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Nucleic Acids Research, 2003, Vol. 31, No. 11 2890-2899
© 2003 Oxford University Press

Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4

Jörg Vogel, Ilka M. Axmann1,2, Hanspeter Herzel1 and Wolfgang R. Hess2

Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem, Israel, 1 Institute for Theoretical Biology, Humboldt-University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 Department of Biology/Genetics, Humboldt-University, Chausseestrasse 117, D-10115 Berlin, Germany

*To whom correspondence should be addressed at present address: Ocean Genome Legacy, 32 Tozer Road, Beverly, MA 01915, USA. Tel: +1 978 927 5054; Fax: +1 978 921 1527; Email: hessw{at}neb.com
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25 transcription start sites (TSS) of 21 different genes of Prochlorococcus sp. MED4 were determined experimentally. The data suggest more than one TSS for the genes ftsZ, petH, psbD and ntcA. In contrast, the rbcL-rbcS operon encoding ribulose 1,5-bisphosphate carboxylase/oxygenase lacks a detectable promoter and is co-transcribed with the upstream located gene ccmK. The entire set of experimental data was used in a genome-wide scan for putative TSS in Prochlorococcus. A –10 element could be defined, whereas at the –35 position there was no element common to all investigated sequences. However, splitting the data set into sub-classes revealed different types of putative –35 boxes. Only one of them resembled the consensus sequence TTGACA recognized by the vegetative {sigma} factor ({sigma}70) of enterobacteria. Using a scoring matrix of the –10 element, more than 3000 TSS were predicted, about 40% of which were estimated to be functional. This is the first systematic study of transcription initiation sites in a cyanobacterium.


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