Genome Analysis Extracytoplasmic function sigma factors in Pseudomonas syringae Jose ´ A. Oguiza 1 , Kristoffer Kiil 2 and David W. Ussery 2 1 Departamento de Produccio ´ n Agraria, Universidad Pu ´ blica de Navarra, 31006 Pamplona, Spain 2 Center for Biological Sequence Analysis, Biocentrum-DTU, The Technical University of Denmark, DK-2800 Lyngby, Denmark Genome analyses of the plant pathogens Pseudomonas syringae pv. tomato DC3000, pv. syringae B728a and pv. phaseolicola 1448A reveal fewer extracytoplasmic func- tion (ECF) sigma factors than in related Pseudomonads with different lifestyles. We highlight the presence of a P. syringae-specific ECF sigma factor that is an interest- ing target for future studies because of its potential role in the adaptation of P. syringae to its specialized phytopathogenic lifestyle. In bacteria, the sigma factor protein binds to the core RNA polymerase and forms a holoenzyme able to recognize the promoter and initiate transcription. Bacterial sigma factors belong to two protein families: the s 54 and the s 70 families. The s 70 family can be further divided into four phylogenetic groups, with the extracytoplasmic function (ECF) group being the largest and most diverse [1–3]. Adaptation to a particular lifestyle clearly contributes to the final shape of bacterial genomes, and the number of transcription- associated proteins, namely sigma factors and two-component regulatory systems, might mirror the adaptability of the bacterium. Accordingly, it has been proposed that the number of sigma factors and transcription-associated proteins encoded in a genome correlates with the different lifestyles of bacteria [4–7]. ECF sigma factors offer a convenient mechanism for transcriptional regulation in response to specific environmental signals, and a correlation between bacterial lifestyles and the number of ECF sigma factors has become evident: bacteria with complex lifestyles involving different habitats have more ECF sigma factors than bacteria with simple lifestyles living in stable niches [7,8]. Genome sequences of Pseudomonas syringae pathovars P. syringae is a common leaf-inhabiting Proteobac- terium, existing either as a harmless commensal on the surface of leaves or as an agriculturally important plant pathogen [9]. P. syringae is a highly specialized plant parasite that interacts with a wide range of plants, and strains of P. syringae are assigned to a pathovar on the basis of their different host specificities. Disease development by P. syringae is often preceded by growth on leaf surfaces as an epiphyte that enters plant leaves through stomata, grows to large populations in intercellular spaces and injects virulence effector proteins into the cytoplasm of plant cells by means of the Hrp type III secretion system [9]. The genomes of P. syringae pv. tomato DC3000, pv. syringae B728a and pv. phaseolicola 1448A have been sequenced [10–12]. In P. syringae pathovars, between 10 and 12% of the genes have a regulatory role, which could reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth, plant colonization and pathogenesis [10–12]. The identification of genomic features that underlie the adaptation of P. syringae to its phytopathogenic lifestyle and the interactions with plant hosts is a major challenge. Hence, the ECF sigma factors of P. syringae are attractive goals for genomic studies that could help to elucidate their regulatory functions and molecular mechanisms, and to establish which gene sets contri- bute to the phytopathogenic lifestyle. The aim of this article is to analyze the ECF sigma factors in the complete genomic sequences of P. syringae pathovars and to compare them with the ECFs in the genomes of related Pseudomonads with different lifestyles. These are the completely sequenced genomes of the opportu- nistic animal and plant pathogen Pseudomonas aeruginosa PAO1 [13], the non-pathogenic saprophytic soil bacterium Pseudomonas putida KT2440 [14], the plant commensal Pseudomonas fluorescens Pf-5 [15], and the genomes in progress of the P. aeruginosa strain UCBPP-PA14, the nitrogen-fixing Azotobacter vinelandii AvOP and the P. fluorescens strains PfO-1 and SBW25 (http://www.ncbi. nlm.nih.gov/genomes/lproks.cgi). A reduced number of ECF sigma factors in P. syringae A limited number of ECF sigma factors have been characterized in plant pathogenic Proteobacteria, and two ECF sigma factors of P. syringae (HrpL and AlgT) have been studied in detail with regard to the trans- criptional regulation of virulence genes [16–18]. The related species P. aeruginosa PAO1 and P. putida KT2440 contain 19 ECF sigma factors and many of the ECF sigma factors of P. aeruginosa PAO1 have a counterpart in P. putida Corresponding author: Oguiza, J.A. (jose.oguiza@unavarra.es). DTD 5 ARTICLE IN PRESS Update TRENDS in Microbiology Vol.xx No.xx Monthxxxx www.sciencedirect.com 0966-842X/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tim.2005.10.005