Microbiology 2007 153 Pt 9 2817 2822 10.1099/mic.0.2007/009480-0 17768226
4. Bound Carbohydrates in Nature. L Warren, Cambridge University press 1994
5. Achievements and challenges of sialic acid research. R Schauer, Glycoconj J 2000 17 79 485 499 10.1023/A:1011062223612 11421344
6. Biological roles of oligosaccharides: all of the theories are correct. A Varki, Glycobiology 1993 3 2 97 130 10.1093/glycob/3.2.97 8490246 (Pubitemid 23132602)
7. Sialylation is essential for early development in mice. M Schwarzkopf KP Knobeloch E Rohde S Hinderlich N Wiechens L Lucka I Horak W Reutter R Horstkorte, Proc Natl Acad Sci USA 2002 99 8 5267 5270 11929971 10.1073/pnas.072066199
8. The presence of N-acetylneuraminic acid in Malpighian tubules of larvae of the cicada Philaenus spumarius. YN Malykh B Krisch R Gerardy-Schahn EB Lapina L Shaw R Schauer, Glycoconj J 1999 16 11 731 739 10.1023/A:1007115627708 11003558
9. Occurrence of sialic acids in Drosophila melanogaster. J Roth A Kempf G Reuter R Schauer WJ Gehring, Science 1992 256 5057 673 675 10.1126/science. 1585182 1585182
10. Occurrence of gangliosides in the common squid and pacific octopus among protostomia. M Saito H Kitamura K Sugiyama, Biochim Biophys Acta 2001 1511 2 271 280 10.1016/S0005-2736(01)00282-6 11286970
11. Sialic acids in fungi: a minireview. CS Alviano LR Travassos R Schauer, Glycoconj J 1999 16 9 545 554 10.1023/A:1007078106280 10815991
12. The surface trans-sialidase family of Trypanosoma cruzi. GA Cross GB Takle, Annu Rev Microbiol 1993 47 385 411 10.1146/annurev.mi.47.100193.002125 8257103
13. The occurrence of N-acetyl- and N-glycoloylneuraminic acid in Trypanosoma cruzi. R Schauer G Reuter H Muhlpfordt AF Andrade ME Pereira, Hoppe Seylers Z Physiol Chem 1983 364 8 1053 1057 6354906
14. Cytidine 5'-monophospho-N-acetyl neuraminic acid and a low molecular weight factor from human blood cells induce lipopolysaccharide alteration in gonococci when conferring resistance to killing by human serum. NJ Parsons PV Patel EL Tan JR Andrade CA Nairn M Goldner JA Cole H Smith, Microb Pathog 1988 5 4 303 309 10.1016/0882-4010(88)90103-9 3148816
15. Sialic acid metabolism's dual function in Haemophilus influenzae. E Vimr C Lichtensteiger S Steenbergen, Mol Microbiol 2000 36 5 1113 1123 10.1046/j.1365-2958.2000.01925.x 10844695
16. Biosynthesis of the polysialic acid capsule in Escherichia coli K1. E Vimr S Steenbergen M Cieslewicz, J Ind Microbiol 1995 15 4 352 360 10.1007/BF01569991 8605072
17. Role of lipopolysaccharide sialylation in serum resistance of serogroup B and C meningococcal disease isolates. U Vogel H Claus G Heinze M Frosch, Infect Immun 1999 67 2 954 957 9916114 (Pubitemid 29059242)
18. Carbon nutrition of Escherichia coli in the mouse intestine. DE Chang DJ Smalley DL Tucker MP Leatham WE Norris SJ Stevenson AB Anderson JE Grissom DC Laux PS Cohen, Proc Natl Acad Sci USA 2004 101 19 7427 7432 15123798 10.1073/pnas.0307888101
19. Derived structure of the putative sialic acid transporter from Escherichia coli predicts a novel sugar permease domain. J Martinez S Steenbergen E Vimr, J Bacteriol 1995 177 20 6005 6010 7592358
20. Sialic acids: their analysis and enzymic modification in relation to the synthesis of submandibular-gland glycoproteins. R Schauer HP Buscher J Casals-Stenzel, Biochem Soc Symp 1974 40 87 116 4620387
21. Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. E Severi G Randle P Kivlin K Whitfield R Young R Moxon D Kelly D Hood GH Thomas, Mol Microbiol 2005 58 4 1173 1185 10.1111/j.1365-2958.2005.04901.x 16262798
22. Sialic Acid metabolism and systemic pasteurellosis. SM Steenbergen CA Lichtensteiger R Caughlan J Garfinkle TE Fuller ER Vimr, Infect Immun 2005 73 3 1284 1294 15731025 10.1128/IAI.73.3.1284-1294.2005
23. Sialic Acid (N-acetyl Neuraminic Acid or NANA) Utilization by Bacteroides fragilis Requires A Novel N-acetyl Mannosamine (manNAc) Epimerase. C Brigham R Caughlan R Gallegos MB Dallas VG Godoy MH Malamy, J Bacteriol 2009 191 11 3629 38 10.1128/JB.00811-08 19304853
24. The sialic acids. I. The structure and enzymatic synthesis of N-acetylneuraminic acid. DG Comb S Roseman, J Biol Chem 1960 235 2529 2537 13811398
25. Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli. J Plumbridge E Vimr, J Bacteriol 1999 181 1 47 54 9864311 (Pubitemid 29013652)
26. The first committed step in the biosynthesis of sialic acid by Escherichia coli K1 does not involve a phosphorylated N-acetylmannosamine intermediate. MA Ringenberg SM Steenbergen ER Vimr, Mol Microbiol 2003 50 3 961 975 10.1046/j.1365-2958.2003.03741.x 14617154
27. Regulation of sialic acid metabolism in Escherichia coli: role of N-acylneuraminate pyruvate-lyase. ER Vimr FA Troy, J Bacteriol 1985 164 2 854 860 3902800 (Pubitemid 16191862)
28. Identification of an inducible catabolic system for sialic acids (nan) in Escherichia coli. ER Vimr FA Troy, J Bacteriol 1985 164 2 845 853 3902799 (Pubitemid 16191861)
29. Purification and characterization of N-acetylneuraminate lyase from Clostridium perfringens. S Nees R Schauer F Mayer, Hoppe Seylers Z Physiol Chem 1976 357 6 839 853 182637
30. Genomics. Are there bugs in our genome? JO Andersson WF Doolittle CL Nesbo, Science 2001 292 5523 1848 1850 10.1126/science.1062241 11358998
31. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. AP de Koning FS Brinkman SJ Jones PJ Keeling, Mol Biol Evol 2000 17 11 1769 1773 11070064 (Pubitemid 30809696)
32. The complete genome sequence of Escherichia coli K-12. FR Blattner G Plunkett 3rd CA Bloch NT Perna V Burland M Riley J Collado-Vides JD Glasner CK Rode GF Mayhew, Science 1997 277 5331 1453 1474 10.1126/science.277.5331.1453 9278503
33. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. JF Heidelberg JA Eisen WC Nelson RA Clayton ML Gwinn RJ Dodson DH Haft EK Hickey JD Peterson L Umayam, Nature 2000 406 6795 477 483 10.1038/35020000 10952301
34. Haemophilus ducreyi strain ATCC 27722 contains a genetic element with homology to the vibrio RS1 element that can replicate as a plasmid and confer NAD independence on haemophilus influenzae. RS Munson Jr H Zhong R Mungur WC Ray RJ Shea GG Mahairas MH Mulks, Infect Immun 2004 72 2 1143 1146 14742562 10.1128/IAI.72.2.1143-1146.2004
35. Clustal W and Clustal X version 2.0. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez, Bioinformatics 2007 23 21 2947 2948 10.1093/bioinformatics/btm404 17846036
36. GeneDoc: Analysis and Visualization of Genetic Variation. KBNH Nicholas DW Deerfield, EMBNEW 1997
37. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 9 817 818 10.1093/bioinformatics/14.9.817 9918953 (Pubitemid 28552116)
38. A new method for calculating evolutionary substitution rates. C Lanave G Preparata C Saccone G Serio, J Mol Evol 1984 20 1 86 93 10.1007/BF02101990 6429346 (Pubitemid 14116237)
39. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. N Goldman S Whelan, Mol Biol Evol 2000 17 6 975 978 10833204 (Pubitemid 30346557)
40. Mathematics vs. Evolution: Mathematical Evolutionary Theory. J Felsenstein, Science 1989 246 4932 941 942 10.1126/science.246.4932.941 17812579
41. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 8 754 755 10.1093/bioinformatics/17.8.754 11524383 (Pubitemid 32851390)
42. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
43. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738
44. Application of phylogenetic networks in evolutionary studies. DH Huson D Bryant, Mol Biol Evol 2006 23 2 254 267 10.1093/molbev/msj030 16221896
45. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. S Karlin, Trends Microbiol 2001 9 7 335 343 10.1016/S0966-842X(01)02079-0 11435108
46. Interconversion of Purine Mononucleotides in Pasteurella pestis. RR Brubaker, Infect Immun 1970 1 5 446 454 16557756
47. Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. T Kuwahara A Yamashita H Hirakawa H Nakayama H Toh N Okada S Kuhara M Hattori T Hayashi Y Ohnishi, Proc Natl Acad Sci USA 2004 101 41 14919 14924 15466707 10.1073/pnas.0404172101
48. Identification of a novel sialic acid transporter in Haemophilus ducreyi. DM Post R Mungur BW Gibson RS Munson Jr, Infect Immun 2005 73 10 6727 6735 16177350 10.1128/IAI.73.10.6727-6735.2005
49. To sialylate, or not to sialylate: that is the question. E Vimr C Lichtensteiger, Trends Microbiol 2002 10 6 254 257 10.1016/S0966-842X(02)02361-2 12088651
50. The origin and evolution of operons: the piecewise building of the proteobacterial histidine operon. R Fani M Brilli P Lio, J Mol Evol 2005 60 3 378 390 10.1007/s00239-004-0198-1 15871048
51. Selfish operons: horizontal transfer may drive the evolution of gene clusters. JG Lawrence JR Roth, Genetics 1996 143 4 1843 1860 8844169 (Pubitemid 26286959)
52. The universal ancestor. C Woese, Proc Natl Acad Sci USA 1998 95 12 6854 6859 9618502 10.1073/pnas.95.12.6854
53. Conservation of gene order: a fingerprint of proteins that physically interact. T Dandekar B Snel M Huynen P Bork, Trends Biochem Sci 1998 23 9 324 328 10.1016/S0968-0004(98)01274-2 9787636
54. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. T Itoh K Takemoto H Mori T Gojobori, Mol Biol Evol 1999 16 3 332 346 10331260 (Pubitemid 29119970)
55. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. MV Omelchenko KS Makarova YI Wolf IB Rogozin EV Koonin, Genome Biol 2003 4 9 R55 12952534 10.1186/gb-2003-4-9-r55
56. Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates. WS Jermyn EF Boyd, Microbiology 2002 148 Pt 11 3681 3693 12427958 (Pubitemid 35414477)
57. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. AT Vasconcelos HB Ferreira CV Bizarro SL Bonatto MO Carvalho PM Pinto DF Almeida LG Almeida R Almeida L Alves-Filho, J Bacteriol 2005 187 16 5568 5577 16077101 10.1128/JB.187.16.5568-5577.2005
58. The cell cycle of the planctomycete Gemmata obscuriglobus with respect to cell compartmentalization. KC Lee RI Webb JA Fuerst, BMC Cell Biol 2009 10 1 4 19144151 10.1186/1471-2121-10-4
59. Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. KC Lee RI Webb PH Janssen P Sangwan T Romeo JT Staley JA Fuerst, BMC Microbiol 2009 9 1 5 19133117 10.1186/1471-2180-9-5
60. Allen S. Zaleski A. Johnston J.W. Gibson B.W. Apicella M.A., Novel sialic acid transporter of Haemophilus influenzae, Infect Immun, 2005 73 9 5291-5300.