{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:05:58Z","timestamp":1789985158098,"version":"4.0.1"},"reference-count":48,"publisher":"American Society for Microbiology","issue":"23","license":[{"start":{"date-parts":[[2006,12,1]],"date-time":"2006-12-01T00:00:00Z","timestamp":1164931200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Many microbial pathogens express specific virulence traits at distinct growth phases. To understand the molecular pathways linking bacterial growth to pathogenicity, we have characterized the growth transcriptome of\n            <jats:italic>Burkholderia pseudomallei<\/jats:italic>\n            , the causative agent of melioidosis. Using a fine-scale sampling approach, we found approximately 17% of all\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            genes displaying regulated expression during growth in rich medium, occurring as broad waves of functionally coherent gene expression tightly associated with distinct growth phases and transition points. We observed regulation of virulence genes across all growth phases and identified\n            <jats:italic>serC<\/jats:italic>\n            as a potentially new virulence factor by virtue of its coexpression with other early-phase virulence genes.\n            <jats:italic>serC<\/jats:italic>\n            -disrupted\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            strains were serine auxotrophs and in mouse infection assays exhibited a dramatic attenuation of virulence compared to wild-type\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            . Immunization of mice with\n            <jats:italic>serC<\/jats:italic>\n            -disrupted\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            also conferred protection against subsequent challenges with different wild-type\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            strains. At a genomic level, early-phase genes were preferentially localized on chromosome 1, while stationary-phase genes were significantly biased towards chromosome 2. We detected a significant level of chromosomally clustered gene expression, allowing us to predict \u223c100 potential operons in the\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            genome. We computationally and experimentally validated these operons by showing that genes in these regions are preferentially transcribed in the same 5\u2032\u21923\u2032 direction, possess significantly shorter intergenic lengths than the overall genome, and are expressed as a common mRNA transcript. The availability of this transcriptome map provides an important resource for understanding the transcriptional architecture of\n            <jats:italic>B. pseudomallei<\/jats:italic>\n            .\n          <\/jats:p>","DOI":"10.1128\/jb.01006-06","type":"journal-article","created":{"date-parts":[[2006,11,16]],"date-time":"2006-11-16T03:29:02Z","timestamp":1163647742000},"page":"8178-8188","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":35,"title":["Global Map of Growth-Regulated Gene Expression in\n            <i>Burkholderia pseudomallei<\/i>\n            , the Causative Agent of Melioidosis"],"prefix":"10.1128","volume":"188","author":[{"given":"Fiona","family":"Rodrigues","sequence":"first","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitali","family":"Sarkar-Tyson","sequence":"additional","affiliation":[{"name":"Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 OJQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah V.","family":"Harding","sequence":"additional","affiliation":[{"name":"Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 OJQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siew Hoon","family":"Sim","sequence":"additional","affiliation":[{"name":"Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, no. 13-14, Singapore 117510, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui Hoon","family":"Chua","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi Ho","family":"Lin","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Han","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. Krishna M.","family":"Karuturi","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Sung","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kun","family":"Yu","sequence":"additional","affiliation":[{"name":"National Cancer Centre, 11 Hospital Drive, Singapore 169610, Republic of Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Agenica Research"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy P.","family":"Atkins","sequence":"additional","affiliation":[{"name":"Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 OJQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard W.","family":"Titball","sequence":"additional","affiliation":[{"name":"Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 OJQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Tan","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, 60 Biopolis Street, no. 02-01, Genome, Singapore 138672, Republic of Singapore"},{"name":"Agenica Research"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/CDLI.5.2.225-229.1998"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.70.9.5290-5294.2002"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.72.5.2468-2476.2004"},{"key":"e_1_3_2_5_2","doi-asserted-by":"crossref","first-page":"E5","DOI":"10.1371\/journal.pbio.0000005","volume":"1","year":"2003","unstructured":"Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, and J. L. DeRisi. 2003. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS. Biol. 1 : E5.","journal-title":"PLoS. Biol."},{"key":"e_1_3_2_6_2","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1093\/nar\/gkh510","volume":"32","year":"2004","unstructured":"Chen, X., Z. Su, P. Dam, B. Palenik, Y. Xu, and T. Jiang. 2004. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res. 32 : 2147-2157.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.18.2.383-416.2005"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.71.4.1622-1629.2003"},{"key":"e_1_3_2_9_2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1080\/01621459.1979.10481038","volume":"74","year":"1979","unstructured":"Cleveland, W. S. 1979. Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74 : 829-836.","journal-title":"J. Am. Stat. Assoc."},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1998.01139.x"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.170.9.3991-3995.1988"},{"key":"e_1_3_2_12_2","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","year":"1998","unstructured":"Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95 : 14863-14868.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.7.4398-4406.2001"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.163.1.355-361.1985"},{"key":"e_1_3_2_15_2","doi-asserted-by":"crossref","first-page":"14240","DOI":"10.1073\/pnas.0403302101","volume":"101","year":"2004","unstructured":"Holden, M. T., R. W. Titball, S. J. Peacock, A. M. Cerdeno-Tarraga, T. Atkins, L. C. Crossman, T. Pitt, C. Churcher, K. Mungall, S. D. Bentley, M. Sebaihia, N. R. Thomson, N. Bason, I. R. Beacham, K. Brooks, K. A. Brown, N. F. Brown, G. L. Challis, I. Cherevach, T. Chillingworth, A. Cronin, B. Crossett, P. Davis, D. DeShazer, T. Feltwell, A. Fraser, Z. Hance, H. Hauser, S. Holroyd, K. Jagels, K. E. Keith, M. Maddison, S. Moule, C. Price, M. A. Quail, E. Rabbinowitsch, K. Rutherford, M. Sanders, M. Simmonds, S. Songsivilai, K. Stevens, S. Tumapa, M. Vesaratchavest, S. Whitehead, C. Yeats, B. G. Barrell, P. C. Oyston, and J. Parkhill. 2004. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc. Natl. Acad. Sci. USA 101 : 14240-14245.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_16_2","doi-asserted-by":"crossref","first-page":"428","DOI":"10.3201\/eid0703.017310","volume":"7","year":"2001","unstructured":"Hsueh, P. R., L. J. Teng, L. N. Lee, C. J. Yu, P. C. Yang, S. W. Ho, and K. T. Luh. 2001. Melioidosis: an emerging infection in Taiwan? Emerg. Infect. Dis. 7 : 428-433.","journal-title":"Emerg. Infect. Dis."},{"key":"e_1_3_2_17_2","doi-asserted-by":"crossref","first-page":"3183","DOI":"10.1101\/gad.943401","volume":"15","year":"2001","unstructured":"Huang, J., C.-J. Lih, K.-H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev. 15 : 3183-3192.","journal-title":"Genes Dev."},{"key":"e_1_3_2_18_2","first-page":"252:243","volume":"15","year":"2005","unstructured":"Korbsrisate, S., M. Vanaporn, P. Kerdsuk, W. Kespichayawattana, P. Vattanaviboon, P. Kiatpapan, and G. Lertmemongkolchai. 2005. The Burkholderia pseudomallei RpoE (AlgU) operon is involved in environmental stress tolerance and biofilm formation. FEMS Microbiol. Lett. 15 : 252:243-249.","journal-title":"FEMS Microbiol. Lett."},{"key":"e_1_3_2_19_2","doi-asserted-by":"crossref","first-page":"2144","DOI":"10.1126\/science.290.5499.2144","volume":"290","year":"2000","unstructured":"Laub, M. T., H. H. McAdams, T. Feldblyum, C. M. Fraser, and L. Shapiro. 2000. Global analysis of the genetic network controlling a bacterial cell cycle. Science 290 : 2144-2148.","journal-title":"Science"},{"key":"e_1_3_2_20_2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1055\/s-2007-972984","volume":"16","year":"1995","unstructured":"Lehmann, M., M. Huonker, F. Dimeo, N. Heinz, U. Gastmann, N. Treis, J. M. Steinacker, J. Keul, R. Kajewski, and D. Haussinger. 1995. Serum amino acid concentrations in nine athletes before and after the 1993 Colmar ultra triathlon. Int. J. Sports Med. 16 : 155-159.","journal-title":"Int. J. Sports Med."},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.1.164-178.2004"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.11.3433-3437.1999"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.61.9.3756-3760.1993"},{"key":"e_1_3_2_24_2","first-page":"733","volume":"38","year":"1938","unstructured":"Miles, A. A., S. S. Misra, and J. O. Irwin. 1938. The estimation of bactericidal power of blood. J. Hyg. 38 : 733-749.","journal-title":"J. Hyg."},{"key":"e_1_3_2_25_2","doi-asserted-by":"crossref","first-page":"S329","DOI":"10.1093\/bioinformatics\/18.suppl_1.S329","volume":"18","year":"2002","unstructured":"Moreno-Hagelsieb, G., and J. Collado-Vides. 2002. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18(Suppl. 1): S329-S336.","journal-title":"Bioinformatics"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.10.3179-3189.2003"},{"key":"e_1_3_2_27_2","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1101\/gr.1608904","volume":"14","year":"2004","unstructured":"Ong, C., C. H. Ooi, D. Wang, H. Chong, K. C. Ng, F. Rodrigues, M. A. Lee, and P. Tan. 2004. Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species. Genome Res. 14 : 2295-2307.","journal-title":"Genome Res."},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.12.4276-4285.2005"},{"key":"e_1_3_2_29_2","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1091\/mbc.e04-04-0299","volume":"16","year":"2005","unstructured":"Peng, X., R. K. Karuturi, L. D. Miller, K. Lin, Y. Jia, P. Kondu, L. Wang, L. S. Wong, E. T. Liu, M. K. Balasubramanian, and J. Liu. 2005. Identification of cell cycle-regulated genes in fission yeast. Mol. Biol. Cell 16 : 1026-1042.","journal-title":"Mol. Biol. Cell"},{"key":"e_1_3_2_30_2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1007\/s00726-002-0338-0","volume":"24","year":"2003","unstructured":"Pitkanen, H. T., S. S. Oja, K. Kemppainen, J. M. Seppa, and A. A. Mero. 2003. Serum amino acid concentrations in aging men and women. Amino Acids 24 : 413-421.","journal-title":"Amino Acids"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki232"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.1.34-44.2001"},{"key":"e_1_3_2_33_2","first-page":"493","volume":"27","year":"1938","unstructured":"Reed, L. J., and H. Muench. 1938. A simple method of estimating 50 percent end-points. Am. J. Hyg. 27 : 493-497.","journal-title":"Am. J. Hyg."},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.27.3.910-914.1980"},{"key":"e_1_3_2_35_2","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.3201\/eid1109.050493","volume":"11","year":"2005","unstructured":"Rolim, D. B. 2005. Melioidosis, northeastern Brazil. Emerg. Infect. Dis. 11 : 1458-1460.","journal-title":"Emerg. Infect. Dis."},{"key":"e_1_3_2_36_2","doi-asserted-by":"crossref","first-page":"2886","DOI":"10.1093\/nar\/gkf388","volume":"30","year":"2002","unstructured":"Sabatti, C., L. Rohlin, M. K. Oh, and J. C. Liao. 2002. Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res. 30 : 2886-2893.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_37_2","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1099\/mic.0.28452-0","volume":"152","year":"2006","unstructured":"Scully, L. R., and M. J. Bidochka, M. J. 2006. A cysteine\/methionine auxotroph of the opportunistic fungus Aspergillus flavus is associated with host-range restriction: a model for emerging diseases. Microbiology 152 : 223-232.","journal-title":"Microbiology"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.134.3.944-949.1978"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.2.1442-1150.2001"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.72.11.6373-6381.2004"},{"key":"e_1_3_2_41_2","doi-asserted-by":"crossref","first-page":"34183","DOI":"10.1074\/jbc.M313491200","volume":"279","year":"2004","unstructured":"Song, M., H.-J. Kim, E. Y. Kim, M. Shin, H. C. Lee, Y. Hong, J. H. Rhee, H. Yoon, S. Ryu, S. Lim, and H. E. Choy. 2004. ppGpp-dependent stationary phase induction of genes on Salmonella pathogenicity island 1. J. Biol. Chem. 279 : 34183-34190.","journal-title":"J. Biol. Chem."},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.2.785-790.2005"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.16.4992-4996.2003"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.71.5.2643-2655.2003"},{"key":"e_1_3_2_45_2","doi-asserted-by":"crossref","first-page":"3732","DOI":"10.1093\/nar\/gkf505","volume":"30","year":"2002","unstructured":"Tjaden, B., R. M. Saxena, S. Stolyar, D. R. Haynor, E. Kolker, and C. Rosenow, C. 2002. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30 : 3732-3738.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_46_2","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1093\/bioinformatics\/17.6.520","volume":"17","year":"2001","unstructured":"Troyanskaya, O., M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, and R. B. Altman. 2001. Missing value estimation methods for DNA microarrays. Bioinformatics 17 : 520-525.","journal-title":"Bioinformatics"},{"key":"e_1_3_2_47_2","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1099\/jmm.0.45661-0","volume":"53","year":"2004","unstructured":"Ulrich, R. L., D. DeShazer, E. E. Brueggemann, H. B. Hines, P. C. Oyston, and J. A. Jeddeloh. 2004. Role of quorum sensing in the pathogenicity of Burkholderia pseudomallei. J. Med. Microbiol. 53 : 1053-1064.","journal-title":"J. Med. Microbiol."},{"key":"e_1_3_2_48_2","first-page":"213","volume":"65","year":"1998","unstructured":"Van Der Walt, M. L., and A. S. Greeff. 1998. The production of an auxotrophic marked, plasmid-cured Salmonella ser. Typhimurium as a live attenuated vaccine. Onderstepoort J. Vet. Res. 65 : 213-220.","journal-title":"Onderstepoort J. Vet. Res."},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.7.2080-2095.2003"}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01006-06","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01006-06","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T17:31:06Z","timestamp":1627579866000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JB.01006-06"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,12]]},"references-count":48,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["10.1128\/JB.01006-06"],"URL":"https:\/\/doi.org\/10.1128\/jb.01006-06","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,12]]},"assertion":[{"value":"2006-07-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2006-09-13","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-12-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}