{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T14:52:04Z","timestamp":1763563924348},"reference-count":79,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T00:00:00Z","timestamp":1472688000000},"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":["Infect Immun"],"published-print":{"date-parts":[[2016,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            In evolving to an obligate intracellular niche,\n            <jats:named-content content-type=\"genus-species\">Chlamydia<\/jats:named-content>\n            has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However,\n            <jats:named-content content-type=\"genus-species\">Chlamydia<\/jats:named-content>\n            can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-\u03b3), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from\n            <jats:named-content content-type=\"genus-species\">Chlamydia<\/jats:named-content>\n            . Thus, how\n            <jats:named-content content-type=\"genus-species\">Chlamydia<\/jats:named-content>\n            , a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that\n            <jats:named-content content-type=\"genus-species\">C. pneumoniae<\/jats:named-content>\n            responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from\n            <jats:named-content content-type=\"genus-species\">C. pneumoniae<\/jats:named-content>\n            genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous\n            <jats:named-content content-type=\"genus-species\">C. pneumoniae<\/jats:named-content>\n            microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis.\n          <\/jats:p>","DOI":"10.1128\/iai.00377-16","type":"journal-article","created":{"date-parts":[[2016,7,12]],"date-time":"2016-07-12T10:43:18Z","timestamp":1468320198000},"page":"2703-2713","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":33,"title":["Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation"],"prefix":"10.1128","volume":"84","author":[{"given":"Scot P.","family":"Ouellette","sequence":"first","affiliation":[{"name":"Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelsey J.","family":"Rueden","sequence":"additional","affiliation":[{"name":"Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth A.","family":"Rucks","sequence":"additional","affiliation":[{"name":"Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","first-page":"443","article-title":"Chlamydiae as agents of human and animal diseases","volume":"49","author":"Schachter J","year":"1973","unstructured":"Schachter J, Storz J, Tarizzo ML, Bogel K. 1973. Chlamydiae as agents of human and animal diseases. Bull World Health Organ 49:443\u2013449.","journal-title":"Bull World Health Organ"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/clind\/15.5.757"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(03)13914-1"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.7326\/0003-4819-147-2-200707170-00007"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsre.2005.03.002"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2014.00157"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.282.5389.754"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/152.6.1275"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/0140-6736(92)90399-N"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(88)90741-6"},{"key":"e_1_3_3_12_2","first-page":"345","article-title":"Treatment of Chlamydia pneumoniae infection in adult asthma: a before-after trial","volume":"41","author":"Hahn DL","year":"1995","unstructured":"Hahn DL. 1995. Treatment of Chlamydia pneumoniae infection in adult asthma: a before-after trial. J Fam Pract 41:345\u2013351.","journal-title":"J Fam Pract"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.58.4.686-699.1994"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1086\/652394"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.9.3998"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.65.11.4539-4547.1997"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2011\/00020"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.12.1.211-220.1975"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.3.1457-1464.2000"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1006\/mpat.2001.0433"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2014.00071"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.53.2.347-351.1986"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.62.9.4059-4062.1994"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.81.3.908"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016783"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.63.1.199-205.1995"},{"key":"e_1_3_3_27_2","first-page":"5529","article-title":"IFN-gamma-mediated antimicrobial response. Indoleamine 2,3-dioxygenase-deficient mutant host cells no longer inhibit intracellular Chlamydia spp","volume":"150","author":"Thomas SM","year":"1993","unstructured":"Thomas SM, Garrity LF, Brandt CR, Schobert CS, Feng GS, Taylor MW, Carlin JM, Byrne GI. 1993. IFN-gamma-mediated antimicrobial response. Indoleamine 2,3-dioxygenase-deficient mutant host cells no longer inhibit intracellular Chlamydia spp. or Toxoplasma growth. J Immunol 150:5529\u20135534.","journal-title":"or Toxoplasma growth. J Immunol"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.74.1.225-238.2006"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.05659-11"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2683(19990101)20:4\/5<775::AID-ELPS775>3.0.CO;2-Z"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.9.5423-5429.2001"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2001.02550.x"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1006\/mpat.2000.0435"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1286-4579(01)01504-0"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.70.6.2976-2981.2002"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2535394100"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr0400031"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01487-05"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2005.05.018"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2008.01446.x"},{"key":"e_1_3_3_41_2","first-page":"27","article-title":"Differential transcriptional responses between the interferon-gamma-induction and iron-limitation models of persistence for Chlamydia pneumoniae","volume":"42","author":"Timms P","year":"2009","unstructured":"Timms P, Good D, Wan C, Theodoropoulos C, Mukhopadhyay S, Summersgill JT, Mathews S. 2009. Differential transcriptional responses between the interferon-gamma-induction and iron-limitation models of persistence for Chlamydia pneumoniae. J Microbiol Immunol Infect 42:27\u201337.","journal-title":"J Microbiol Immunol Infect"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.22.7853-7856.2005"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2006.05465.x"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.10.6038-6040.2000"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.67.4.1666-1671.1999"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03638.x"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1331135100"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.165.2.379-385.1986"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.173.12.3821-3830.1991"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.175.10.2936-2942.1993"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2012.08100.x"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00279"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2010.12.005"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.6.1958-1966.2003"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2007.04.076"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005125"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.23.6983-6990.1996"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13093"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1369-5274(00)00182-X"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2005.03.008"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2012.08177.x"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/0002-9378(89)90080-X"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1111\/aji.12008"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.70.3.689"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2001.tb10732.x"},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-11-17"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.12867"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-7-230"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00288-08"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2008.06229.x"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00692-15"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2004.04029.x"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI17993"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2014.00071"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.270.9.4563"},{"key":"e_1_3_3_76_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2015.03.018"},{"key":"e_1_3_3_77_2","unstructured":"Reference deleted."},{"key":"e_1_3_3_78_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00330-07"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.03.036"},{"key":"e_1_3_3_80_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002258"}],"container-title":["Infection and Immunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00377-16","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00377-16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T10:27:01Z","timestamp":1646476021000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/IAI.00377-16"}},"subtitle":[],"editor":[{"given":"C. R.","family":"Roy","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,9]]},"references-count":79,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2016,9]]}},"alternative-id":["10.1128\/IAI.00377-16"],"URL":"https:\/\/doi.org\/10.1128\/iai.00377-16","relation":{},"ISSN":["0019-9567","1098-5522"],"issn-type":[{"value":"0019-9567","type":"print"},{"value":"1098-5522","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9]]},"assertion":[{"value":"2016-05-02","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-07-05","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-08-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}