{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T15:21:39Z","timestamp":1781104899319,"version":"3.54.1"},"reference-count":23,"publisher":"National Academy of Sciences","issue":"12","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2003,6,10]]},"abstract":"<jats:p>\n                    Predicted highly expressed (PHX) genes in five currently available high G+C  complete \u03b1-proteobacterial genomes are analyzed. These include: the  nitrogen-fixing plant symbionts\n                    <jats:italic>Sinorhizobium meliloti<\/jats:italic>\n                    (SINME) and\n                    <jats:italic>Mesorhizobium loti<\/jats:italic>\n                    (MESLO), the nonpathogenic aquatic bacterium\n                    <jats:italic>Caulobacter crescentus<\/jats:italic>\n                    (CAUCR), the plant pathogen\n                    <jats:italic>Agrobacterium  tumefaciens<\/jats:italic>\n                    (AGRTU), and the mammalian pathogen\n                    <jats:italic>Brucella  melitensis<\/jats:italic>\n                    (BRUME). Three of these genomes, SINME, AGRTU, and BRUME,  contain multiple chromosomes or megaplasmids (&gt;1 Mb length). PHX genes in  these genomes are concentrated mainly in the major (largest) chromosome with  few PHX genes found in the secondary chromosomes and megaplasmids.  Tricarboxylic acid cycle and aerobic respiration genes are strongly PHX in all  five genomes, whereas anaerobic pathways of glycolysis and fermentation are  mostly not PHX. Only in MESLO (but not SINME) and BRUME are most glycolysis  genes PHX. Many flagellar genes are PHX in MESLO and CAUCR, but mostly are not  PHX in SINME and AGRTU. The nonmotile BRUME also carries many flagellar genes  but these are generally not PHX and all but one are located in the second  chromosome. CAUCR stands out among available prokaryotic genomes with 25 PHX  TonB-dependent receptors. These are putatively involved in uptake of iron ions  and other nonsoluble compounds.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1232298100","type":"journal-article","created":{"date-parts":[[2003,6,10]],"date-time":"2003-06-10T13:06:36Z","timestamp":1055250396000},"page":"7313-7318","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":37,"title":["Predicting gene expression levels from codon biases in  \u03b1-proteobacterial genomes"],"prefix":"10.1073","volume":"100","author":[{"given":"Samuel","family":"Karlin","sequence":"first","affiliation":[{"name":"Departments of Mathematics and  Biological Sciences, Stanford University,  Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie J.","family":"Barnett","sequence":"additional","affiliation":[{"name":"Departments of Mathematics and  Biological Sciences, Stanford University,  Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allan M.","family":"Campbell","sequence":"additional","affiliation":[{"name":"Departments of Mathematics and  Biological Sciences, Stanford University,  Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert F.","family":"Fisher","sequence":"additional","affiliation":[{"name":"Departments of Mathematics and  Biological Sciences, Stanford University,  Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Mr\u00e1zek","sequence":"additional","affiliation":[{"name":"Departments of Mathematics and  Biological Sciences, Stanford University,  Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2003,5,29]]},"reference":[{"key":"e_1_3_2_1_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.061029298"},{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1060966"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/7.6.331"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1066803"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1066804"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.221575398"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.161294398"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.161294698"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.161294798"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.12.3582-3586.2000"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.192319099"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.18.5238-5250.2000"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.17.5025-5040.2001"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.7.1590"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1749-6632.1999.tb08893.x"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0966-842X(01)02079-0"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.081077598"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-4838(99)00119-3"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.22"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.16.9184"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.062065699"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1042\/bst0300150"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.11.6456"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1232298100","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T21:23:58Z","timestamp":1650921838000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1232298100"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,5,29]]},"references-count":23,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2003,6,10]]}},"alternative-id":["10.1073\/pnas.1232298100"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1232298100","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2003,5,29]]},"assertion":[{"value":"2003-05-29","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}