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Wolff BJ, Morrison SS, Pesti D, Ganakammal SR, Srinivasamoorthy G, Changayil S, Weil MR, MacCannell D, Rowe L, Frace M, Ritchie BW, Dean D, Winchell JM. Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes. Microbiology (Reading) 2015; 161:1378-91. [PMID: 25887617 PMCID: PMC4635502 DOI: 10.1099/mic.0.000097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.
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Affiliation(s)
- Bernard J Wolff
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shatavia S Morrison
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Denise Pesti
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Satishkumar Ranganathan Ganakammal
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ganesh Srinivasamoorthy
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shankar Changayil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Ryan Weil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan MacCannell
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lori Rowe
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Frace
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Branson W Ritchie
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Deborah Dean
- 4Children's Hospital Oakland Research Institute, Oakland, CA 5UCSF and UC Berkeley Joint Graduate Program in Bioengineering, Oakland, CA
| | - Jonas M Winchell
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Lozupone C, Changayil S, Majerfeld I, Yarus M. Selection of the simplest RNA that binds isoleucine. RNA 2003; 9:1315-22. [PMID: 14561881 PMCID: PMC1287053 DOI: 10.1261/rna.5114503] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Accepted: 07/30/2003] [Indexed: 05/20/2023]
Abstract
We have identified the simplest RNA binding site for isoleucine using selection-amplification (SELEX), by shrinking the size of the randomized region until affinity selection is extinguished. Such a protocol can be useful because selection does not necessarily make the simplest active motif most prominent, as is often assumed. We find an isoleucine binding site that behaves exactly as predicted for the site that requires fewest nucleotides. This UAUU motif (16 highly conserved positions; 27 total), is also the most abundant site in successful selections on short random tracts. The UAUU site, now isolated independently at least 63 times, is a small asymmetric internal loop. Conserved loop sequences include isoleucine codon and anticodon triplets, whose nucleotides are required for amino acid binding. This reproducible association between isoleucine and its coding sequences supports the idea that the genetic code is, at least in part, a stereochemical residue of the most easily isolated RNA-amino acid binding structures.
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Affiliation(s)
- Catherine Lozupone
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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