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Genomics-Enabled Studies of the Photosynthetic Apparatus in Green Sulfur Bacteria and filamentous Anoxygenic Phototrophic Bacteria

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Genomics-Enabled Studies of the Photosynthetic Apparatus in Green Sulfur Bacteria and filamentous Anoxygenic Phototrophic Bacteria Arch Microbiol (2004) 182: 265–276 DOI 10.1007/s00203-004-0718-9 MINI-REVIEW Niels-Ulrik Frigaard Seeing green bacteria in a new light: Donald A. Bryant genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria Abstract Based upon their photo- analysis in Cfx. aurantiacus, and Received: 18 April 2004 Revised: 21 July 2004 synthetic nature and the presence of gene inactivation studies in Chl. Accepted: 22 July 2004 a unique light-harvesting antenna tepidum. Based on these results, Published online: 1 September 2004 structure, the chlorosome, the pho- BChl a and BChl c biosynthesis is Ó Springer-Verlag 2004 tosynthetic green bacteria are de- similar in the two organisms, fined as a distinctive group in the whereas carotenoid biosynthesis Bacteria. However, members of the differs significantly. In agreement two taxa that comprise this group, with its facultative anaerobic nature, the green sulfur bacteria (Chlorobi) Cfx. aurantiacus in some cases and the filamentous anoxygenic apparently produces structurally phototrophic bacteria (‘‘Chloroflex- different enzymes for heme and BChl ales’’), are otherwise quite different, biosynthesis, in which one enzyme both physiologically and phyloge- functions under anoxic conditions netically. This review summarizes and the other performs the same how genome sequence information reaction under oxic conditions. The facilitated studies of the biosynthesis Chl. tepidum mutants produced with and function of the photosynthetic modified BChl c and carotenoid apparatus and the oxidation of species also allow the functions of inorganic sulfur compounds in two these pigments to be studied in vivo. model organisms that represent these taxa, Chlorobium tepidum and N.-U. Frigaard (&) Æ D. A. Bryant Chloroflexus aurantiacus. The genes Keywords Bacteriochlorophyll a Æ Department of Biochemistry involved in bacteriochlorophyll Bacteriochlorophyll biosynthesis Æ and Molecular Biology, The Pennsylvania (BChl) c and carotenoid biosynthesis Bacteriochlorophyll c Æ Carotenoid State University, University Park, in these two organisms were identi- biosynthesis Æ Chlorobium Æ PA 16801, USA fied by sequence homology with E-mail: [email protected] Chloroflexus Æ Chlorosome Æ Tel.: +1-814-8637405 known BChl a and carotenoid bio- Functional genomics Æ Inorganic Fax: +1-814-8637024 synthesis enzymes, gene cluster sulfur metabolism Introduction or chlorosomes, of these bacteria are large structures and mostly consist of bacteriochlorophyll (BChl) c, d,ore in Members of the phylum Chlorobi, or green sulfur bac- addition to smaller amounts of BChl a and carotenoids teria, are strictly anaerobic and obligately photoauto- with aromatic end groups (Blankenship et al. 1995; trophic Bacteria, which form a distinct phylogenetic Blankenship and Matsuura 2003; Fig. 1)]. Chlorobium group that shares a common root with the Bacteroidetes tepidum (Wahlund et al. 1991) has emerged as the model (Garrity and Holt 2001a). The light-harvesting antennae, organism of choice for the green sulfur bacteria, because 266 Fig. 1 Simplified model of the photosynthetic apparatus in Chl. tepidum. Carotenoids (not shown) are associated with all complexes containing BChls, except the Fenna–Matthews– Olson (FMO) protein. Under oxic conditions (which are det- rimental to the bacteria), the quencher in the chlorosome prevents excitation transfer from BChl c to the reaction center and thus prevents pho- tosynthetic electron transfer. The quencher is activated by oxidation, with the electrons probably being delivered di- rectly or indirectly to O2; and it is inactivated by reduction by the chlorosome (Csm) proteins CsmI and CsmJ. Excitation transfer is shown by red lines and electron transfer is shown by blue lines it is naturally transformable (Frigaard and Bryant 2001; synthesize BChl c and/or d and contain chlorosomes. Frigaard et al. 2004d) and because its genome has been Chloroflexus aurantiacus is the best-studied member of completely sequenced (Eisen et al. 2002). Much has al- the Chloroflexi (Pierson and Castenholz 1974a). This ready been learned about the biosynthesis of carotenoids, bacterium is facultatively phototrophic and only induces BChls, and other structures and processes in this the synthesis of its photosynthetic apparatus, including organism by a combination of bioinformatic and gene chlorosomes, under anoxic conditions. The synthesis of inactivation approaches (Frigaard et al. 2002, 2003, BChl c and BChl a is inhibited under oxic conditions, 2004a, b, c; Hanson and Tabita 2001, 2003; Maresca whereas carotenoid biosynthesis persists. However, the et al. 2004). A new nomenclature of the green sulfur carotenoid composition is different under oxic and an- bacteria was recently proposed, in which Chl. tepidum is oxic conditions (see below). As Cfx. aurantiacus syn- renamed Chlorobaculum tepidum (Imhoff 2003). thesizes BChl c, it is commonly known as a green The phylum Chloroflexi, which is divided into two filamentous bacterium or a green ‘‘non-sulfur’’ bacte- orders, the ‘‘Chloroflexales’’ and the ‘‘Herpetosipho- rium. However, in recognition of the fact that some nales,’’ is a deep-branching lineage of the Bacteria members of the ‘‘Chloroflexales’’ are not ‘‘green’’ and do (Garrity and Holt 2001b). Members of the former order not synthesize BChl c/d and chlorosomes, members of synthesize BChls and are obligately or facultatively this group are now commonly referred to as ‘‘filamen- phototrophic, while members of the latter order do not tous anoxygenic phototrophic bacteria’’ or ‘‘photosyn- synthesize BChls and are not phototrophs. Although thetic flexibacteria.’’ The genome of Cfx. aurantiacus has members of both groups are designated as Gram-nega- been partially sequenced (see http://www.jgi.doe.gov tive, they do not synthesize lipopolysaccharide and thus and below) and currently is being sequenced to com- do not possess outer membranes. Like all members of pletion (R.E. Blankenship and J. Raymond, personal the Chlorobi, some but not all of the ‘‘Chloroflexales’’ communication). At present, this is the only genome 267 information available for the phylum Chloroflexi, and to comprises a single, circular DNA molecule and contains date there has been no demonstration that Cfx. auran- 2,288 assigned coding sequences, two rRNA operons tiacus is amenable to genetic manipulation. (16S-23S-5S), 50 tRNAs, and two small stable RNAs. Green sulfur bacteria are typically found in anoxic More than half of the proteins (1,217) were similar to aquatic or terrestrial environments where both sulfide proteins of known function and role category and an- and light occur. Green filamentous bacteria are often other 98 proteins were similar to proteins of known found in the anoxic layer of microbial mats but also function but unknown role category. Of the remaining occur in some aquatic environments. The light intensi- 973 proteins of unknown function, the majority ties are exceedingly low in the anoxic layers of stratified (680 proteins) encoded purely hypothetical proteins. lakes or microbial mats in which these organisms typi- Phylogenetic analyses of the genomic data support the cally occur. For example, a layer of Chl. phaeobactero- hypothesis that the Chlorobi are closely related to the ides occurs at the chemocline of the Black Sea at a depth Bacteroidetes (Cytophaga–Flavobacteria–Bacteroides) of approx. 100 m. The light intensity at this depth is grouping. Interestingly, a rather high percentage (12%) nearly 106 times less than at the surface and has been of the predicted proteins are most similar to proteins determined to be ca. 3 nmol photons m)2 s)1 (Over- from archaeal species. mann et al. 1992). Under these conditions, a single The Joint Genome Institute (JGI; Walnut Creek, chlorophyll molecule will absorb one photon in a period Calif., USA) of the United States Department of Energy of ca. 6 h. In order to survive under such low light (DOE) has determined a draft genome sequence for Cfx. intensities, green bacteria evolved highly specialized aurantiacus strain J-10-fl (Table 1). The genomic infor- light-harvesting antennae, known as chlorosomes, which mation presently resides on 1,142 contigs containing a contain the largest numbers of chromophores known in total of 4.9 Mbp. Of these contigs, 541 are larger than nature. In Chl. tepidum, each chlorosome can contain 2 kb and contain a total of 4.3 Mbp. Based on this more than 200·103 BChl c molecules (Martinez-Planells information, the total genome size is probably roughly et al. 2002; Montan˜ o et al. 2003a) and a cell can contain 5 Mbp and perhaps even larger. The data are available about 200–250 chlorosomes. Thus, a Chl. tepidum cell from JGI (http://genome.jgi-psf.org/draft_microbes/ can contain up to 50·106 BChl c molecules, or ten times chlau/chlau.download.html) or GenBank (accession the estimated number of protein molecules per cell. number NZ_AAAH00000000). Because of the incom- plete nature of the Cfx. aurantiacus data and the imprecise size-prediction for its genome, it is not possible Overview of the Chl. tepidum and Cfx. aurantiacus to estimate reliably the number and nature of the coding genomes sequences and stable RNA genes. Although the current genomic sequence information is sufficient for identify- The Institute for Genomic Research (Rockville, Md.) ing many genes of interest, the fragmented nature of the sequenced the genome of Chl. tepidum (Table 1; Eisen data is a serious limitation in whole-organism analyses et al. 2002). The 2.15-Mbp Chl. tepidum genome and comparative genomics. Efforts are therefore Table 1 Comparison of Chl. tepidum and Cfx. aurantiacus and their genomes. Data are taken from Eisen et al. (2002), Frigaard et al. (2004c), and Garrity and Holt (2001b) Chl. tepidum strain TLS Cfx. aurantiacus strain J-10-fl Genome size (bp) 2,154,946 Estimated at ca. 5,000,000 Number of predicted coding 2,288 Estimated at ca. 5,000 sequences Number of rRNA operons 2 Estimated at 2 G+C content (mol%) 56.5 57 Optimum growth temperature 48°C ca. 55°C Growth mode Photolithoautotrophic, Photoheterotrophic or photoautotrophic strictly anaerobic under anoxic conditions; chemoheterotrophic under oxic conditions Morphology Rods (ca.
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