Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts

doi:10.1073/pnas.0806554105

Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts

*Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;
^§Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543; and
^††Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden

↵^†I.T. and J.J.W. contributed equally to this work.
Edited by Nancy A. Moran, University of Arizona, Tucson, AZ, and approved August 15, 2008 (received for review July 9, 2008)

Abstract

Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160–790 kb) and most A + T-rich (>70%) bacterial genomes known to date. These genomes are riddled with poly(A) tracts, and 5–50% of genes contain tracts of 10 As or more. Here, we demonstrate transcriptional slippage at poly(A) tracts within genes of Buchnera aphidicola associated with aphids and Blochmannia pennsylvanicus associated with ants. Several tracts contain single frameshift deletions; these apparent pseudogenes showed patterns of constraint consistent with purifying selection on the encoded proteins. Transcriptional slippage yielded a heterogeneous population of transcripts with variable numbers of As in the tract. Across several frameshifted genes, including B. aphidicola cell wall biosynthesis genes and a B. pennsylvanicus histidine biosynthesis gene, 12–50% of transcripts contained corrected reading frames that could potentially yield full-length proteins. In situ immunostaining confirmed the production of the cell wall biosynthetic enzyme UDP-N-acetylmuramyl pentapeptide synthase encoded by the frameshifted murF gene. Simulation studies indicated an overrepresentation of poly(A) tracts in endosymbiont genomes relative to other A + T-rich bacterial genomes. Polymerase infidelity at poly(A) tracts rescues the functionality of genes with frameshift mutations and, conversely, reduces the efficiency of expression for in-frame genes carrying poly(A) regions. These features of homopolymeric tracts could be exploited to manipulate gene expression in small synthetic genomes.

Footnotes

^¶To whom correspondence may be addressed. E-mail: siv.andersson{at}ebc.uu.se. Requests for material: jwernegreen{at}mbl.edu(ant experiments), anthony.poole{at}molbio.su.se or siv.andersson{at}ebc.uu.se(aphid experiments).
Author contributions: I.T., J.J.W., A.M.P., and S.G.E.A. designed research; I.T., S.N.K., A.C.D., L.G.-V., and D.L. performed research; I.T., J.J.W., B.N., A.M.P., and S.G.E.A. analyzed data; and I.T., J.J.W., A.M.P., and S.G.E.A. wrote the paper.
↵^‡Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, B3H 1X5 Halifax, Canada.
↵^‖Present address: Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, U.K.
↵**Present address: Institute Pasteur, 75724 Paris, France.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.