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Applied and Environmental Microbiology, March 2004, p. 1658-1668, Vol. 70, No. 3
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.3.1658-1668.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Diverse Organization of Genes of the ß-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage

Alison Buchan,1* Ellen L. Neidle,2 and Mary Ann Moran1

Departments of Marine Sciences,1 Microbiology, University of Georgia, Athens, Georgia 306022

Received 23 September 2003/ Accepted 20 November 2003

Members of the Roseobacter lineage, an ecologically important marine clade within the class {alpha}-Proteobacteria, harbor genes for the protocatechuate branch of the ß-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. The genes of this pathway are typically clustered, although gene order varies among organisms. Here we characterize genes linked to pcaH and -G, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the Roseobacter lineage (pairwise 16S rRNA gene sequence identities, 92 to 99%). Sequence analysis of genomic fragments revealed five unique pca gene arrangements. Identical gene organization was found for isolates demonstrating species-level identity (i.e., >99% 16S rRNA gene similarity). In one isolate, six functionally related genes were clustered: pcaQ, pobA, pcaD, pcaC, pcaH, and pcaG. The remaining seven isolates lacked at least one of these genes in their clusters, although the relative order of the remaining genes was preserved. Three genes (pcaC, -H, and -G) were physically linked in all isolates. A highly conserved open reading frame (ORF) was found immediately downstream of pcaG in all eight isolates. Reverse transcription-PCR analysis of RNA from one isolate, Silicibacter pomeroyi DSS-3, provides evidence that this ORF is coexpressed with upstream pca genes. The absence of this ORF in similar bacterial pca gene clusters from diverse microbes suggests a niche-specific role for its protein product in Roseobacter group members. Collectively, these comparisons of bacterial pca gene organization illuminate a complex evolutionary history and underscore the widespread ecological importance of the encoded ß-ketoadipate pathway.

* Corresponding author. Present address: Department of Molecular, Cellular, and Developmental Biology, P.O. Box 208103, Yale University, New Haven, CT 06520. Phone: (203) 432-3505. Fax: (203) 432-3350. E-mail: alison.buchan{at}yale.edu.

Applied and Environmental Microbiology, March 2004, p. 1658-1668, Vol. 70, No. 3
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.3.1658-1668.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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