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General Overview
modern-day cyanobacteria. It is widely assumed that in the process of endosymbiosis, most endosymbiont genes were either lost together with the corresponding function or transferred to the host
nucleus and merged into the chromosomes during the course of plastid integration. This migration
of genes between two genomes is known as endosymbiotic gene transfer, a special case of horizontal gene transfer (HGT). Over time, some acquired targeting sequences that enabled their products
synthesized on cytoplasmic ribosomes were targeted back to the organelle. In addition, some host
genes acquired targeting sequences that enabled their products to be imported into the organelle.
All these processes played a fundamental role in the integration of endosymbiont and host.
“Primary plastids” are surrounded by two bounding membranes and are only found in three major
eukaryotic photosynthetic groups of Plantae, that is, Glaucophyta, Chlorophyta, and Rhodopyta.
Glaucophyta occupy a key position in the evolution of plastids; in fact, the plastids of glaucophytes
contain chlorophyll a, present in cyanobacteria, and retain the remnant of a Gram-negative bacterial peptidoglycan wall that would have been between the two membranes of the cyanobacterial
ancestor symbiont. The retention of this ancestral character is absent in both green and red plastids.
Chlorophyta (green algae and plants) constitute the second lineage of primary plastids. The
simple two-membrane system surrounding the plastid, the congruence of phylogenies based on
nuclear and organellar genes, and the antiquity of the green algae in the fossil record all indicate
that the green algal plastid is of primary origin. In these chloroplasts, chlorophyll b was synthesized
as a secondary pigment, phycobiliproteins were lost, and starch was stored. Another hypothesis
suggested that the photosynthetic ancestor of green lineage was a prochlorophyte that possessed
chlorophylls a and b and lacked phycobiliproteins.
The green lineage played a major role in oceanic food webs and the carbon cycle from about 2.2
billion years ago until the end-Permian extinction, approximately 250 million years ago. It was this
similarity to the pigments of plants that led to the inference that the ancestors of land plants (i.e.,
embryophytes) would be among the green algae and is clear that phylogenetically plants are a group
of green algae adapted to life on land.
The plastids of Rhodophyta (red algae) constitute the third primary plastid lineage. Like the
green algae, the red algae are also an ancient group in the fossil record, and some of the oldest fossils interpreted as being of eukaryotic origin are often referred to the red algae, although clearly
these organisms were very different from any extant alga. Like those of green algae, the plastids
of red algae are surrounded by two membranes. However, they are pigmented with chlorophyll a,
phycobiliproteins, organized into phycobilisomes, and are distinguished by the presence of phycoerithrin. Phycobilisomes are relatively large extrinsic antennas, water-soluble, and attached to the
surface of the thylakoid membrane. Thylakoids with phycobilisomes do not form stacks like those
in other plastids and consequently the plastids of red algae (and glaucophytes) bear an obvious ultrastructural resemblance to cyanobacteria.
Though the plastids of these three lineages are all primary plastids, that is, having only two
membranes around them, they differ more noticeably in their light-harvesting machinery. Green
algae and plants have membrane-intrinsic antenna proteins (members of the light-harvesting complex superfamily) that bind both chlorophylls a and b and are associated with both photosystems.
Red algae have proteins of the same family that bind only chlorophyll a and are associated with
photosystem I. Glaucophytes do not have this type of antenna, but along with the red algae they have
phycobilisomes, extrinsic antennas which bind linear tetrapyrroles.
Molecular phylogeny supports two possible evolutionary scenarios for the branching order
within Plantae, the red-first and glaucophyte-first hypotheses. The inability to unambiguously
decide between these two using genome-wide analyses may be explained by the more than 1 billion years that have passed since primary endosymbiosis. The early period of Plantae evolution was
likely characterized by a rapid radiation, reticulate evolution (by HGT) among taxa, and high rates
of gene divergence, loss, and replacement that have diffused the evolutionary signal. This idea is
supported by the findings regarding mitochondrial gene order and gene content that do not favor a
particular order of branching.
General Overview
modern-day cyanobacteria. It is widely assumed that in the process of endosymbiosis, most endosymbiont genes were either lost together with the corresponding function or transferred to the host
nucleus and merged into the chromosomes during the course of plastid integration. This migration
of genes between two genomes is known as endosymbiotic gene transfer, a special case of horizontal gene transfer (HGT). Over time, some acquired targeting sequences that enabled their products
synthesized on cytoplasmic ribosomes were targeted back to the organelle. In addition, some host
genes acquired targeting sequences that enabled their products to be imported into the organelle.
All these processes played a fundamental role in the integration of endosymbiont and host.
“Primary plastids” are surrounded by two bounding membranes and are only found in three major
eukaryotic photosynthetic groups of Plantae, that is, Glaucophyta, Chlorophyta, and Rhodopyta.
Glaucophyta occupy a key position in the evolution of plastids; in fact, the plastids of glaucophytes
contain chlorophyll a, present in cyanobacteria, and retain the remnant of a Gram-negative bacterial peptidoglycan wall that would have been between the two membranes of the cyanobacterial
ancestor symbiont. The retention of this ancestral character is absent in both green and red plastids.
Chlorophyta (green algae and plants) constitute the second lineage of primary plastids. The
simple two-membrane system surrounding the plastid, the congruence of phylogenies based on
nuclear and organellar genes, and the antiquity of the green algae in the fossil record all indicate
that the green algal plastid is of primary origin. In these chloroplasts, chlorophyll b was synthesized
as a secondary pigment, phycobiliproteins were lost, and starch was stored. Another hypothesis
suggested that the photosynthetic ancestor of green lineage was a prochlorophyte that possessed
chlorophylls a and b and lacked phycobiliproteins.
The green lineage played a major role in oceanic food webs and the carbon cycle from about 2.2
billion years ago until the end-Permian extinction, approximately 250 million years ago. It was this
similarity to the pigments of plants that led to the inference that the ancestors of land plants (i.e.,
embryophytes) would be among the green algae and is clear that phylogenetically plants are a group
of green algae adapted to life on land.
The plastids of Rhodophyta (red algae) constitute the third primary plastid lineage. Like the
green algae, the red algae are also an ancient group in the fossil record, and some of the oldest fossils interpreted as being of eukaryotic origin are often referred to the red algae, although clearly
these organisms were very different from any extant alga. Like those of green algae, the plastids
of red algae are surrounded by two membranes. However, they are pigmented with chlorophyll a,
phycobiliproteins, organized into phycobilisomes, and are distinguished by the presence of phycoerithrin. Phycobilisomes are relatively large extrinsic antennas, water-soluble, and attached to the
surface of the thylakoid membrane. Thylakoids with phycobilisomes do not form stacks like those
in other plastids and consequently the plastids of red algae (and glaucophytes) bear an obvious ultrastructural resemblance to cyanobacteria.
Though the plastids of these three lineages are all primary plastids, that is, having only two
membranes around them, they differ more noticeably in their light-harvesting machinery. Green
algae and plants have membrane-intrinsic antenna proteins (members of the light-harvesting complex superfamily) that bind both chlorophylls a and b and are associated with both photosystems.
Red algae have proteins of the same family that bind only chlorophyll a and are associated with
photosystem I. Glaucophytes do not have this type of antenna, but along with the red algae they have
phycobilisomes, extrinsic antennas which bind linear tetrapyrroles.
Molecular phylogeny supports two possible evolutionary scenarios for the branching order
within Plantae, the red-first and glaucophyte-first hypotheses. The inability to unambiguously
decide between these two using genome-wide analyses may be explained by the more than 1 billion years that have passed since primary endosymbiosis. The early period of Plantae evolution was
likely characterized by a rapid radiation, reticulate evolution (by HGT) among taxa, and high rates
of gene divergence, loss, and replacement that have diffused the evolutionary signal. This idea is
supported by the findings regarding mitochondrial gene order and gene content that do not favor a
particular order of branching.