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IS PHOTOSYNTHESIS REALLY DERIVED
FROM PURPLE BACTERIA?
The ability to convert light energy into chemical
energy must have arisen very early in the history of
life. Three and a half billion years later, our problem
is to reconstruct the subsequent evolution of photosynthesis by examining the five extant groups of photosynthetic prokaryotes, none of which is closely related to any of the others on the basis of rRNA
sequences or physiological/morphological characteristics. Recent progress in x-ray and electron crystallography has shown that the three-dimensional structures of both photosystem I and photosystem II of
cyanobacteria and the single photosystem of purple
bacteria have the same molecular design (Schubert et
al. 1998), even though protein sequence similarity is
fragmentary and not statistically significant. The fact
that any molecular resemblances at all can be detected over this time scale is a testament to the conservative nature of cellular evolution. This structural conservation tells us that all photosynthetic reaction
centers probably had a common ancestor; however, it
does not mean that all photosynthetic prokaryotes
had a common ancestor.
In a recent paper in Science, Xiong et al. (2000) have
put forward the hypothesis that purple bacteria were
the earliest branching photosynthetic lineage and
challenged the long favored hypothesis that chlorophyll biosynthesis preceded bacteriochlorophyll biosynthesis (Granick 1965). They obtained sequences
for a number of genes involved in photosynthesis from
representatives of the two groups of green bacteria,
the green filamentous bacterium Chloroflexus and the
green sulfur bacterium Chlorobium, and compared them
with previously obtained sequences from Heliobacillus
(Xiong et al. 1998), representative of a third group, and
with the corresponding purple bacterial and cyanobacterial sequences. Phylogenic trees for seven enzymes
of chlorophyll/bacteriochlorophyll synthesis were constructed using the three standard methods (neighborjoining distance, maximum parsimony, and maximum
984
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likelihood), with both DNA and protein sequences; in
addition, trees were made from the concatenated sequences of all seven genes/proteins.
The results were somewhat surprising. In most of
the trees, Chlorobium and Chloroflexus genes were clustered, and the gram-positive obligate anaerobe Heliobacillus was sister group to the gram-negative oxygenic
cyanobacteria. This flies in the face of all we know
about the relationships of these four groups of prokaryotes (Stackebrandt et al. 1996, Madigan et al. 1996).
Even more surprising, the majority of the trees showed
the purple proteobacterial genes as the earliest branch,
even though the proteobacteria are generally considered the most advanced of the Eubacteria (Madigan
et al. 1996).
This branching pattern needs to be viewed with
some caution. When a molecular sequence branches
off at the base of a tree, it means that this sequence is
the most divergent of the group of sequences, that is,
it has accumulated more changes compared to the
other sequences with which it shared a common ancestor. This can be the result of two things: it has had
more time to accumulate changes since it branched
off from the last common ancestor, OR it has a higher
rate of evolution (i.e. of fixation of mutational changes).
The mathematical methods for minimizing the effects of
different rates cannot completely remove this problem,
especially over large evolutionary distances (e.g. Zhang
et al. 2000). A lucid explanation of this “long-branch
problem” and its effect on deep-branching trees is
given by Philippe and Laurent (1998). The deep purple bacterial branch may simply mean that the pigment biosynthesis genes are evolving faster in the proteobacterial line than in the other lines.
Another problem is that only a very limited number of genes were available for comparison in all five
photosynthetic groups. Although the title of the Xiong
et al. paper (2000) is rather sweeping, only genes for
bacteriochlorophyll/chlorophyll synthesis enzymes were
analyzed. In fact, three of the genes encode subunits of
the Mg chelatase (bchHDI/chlHDI), three encode subunits of the light-independent protochlorophyllide
reductase (bchBLN/chlBLN), and one encodes the enzyme that adds the phytol tail (bchG/chlG), so only
three independent enzymes were actually studied.
The authors concluded that because purple bacteria
gave rise to the earliest branch, bacteriochlorophyll
synthesis must have come first. This idea was first put
forward by Burke et al. (1993), but the conclusions
were challenged by a reanalysis of the data (Lockhart
et al. 1996). Both molecules are synthesized from chlorophyllide a, but bacteriochlorophyll synthesis requires three additional steps, one of which is catalyzed
by the products of three genes (bchXYZ) in purple bacteria (Fig. 1). These three genes appear to have arisen
by duplication of the three genes for protochlorophyllide reductase (Burke et al. 1993). At some point,
therefore, there must have been a prokaryotic ancestor that only went as far as chlorophyllide a. Unfortunately, bchXYZ have not yet been found in the two
Fig. 1. Simplified schematic showing relationship between
chlorophyll and bacteriochlorophyll biosynthesis pathways and
the genes encoding the enzymes involved. Chlorophyllide a is
the last common intermediate in both pathways.
green bacterial groups. (They would not be expected
in the heliobacteria, because Bchl g is actually an isomer of chlorophyllide a.)
Considerable caution needs to be exercised in
jumping from the phylogenetic tree of a gene family
to the family tree of its owners. One of the strongest
messages coming from the explosion of bacterial genome projects is that lateral gene transfer between
distantly-related prokaryotes has been rampant, is ongoing, and, in some cases, involves very large blocks of
DNA (Doolittle 1999, Ochman et al. 2000). It may be
significant that all the genes required for synthesis of
bacteriochlorophylls, carotenoids, reaction center proteins, and antenna proteins are found in single large
clusters in two of these prokaryotic groups, the heliobacteria and the purple bacteria (Xiong et al. 2000).
The surest way to acquire photosynthesis would be to
appropriate a complete photosynthetic package from
a neighbor’s genome. Whether modern gene clusters
identify the owners as recipients or donors is not yet
clear. Xiong et al. (2000) considered the possibility that
genes were horizontally transferred from purple bacteria to the other groups but not in other directions.
We should like to propose that lateral gene transfer
may have been much more multidirectional. The
green filamentous Chloroflexus shares a unique extrinsic antenna structure (the chlorosome) with the green
sulfur Chlorobium as well as having the greatest similarity
in bacteriochlorophyll synthesis enzymes, whereas its
reaction center and antenna polypeptides are closely related to those of purple bacteria and not at all like those
of Chlorobium. Chloroflexus is not related to either of these
groups on the basis of rRNA trees or cell wall structure,
and most of its relatives are nonphotosynthetic (Stackebrandt et al. 1996). Both Heliobacillus and the green sulfur Chlorobium have what appear to be “primitive” photosystem I–like reaction centers where the chromophores
are protected by a homodimer of a single protein, rather
than a heterodimer of two subunits related by gene duplication (Blankenship 1994). Did one of them acquire
its reaction center genes from the other?
Modern microbial mat communities provide ample
opportunity for gene swapping, with Chloroflexus, Chlorobium, and purple bacteria in close proximity, often un-
ALGAE • HIGHLIGHTS
derlying a layer of cyanobacteria (Pierson 1994). Microbial mats are believed to have been very common in the
Precambian era and to have given rise to sedimentary
structures known as stromatolites, in which many
prokaryotic microfossils have been found (Schopf and
Packer 1987). The primary question of phylogenetics is
to guess who came first, that is, whose ancestors were
around 3.5 billion years ago when photosynthesis presumably first existed? Some authors have considered the
possibility that cyanobacteria came first because many of
the early microfossils resemble modern cyanobacteria in
size and segmentation of wall outlines (Schopf and
Packer 1987). This would imply that the other four
groups acquired their photosynthesis genes piecemeal
from cyanobacteria. Pierson (1994), however, has argued persuasively that Chloroflexus-like cells could equally
well have given rise to similar structures.
A final point. Any hypothesis on the origin of chlorophyll biosynthesis is obligated to consider carotenoid
biosynthesis for any meaningfully predictive scheme because carotenoids are required for functional photosynthetic proteins. Isoprenoid biosynthesis supplies the required precursors (isopentenyl pyrophosphate and
dimethylallyl pyrophosphate) by two pathways, the 1deoxyxylulose-5-phosphate (DOXP) and mevalonate
(MVA) pathways. The apparently more “primitive”
DOXP pathway occurs in cyanobacteria and is common
in many bacteria. There is considerable evidence, however, for lateral gene transfer as well as selection of genes
from both pathways (Boucher and Doolittle 2000).
In spite of our reservations about their conclusions,
Carl Bauer and his colleagues are to be commended
for undertaking the first comprehensive gene sequencing of two major prokaryotic groups (Xiong et
al. 1998, 2000). We look forward to seeing more sequences from Chloroflexus and Heliobacillus and anticipate with great interest the publication of the completed
Chlorobium genome (http://www.tigr.org/). Once a wider
range of sequence information is available, including
more information on the phylogenetic relationships of
the isoprenoid pathways, it should be possible to get a
clearer idea of the ancestry of photosynthetic genes.
We should like to thank J.T. Beatty and S.I. Beale for helpful
comments.
Beverley R. Green
Department of Botany
University of British Columbia
Vancouver, BC, Canada V6T 1Z4
e-mail: [email protected]
985
Elisabeth Gantt
University of Maryland
Cell Biology and Molecular Genetics Dept.
College Park, MD 29742
e-mail: [email protected]
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