View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Molecular Microbiology (2008) 70(4), 1037–1050 ᭿ doi:10.1111/j.1365-2958.2008.06473.x First published online 9 October 2008 Intermediate filament-like proteins in bacteria and a cytoskeletal function in Streptomyces ᭿ OnlineOpen: This article is available free online at www.blackwell-synergy.com Sonchita Bagchi1, Henrik Tomenius1, Introduction Lyubov M. Belova2 and Nora Ausmees1* 1Department of Cell and Molecular Biology, Uppsala Research of the two past decades has revealed that University, Box 596, 75124 Uppsala, Sweden. bacterial cells are architecturally surprisingly complex. 2Department of Materials Science and Engineering, Bacteria, like eukaryotes, use protein filaments for The Royal Institute of Technology, Brinellvägen 23, spatial organization of their cells, and a large variety of 10044 Stockholm, Sweden. cytoskeletal elements has already been identified in bac- teria (Graumann, 2007). Best studied of these are the FtsZ- and MreB-family proteins, which are structurally Summary and evolutionarily related to tubulin and actin of eukary- Actin and tubulin cytoskeletons are conserved and otic organisms. FtsZ and MreB are widespread and con- widespread in bacteria. A strikingly intermediate fila- served in bacteria and fulfil important functions, including ment (IF)-like cytoskeleton, composed of crescentin, spatial orchestration of cell division, growth and morpho- is also present in Caulobacter crescentus and deter- genesis [recently reviewed in Michie and Lowe (2006), mines its specific cell shape. However, the broader Cabeen and Jacobs-Wagner (2007), Graumann (2007), significance of this finding remained obscure, Harold (2007), Pichoff and Lutkenhaus (2007), Than- because crescentin appeared to be unique to bichler and Shapiro (2008)]. The morphogenetic function Caulobacter. Here we demonstrate that IF-like func- of the bacterial cytoskeleton appears to depend greatly tion is probably a more widespread phenomenon in on its ability to recruit and spatially organize proteins bacteria. First, we show that 21 genomes of 26 phy- involved in the synthesis of the cell wall peptidoglycan logenetically diverse species encoded uncharacter- (PG). PG consists of long glycan strands cross-linked by ized proteins with a central segmented coiled coil rod short peptide side-chains into one huge molecule encas- domain, which we regarded as a key structural feature ing the cell and functions as an exoskeleton to maintain of IF proteins and crescentin. Experimental studies of cell shape and to withstand turgor pressure. At the same three in silico predicted candidates from Mycobacte- time, turgor pressure may act as a driving force in cell rium and other actinomycetes revealed a common wall expansion during growth (Koch, 1985; Harold, IF-like property to spontaneously assemble into fila- 2002). Thus, according to this model, growth and mor- ments in vitro. Furthermore, the IF-like protein FilP phogenesis are intimately coupled in bacteria. By allow- formed cytoskeletal structures in the model actino- ing cell wall expansion only at certain positions dictated mycete Streptomyces coelicolor and was needed for by cytoskeletal structures and driven by turgor pressure normal growth and morphogenesis. Atomic force (and/or other forces), different shapes can be generated microscopy of living cells revealed that the FilP (Cabeen and Jacobs-Wagner, 2007; Harold, 2007). The cytoskeleton contributed to mechanical fitness of the helical cytoskeletal structure formed in vivo by the bac- hyphae, thus closely resembling the function of meta- terial actin MreB defines a cylinder and thus determines zoan IF. Together, the bioinformatic and experimental the common rod shape of many bacteria (Jones et al., data suggest that an IF-like protein architecture is a 2001; Kruse et al., 2003; Figge et al., 2004; Dye et al., versatile design that is generally present in bacteria 2005; Carballido-Lopez, 2006; Carballido-Lopez et al., and utilized to perform diverse cytoskeletal tasks. 2006; Divakaruni et al., 2007; Mohammadi et al., 2007). Ends of the cell cylinder are capped by hemispherical poles, generated by a cell division process guided by the action of bacterial tubulin FtsZ, which forms a con- Accepted 18 September, 2008. *For correspondence. E-mail Nora. stricting ring structure at the cell division site (Bi and [email protected]; Tel. (+46) 18 4714058; Fax (+46) 18 530396. Lutkenhaus, 1991; Daniel and Errington, 2003; Varma Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial and Young, 2004; Margolin, 2005; Aaron et al., 2007). exploitation. Cocci generally do not contain MreB and are made up of © 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd 1038 S. Bagchi, H. Tomenius, L. M. Belova and N. Ausmees ᭿ two poles created by FtsZ-directed cell division (Jones common? Here we demonstrate that proteins with a basi- et al., 2001; Pinho and Errington, 2003). However, the cally IF- or crescentin-like architecture are in fact present cell shape arsenal of bacteria contains much more than and widespread in bacteria. Experimental analysis of a just spheres and straight rods. Obviously, other spatial conserved group of such proteins from actinobacteria organizers besides MreB and FtsZ must exist in bacteria demonstrated that IF-like biochemical properties accom- to determine more complicated forms. A step further in panied the basic IF-like architecture of these proteins and understanding bacterial morphogenesis was the identi- also revealed a novel cytoskeletal function in actinobac- fication of the intermediate filament (IF)-like protein terial growth and morphogenesis. Together our data crescentin in an aquatic bacterium with a characteristic suggest that an IF-like cytoskeleton, based on a versatile crescent-like cell shape, Caulobacter crescentus structural element of a segmented coiled coil rod, is more (Ausmees et al., 2003). The laterally localized crescentin widespread in bacteria than previously thought. cytoskeleton converts the FtsZ- and MreB-dependent simple straight rod into a curved or helical rod, depend- ing on the length of the cell (Ausmees et al., 2003). Results Surprisingly, despite the remarkable architectural and Proteins with a potential segmented coiled coil rod biochemical relatedness of crescentin to IF proteins, a domain are widespread in bacteria sequence similarity search failed to reveal crescentin homologues in other bacteria. Thus, the additional mor- Despite poor sequence conservation all eukaryotic IF phogenetic factors in other MreB/FtsZ-bacteria with proteins share a similar building plan, consisting of a complex shapes remain to be uncovered. How general central rod domain of alternating coiled coil segments is the above outlined morphogenetic model based on and linkers, flanked by more globular head and tail the actions of MreB, FtsZ and additional cytoskeletal domains (Fig. 1, top) (Herrmann and Aebi, 2004). The elements, such as crescentin? Remarkably, at least one rod domain is absolutely essential for filament formation large and important group of bacteria, the actino- (Parry et al., 2007). The bacterial IF-like protein crescen- mycetes, seem to use a different modus operandi for tin also possesses an apparent rod domain with a dif- cell growth and morphogenesis that is independent of ferent arrangement of coiled coil segments and linkers MreB and FtsZ. These bacteria grow in a polarized (Fig. 1) yet exhibits remarkably IF-like biochemical prop- fashion: rod-shaped species, such as Mycobacterium erties and has a cytoskeletal function (Ausmees et al., and Corynebacterium assemble new cell wall at both 2003). We chose arbitrarily 26 bacterial genomes to cell poles, while filamentous ones, such as Streptomy- survey for the presence of rod-domain proteins among ces, grow by hyphal tip extension analogously to how the encoded proteomes (Table 1). A rod domain was filamentous fungi grow (Daniel and Errington, 2003; defined as a sequence of more than 80 amino acids in Flärdh, 2003a,b; Ramos et al., 2003; Nguyen et al., coiled coil conformation, positioned either as one con- 2007; Letek et al., 2008). The actinomycetes exhibit tinuous block or interrupted by short non-coiled coil extraordinary diversity, regarding their morphology (from sequences. An additional condition was that the candi- simple coccoid to complex branching and multicellular dates should contain no known functional domains, such filaments), lifestyle (e.g. pathogenic like Mycobacterium as a signal sequence, transmembrane segments, enzy- or symbiotic like Frankia), physiology, metabolism (e.g. matic activity, etc. Out of 26 genomes 21 encoded at production of a multitude of secondary metabolites by least one candidate protein with above mentioned prop- Streptomyces) and colonization of various environmental erties, and 16 genomes encoded several (Table 1). One niches (Ventura et al., 2007). The coiled coil protein putative crescentin-like rod-domain protein from each DivIVA seems to have an important role in generation of genome is schematically shown in Fig. 1. The analysed polarity in these bacteria (Flärdh, 2003a; Letek et al., genomes represent distant phylogenetic groups, sug- 2008), but other than that, the molecular mechanisms gesting that proteins with a rod-like architecture are underlying the diverse morphologies of actinomycetes widespread among bacteria. Further