Supplementary table 1- Chromosomes used in the analysis, their estimated optimal doubling time (d) in hours and their size (kb). Not all genes or chromosomes are present for all genomes. This is because some genes are absent from smaller replicons, or because the origin of replication could not be identified reliably (hence they were not used in the analysis), because some genes were not annotated, or finally because their orthology was not reliably assessed.
replicon / size / d / ReferenceAcinetobacter ADP1 / 3598621 / 0,5 / (Parke et al., 2001)
Agrobacterium tumefaciens C58 I / 2841581 / 3 / (Bell, 1990)
Agrobacterium tumefaciens C58 II / 2074782 / 3 / (Bell, 1990)
Azoarcus sp EbN1 / 4296230 / 4,3 / (Chee-Sanford et al., 1996)
Bacillus cereus ATCC 14579 / 5411809 / 0,3 / (Olmez and Aran, 2005)
Bacteroides fragilis
/ 5277274 / 0,63 / (Mangels et al., 1978)Bacillus halodurans
/ 4202352 / 0,6 / (Sturr et al., 1994)Bartonella henselae Houston-1 / 1931047 / 3 / (Chenoweth et al., 2004)
Bacillus licheniformis ATCC14580 / 4222336 / 0,58 / (van Dijk-Salkinoja and Planta, 1971)
Bartonella quintana Toulouse / 1581384 / 3 / (Huang, 1967)
Bacillus subtilis 168 / 4214630 / 0,43 / (Yoshikawa et al., 1964)
Bacteroides thetaiotaomicron VPI-5482 / 6260361 / 1,47 / (Anderson and Salyers, 1989)
Bdellovibrio bacteriovorus
/ 3782950 / 1,4 / (Pritchard et al., 1975)Borrelia burgdorferi
/ 910724 / 4 / (De Silva and Fikrig, 1995)Bordetella pertussis 12822 / 4086189 / 6 / (Frohlich et al., 1995)
Brucella abortus biovar1 9-941 I / 2124241 / 2 / (Hoover and Friedlander, 2005)
Brucella abortus biovar1 9-941 II / 1162204 / 2 / (Hoover and Friedlander, 2005)
Bradyrhizobium japonicum USDA110 / 9105828 / 20 / (Lopez-Garcia et al., 2001)
Brucella melitensis 16M I / 2117144 / 2 / (Gallot-Lavallee et al., 1995)
Brucella melitensis 16M II / 1177787 / 2 / (Gallot-Lavallee et al., 1995)
Brucella suis 1330 I / 2107794 / 2 / (Ekaza et al., 2000)
Brucella suis 1330 II / 1207381 / 2 / (Ekaza et al., 2000)
Buchnera aphidicola Sg / 641454 / 36 / (Baumann et al., 1995)
Burkholderia mallei ATCC23344 / 2325379 / 0,4 / (Personal communication)
Burkholderia pseudomallei K96243 I / 4074542 / 0,7 / (Personal communication)
Burkholderia pseudomallei K96243 II / 3173005 / 0,7 / (Personal communication)
Candidatus Blochmannia floridanus
/ 705557 / 36 / (Holt, 1984)Caulobacter crescentus
/ 4016947 / 1,5 / (Iba et al., 1977)Campylobacter jejuni
/ 1641481 / 1,5 / (Rollins et al., 1983)Chlamydophila abortus S26/3 / 1144377 / 24 / (Holt, 1989)
Chlamydophila caviae GPIC / 1173390 / 24 / (Holt, 1989)
Chlamydia trachomatis M / 1072950 / 24 / (Holt, 1989)
Chlamydophyla pneumoniae A / 1229853 / 24 / (Holt, 1989)
Chlorobium tepidum TLS / 2154946 / 2 / (Frigaard et al., 2004)
Chlamydia trachomatis
/ 1042519 / 24 / (Holt, 1989)Chromobacterium violaceum ATCC12472 / 4751080 / 0,8 / (Bazylinski et al., 1986)
Clostridium acetobutylicum ATCC824 / 3940880 / 0,58 / (Holt, 1986)
Clostridium perfringens 13 / 3031430 / 0,2 / (Bryant and Stevens, 1997)
Coxiella burnetii RSA 493 / 1995275 / 8 / (Heinzen et al., 1999)
Corynebacterium glutamicum
/ 3282708 / 1,2 / (Cocaign-Bousquet et al., 1996)Dehalococcoides ethenogenes 195 / 1469720 / 19 / (Maymo-Gatell et al., 1997)
Desulfotalea psychrophila
/ 3523383 / 0,37 / (Rabus et al., 2005)Desulfovibrio vulgaris Hildenborough / 3570858 / 14 / (Pohorelic et al., 2002)
Enterococcus faecalis V583 / 3218031 / 0,5 / (Sarantinopoulos et al., 2003)
Erwinia carotovora atroseptica SCRI1043 / 5064019 / 0,2 / (Ding et al., 2001)
Escherichia coli MG1655 / 4639675 / 0,35 / (Rubin, 1986)
Fusobacterium nucleatum
/ 2174500 / 0,72 / (Mangels et al., 1978)Geobacter sulfurreducens PCA / 3814139 / 6 / (Cord-Ruwisch et al., 1998)
Gluconobacter oxydans 621H / 2702173 / 1 / (Bonomi et al., 1997)
Haemophilus ducreyi 35000HP / 1698955 / 1,8 / (Trees and Morse, 1995)
Haemophilus influenzae
/ 1830138 / 0,5 / (Rubin, 1986)Helicobacter hepaticus ATCC51449 / 1799146 / 4,2 / (Mehta et al., 2005)
Helicobacter pylori
/ 1667867 / 2,4 / (Vega et al., 2003)Lactobacillus acidophilus NCFM / 1993564 / 1,8 / (Adamberg et al., 2003)
Lactobacillus johnsonii NCC533 / 1992676 / 0,9 / (van der Kaaij et al., 2004)
Lactococcus lactis IL1403 / 2365589 / 0,7 / (Andersen et al., 2001)
Lactobacillus plantarum WCFS1 / 3308274 / 1,6 / (Barcena et al., 1998)
Leptospira interrogans lai 56601 I / 4332241 / 9 / (Shenberg, 1967)
Leptospira interrogans lai 56601 II / 358943 / 9 / (Shenberg, 1967)
Legionella pneumophila Philadelphia 1 / 3397754 / 3,3 / (Saito et al., 1981)
Leifsonia xyli xyli CTCB07 / 2584158 / 5 / (Turner et al., 1991)
Listeria innocua Clip11262 / 3011208 / 0,6 / (Houtsma et al., 1996)
Listeria monocytogenes strain EGD / 2944528 / 1 / (Rubin, 1986)
Mycobacterium avium paratuberculosis k10 / 4829781 / 10 / (Falkinham, 2003)
Mycoplasma gallisepticum R / 996422 / 1 / (Personal communication)
Mycoplasma genitalium
/ 580074 / 12 / (Peterson and Fraser, 2001)Mycobacterium leprae
/ 3268203 / 240 / (Cole et al., 2001)Mycoplasma pneumoniae
/ 816394 / 6 / (Peterson and Fraser, 2001)Mycoplasma pulmonis UAB CTIP / 963879 / 2 / (Lartigue et al., 2003)
Mycobacterium tuberculosis
/ 4411532 / 24 / (Hiriyanna and Ramakrishnan, 1986)Neisseria gonorrhoeae FA1090 / 2153922 / 1,1 / (Morse and Hebeler, 1978)
Neisseria meningitidis A / 2184406 / 1 / (Takahashi et al., 2004)
Nitrosomonas europaea ATCC19718 / 2812094 / 18,5 / (Holt, 1989)
Nocardia farcinica / 6021225 / 3 / (Heinzen and Ensign, 1975)
Pasteurella multocida PM70 / 2257487 / 1 / (Xia et al., 2002)
Parachlamydia sp UWE25 / 2414465 / 48 / (Greub et al., 2003)
Photorhabdus luminescens laumondii TTO1 / 5688987 / 0,5 / (Personal communication)
Photobacterium profundum SS9 I / 4085304 / 2,5 / (Bidle and Bartlett, 1999)
Photobacterium profundum SS9 II / 2237943 / 2,5 / (Bidle and Bartlett, 1999)
Pirellula sp / 7145576 / 10 / (Rabus et al., 2002)
Porphyromonas gingivalis W83 / 2343476 / 2,7 / (Marsh et al., 1994)
Propionibacterium acnes KPA171202 / 2560265 / 5,1 / (Kunishima et al., 2001)
Prochlorococcus marinus CCMP1375 / 1751080 / 17 / (Shalapyonok et al., 1998)
Pseudomonas aeruginosa PA01 / 6264403 / 0,5 / (Rubin, 1986)
Pseudomonas putida KT2440 / 6181863 / 1,1 / (Ahn et al., 1998)
Pseudomonas syringae tomato DC3000 / 6397126 / 1,47 / (Keith et al., 1999)
Ralstonia solanacearum GMI1000 / 3716413 / 4 / (Marangoni et al., 2001)
Rhodopseudomonas palustris
/ 5459213 / 9 / (Oda et al., 2004)Rickettsia conorii Malish 7 / 1268755 / 4,1 / (Oaks and Osterman, 1979)
Rickettsia prowazekii
/ 1111523 / 10 / (Pang and Winkler, 1994)Rickettsia typhi wilmington / 1111496 / 10 / (Higgins et al., 1998)
Salmonella typhimurium LT2 / 4857432 / 0,4 / (Rubin, 1986)
Shewanella oneidensis MR-1 / 4969803 / 0,66 / (Abboud et al., 2005)
Sinorhizobium meliloti 1021 / 3654135 / 1,5 / (Ampe et al., 2003)
Streptococcus agalactiae 2603VR / 2160267 / 1,8 / (Malin and Paoletti, 2001)
Staphylococcus aureus strain N315 / 2814816 / 0,4 / (Somerville et al., 2003)
Streptomyces coelicolor A3(2) / 8667507 / 2,2 / (Shahab et al., 1996)
Staphylococcus epidermidis ATCC 12228 / 2499279 / 0,8 / (Gottenbos et al., 2000)
Streptococcus mutans UA159 / 2030921 / 0,75 / (Shimamoto et al., 1990)
Streptococcus pneumoniae TIGR4 / 2160837 / 0,5 / (Small et al., 1986)
Streptococcus pyogenes M1 / 1852441 / 0,4 / (Biswas et al., 2001)
Streptococcus thermophilus LMG18311 / 1796846 / 0,43 / (O'Sullivan and Fitzgerald, 1999)
Symbiobacterium thermophilum
/ 3566135 / 4,2 / (Ohno et al., 1999)Synechococcus sp WH8102 / 2434428 / 6 / (Mori et al., 1996)
Thermotoga maritima
/ 1860725 / 1,2 / (Chhabra et al., 2002)Thermoanaerobacter tengcongensis
/ 2689445 / 1,1 / (Xue et al., 2001)Thermus thermophilus HB27 / 1894877 / 2,5 / (Demirtas et al., 2003)
Treponema denticola ATCC35405 / 2843201 / 5 / (Dollhopf et al., 2003)
Treponema pallidum
/ 1138011 / 33 / (Cox et al., 1990)Ureaplasma urealyticum
/ 751719 / 0,9 / (Personal communication)Vibrio cholerae I / 2961149 / 0,2 / (Holt, 1984)
Vibrio cholerae II / 1072315 / 0,2 / (Holt, 1984)
Vibrio fischeri ES114 I / 2906179 / 0,3 / (McFall-Ngai, 2000)
Vibrio fischeri ES114 II / 1332022 / 0,3 / (McFall-Ngai, 2000)
Vibrio parahaemolyticus I / 3288558 / 0,2 / (Twedt and Novelli, 1971)
Vibrio parahaemolyticus II / 1877212 / 0,2 / (Twedt and Novelli, 1971)
Vibrio vulnificus CMCP6 I / 3281945 / 0,16 / (Holt, 1984)
Vibrio vulnificus CMCP6 II / 1844853 / 0,16 / (Holt, 1984)
Wolbachia endosymbiont TRS Brugia malayi / 1080084 / 14 / (Fenollar et al., 2003)
Wolinella succinogenes
/ 2110355 / 1 / (Ullmann et al., 2000)Xanthomonas axonopodis
/ 5175554 / 7 / (Wichmann et al., 2005)Xanthomonas campestris
/ 5076188 / 3 / (Pena et al., 2002)Xanthomonas oryzae oryzae KACC10331 / 4941439 / 2 / (Ehrlich et al., 1977)
Xylella fastidiosa 9a5c / 2679306 / 96 / (Leite et al., 2004)
Yersinia pestis CO92 / 4653728 / 1,25 / (Chu, 2001)
Yersinia pseudotuberculosis
/ 4744671 / 0,5 / (Dreyfus and Brubaker, 1978)References:
Abboud, R., Popa, R., Souza-Egipsy, V., Giometti, C.S., Tollaksen, S., Mosher, J.J., et al. (2005) Low-temperature growth of Shewanella oneidensis MR-1. Appl Environ Microbiol 71: 811-816.
Adamberg, K., Kask, S., Laht, T.M., and Paalme, T. (2003) The effect of temperature and pH on the growth of lactic acid bacteria: a pH-auxostat study. Int J Food Microbiol 85: 171-183.
Ahn, I.S., Ghiorse, W.C., Lion, L.W., and Shuler, M.L. (1998) Growth kinetics of Pseudomonas putida G7 on naphthalene and occurrence of naphthalene toxicity during nutrient deprivation. Biotechnol Bioeng 59: 587-594.
Ampe, F., Kiss, E., Sabourdy, F., and Batut, J. (2003) Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biol 4: R15.
Andersen, H.W., Solem, C., Hammer, K., and Jensen, P.R. (2001) Twofold reduction of phosphofructokinase activity in Lactococcus lactis results in strong decreases in growth rate and in glycolytic flux. J Bacteriol 183: 3458-3467.
Anderson, K.L., and Salyers, A.A. (1989) Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 171: 3199-3204.
Barcena, J.M., Sineriz, F., Gonzalez de Llano, D., Rodriguez, A., and Suarez, J.E. (1998) Chemostat production of plantaricin C by Lactobacillus plantarum LL441. Appl Environ Microbiol 64: 3512-3514.
Baumann, P., Baumann, L., Lai, C.-H., and Rouhbakhsh, D. (1995) Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Annu Rev Microbiol 49: 55-94.
Bazylinski, D.A., Palome, E., Blakemore, N.A., and Blakemore, R.P. (1986) Denitrification by Chromobacterium violaceum. Appl Environ Microbiol 52: 696-699.
Bell, C.R. (1990) Growth of Agrobacterium tumefaciens under octopine limitation in chemostats. Appl Environ Microbiol 56: 1775-1781.
Bidle, K.A., and Bartlett, D.H. (1999) RecD function is required for high-pressure growth of a deep-sea bacterium. J Bacteriol 181: 2330-2337.
Biswas, I., Germon, P., McDade, K., and Scott, J.R. (2001) Generation and surface localization of intact M protein in Streptococcus pyogenes are dependent on sagA. Infect Immun 69: 7029-7038.
Bonomi, A., Fleury, A.T., Augusto, E.F.P., Mattos, M.N., and Magossi, L.R. (1997) Mathematical modeling, automation and control of the bioconversion of sorbitol to sorbose in the vitamic C production process. I. Mathematical modeling. Braz J Chem Eng 14: ISSN 0104-6632.
Bryant, A.E., and Stevens, D.L. (1997) The pathogenesis of gas gangrene. In The clostridia: molecular biology and pathogenesis. Rood, J.I. (ed). San Diego: Academic Press, pp. 185-196.
Chee-Sanford, J.C., Frost, J.W., Fries, M.R., Zhou, J., and Tiedje, J.M. (1996) Evidence for acetyl coenzyme A and cinnamoyl coenzyme A in the anaerobic toluene mineralization pathway in Azoarcus tolulyticus Tol-4. Appl Environ Microbiol 62: 964-973.
Chenoweth, M.R., Somerville, G.A., Krause, D.C., O'Reilly, K.L., and Gherardini, F.C. (2004) Growth characteristics of Bartonella henselae in a novel liquid medium: primary isolation, growth-phase-dependent phage induction, and metabolic studies. Appl Environ Microbiol 70: 656-663.
Chhabra, S.R., Shockley, K.R., Ward, D.E., and Kelly, R.M. (2002) Regulation of endo-acting glycosyl hydrolases in the hyperthermophilic bacterium Thermotoga maritima grown on glucan- and mannan-based polysaccharides. Appl Environ Microbiol 68: 545-554.
Chu, M. (2001) Basic laboratory protocols for the presumptive identification of Yersinia pestis. Atlanta: CDC, pp. 1-19.
Cocaign-Bousquet, M., Guyonvarch, A., Lindley, N.D., GUYONVARCH, A., and Lindley, N.D. (1996) Growth Rate-Dependent Modulation of Carbon Flux through Central Metabolism and the Kinetic Consequences for Glucose-Limited Chemostat Cultures of Corynebacterium glutamicum. Appl Environ Microbiol 62: 429-436.
Cole, S.T., Eiglmeier, K., Parkhill, J., James, K.D., Thomson, N.R., Wheeler, P.R., et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409: 1007-1011.
Cord-Ruwisch, R., Lovley, D.R., and Schink, B. (1998) Growth of geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. Appl Environ Microbiol 64: 2232-2236.
Cox, D.L., Riley, B., Chang, P., Sayahtaheri, S., Tassell, S., and Hevelone, J. (1990) Effects of molecular oxygen, oxidation-reduction potential, and antioxidants upon in vitro replication of Treponema pallidum subsp. pallidum. Appl Environ Microbiol 56: 3063-3072.
De Silva, A.M., and Fikrig, E. (1995) Growth and migration of Borrelia burgdorferi in Ixodes ticks during blood feeding. Am J Trop Med Hyg 53: 397-404.
Demirtas, M.U., Kolhatkar, A., and Kilbane, J.J., 2nd (2003) Effect of aeration and agitation on growth rate of Thermus thermophilus in batch mode. J Biosci Bioeng 95: 113-117.
Ding, F., Noritomi, H., and Nagahama, K. (2001) Optimization of Fermentation Conditions for Preparation of Polygalacturonic Acid Transeliminase by Erwinia carotovora IFO3830. Biotechnol Prog 17: 311-317.
Dollhopf, S.L., Pariseau, M.L., Hashsham, S.A., and Tiedje, J.M. (2003) Competitive and interactions affecting a fermentative spirochete in anaerobic chemostats. Microb Ecol 46: 1-11.
Dreyfus, L.A., and Brubaker, R.R. (1978) Consequences of aspartase deficiency in Yersinia pestis. J Bacteriol 136: 757-764.
Ehrlich, M., Lin, F.H., Ehrlich, K., Brown, S.L., and Mayo, J.A. (1977) Changes in macromolecular synthesis in Xanthomonas oryzae infected with bacteriophage XP-12. J Virol 23: 517-523.
Ekaza, E., Guilloteau, L., Teyssier, J., Liautard, J.P., and Kohler, S. (2000) Functional analysis of the ClpATPase ClpA of Brucella suis, and persistence of a knockout mutant in BALB/c mice. Microbiology 146: 1605-1616.