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Open Access Research article

Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942

Luis Delaye12, Carmen M González-Domenech13, María P Garcillán-Barcia4, Juli Peretó15, Fernando de la Cruz4 and Andrés Moya16*

Author Affiliations

1 Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain

2 Departamento de Ingeniería Genética CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México

3 Facultad de Farmacia, Universidad de Granada, Granada, Spain

4 Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Santander, Spain

5 Departament de Bioquimica i Biologia Molecular, Universitat de València, València, Spain

6 Departament de Genètica, Universitat de València, València, Spain

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BMC Genomics 2011, 12:25  doi:10.1186/1471-2164-12-25

Published: 12 January 2011

Abstract

Background

Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.

Results

By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.

Conclusions

Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.