The Open Systems Biology Journal, 2009, 2, 1-7 1 Open Access Ureaplasma Urease Genes have Undergone a Unique Evolutionary Process Hiromi Nishida* Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1- 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan Abstract: Ureaplasma, a member of mycoplasmas, has a unique ATP synthesis system, which is coupled to the urea hy- drolysis. Urease catalyzes the hydrolysis of urea into carbon dioxide and ammonia. Phylogenetic analyses of the urease genes indicated that Ureaplasma urease genes were not gained by recent horizontal transfer and have a unique evolution- ary process. Ureaplasma unique ATP synthesis system leaded to breakdown of the glycolysis pathway. Some glycolytic genes are absent and some glycolytic genes are evolving under relaxed selection in Ureaplasma. Probably glycolytic genes can be used as an indicator of ATP synthesis system. Thus, the organisms that have incomplete glycolysis pathway or glycolytic genes evolving under relaxed selection would have an ATP synthesis system independently of the glycolysis. Mycoplasmas are widespread in nature as parasites of is coupled to ATP synthesis in Ureaplasma [9]. This unique mammals, reptiles, fishes, arthropods, and plants [1]. During system of Ureaplasma leaded to breakdown of the glycolysis the mycoplasma evolution, gene loss has occurred fre- pathway. For example, Ureaplasma does not have any genes quently, resulting in very small genome size [1-3]. The re- encoding glucose-6-phosphate isomerae [10]. It suggests that ductive evolution of mycoplasmas is still in progress. The the glycolysis system had been important for ATP synthesis genus Ureaplasma is a member of mycoplasmas, which gen- rather than glucose metabolism at least in Ureaplasma (Fig. erates 95% of its ATP using the hydrolysis of urea [4]. 1). Generally the TCA (tricarboxylic acid) cycle is linked to Growth of Ureaplasma is dependent on urea [5]. This unique the glycolysis pathway, which has played an important role ATP synthesis is not found in the other mycoplasmas. In in ATP synthesis of many organisms and conserved in the fact, key enzymes in the glycolytic pathway are absent in course of evolution. On the other hand, the urea hydrolysis is Ureaplasma [6]. In addition, some glycolytic genes of Urea- not linked to the glycolysis pathway. Ureaplasma generates plasma are evolving under relaxed selection [7, 8]. Thus, the ATP through the urea hydrolysis not through the glycolysis. glycolysis pathway is collapsing in Ureaplasma. Probably Ureaplasma glycolysis pathway was not able to be PAST SYSTEM Urea hydrolysis Glycolysis ATP synthesis Urea hydrolysis ATP synthesis Glycolysis ATP synthesis PRESENT SYSTEM Urea hydrolysis ATP synthesis Glycolysis Fig. (1). Model of change of ATP synthesis system in Ureaplasma . In Ureaplasma, the ATP synthesis through the glycolysis had been changed to that through the urea hydrolysis. The glycolysis pathway was broken after the urea hydrolysis was coupled to ATP synthesis. Urea is hydrolyzed into carbon dioxide and ammonia in broken before the urea hydrolysis was coupled to ATP syn- many organisms. However, it is unique that the urea hydrolysis thesis. Therefore, after the coupling of the urea hydrolysis and ATP synthesis, dominant ATP synthesis had been *Address correspondence to this author at the Agricultural Bioinformatics changed from through the glycolysis to through the urea hy- Research Unit, Graduate School of Agricultural and Life Sciences, The drolysis during the Ureaplasma evolution (Fig. 1). University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; E-mail: [email protected] 1876-3928/09 2009 Bentham Open 2 The Open Systems Biology Journal, 2009, Volume 2 Hiromi Nishida (A) Rhizobium leguminosarum WSM 2304 88 Rhizobium etli CIAT 652 66 Rhizobium leguminosarum 3841 63 Rhizobium etli CFN 42 Agrobacterium tumefaciens C58 Cereon 22 99 Agrobacterium tumefaciens U.W./Dupont Bradyrhizobium japonicum USDA 110 26 15 Sinorhizobium meliloti 1021 14 99 Sinorhizobium medicae WSM 419 Alphaproteobacteria 10 Mesorhizobium sp. BNC 1 Beijerinckia indica ATCC 9039 54 Jannaschia sp. CCS 1 83 Silicibacter pomeroyi DSS-3 95 Silicibacter sp. TM 1040 26 Dinoroseobacter shibae DFL 12 65 Rhodobacter sphaeroides ATCC 17025 Methylobacterium radiotolerans JCM 2831 Saccharopolyspora erythraea NRRL 2338 Actinobacteria Ureaplasma urealyticum ATCC 33699 42 100 Ureaplasma parvum ATCC 700970 Firmicutes 99 Ureaplasma parvum ATCC 27815 100 Mycobacterium marinum M 85 Mycobacterium ulcerans Agy 99 82 Nocardia farcinica IFM 10152 Actinobacteria 88 Rhodococcus sp. RHA 1 Streptomyces avermitilis MA-4680 37 100 Bordetella bronchiseptica RB 50 Bordetella parapertussis 12822 Betaproteobacteria 88 Shewanella halifaxensis HAW-EB4 Vibrio fischeri MJ 11 95 Gammaproteobacteria 100 Vibrio fischeri ES 114 0.05 (B) Nocardia farcinica IFM 10152 Rhodococcus sp. RHA 1 Streptomyces avermitilis MA-4680 Shewanella halifaxensis HAW-EB4 89 Vibrio fischeri ES 114 72 93 100 Vibrio fischeri MJ 11 Bordetella parapertussis 12822 100 Bordetella bronchiseptica RB 50 Saccharopolyspora erythraea NRRL 2338 47 Ureaplasma urealyticum ATCC 33699 100 100 Ureaplasma parvum ATCC 27815 75 Ureaplasma parvum ATCC 700970 52 Methylobacterium radiotolerans JCM 2831 Beijerinckia indica ATCC 9039 Bradyrhizobium japonicum USDA 110 12 23 Sinorhizobium medicae WSM 419 24 64 27 Sinorhizobium meliloti 1021 24 Mesorhizobium sp. BNC 1 66 Rhizobium etli CFN 42 39 23 Rhizobium leguminosarum WSM 2304 29 67 Rhizobium etli CIAT 652 53 31 Rhizobium leguminosarum 3841 70 Agrobacterium tumefaciens C58 Cereon 100 Agrobacterium tumefaciens U.W./Dupont Jannaschia sp. CCS 1 47 Rhodobacter sphaeroides ATCC 17025 63 Dinoroseobacter shibae DFL 12 83 Silicibacter pomeroyi DSS-3 Silicibacter sp. TM 1040 99 Mycobacterium ulcerans Agy 99 Mycobacterium marinum M Fig. (2). Phylogenetic relationships among Ureaplasma UreA and the homologues. (A) Neighbo r-joining tree. The BLAST program was used to search the GenomeNet website for proteins homologous to Ureaplasma UreA with E-value < 10-23. Ureaplasma UreA and 30 homologous proteins were multiple aligned using the CLUSTAL W program. Phylogenetic tree was recon- structed, based on the multiple-alignment with complete deletion of gap sites using the neighbor-joining method of MEGA software with 1000 bootstrap replicates. (B) Maximum likelihood tree. Phylogenetic tree was reconstructed using the maximum likelihood method of the PHYLIP program with 100 bootstrap replicates. The JTT model was used as the model of amino acid substitution. Number of times to jumble in the PROML program was 2. Ureaplasma Unique ATP Synthesis System The Open Systems Biology Journal, 2009, Volume 2 3 Staphylococcus aureus MSSA 476 (A) Staphylococcus aureus JH 1 Staphylococcus aureus MRSA 252 Staphylococcus aureus MW 2 Staphylococcus aureus Newman Staphylococcus aureus NCTC 8325 100 Staphylococcus aureus COL Staphylococcus aureus N 315 Firmicutes Staphylococcus aureus JH 9 Staphylococcus aureus Mu 3 97 Staphylococcus aureus Mu 50 Staphylococcus aureus TCH 1516 Staphylococcus aureus RF 122 Staphylococcus aureus USA 300 15 Staphylococcus saprophyticus ATCC 15305 21 Microcystis aeruginosa NIES-843 Synechocystis sp. PCC 6803 100 Anabaena sp. PCC 7120 74 23 Anabaena variabilis ATCC 29413 Nostoc punctiforme PCC 73102 47 Trichodesmium erythraeum IMS 101 Cyanobacteria 5 Synechococcus sp. PCC 7002 10 Prochlorococcus marinus MED 4 90 Prochlorococcus marinus MIT 9215 99 Prochlorococcus marinus MIT 9312 Methylobacillus flagellatus KT Betaproteobacteria 52 Methylobacterium populi BJ 001 Alphaproteobacteria 27 Arthrobacter aurescens TC 1 Corynebacterium urealyticum DSM 7109 Actinobacteria 21 Helicobacter acinonychis Sheeba Epsilomproteobacteria Ureaplasma urealyticum ATCC 33699 21 Ureaplasma parvum ATCC 700970 100 Firmicutes 95 Ureaplasma parvum ATCC 27815 0.05 (B) Ureaplasma urealyticum ATCC 33699 Ureaplasma parvum ATCC 27815 Ureaplasma parvum ATCC 700970 Staphylococcus saprophyticus ATCC 15305 Staphylococcus aureus Mu 3 2 Staphylococcus aureus JH 9 92 Staphylococcus aureus MW 2 100 Staphylococcus aureus Newman Staphylococcus aureus N 315 100 4 Staphylococcus aureus JH 1 3 Staphylococcus aureus RF 122 Staphylococcus aureus USA 300 Staphylococcus aureus Mu 50 50 2 Staphylococcus aureus MSSA 476 11 3 Staphylococcus aureus COL 36 Staphylococcus aureus MRSA 252 4 Staphylococcus aureus NCTC 8325 Staphylococcus aureus TCH 1516 Synechocystis sp. PCC 6803 Synechococcus sp. PCC 7002 9 38 Prochlorococcus marinus MED 4 98 Prochlorococcus marinus MIT 9312 13 59 Prochlorococcus marinus MIT 9215 26 20 Microcystis aeruginosa NIES-843 100 Trichodesmium erythraeum IMS 101 Nostoc punctiforme PCC 73102 22 52 Anabaena variabilis ATCC 29413 91 Anabaena sp. PCC 7120 51 Methylobacterium populi BJ 001 Methylobacillus flagellatus KT Arthrobacter aurescens TC 1 45 Corynebacterium urealyticum DSM 7109 48 Helicobacter acinonychis Sheeba Fig. (3). Phylogenetic relationships among Ureaplasma UreB and the homologues. (A) Neighbor-joining tree. The BLAST program was used to search the GenomeNet website for proteins homologous to Ureaplasma UreB with E-value < 10-25. Ureaplasma UreA and 32 ho- mologous proteins were multiple aligned using the CLUSTAL W program. Phylogenetic tree was reconstructed, based on the multiple- alignment with complete deletion of gap sites using the neighbor-joining method of MEGA software with 1000 bootstrap replicates. (B) Maximum likelihood tree.