Download Prokaryotic photosynthesis and phototrophy illuminated

Review
TRENDS in Microbiology
Vol.14 No.11
Prokaryotic photosynthesis and
phototrophy illuminated
Donald A. Bryant1 and Niels-Ulrik Frigaard2
1
2
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
Institute of Molecular Biology and Physiology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark
Genome sequencing projects are revealing new
information about the distribution and evolution of
photosynthesis and phototrophy. Although coverage
of the five phyla containing photosynthetic prokaryotes
(Chlorobi, Chloroflexi, Cyanobacteria, Proteobacteria
and Firmicutes) is limited and uneven, genome
sequences are (or soon will be) available for >100 strains
from these phyla. Present knowledge of photosynthesis
is almost exclusively based on data derived from cultivated species but metagenomic studies can reveal new
organisms with novel combinations of photosynthetic
and phototrophic components that have not yet been
described. Metagenomics has already shown how the
relatively simple phototrophy based upon rhodopsins
has spread laterally throughout Archaea, Bacteria and
eukaryotes. In this review, we present examples that
reflect recent advances in phototroph biology as a result
of insights from genome and metagenome sequencing.
Photosynthesis and phototrophy
Photosynthesis is arguably the most important biological
process on Earth, and only two mechanisms for collecting
light energy and converting it into chemical energy have
been described (Box 1). The first mechanism, which is
dependent upon photochemical reaction centers (RCs;
see Glossary) that contain (bacterio)-chlorophyll
[(B)Chl], is found in five bacterial phyla: Cyanobacteria,
Proteobacteria, Chlorobi, Chloroflexi and Firmicutes. All
currently described Chlorobi and Cyanobacteria strains
are photoautotrophs but only some strains of Chloroflexi
[filamentous anoxygenic phototrophs (FAPs)], Proteobacteria (purple sulfur and purple non-sulfur bacteria) and
Firmicutes (heliobacteria) are phototrophic (Figure 1).
The second mechanism employs rhodopsins, retinalbinding proteins that respond to light stimuli [1]. Several
homologous types of rhodopsins are known in microbes
and include energy-conserving transmembrane proton
pumps [bacteriorhodopsin (BR), proteorhodopsin (PR),
xanthorhodopsin] (Figure 2), transmembrane chloride
pumps (halorhodopsins) and light sensors (sensory rhodopsins) [1,2]. Here, we review how genome and metagenome sequencing studies are providing new insights into
the physiology, metabolism and evolution of the organisms that perform these two processes for the capture of
light energy.
Corresponding author: Bryant, D.A. ([email protected]).
Available online 25 September 2006.
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Glossary
Anoxygenic photosynthesis: photosynthesis performed by organisms that do
not evolve oxygen; it uses electron donors other than water for carbon dioxide
reduction.
Bacteriorhodopsin (BR): a rhodopsin first identified in haloarchaea; translocates protons to the periplasm after light-induced isomerization of retinal.
Chlorobi: bacterial phylum that includes the green-colored and brown-colored
green sulfur bacteria; these bacteria have type 1 reaction centers (containing
BChl a and Chl a) and chlorosomes containing BChl c, d or e. They fix carbon by
the reverse tricarboxylic cycle and oxidize sulfide, sulfur, thiosulfate, Fe2+ or H2.
Chloroflexi: bacterial phylum that includes the filamentous anoxygenic
phototrophs (FAPs), formerly known as the green gliding or green filamentous
bacteria.
Cyanobacteria: bacterial phylum that includes all oxygen-evolving photosynthetic bacteria; they have Chl a-containing type 1 and type 2 reaction centers
and fix carbon by the reductive pentose-phosphate (Calvin–Benson–Bassham)
cycle; most have phycobilisomes as light-harvesting antennae (but see
Prochlorophytes).
Filamentous anoxygenic phototrophs (FAPs): Chloroflexi that have BChl acontaining, type 2 reaction centers. They might have chlorosomes that contain
BChl c and most fix carbon by the 3-hydroxypropionate cycle whereas some
oxidize sulfide or H2.
Heliobacteria: endospore-producing photoheterotrophic bacteria of the phylum Firmicutes that have type 1 reaction centers and BChl g.
Oxygenic photosynthesis: photosynthesis that uses water as the electron
donor and leads to oxygen evolution.
Photochemical reaction center: a multisubunit protein complex containing
chlorophylls or bacteriochlorophylls, in which light energy is transduced into
redox chemistry.
Photosynthesis: the reduction of carbon dioxide into biomass using energy
derived from light.
Phototrophy: a metabolic mode in which organisms convert light energy into
chemical energy for growth.
Prochlorophyte: a cyanobacterium such as Prochlorococcus spp. that synthesizes both divinyl-Chl a and divinyl-Chl b but lacks phycobilisomes.
Proteorhodopsin (PR): a rhodopsin first identified in marine proteobacteria,
which translocates protons to the periplasm after light-induced isomerization
of retinal.
Purple bacteria: bacteria of the phylum Proteobacteria that produce BChl a or b
under oxic or anoxic conditions. They have type 2 reaction centers and
membrane-intrinsic caroteno-BChl antennae; many oxidize sulfide, thiosulfate,
or H2 and they fix carbon by the reductive pentose-phosphate (Calvin–Benson–
Bassham) cycle.
Rhodopsin: a membrane-intrinsic protein characterized by seven transmembrane a-helices and a covalently attached carotenoid, retinal.
Type 1 reaction center: RC family found in cyanobacteria, green sulfur bacteria
and heliobacteria. They have either homodimeric or heterodimeric cores with
[4Fe-4S] clusters as their terminal electron acceptors and produce weak
oxidants and strong reductants (reduced ferredoxin).
Type 2 reaction center: RC family found in cyanobacteria, purple bacteria and
filamentous anoxygenic bacteria; all have heterodimeric cores with quinones
as terminal electron acceptors. They produce strong oxidants and weak
reductants (hydroquinone).
Genome sequencing projects for photosynthetic
prokaryotes
Synechocystis sp. PCC6803, a unicellular cyanobacterium,
was the third prokaryote and the first photosynthetic organism to have its chromosome completely sequenced [3]. Over
the past decade, there has been explosive growth in the
0966-842X/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tim.2006.09.001
Review
TRENDS in Microbiology
Box 1. Photosynthesis and phototrophy
Photosynthesis is the reduction of CO2 into biomass using energy
derived from light. Biological CO2 reduction requires both ATP and
electrons, which can be provided as NADPH or reduced ferredoxin.
However, the ultimate electron source is organism-dependent and
can be H2O, H2S, H2 or other reduced inorganic compounds.
Phototrophy refers to a metabolic mode in which organisms convert
light energy into chemical energy for growth. Thus, all photosynthetic bacteria are phototrophic but not all phototrophic bacteria are
photosynthetic.
Two mechanistically distinct processes empower phototrophy. In
the first and simplest case, light energy directly drives proton
expulsion from cells through the proteins BR or PR, thereby creating
a proton-motive force that can be used either to drive ATP synthesis
through ATP synthase or to drive various secondary transport
processes [1,47] (Figure 2). Because PRs and BRs do not mediate
electron transfer reactions, organisms that use these proteins are
phototrophs but they have not yet been shown to be photosynthetic.
In the second and more complex type of phototrophy, light
initiates electron transfer through oxidation of a chlorophyll and
reduction of an electron acceptor; secondary electron transfer
reactions that do not require light subsequently lead to the
production of proton-motive force that can be coupled to ATP
synthesis. This second mechanism is absolutely dependent upon
(B)Chl-containing proteins known as photochemical RCs (Figure 1).
Type 1 RCs produce weak oxidants and strong reductants through
their terminal, electron-accepting [4Fe-4S] clusters; type 2 RCs
produce strong oxidants and a weak reductant (a reduced quinone
molecule). The two types of RCs have similar structures [57,62–64]
and seem to share a common evolutionary origin [57,65]. To date,
(B)Chl biosynthesis has not been detected in any archaeal organism,
so photosynthesis most probably evolved after the divergence of
the archaeal–eukaryal and bacterial lineages. Although most RCcontaining bacteria are autotrophs and are thus photosynthetic,
some bacteria (e.g. heliobacteria) that have a single type of RC do
not grow autotrophically when provided with CO2 and an electron
source [39]; presumably, they only perform cyclic electron transfer
for ATP synthesis. Similar to rhodopsin-containing organisms, these
bacteria are not photosynthetic but are photoheterotrophs. Photosynthetic organisms produce a variety of light-harvesting antenna
structures (the protein components of which do not share a
common evolutionary ancestor) to enhance the rate of light-driven
electron transport [57,65,66]. Examples include phycobilisomes,
chlorosomes and a variety of light-harvesting (B)Chl and caroteno(B)Chl proteins [25,57,66] (Figure 1).
genome sequencing of photosynthetic prokaryotes, and the
Genomes On-Line Database (http://www.genomesonline.
org/) and other sources currently indicate that 55 Cyanobacteria, 12 Chlorobi, nine Chloroflexi, 24 Proteobacteria
and two Firmicutes (heliobacteria) are or soon will be completely sequenced. These data will have a substantial
impact on the understanding of the origins and evolution
of photosynthesis while providing many exciting new
insights into the properties of these ecologically and environmentally important organisms.
Cyanobacteria: the oxyphototrophs
Cyanobacteria are such an ancient and remarkably diverse
group of Bacteria that even data for 55 organisms provide
an extremely limited view of their complexity. There are
>475 pure strains in the Pasteur Culture Collection of
Cyanobacteria, and yet this collection includes only a small
number of the several thousand described species. To
illustrate the magnitude of this problem, the smallest
genomes for photosynthetic bacteria are 1.7 Mb and
are found in the marine, unicellular Prochlorococcus spp.
[4,5] whereas Nostoc punctiforme has the largest genome
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(9 Mb) sequenced thus far [6]. N. punctiforme can differentiate into multiple specialized cells (hormogonia, akinetes and heterocysts), establishes cellular patterns of
development for heterocysts within its filaments and forms
symbioses with fungi and plants. Genome size estimates
indicate that some Calothrix sp. genomes are even larger at
12–15 Mb [7]. These prokaryotes have genomes that are as
large as those of yeast and gene contents approaching that
of Drosophila melanogaster! As additional, morphologically and developmentally distinctive cyanobacteria are
studied by genomic methods, new mechanisms that regulate cellular interactions are likely to emerge. Unlike
other Gram-negative bacteria, colonial cyanobacteria do
not appear to employ autoinducer-2 (a furanosyl borate
diester [8]) or acyl-homoserine lactones [9] as quorumsensing and signaling molecules for biofilm development
or other cellular interactions.
Comparisons of cyanobacterial genome sequences from
ecotypes of the same species and from closely related
species are already providing new insights into the relationships between ecological niche, gene content and speciation for environments as different as the oligotrophic
ocean and dense, nutrient-rich microbial mats. The most
detailed studies to date of the closely related marine
Synechococcus and Prochlorococcus species have provided
important insights into the ecophysiology of these genera
[4,5,10–12], and this information has been substantially
extended by metagenomic data from the Sargasso Sea [13].
Specific gene-content differences have been correlated with
the physiological properties of high-light and low-light
adapted ecotypes of these genera. In turn, these properties
can be correlated with the chemical and physical differences that are found in the upper and lower portions of the
photic zone in the ocean [4,5,10–12].
Delong et al. [14] have recently expanded this concept by
examining both organismal and gene-content variation as
a function of depth in the planktonic microbial communities in the North Pacific subtropical gyre. Their results
show that the distribution of taxonomic groups, functional
gene repertoires and metabolic potentials vary with depth
in ways that relate to carbon and energy metabolism,
adhesion and motility, gene mobility and host–virus interactions. These studies raise interesting questions about
how different ecotypes arise and how they persist in the
oceans [12]. Ambient temperature and growth temperature optima seem to be important along with light, nutrients and competitor abundances [15]. The observation that
cyanophages sometimes carry photosynthesis genes [16–
20] provides one explanation for how genes can be rapidly
exchanged throughout these populations. The genome
sequencing, metagenomics and ‘metatranscriptomics’ of
Ward and coworkers [21] are addressing similar issues
in the integrated ‘community metabolism’ and ecophysiology of the cyanobacteria of a different physicochemical
environment: the phototrophic mats of the Octopus and
Mushroom Springs in Yellowstone National Park. Stenou
et al. [21] have recently shown that two populations of
thermophilic Synechococcus spp. in these mats perform
photosynthesis by day and seem to ferment stored carbohydrates to generate reductant for nitrogen fixation by
night.
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TRENDS in Microbiology Vol.14 No.11
Figure 2. Simple scheme for phototrophy based on BR or PR and ATP synthase.
Absorption of light by retinal leads to isomerization of retinal causing a
conformational change in PR or BR, which in turn leads to the expulsion of a
proton to the periplasmic space. Translocation of protons to the cytoplasm is
coupled to the synthesis and release of cytoplasmic ATP by ATP synthase. Image
of BR molecules (left) reproduced, with permission, from Ref. [58]. ß (2004)
Elsevier. ATP synthase image (right) reproduced, with permission, from Ref. [59].
ß (2004) Nature Publishing Group.
Figure 1. Distribution of reaction center types and antenna systems in
photosynthetic bacteria, which are found in the Cyanobacteria, Chlorobi,
Proteobacteria, Chloroflexi and Firmicutes. Type 1 RCs (left) have [4Fe-4S] clusters
(Fe-S) as terminal electron acceptors, whereas type 2 RCs (right) have quinones (Q)
as electron acceptors. Colors indicate whether a RC is a homodimer (e.g.
heliobacteria and green sulfur bacteria) or a heterodimer [photosystem (PS) I and
all type 2 RCs]. Cyanobacteria have Chl-a-containing PS I (left) and PS II (right) and
have light-harvesting phycobilisomes that are principally associated with PS II.
Dotted lines in the type 1 RC subunits indicate the existence of both a light-harvesting
domain, which is structurally related to subunits CP43 and CP47 of PS II, and an
electron transfer domain, which is structurally related to the subunits of both the PS II
core and other bacterial type 2 RCs. Prochlorophytes lack phycobilisomes and,
instead, have light-harvesting PCB proteins, which are structurally related to CP43
and bind to both divinyl-Chl a and divinyl-Chl b. Heliobacteria have homodimeric
type 1 RCs with BChl g. Green sulfur bacteria (Chlorobi) have homodimeric type 1
RCs that bind to BChl a and a small amount of Chl a; their chlorosomes contain
>200 000 BChl c, d or e molecules and a small amount of BChl a that is bound to the
CsmA protein. The BChl-a-binding FMO protein connects chlorosomes to the RCs.
Purple bacteria and FAPs are similar and have type 2 bacterial RCs that carry either
BChl a (or BChl b in some purple bacteria). The antennae for these RCs are formed by
ring-shaped, BChl-a-binding LH1 and LH2 complexes in purple bacteria or
chlorosomes containing BChl c and BChl a in some FAPs. The LH1-like complexes
of FAPs can also form rings around their type 2 RCs. ‘Red’ FAPs lack the chlorosomes
that are found in ‘green’ FAPs. The chlorosomes of FAPs are usually smaller and
contain fewer BChl c molecules than those found in the Chlorobi.
Chlorobi: green sulfur bacteria
In contrast to the extraordinary richness of cyanobacterial
diversity, the phylum Chlorobi (comprising the green sulfur bacteria) is a metabolically limited, physiologically
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well-defined and genetically closely related bacterial
group, which shares a common root with the Bacteroidetes.
Comparative genomic analyses have enabled the elucidation of their unique BChl and carotenoid biosynthetic
pathways. Chlorobi are obligately anaerobic photoautotrophs that (i) oxidize sulfur compounds, H2 or ferrous
iron; (ii) fix carbon by the reverse tricarboxylic acid cycle;
(iii) synthesize BChl c, d or e along with BChl a and Chl a;
and (iv) have a photosynthetic apparatus that comprises a
type 1 reaction center, the Fenna-Matthews-Olson (FMO)
BChl-a-binding protein and chlorosomes that each contain
>200 000 BChl c, d or e molecules (Figure 1) [22–25].
Because of the availability of an efficient natural transformation system and its ability to grow rapidly with thiosulfate as an electron donor, Chlorobium tepidum – the
2.15 Mb genome of which was sequenced by The Institute
for Genomic Research [26] – has become the model organism for this group of phototrophs. Insights into the physiology, metabolism and light-harvesting apparatus of this
organism have been reviewed elsewhere [22–25].
Although fewer Chlorobi genomes have been sequenced
than cyanobacterial genomes, the ten sequenced and two
anticipated genomes encompass most of the currently
known diversity of this group. The Joint Genome Institute
of the Department of Energy (JGI-DOE) has sequenced
most of the type strains of the Chlorobi, and these data
provide benchmarks for comparisons of future isolates.
Complete genomes are already available for two additional
strains, Pelodictyon luteolum DSM273 and Chlorobium
chlorochromatii (Box 2 and Figure 3), and draft genomes
are available for seven additional strains (C. ferrooxidans,
C. phaeobacteroides DSM 266, C. limicola DSM245, C.
vibrioforme DSM 265, Prosthecochloris aestuarii SK413,
Pelodictyon phaeoclathratiforme and an enrichment
culture, C. phaeobacteroides BS-1, isolated from 100 m
below the surface of the Black Sea [27]). Sequencing of
Chloroherpeton thalassium and C. vibrioforme 8327d
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TRENDS in Microbiology
Box 2. Phototrophic consortia
With the exception of Chloroherpeton thalassium, which exhibits
gliding motility, all known green sulfur bacteria are non-motile.
Some green sulfur bacteria (‘epibionts’) become motile by forming
phototrophic consortia through a specific association with a bproteobacterium, denoted the ‘central rod’ [60,61,67] (Figure 3).
Each polarly flagellated central rod carries 20–60 epibiont cells and
the entire consortium is phototactic in response to light signals
perceived by the epibiont. The nature of any metabolic coupling
between the two organisms is not yet known but possibilities
include transfer of reduced carbon and/or nitrogen from the epibiont
to the central rod and possibly the provision of sulfide from sulfate
reduction or H2 from the central rod to the epibiont. At present, the
mechanisms of cell-to-cell signaling for phototaxis and coordination
of cell division are completely unknown.
Genome sequencing of the two partners of ‘Chlorochromatium
aggregatum’, which was isolated as an enrichment culture from
Lake Dagow [60,67], should help to answer many of these questions.
The 2.57 Mb genome of the epibiont, Chlorobium chlorochromatii,
which is not an obligate symbiont [67], has already been completely
sequenced (http://img.jgi.doe.gov/). Sequencing of the b-proteobacterial central rod, which cannot be grown independently from C.
chlorochromatii and is most closely related to Rhodoferax sp. [60], is
now in progress at JGI-DOE. C. chlorochromatii encodes a family of
calcium-dependent, RTX-toxin-like proteins that might be involved
in cellular adhesion to the central rod [68]. The largest gene is
predicted to encode a protein of 36 805 amino acids, one of the
largest predicted proteins known to date. This gene occurs in an
apparent operon with a sequence-related gene of 20 646 codons,
producing an operon of >170 kb. Homologs of these genes occur in
Magnetococcus sp. MC-1 (15 245 codons) and Synechococcus sp.
RS9917 (28 178 codons) but their functions are unknown.
should be completed later this year. The sequenced
Chlorobi have 2–3 Mb genomes that encode 1750–
2800 genes (http://img.jgi.doe.gov/) and pairwise comparisons show that Chlorobi strains share a common core-set
of 1400–1500 genes. Chlorobi genomes encode only a few
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491
predicted transporters for organic molecules, have a small
number of predicted transcription regulators, and are
largely devoid of two-component histidine kinases and
response regulators. These observations suggest that
Chlorobi live in relatively constant (and energy-limited)
conditions and that they probably have a limited capacity
to respond to changes in their physicochemical environment [22,26]. This is a trait that is shared by members of
the cyanobacteria with reduced genomes, such as Prochlorococcus and marine Synechococcus [4,5,10].
Pigment biosynthetic pathways in Chlorobi
The availability of multiple Chlorobi genome sequences
and of a highly efficient natural transformation system for
C. tepidum has facilitated the identification of genes that
encode enzymes for pigment biosynthesis and other physiological processes in green sulfur bacteria. C. tepidum
synthesizes three chlorophylls: BChl c, BChl a and Chl a
[24]. Before the completion of its genome sequence, no
enzyme specifically involved in BChl c, d or e biosynthesis
had been identified, and now all steps but one in the
pathway leading from chlorophyllide a to BChl c are
known. Only the enzyme responsible for the removal of
the C-132 methylcarboxyl group has not yet been identified. Moreover, the erroneous identification of the 8-vinyl
reductase as BchJ has recently been corrected [24]. Similarly, although nothing was known about the pathway for
carotenoid biosynthesis in Chlorobi before the availability
of the genome sequence, all of the enzymes required for
synthesis of chlorobactene and isorenieratene have been
identified [28,29]. Through these analyses, it is now clear
that carotenoid biosynthesis in Chlorobi is more similar to
the pathway in Cyanobacteria than to that in other bacteria
[28]. Although no member of the three known families of
Figure 3. Phototrophic consortia. (a) Transmission electron micrograph of a thin section of the phototrophic consortium ‘Chlorochromatium aggregatum’. The central
rod (CR; a b proteobacterium with a putative genome size of 4–5 Mb) and the epibiont cells (EB; the green sulfur bacterium Chl. Chlorochromatii with a genome size of
2 572 079 bp) are indicated. (b) Light micrograph of ‘Chlorochromatium aggregatum’. Scale bar = 5 mm. Scanning electron micrographs of ‘Pelochromatium roseum’ before
(c) and after (d) division of the EB. Scale bar = 1 mm. (e) Thin-section electron micrograph of the junction of an EB cell with the central rod. Note that chlorosomes, the
electron-dense ellipsoids on the inner surface of the cytoplasmic membrane of the EB cells, do not occur at the junction with the CR and that an additional wall layer
between the cells can be seen at this junction [60]. Additionally, a paracrystalline structure is seen at the cell junctions at the inner surface of the CR (boxed region). Scale
bar = 0.5 mm. Parts (b), (c) and (d) reproduced, with permission, from Ref. [61]. ß (2002) Springer.
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lycopene cyclases could be identified in the C. tepidum
genome, phylogenetic profiling (using data from multiple
photosynthetic bacteria) and complementation of a
lycopene-producing strain of Escherichia coli both identified
a fourth type of lycopene cyclase encoded by the C. tepidum
open reading frame CT0456 [29] (J.A. Maresca et al.,
unpublished). The identification of the ‘missing’ lycopene
cyclase in C. tepidum also enabled the identification of
‘missing’ lycopene cyclases in several cyanobacteria.
Interestingly, many cyanobacteria have an ortholog and a
paralog of CT0456, and both of these enzymes seem to be
involved in cyclase reactions with lycopene (J.E. Graham
and D.A. Bryant, unpublished). Synechococcus sp. PCC7942
has lycopene cyclases that belong to two of the four families,
which demonstrates the mosaic nature of carotenoid
biosynthesis and is a likely example of lateral gene
transfer.
The sequenced Chlorobi strains are metabolically similar
but can be separated according to particular phenotypes
(e.g. green-colored strains that contain BChl c and chlorobactene versus brown-colored strains that contain BChl e
and isorenieratene, or strains that oxidize sulfur compounds
versus ferrous iron). Thus, whole-genome comparisons can
identify candidate genes that are responsible for defined
physiological differences among these strains. This
approach was recently used to search for candidate gene(s),
the product(s) of which could convert BChl c into BChl e. This
analysis identified a radical SAM enzyme and an adjacent
dehydrogenase as the most likely candidates for this transformation (J.A. Maresca and D.A. Bryant, unpublished).
Interestingly, these two genes occur adjacent to the gene
encoding g-carotene cyclase, which produces b-carotene,
the precursor of isorenieratene [29] (J.A. Maresca et al.,
unpublished). The proximity of these genes on a 6 kb
segment of the chromosome provides a possible explanation for the polyphyletic nature of the ‘brown’ phenotype
among green sulfur bacteria. This gene proximity would
greatly facilitate their lateral transfer among the Chlorobi, and such transfer would immediately confer the
ability to populate a new environmental niche. The
synthesis of BChl e is another example of a reaction for
which both oxygen-independent and oxygen-dependent
enzymes occur in nature [23,30]. The C-7 formyl group
introduced during BChl e biosynthesis must be derived
from water because this reaction occurs under anoxic
conditions; however, the C-7 formyl group of Chl b in
Prochlorococcus sp., green algae and higher plants is
derived from oxygen [31].
Chloroflexi: filamentous anoxygenic phototrophs
Because of their diverse metabolic and physiological properties, genomic analyses of diverse strains of Chloroflexi
are likely to produce novel insights into the evolution of
photosynthesis. The phylum Chloroflexi is one of the earliest diverging lineages of the Bacteria, and it contains
several genera of filamentous, gliding bacteria that perform anoxygenic photosynthesis (FAPs) [32]. The phylum
contains two orders, the ‘Chloroflexales’ and ‘Herpetosiphonales’. Herpetosiphon aurantiacus, the type strain of
the latter order, has recently been sequenced by JGI-DOE.
The 6.6 Mb genome of this heterotrophic bacterium
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encodes the enzymes for carotenoid biosynthesis but has
no genes for the enzymes of BChl biosynthesis or
components of the photosynthetic apparatus. Pierson
and Castenholz first isolated Chloroflexus aurantiacus,
the type strain of the Chloroflexi and ‘Chloroflexales’, in
the early 1970s from Yellowstone National Park and other
thermal features [32]. Cfx. aurantiacus synthesizes BChl a
and BChl c and has type 2 RCs and chlorosomes but lacks
the FMO protein (Figure 1). The ‘red/orange’ FAPs of the
genera Roseiflexus and Heliothrix do not synthesize BChl c
and lack chlorosomes [32,33] (Figure 1).
Until recently, the incomplete 5.2 Mb draft sequence of
Cfx. aurantiacus was the only genomic information available for any photosynthetic member of the Chloroflexi.
However, JGI-DOE will soon release the draft genomes
of four additional Chloroflexi: Cfx. aggregans (4.5 Mb),
Roseiflexus sp. strain RS-1 (5.8 Mb; from Octopus Springs,
Yellowstone National Park), Roseiflexus castenholzii
(5.6 Mb; from Nakabusa Hot Springs, Japan) and the
heterotroph Herpetosiphon aurantiacus (6.6 Mb). In addition, three sulfide-oxidizing FAPs (Chlorothrix halophila,
Oscillochloris sp. strain UdG 9002 and Chloronema giganteum strain UdG 9001) are scheduled for sequencing by
JGI-DOE later this year. A consortium of Russian scientists is sequencing the genome of Oscillochloris trichoides
(R. Ivanovskii and B. Kuznetsov, personal communication). O. trichoides produces a type I ribulose-1,5-bisphosphate carboxylase–oxygenase (RubisCO) and fixes carbon
dioxide by the Calvin cycle rather than by the 3-hydroxypropionate cycle [34]. However, it is not known whether
other FAPs have RubisCO and use the Calvin cycle. It will
be interesting to see whether the sulfide-oxidizing FAPs
have type 1 RCs like the Chlorobi or have type 2 RCs (and
reverse electron transport) like Cfx. aurantiacus and purple bacteria. Roseiflexus sp. and O. trichoides have nitrogenase genes, and other FAPs also probably fix dinitrogen.
Much more information will soon be available for these
poorly characterized phototrophs.
Like purple non-sulfur bacteria, Cfx. aurantiacus
exhibits considerable metabolic diversity and it can grow
as an aerobic chemoheterotroph or as an anaerobic photoheterotroph. Using electrons derived from H2 or H2S under
anoxic or microaerophilic conditions, some strains of Chloroflexus sp. grow photoautotrophically by fixing CO2
through the 3-hydroxypropionate pathway [32]. In nature,
Cfx. aurantiacus probably grows under microaerophilic or
alternating oxic and anoxic conditions but it only fully
develops its photosynthetic apparatus under anoxic conditions. As a result, Cfx. aurantiacus encodes some
enzymes that can function under either oxic or anoxic
conditions [23,30]. For example, both bchE and acsF genes
are found in the Cfx. aurantiacus genome; these genes
encode the oxygen-independent isocyclic ring cyclase and
the oxygen-dependent isocyclic ring cyclase, respectively.
Both Roseiflexus sp. strains and Cfx. aggregans also produce both of these enzymes. Interestingly, the same pattern is not found for hemF and hemN, which encode
oxygen-dependent and oxygen-independent coproporphyrinogen oxidases, respectively. The two Chloroflexus strains
have both genes, whereas the Roseiflexus sp. strains do not
encode hemF.
Review
TRENDS in Microbiology
Proteobacteria: purple non-sulfur and purple sulfur
bacteria
Photosynthesis is a trait that is widespread but not
universal among members of the Proteobacteria and is
found in morphologically and metabolically diverse species.
Genome sequence information has largely confirmed the
physiological versatility and corresponding large genome
sizes of these organisms. Some of the photosynthetic proteobacteria are well suited for studies of global gene regulation because many members are facultatively phototrophic
or photosynthetic under anoxic conditions. Photosynthetic
Proteobacteria can be found in the a, b and g subdivisions
but, to date, almost all available genome sequences are from
members of the a subdivision. Several genomes have been
determined (http://www.genomesonline.org), including
those of Rhodopseudomonas palustris (5.5 Mb) [35], two
Rhodobacter sphaeroides strains (4.6 Mb) [36] (http://
www.ncbi.nlm.nih. gov/), Rhodospirillum rubrum (4.4 Mb)
(http://www.ncbi. nlm.nih.gov/), Roseobacter denitrificans
(http://genomes. tgen.org/rhodobacter.html), Bradyrhizobium sp. (9.1 Mb) and Roseobacter sp. (4.1 Mb) (http://
www.genomesonline. org).
Only two g-subdivision members have been studied and
no photosynthetic b-proteobacterium has been sequenced.
Thus, the environmentally important purple sulfur bacteria, all of which belong to the g subdivision, along with
purple bacteria of the b subdivision (many of which can
also use sulfur or H2 as electron donors), represent groups
about which little genome sequence information is available. Finally, a large number of mostly a-proteobacteria in
diverse freshwater, saline, marine, soil and hot-spring
environments seem to have photosynthesis gene clusters
but, in many cases, the function of the relatively low levels
of BChl a produced under aerobic conditions is unknown
[37,38]. Projected sequencing projects and comparative
analyses will help to define the genetic, physiological
and metabolic differences among these aerobic anoxygenic
phototrophs, photoheterotrophs like Rhodobacter sp., and
the photolithoautotrophic purple sulfur bacteria. Genome
sequence data, in combination with the physiological and
metabolic versatility of these organisms, should lead to
engineered strains for diverse applications in biotechnology, including bioremediation, lignin degradation and biofuels and hydrogen production [35].
Heliobacteria
Heliobacteria, first described by Gest and Favinger in 1983
[39], are the most recently discovered group of bacteria
containing RCs and they remain the most poorly characterized overall. Heliobacteria are members of the phylum
Firmicutes and are closely related to clostridia. Like
Bacillus or Clostridium sp., heliobacteria produce heatresistant endospores and, to date, no characterized member of this group is known to grow photoautotrophically.
Studies with Heliobacillus mobilis have shown that
many of the genes for synthesis of BChl g and the RC
are located in a 30 kb cluster similar to the photosynthesis gene clusters found in purple bacteria [40,41]. Thus,
it is possible that the heliobacteria obtained their
photosystem components through a lateral gene transfer
event. However, a recent detailed analysis of RC and
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493
light-harvesting protein sequences argues that lateral
gene transfer is not required to explain the current distribution of RC sequences [42]. No complete heliobacterial
genome sequence is yet available, although the 3.1 Mb
draft genome of Heliobacterium modesticaldum has
recently been made available for searches (http://genomes.
tgen.org/helio.html). The H. modesticaldum genome
sequence will help to clarify the possible lateral acquisition
of photosynthesis genes and it will also help to identify
genes that are required for carotenoid, BChl, and RC
synthesis and function. The relatively small genome of
H. modesticaldum is likely to provide new insights into
genes that are functionally important in sporulation and
regulation of this process.
Bacteriorhodopsin-based phototrophy in halophilic
prokaryotes
Comparative analyses of sequenced genomes and
metagenomic data from the ocean have shown the great
diversity in the structure and function of rhodopsins and
have demonstrated how easily lateral gene transfer can
occur among unrelated organisms. Bacteriorhodopsin (BR)
in the so-called ‘purple membrane’ of halophilic archaea
has been studied for three decades and the structure and
function of BR is known in great detail [1] (Figure 2). The
halophilic archaea grow well in the dark as aerobic chemoheterotrophs; however, strains that synthesize BR exhibit light-enhanced growth under anoxic conditions and are,
therefore, facultatively phototrophic [43].
Among these haloarchaea, multiple rhodopsins with
diversified functions can exist within a single cell. The
genome of the haloarchaeon Haloarcula marismortui
encodes six homologous rhodopsins: one proton-pumping
BR, one chloride-pumping halorhodopsin, two sensory
rhodopsins and two opsins of unknown function [44].
The importance of these rhodopsins for environmental
adaptation was recently and elegantly illustrated
through the genome sequence of a halophilic bacterium,
Salinibacter ruber, which taxonomically belongs to the
Cytophaga–Flexibacter–Bacteroides group [45]. Genomewide analyses showed that S. ruber has evolved convergently towards halophilic archaea at both the physiological
level (different genes producing a similar overall phenotype) and at the molecular level (independent mutations
yielding proteins with similar sequences or structures).
Although the identity of the donor organism (or organisms)
is uncertain, the genome of S. ruber encodes four rhodopsins – the obvious result of lateral gene exchange with the
haloarchaea. One rhodopsin resembles a chloride pump
and two resemble sensory rhodopsins. The fourth is a
proton-pumping rhodopsin, xanthorhodopsin, which is
related to proteorhodopsins but contains a salinixanthin
carotenoid chromophore in addition to retinal [46].
Proteorhodopsin in marine prokaryotes
Other than those in haloarchaea, the first example of a
prokaryotic rhodopsin was one found in a marine proteobacterium and, thus, it was named proteorhodopsin (PR)
[47,48]. This identification was based on a metagenomics
approach in which large fragments of genomic DNA
isolated from marine picoplankton were cloned and
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TRENDS in Microbiology Vol.14 No.11
sequenced. Like BR, PR has been shown by heterologous
expression to function as a light-driven, transmembrane
proton pump in E. coli [47] and, thus, it could contribute
substantially to the energy budget in cells living in the
photic zone of oceans. Therefore, it is not surprising that
sequencing of both short and long fragments of environmental DNA has shown that a wide range of PRs exist in
highly different types of marine prokaryotic plankton
[13,49–51]. For example, PR is present in marine euryarchaeotes in the photic zone of the North Pacific subtropical
gyre, whereas the marine euryarchaeotes living below the
photic zone do not have PR, clearly as a consequence of
environmental adaptation [51].
Recently, Pelagibacter ubique, a representative of the
ubiquitous SAR11 marine proteobacteria, was axenically
cultivated and its genome was sequenced [52]. This
genome contains one gene encoding PR [52,53] but has
no genes that are characteristic for CO2 fixation. The
genomes of other marine proteobacteria (Photobacterium
sp. SKA34 and Vibrio angustum S14) and marine
Bacteroidetes (Polaribacter irgensii, Cellulophaga sp.
MED134, Tenacibaculum sp. MED152 and Psychroflexus
torquis ATCC700755), which are currently being
sequenced by the J. Craig Venter Institute (https://
research.venterinstitute.org/moore/), also contain PRs.
Although laboratory growth experiments with P. ubique
have not yet demonstrated that this bacterium grows
faster in the light than in the dark [53], it seems likely
that PR enables the bacterium to benefit from light even
though the experimental conditions to show this have not
yet been identified. Although the structure of this PR is
consistent with a function in proton pumping, it remains
possible that this molecule could instead transport another
substrate or function as a sensory molecule.
To put it briefly, it seems that many, if not most, of the
planktonic prokaryotes in the photic zone of the oceans
that do not contain photosynthetic reaction centers nevertheless exploit light by having acquired PR through lateral
gene transfer. The exact physiology of the marine prokaryotes that harbor these PRs is not always clear. For
example, a recently characterized 95 kb genomic fragment
from a marine proteobacterium that encodes a PR also
encodes a putative reverse dissimilatory sulfite reductase
operon, which could provide reducing equivalents for autotrophic growth by oxidizing a reduced sulfur compound
[54].
The ‘cosmopolitan’ rhodopsins versus the ‘refined’
reaction centers
Shotgun sequencing of DNA from the Sargasso Sea
illustrated how PRs are widespread in oceanic microorganisms [13]. Although the exact functions of the rhodopsins are
often not known, genome sequencing projects of organisms
in pure culture have also confirmed that rhodopsins are
much more widely distributed among different organismal
lineages than first anticipated. For example, rhodopsins of
unknown function have been found in the genomes of
organisms as diverse as halophilic archaea and bacteria,
marine proteobacteria, marine Bacteroidetes, marine
euryarchaeotes,
g-radiation-resistant
actinobacteria
(Rubrobacter xylanophilus and Kineococcus radiotolerans)
www.sciencedirect.com
and the Gram-positive Exiguobacterium sp. 255–15, in
addition to certain cyanobacteria, fungi, green algae and
a dinoflagellate (Pyrocystis lunula). The single rhodopsins
encoded by the genomes of the cyanobacteria Nostoc
sp. PCC7120 (Alr3165) and of the fungus Leptosphaeria
maculans have recently been shown by experimental
characterization to be a sensory rhodopsin [55] and a
proton-pumping rhodopsin [56], respectively. As a last
example, the early-diverging cyanobacterium, Gloeobacter
violaceus, encodes a rhodopsin (Gll0198) that seems to be
most similar to the proton-pumping xanthorhodopsin of
S. ruber.
If rhodopsin-based phototrophy is transferred so
easily among organisms, why do only a few groups of
RC-based phototrophs dominate phototrophic niches?
Part of the answer might be that rhodopsin-based phototrophy uses light energy relatively inefficiently. First, to
produce the proton-motive force required to produce one
ATP, three to four BR molecules must each absorb a
photon and release a proton to the periplasmic space.
When a proteobacterial RC absorbs four photons, two
ubiquinol molecules are produced and their dark re-oxidation by the cytochrome bc1 complex enables the production
of two ATP molecules [57]. Second, the single retinal
chromophore in the photochemical units of most rhodopsin-based phototrophs has a much smaller absorption
cross-section than the photochemical units of RC-based
phototrophs, which can have hundreds to thousands of
chromophores [57]. Thus, a rhodopsin-based phototroph
would have to synthesize many more energetically
expensive BR or PR molecules to absorb the same amount
of light energy. The highly efficient and extensive lightharvesting antenna systems of photosynthetic bacteria
Box 3. Are there more phototrophs out there?
Our current knowledge of photosynthesis is based almost
exclusively on cultivated strains but, given the vast diversity of
microorganisms on Earth, these organisms are unlikely to represent
the full spectrum of light utilization. Continued genome sequencing
of cultivated and uncultivated organisms will undoubtedly reveal
many more microbial groups that harbor rhodopsins. It will be
interesting to see if there are any organisms that combine
rhodopsin-based phototrophy with CO2 fixation because such
organisms could then be classified as Chl-independent photosynthetic organisms. A priori, there seems to be no reason why the
carbon fixation reactions of the Calvin cycle could not be driven by
the combination of PR and sulfide:quinone oxidoreductase coupled
to a type I NADH dehydrogenase for reverse electron flow.
Alternatively, a rhodopsin and hydrogenase could be coupled to
provide the energy and reducing power for photolithoautotrophic
growth.
As more environments are sampled, metagenomics are likely to
reveal photosynthetic organisms with combinations of components
that have not yet been observed in cultivated species (e.g. an
anoxygenic organism with two types of RCs), novel solutions to the
problem of light harvesting or the existence of new phyla that have
not previously been shown to contain phototrophic or photosynthetic members. This latter prediction is not simply an idle
speculation: a new phylum-level, RC-containing phototroph has
recently been discovered in this manner and will be described in
detail elsewhere (D.A. Bryant et al., unpublished). The rapidly
increasing body of genome sequence and metagenomic data will
help to answer questions about the origin and evolution of
photosynthesis [42,69].
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TRENDS in Microbiology
enable the RCs to function at maximal efficiency even at
relatively low light intensities.
If RC-based phototrophy is so much more efficient than
rhodopsin-based systems, why does this type of phototrophy not spread laterally? Perhaps it does on rare occasions,
but because even the simplest chlorophyll-based photosystem requires 30 unique genes, this capability probably
cannot be laterally transferred as easily as rhodopsinbased phototrophy. Lateral transfer of rhodopsin-based
photosystems requires only the genes encoding the rhodopsin apoprotein and a carotenoid oxygenase–lyase that
produces retinal [54] if the recipient already has the capability to produce an appropriate carotenoid. If it does not,
retinal biosynthesis can be performed with just four genes
(crtBIY–blh) [54]. Therefore, rhodopsin-based systems
might be much more prone to lateral transfer and, driven
by the selection of light, could thus distribute themselves
among distantly related but sympatric organisms. Metagenomic analyses of photic environments are likely to
identify many new examples in the near future (Box 3).
Concluding remarks and future perspectives
Genome sequencing of cultured organisms and metagenome
sequencing of DNA from uncultured organisms of photic
environments has already greatly accelerated the pace of
new discoveries for the Cyanobacteria and Chlorobi. As
more genomic sequence data become available for other
phototrophic organisms, comparative bioinformatics will
certainly catalyze advances in knowledge of the metabolism,
gene regulation and physiology of these groups and
might answer many outstanding questions about these
organisms (Box 4). Metagenomic studies will ultimately
lead to insights that transcend the level of individual organisms and will facilitate a broader and deeper understanding
of the community-level dynamics among phototrophs (and
non-phototrophs). This approach has the potential to
Box 4. Outstanding questions
(i) Because photosynthetic reaction centers evolved only once,
which came first: type 1 or type 2 reaction centers?
(ii) How did ancestors of cyanobacteria acquire type 1 and type 2
reaction centers, and how did oxygenic photosynthesis
evolve?
(iii) Did bacteria that principally synthesize BChl a arise before or
after those that principally synthesize Chl a?
(iv) Beyond the five known examples, how many additional
bacterial phyla contain members that can synthesize (B)Chl
and photochemical reaction centers?
(v) Are there organisms that combine a rhodopsin-based ATP
generation system with enzymes for the oxidation of an
inorganic electron donor (e.g. sulfide or H2) to drive autotrophic carbon dioxide reduction?
(vi) What is the physiological role of the low amounts of BChl a
found in aerobic anoxygenic phototrophs that are common in
the oceans?
(vii) Nature has evolved multiple, independent solutions to the
problem of harvesting solar energy. Are there novel types of
light-harvesting antenna complexes yet to be discovered, and
can metagenomics help to identify them?
(viii) What are the principal drivers behind the evolution and
distribution of phototrophy? How do nutrients, temperature,
light and other parameters interact with genomic content to
produce niche partitioning and ecotype distributions in photic
environments?
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495
explain how gene contents map onto taxonomic compositions, physiological and metabolic capabilities and gene
expression patterns of phototrophs in diverse photic environments – all of which together lead to the primary energy
input that ultimately drives life and its evolution on Earth.
Acknowledgements
The authors would like to thank Julia A. Maresca for critical reading of
the manuscript and many helpful comments. We also thank Joachim
Weber (Texas Tech University) for use of the ATP synthase image in
Figure 2 and Jörg Overmann (Ludwig Maximilians Universität,
München) for providing Figure 3 parts (a) and (e), and for use of parts
(b), (c) and (d). D.A.B. gratefully acknowledges support for genomics
studies from the National Science Foundation (MCB-MCB-0519743 and
MCB-0523100) and from the Department of Energy (DE-FG02–
94ER20137). N.-U.F gratefully acknowledges support from The Danish
Natural Science Research Council (grant 21–04–0463).
References
1 Lanyi, J.K. (2004) Bacteriorhodopsin. Annu. Rev. Physiol. 66, 665–688
2 Spudich, J.L. and Luecke, H. (2002) Sensory rhodopsin II: functional
insights from structure. Curr. Opin. Struct. Biol. 12, 540–546
3 Kaneko, T. et al. (1996) Sequence analysis of the genome of the
unicellular cyanobacterium Synechocystis sp. strain PCC6803. II.
Sequence determination of the entire genome and assignment of
potential protein-coding regions. DNA Res. 3, 109–136
4 Rocap, G. et al. (2003) Genome divergence in two Prochlorococcus
ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047
5 Dufresne, A. et al. (2003) Genome sequence of the cyanobacterium
Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic
genome. Proc. Natl. Acad. Sci. U. S. A. 100, 10020–10025
6 Meeks, J.C. et al. (2001) An overview of the genome of Nostoc
punctiforme, a multicellular, symbiotic cyanobacterium. Photosynth.
Res. 70, 85–106
7 Herdman, M. et al. (1979) Genome size of cyanobacteria. J. Gen.
Microbiol. 111, 73–85
8 Sun, J. et al. (2004) Is autoinducer-2 a universal signal for interspecies
communication? A comparative genomic and phylogenetic analysis
of the synthesis and signal transduction pathways. BMC Evol.
Biol. 4, 36, DOI: 10.1186/1471-2148-4-36 (http://www.biomedcentral.
com/bmcevolbiol/)
9 Dittmann, E. et al. (2001) Altered expression of two light-dependent
genes in a microcystin-lacking mutant of Microcystis aeruginosa PCC
7806. Microbiology 147, 3113–3119
10 Palenik, B. et al. (2003) The genome of a motile marine Synechococcus.
Nature 424, 1037–1042
11 Ting, C.S. et al. (2002) Cyanobacterial photosynthesis in the oceans: the
origins and significance of divergent light-harvesting strategies.
Trends Microbiol. 10, 134–142
12 Coleman, M.L. et al. (2006) Genomic islands and the ecology and
evolution of Prochlorococcus. Science 311, 1768–1770
13 Venter, J.C. et al. (2004) Environmental genome shotgun sequencing of
the Sargasso Sea. Science 304, 66–74
14 Delong, E. et al. (2006) Community genomics among stratified
microbial assemblages in the ocean’s interior. Science 311, 496–503
15 Johnson, Z.I. et al. (2006) Niche partitioning among Prochlorococcus
ecotypes along ocean-scale environmental gradients. Science 311,
1737–1740
16 Bailey, S. et al. (2004) Cyanophage infection and photoinhibition in
marine cyanobacteria. Res. Microbiol. 155, 720–725
17 Millard, A. et al. (2004) Genetic organization of the psbAD region in
phages infecting marine Synechococcus strains. Proc. Natl. Acad. Sci.
U. S. A. 101, 11007–11012
18 Lindell, D. et al. (2004) Transfer of photosynthesis genes to and from
Prochlorococcus viruses. Proc. Natl. Acad. Sci. U. S. A. 101, 11013–
11018
19 Sullivan, M.B. et al. (2005) Three Prochlorococcus cyanophage
genomes: signature features and ecological interpretations. PLoS
Biol. 3, e144, DOI: 10.1371/journal.pbio.0030144 (http://biology.
plosjournals.org)
20 Mann, N.H. (2005) The third age of phage. PLoS Biol. 3, e182, DOI:
10.1371/journal.pbio.0030182 (http://biology.plosjournals.org)
496
Review
TRENDS in Microbiology Vol.14 No.11
21 Steunou, A.S. et al. (2006) In situ analysis of nitrogen fixation and
metabolic switching in unicellular thermophilic cyanobacteria
inhabiting hot spring microbial mats. Proc. Natl. Acad. Sci. U. S. A.
103, 2398–2403
22 Frigaard, N-U. et al. (2003) Chlorobium tepidum: insights into the
structure, physiology and metabolism of a green sulfur bacterium
derived from the complete genome sequence. Photosynth. Res. 78,
93–117
23 Frigaard, N-U. and Bryant, D.A. (2004) Seeing green bacteria in a new
light: genomics-enabled studies of the photosynthetic apparatus in
green sulfur bacteria and filamentous anoxygenic phototrophic
bacteria. Arch. Microbiol. 182, 265–276
24 Frigaard, N-U. et al. (2006) Bacteriochlorophyll biosynthesis in green
bacteria. In Chlorophylls and Bacteriochlorophylls: Biochemistry,
Biophysics, Functions and Applications (Grimm, B. et al., eds),
Advances in Photosynthesis and Respiration Vol. 25, pp. 201–221,
Springer
25 Frigaard, N-U. and Bryant, D.A. (2006) Chlorosomes: antenna
organelles in green photosynthetic bacteria. In Complex
Intracellular Structures in Prokaryotes (Microbiology Monographs,
Vol. 2) (Shively, J.M., ed.), pp. 79–114, Springer
26 Eisen, J.A. et al. (2002) The complete genome sequence of the green
sulfur bacterium Chlorobium tepidum. Proc. Natl. Acad. Sci. U. S. A.
99, 9509–9514
27 Manske, A.K. et al. (2005) Physiology and phylogeny of green sulfur
bacteria forming a monospecific phototrophic assemblage at a depth of
100 meters in the Black Sea. Appl. Environ. Microbiol. 71, 8049–8060
28 Frigaard, N-U. et al. (2004) Genetic manipulation of carotenoid
biosynthesis in the green sulfur bacterium Chlorobium tepidum. J.
Bacteriol. 186, 5210–5220
29 Maresca, J.A. et al. (2005) Identification of a novel class of lycopene
cyclases in photosynthetic bacteria. In Photosynthesis: Fundamental
Aspects to Global Perspectives (van der Est, A. and Bruce, D., eds), pp.
884–886, Allen Press
30 Raymond, J. and Blankenship, R.E. (2004) Biosynthetic pathways,
gene replacement and the antiquity of life. Geobiol. 2, 199–203
31 Tomitani, A. et al. (1999) Chlorophyll b and phycobilins in the common
ancestor of cyanobacteria and chloroplasts. Nature 400, 159–162
32 Boone, D.R. and Castenholz, R.W. (2001) Bergey’s Manual of
Systematic Bacteriology (Vol. 1, 2nd edn), Springer
33 Hanada, S. et al. (2002) Roseiflexus castenholzii gen. nov., sp. nov., a
thermophilic, filamentous, photosynthetic bacterium that lacks
chlorosomes. Int. J. Syst. Evol. Microbiol. 52, 187–193
34 Tourova, T.P. et al. (2006) Phylogeny of anoxygenic filamentous
phototrophic bacteria of the family Oscillochloridaceae as inferred
from comparative analyses of the rrs, cbbL, and nifH genes.
Microbiology 75, 192–200
35 Larimer, F.W. et al. (2003) Complete genome sequence of the
metabolically versatile photosynthetic bacterium Rhodopseudomonas
palustris. Nat. Biotechnol. 22, 55–61
36 Mackenzie, C. et al. (2001) The home stretch, a first analysis of the
nearly completed genome of Rhodobacter sphaeroides 2.4.1.
Photosynth. Res. 70, 19–41
37 Yurkov, V.V. and Beatty, J.T. (1998) Aerobic anoxygenic phototrophic
bacteria. Microbiol. Mol. Biol. Rev. 62, 695–724
38 Rathgeber, C. et al. (2004) Aerobic phototrophic bacteria: new evidence
for the diversity, ecological importance and applied potential of this
previously overlooked group. Photosynth. Res. 81, 113–128
39 Gest, H. and Favinger, J.L. (1983) Heliobacterium chlorum gen. nov.
sp. nov., an anoxygenic brownish-green photosynthetic bacterium
containing a new form of bacteriochlorophyll. Arch. Microbiol. 136,
11–16
40 Xiong, J. et al. (1998) Tracking molecular evolution of photosynthesis
by characterization of a major photosynthesis gene cluster from
Heliobacillus mobilis. Proc. Natl. Acad. Sci. U. S. A. 95, 14851–14856
41 Xiong, J. and Bauer, C.E. (2002) Complex evolution of photosynthesis.
Annu. Rev. Plant Biol. 53, 503–521
www.sciencedirect.com
42 Mix, L.J. et al. (2005) Phylogenetic analyses of the core antenna
domain: investigating the origin of photosystem I. J. Mol. Evol. 60,
153–162
43 Oren, A. (2000) The order Halobacteriales. In The Prokaryotes: An
Evolving Electronic Resource for the Microbiological Community
(Dworkin, M. et al., eds) (3rd edn, release 3.2), Springer-Verlag
(http://link.springer-ny.com/link/service/books/10125/).
44 Baliga, N.S. et al. (2004) Genome sequence of Haloarcula marismortui:
a halophilic archaeon from the Dead Sea. Genome Res. 14, 2221–2234
45 Mongodin, E.F. et al. (2005) The genome of Salinibacter ruber:
convergence and gene exchange among hyperhalophilic bacteria and
archaea. Proc. Natl. Acad. Sci. U. S. A. 102, 18147–18152
46 Balashov, S.P. et al. (2005) Xanthorhodopsin: a proton pump with a
light-harvesting carotenoid antenna. Science 309, 2061–2064
47 Béjà, O. et al. (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289, 1902–1906
48 Béjà, O. et al. (2001) Proteorhodopsin phototrophy in the ocean. Nature
411, 786–789
49 de la Torre, J.R. et al. (2003) Proteorhodopsin variants from the
Mediterranean and Red Seas. Proc. Natl. Acad. Sci. U. S. A. 100,
12830–12835
50 Sabehi, G. et al. (2004) Different SAR86 subgroups harbor divergent
proteorhodopsins. Environ. Microbiol. 6, 903–910
51 Frigaard, N-U. et al. (2006) Proteorhodopsin lateral gene transfer
between marine planktonic Bacteria and Archaea. Nature 439, 847–
850
52 Giovannoni, S.J. et al. (2005) Genome streamlining in a cosmopolitan
oceanic bacterium. Science 309, 1242–1245
53 Giovannoni, S.J. et al. (2005) Proteorhodopsin in the ubiquitous marine
bacterium SAR11. Nature 438, 82–85
54 Sabehi, G. et al. (2005) New insights into metabolic properties of
marine bacteria encoding proteorhodopsins. PLoS Biol. 3, e273
55 Jung, K-H. et al. (2003) Demonstration of a sensory rhodopsin in
eubacteria. Mol. Microbiol. 47, 1513–1522
56 Waschuk,
S.A.
et
al.
(2005)
Leptosphaeria
rhodopsin:
bacteriorhodopsin-like proton pump from a eukaryote. Proc. Natl.
Acad. Sci. U. S. A. 102, 6879–6883
57 Blankenship, R.E. (2002) Molecular Mechanisms of Photosynthesis.
Blackwell
58 Bondar, A.N. et al. (2004) Mechanism of primary proton transfer in
bacteriorhodopsin. Structure 12, 1281–1288
59 Senior, A.E. and Weber, J. (2004) Happy motoring with ATP synthase.
Nat. Struct. Mol. Biol. 11, 110–112
60 Kanzler, B.E. et al. (2005) Molecular characterization of the nonphotosynthetic partner in the consortium ‘‘Chlorochromatium
aggregatum’’. Appl. Environ. Microbiol. 71, 7431–7441
61 Overmann, J. and Schubert, K. (2002) Phototrophic consortia: model
systems for symbiotic interrelations between prokaryotes. Arch.
Microbiol. 177, 201–208
62 Jordan, P. et al. (2001) Three-dimensional structure of cyanobacterial
photosystem I. Nature 411, 909–917
63 Ferreira, K.N. et al. (2004) Architecture of the photosynthetic oxygenevolving center. Science 303, 1831–1838
64 Loll, B. et al. (2005) Towards complete cofactor arrangement in the
3.0 Å resolution of Photosystem II. Nature 438, 1040–1044
65 Olson, J.M. and Blankenship, R.E. (2004) Thinking about the evolution
of photosynthesis. Photosynth. Res. 80, 373–386
66 Green, B.R. and Parson, W.W., eds (2003) Light-Harvesting Antennas
in Photosynthesis (Advances in Photosynthesis and Respiration, Vol.
13) (Govindjee, series ed.), Springer
67 Vogl, K. et al. (2006) Chlorobium chlorochromatii sp. nov., a symbiotic
green sulfur bacterium isolated from the phototrophic consortium
‘‘Chlorochromatium aggregatum’’. Arch. Microbiol. 185, 363–372
68 Lally, E.T. et al. (1999) The interaction between RTX toxins and target
cells. Trends Microbiol. 7, 356–361
69 Raymond, J. et al. (2002) Whole-genome analysis of photosynthetic
prokaryotes. Science 298, 1616–1620