UC San Diego UC San Diego Previously Published Works Title Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica. Permalink https://escholarship.org/uc/item/0f85q1z7 Journal Biochimica et biophysica acta, 1838(1 Pt B) ISSN 0006-3002 Authors Paparoditis, Philipp Västermark, Ake Le, Andrew J et al. Publication Date 2014 DOI 10.1016/j.bbamem.2013.08.007 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Biochimica et Biophysica Acta 1838 (2014) 193–215 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamem Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica Philipp Paparoditis a, Åke Västermark a,AndrewJ.Lea, John A. Fuerst b, Milton H. Saier Jr. a,⁎ a Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093–0116, USA b School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 9072, Australia article info abstract Article history: Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its un- Received 12 April 2013 usual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane Received in revised form 8 August 2013 transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Data- Accepted 9 August 2013 base (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a Available online 19 August 2013 high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in Keywords: Marine ecology smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium- Planctomycetes dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and Transport proteins trimethyl-amine-oxide (TMAO) reductases, consistent with its Na+-rich marine environment. R. baltica also Sodium motive force possesses a Na+-translocating NADH:quinone dehydrogenase (Na+-NDH), a Na+ efflux decarboxylase, two Electron transport Na+-exporting ABC pumps, two Na+-translocating F-type ATPases, two Na+:H+ antiporters and two K+:H+ Cellular energization antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H+-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predic- tions regarding the physiology, ecology and evolution of R. baltica. © 2013 Elsevier B.V. All rights reserved. 1. Introduction Planctomycetes are characteristically divided into two and sometimes three major compartments, and all species examined have at least Rhodopirellula baltica is an aerobic marine halotolerant Planctomycete, two such compartments. There is a cytoplasmic membrane, defining a member of a diverse genus of ecological importance with an unusual the protoplast and cytoplasm within it, and this membrane is closely cell structure, including an intracellular membrane-enclosed nucleoid, apposed to the cell wall. Such an arrangement is highly unusual for the pirellulosome [1–6]. It and other Planctomycetes exhibit resistance bacteria, and these organisms lack a peptidoglycan wall polymer to a number of traditionally used antibiotics and heavy metals, and they characteristic of most walled bacteria of both Gram-positive and have the capacity to degrade and utilize a wide range of organic materials Gram-negative types. There are aspects of electron micrographs of in their environments [7–9]. They lack peptidoglycan and instead display sections of the wall in whole cells which might be interpreted by a proteinaceous cell wall, possibly with degradative enzymes anchored to some as murein-like, e.g., electron dense and electron light strati- the external surface [10–12]. These organisms produce a variety of sec- fied layers, and the 10% SDS-resistant walls of several species appear ondary products such as pigments including carotenoids [13]. to retain shape on isolation after SDS treatment in a manner typical of a R. baltica belongs to the phylum Planctomycetes,adivergent classical peptidoglycan-containing murein sacculus [19–21]. phylum which some phylogenetic analyses claim to be deep-branching The suggestion that a murein wall structure, including an outer within the domain Bacteria [14,15]. These organisms are most close- membrane, somehow applies to Planctomycetes on the basis of some ly related to other members of the so-called PVC superphylum also genomic data does not seem justified. However, homologs of Gram- encompassing the phyla Verrucomicrobia, Lentisphaerae, Chlamydiae negative bacterial wall synthesis enzymes are present [22], suggesting and the uncultured OP3 phylum [16–18]. Cells of species in the phylum that the precursor of the Planctomycetes must have been a more typical Gram-negative bacterium. Without localization of the proteins detected ⁎ Corresponding author. Tel.: +1 858 534 4084; fax: +1 858 534 7108. bioinformatically, there is little convincing evidence for the presence of E-mail addresses: [email protected] (J.A. Fuerst), [email protected] (M.H. Saier). a typical Gram-negative bacterial envelope. 0005-2736/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.bbamem.2013.08.007 194 P. Paparoditis et al. / Biochimica et Biophysica Acta 1838 (2014) 193–215 Homologs of outer membrane proteins present in R. baltica might R. baltica was the first Planctomycete to have its genome fully se- serve roles different from those served in most Gram-negative bacteria. quenced [32]. It has a circular chromosome of 7.15 Mbp with genes In all Planctomycetes examined, a single bilayer intracytoplasmic mem- for heterolactic acid fermentation, the interconversion of C1 compounds brane (ICM) lies inside the cytoplasm and defines a region called the [35], and an amazingly large number (110) of putative sulfatases, proba- paryphoplasm lying between the cytoplasmic membrane (CM) and bly related to its association with macroalgae [26]. In addition to encoding this ICM. The ICM displays no obvious continuity with the CM. The a fragmentary peptidoglycan biosynthetic pathway, it has many typical ICM surrounds a compartment termed the pirellulosome containing Gram-negative bacterial enzyme systems such as those involved in lipo- the ribosomes and nucleoid. In some species, a third compartment lies polysaccharide biosynthesis and flagellar motility. The availability of the within the pirellulosome, defined by one membrane as in anaerobic fully sequenced genome of R. baltica immediately led to phylogenetic, anammox plantomycetes such as Kuenenia stuttgartiensis, or two closely proteomic and transcriptomic analyses, providing the first detailed mo- apposed membranes forming a ‘nuclear envelope’ as in the case of aer- lecular description of a Planctomycete [34,36–40]. obic Gemmata obscuriglobus. Thus, in an organism such as Gemmata, Transporters allow communication between the cytoplasm of a cell molecular transport must occur across not only the cytoplasmic mem- and the external medium and are responsible for the uptake of all nutri- brane but also across up to three internal membrane bilayers and be- ents and the export of secondary metabolites and end-products of me- tween up to three internal compartments. It should be noted, however, tabolism. Further, the compartmentalized cell of R. baltica presumably that R. baltica appears to have only two compartments delineated by requires the existence of transport proteins in both the CM and the two phospholipid bilayers, the CM and ICM. ICM. It has been proposed that this complex structure might relate to Marine Planctomycetes include: R. baltica, Blastopirellula marina, a common origin with eukaryotes that also display compartmentaliza- many related unnamed isolates, and several about-to-be-named new tion, but this proposal is highly speculative. species of this genus. Planctomyces maris and P. brasiliensis are hypersaline In this communication, we deduce the full complement of pond organisms. However, to date, no Gemmata or Pirellula strains have bioinformatically recognizable putative integral membrane transport been isolated from marine habitats. Several researchers are currently proteins in R. baltica. Usually, about one quarter of all proteins in a living working on new marine isolates of Planctomycetes [8].Thestudiesre- cell are integral membrane proteins, and about one quarter of these are ported here are likely to be relevant to the various marine Planctomycetes transport proteins. In accordance with this trend, we find that the per- in addition to R. baltica (see Discussion). centage