Serial Endosymbiosis

Serial Endosymbiosis Theory (SET)

2007-12-31T23:59:00.000-08:00

This widely accepted view of cellular evolution holds that the cellular evoluton of eukaryotes arose through the endosymbiotic union of engulfed bacteria with a precursor eukaryotic cell. The advent of oxygen releasing Cyanobacterial photosynthesis about 3 billion years ago (3 Ga) gradually converted the Earth's atmosphere from its primordial reducing state (timeline). Oxygen is toxic to organisms that lack the metabolic machinery to rapidly utilize oxygen, so symbiotic union with bacteria capable of oxidative metabolism would ensure cellular survival in environments with increased oxygen tension (pO₂). This union ultimately resulted in mitochondrial organelles, while a second union with Cyanobacterial cells ultimately resulted in photosynthetic plastids (chloroplasts).

Constantin Mereschkowsky was the first to appreciate the significance of protists in early eukaryotic evolution. A.F.W. Schimper noted that chloroplasts in plant cells very much resembled cyanobacteria. The the ultimate theoretical model was provided by Lynn Margulis: the key step was the endosymbiosis of cyanobacteria within a phagotrophic eukaryotic host, a process she calls symbiogenesis. The symbiotic theory of mitochondrial origin is supported by the different nature of internal and external membranes in mitochondria.

In primary endosymbiosis, 1,000 genes were acquired by the nucleus from an incorporated cyanobacteria. A second round of gene transfer involved the engulfment of another plastid-containing eukaryote in secondary endosymbiosis. [S]

Prior to Lynn Margulis' conception of the Symbiotic Theory in the 1960's, biologists believed that the eukaryote's nuclear DNA coded for cellular organelles. When Margulis initially proposed the Symbiotic Theory, she predicted that organelles of prokaryotic origin would be coded for by their own DNA. In the 1980's, experimental evidence in support of Margulis’ prediction was found in the distinct prokaryotic-DNA of the mitochondria and chloroplasts of eukaryotic cells.

More detail:

“Much advance in evolution is due to the establishment of consortia between two organisms with entirely different genomes. Ecologists have barely begun to describe these interactions.” Ernst Mayr in foreword to Acquiring Genomes: A Theory of the Origins of Species, by Lynn Margulis and Dorion Sagan.

Biologist Lynn Margulis actively promoted endosymbiotic theory in the 1960s – The Endosymbiotic Theory of Eukaryote Evolution. Margulis published "Symbiosis in Cell Evolution" in 1981. Even though the essential idea had a lengthy history, mainstream biologists initially reacted to Margulis’ claims with incredulity and ridicule. On the basis of experimental evidence, Serial Endosymbiotic Theory (SET) is now almost universally accepted as the most plausible explanation for evolution of eukaryotes.

Serial Endosymbiotic Theory proposes that "symbiotic consortiums" of prokaryote cells were the ancestors of eukaryotic cells. In ecology, symbiosis indicates that two different organisms live in association with one another, and nature abounds with examples of ‘economic’ symbiotic relationships. Endosymbiosis is, in Margulis’ words, a ‘topological arrangement’, indicating that protracted symbiotic association generates an interdependent relationship in which the sum-of-the-parts becomes a new whole. As such, endosymbiosis generates evolutionary innovation where metabolic cooperation confers survival advantage.

The mechanism of primary endosymbiosis is envisioned as phagocytosis of a bacterium (or bacteria) by another prokaryotic cell. (3-4) The phagocytozed bacteria survived upon nutrients from the host prokaryotic cell. Subsequently, both host and symbiotic bacterium reproduced co-independently such that subsequent generations of endosymbiotic neocytes would also contain the descendents of the originally ingested bacterium.

Ultimately, both the prokaryotic host and the bacteria endosymbionts developed an interdependence through endosymbiotic gene transfer, by which both entities lost their ability to function without the other (5). It is assumed that Cyanobacteria-generated oxygen in the early atmosphere necessitated endosymbiotic metabolic association between ingested aerobic bacteria and anaerobic host prokaryotes. The ingested bacteria ultimately performed oxidative metabolism necessary to the survival of the original host cell, which would otherwise have been poisoned by atmospheric oxygen. The former free-living aerobic bacteria assumed the role of mitochondria within its host cell (purple organelles within 5).

Similarly, serial ingestion of photosynthetic bacteria by endosymbiontic prokaryotes or eukaryotes (5-6) led to the evolution the ancestors of eukaryotic plants and photosynthetic protists (7). As the ingested photosynthetic bacteria adapted to the ingesting prokaryotic host cell, plastids, such as the chloroplast evolved (green organelle within 7). Primary plastids are found in Chlorophyta and plants, Rhodophyta, and Glaucocystophyta because their plastids are derived directly from a Cyanobacterium. All other lineages of plastids have arisen through secondary (or tertiary) endosymbiosis, in which a eukaryote already possessing plastids is engulfed by a second eukaryote. Considerable gene transfer has occurred among genomes and, at times, between organisms. A particularly complex history of plastid acquisition is found in eukaryotic crown group Alveolata. diagrams

[also]
References

Experimental evidence for Endosymbiosis

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Abundant evidence has been found in support of the concept of serial endosymbiosis:

1. Mitochondria and chloroplasts are similar in size and morphology to bacterial prokaryotic cells (though the mitochondria of some organisms are known to be morphologically variable).

2. Mitochondria and chloroplasts divide by binary fission, just as bacteria do, and not by mitosis as eukaryotes do. Both types of organelle have Fts proteins at their division plane.

3. Chemically distinct membrane systems:

The double membrane found in mitochondria and chloroplasts appears to be a relic of the absorption of the prokaryotic bacteria by the eukaryotic host cells. The inner membrane is of a different chemical composition (similar to that of prokaryotes) than the outer membrane of the organelle. Some organellar enzymes and inner membrane systems resemble prokaryotic inner membrane systems. The outer membrane is of similar composition to the plasma membrane of the eukaryote, as is the membrane of other cellular organelles such as the nuclear membrane, endoplasmic reticulum, and Golgi apparatus of eukaryotes (in support of the invagination hypothesis of their origin). Several primitive eukaryotic microbes, such as Giardia and Trichomonas possess a nuclear membrane yet have no mitochondria.

4. Mitochondria and chloroplasts have their own DNA and their ownribosomes:

The DNA of mitochondria and chloroplasts is different from that of the eukaryotic cell in which they are found. As Margulis predicted, both mitochondria and chloroplasts include DNA that is like that of prokaryotes – circular, not linear. Further, the DNA of mitochondria and chloroplasts, like that of the eubacteria, usually has neither introns nor histones. The first amino acid of mitochondrial and choloroplastic transcripts is equivalent to that of prokaryotes, and is different from that of eukaryotes.

Proteins encoded by mitochondrial DNA do not account for all of the mitochondrial proteins. The ingested prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells, a process known as endosymbiotic gene transfer. For this reason, mitochondria and chloroplasts now depend on their hosts to synthesize most of their components.

The DNA of these mitochondrial and chloroplastic organelles evolves independently – and at a different rate – from the nuclear DNA of the eukaryotic cell. (Mitochondrial DNA is employed to trace evolutionary lines of human maternally-derived cells because virtually all DNA mtDNA is contributed by the oocyte, unlike nuclear DNA which derives from both parents, and unlike the Y-chromosome contributed solely by the human father.)

5. Mitochondria arise from preexisting mitochondria; chloroplastsarise from preexisting chloroplasts (they are not manufacturedthrough the direction of nuclear genes).

6. Organellar ribosomes are more similar in size to prokaryoticribosomes than to eukaryotic ribosomes:Mitochondria and chloroplasts produced their own ribosomes, which have 30S and 50S subunits, unlike the 40S and 60S subunits of the eukaryotic cells in which they occur.

7. Many antibiotics that kill or inhibit bacteria also inhibit proteinsynthesis of these organelles:

Antibiotics such as streptomycin block the synthesis of proteins in eubacteria, mitochondria, and chloroplasts, but not cytoplasmic protein synthesis in eukaryotes. Similarly, the antibiotic rifampicin infibits the RNA polymerase of eubacteria and mitochondria, but does not inhibit the RNA polymerase of the eukaryotic nucleus. Conversely inhibitors of eukaryotic protein synthesis, such as bacterially derived diphtheria toxin, do not affect protein synthesis within eubacteria, mitochondria, or chloroplasts.

8. Phylogenetic studies using comparative ribosomal RNA sequencing demonstrates that both mitochondria and plastids are related to the eubacteria. Phylogenetic analyses have clearly demonstrated that mitochondria and plastids derive from bacterial lines related to modern-day proteobacteria and cyanobacteria, respectively. Experimental observations confirm growth of bacterial endosymbionts in numerous organisms.

9. Microbiologist Kwang Jeon observed Legionella-like x-bacterial infection of strains of Amoeba proteus (xD) with which he was working. The infection killed many of the amoeba, but he raised the most hardy of the survivors. After many generations, the amoeba became dependent upon the bacterium, and endosymbiotic gene switching occurred. Free Full Text Article 2004 Detailed description xD amoeba experiments

References

Secondary endosymbiosis

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Secondary endosymbiosis and nucleomorph genome evolution: modified
The plastids (chloroplasts) of photosynthetic eukaryotes are the product of an ancient symbiosis between a heterotrophic eukaryote and a free-living Cyanobacterium. It is widely believed that this process, known as primary endosymbiosis, occurred only once and that all plastids descend from a single common ancestor. However, plastids have also moved laterally amongst unrelated eukaryotic cells by secondary endosymbiosis, a process that has occured multiple times and has given rise to a staggering array of photosynthetic organisms [diagram, see Archibald & Keeling 2002, Trends Genet. 18, 577- for review].

The Cryptomonads and Chlorarachniophytes are two microalgal lineages that are of particular interest with respect to secondary endosymbiosis. Unlike all other secondary plastid-containing algae, these organisms have retained the nucleus of the eukaryotic endosymbiont in a highly derived form called a nucleomorph. The nucleomorph genomes of Chorarachniophytes and Cryptomonads are very fast evolving and are the smallest eukaryotic genomes known, having transferred most of their genetic material to the nuclear genome of their respective host cells. Within the two groups, nucleomorph genome size varies considerably from lineage to lineage.

Continued evolutionary surprises among dinoflagellates -- Morden and Sherwood 99 (18): 11558 -- Proceedings of the National Academy of Sciences:"It is well established that chloroplasts in green and red algae are derived from a primary endosymbiotic event between a cyanobacterium and a eukaryotic organism 1 billion years ago (Fig. 1; refs. 1 and 2). Although these two groups account for many of the world's photosynthetic species, most other major taxonomic groups of photosynthetic organisms (stramenopiles including diatoms, phaeophytes, chrysophytes, and haptophytes) have plastids derived from a photosynthetic eukaryote implying a secondary endosymbiosis (1, 2). Still other groups, such as the dinoflagellates, have more complicated associations believed to be derived from tertiary endosymbioses involving the engulfment of a secondary endosymbiont. Each endosymbiotic event has characteristic structural changes associated with it, the most notable of which is the addition of two membranes surrounding the plastid (the inner representing the cell membrane of the engulfed organism and the outer representing the phagocytosis vacuole membrane) (2). Dinoflagellates, although believed to be tertiary endosymbionts, have only 3 membranes surrounding their plastids (1, 2), suggesting that the acquisition of too many membranes may be functionally unstable and can cause some to be lost. "
Clifford W. Morden, and Alison R. Sherwood Continued evolutionary surprises among dinoflagellates PNAS September 3, 2002 vol. 99 no. 18 11558-11560

Mitochondrial origins

2007-12-31T23:54:00.000-08:00

The eukaryotic mitochondrion (pl. mitochondria) is the 'power house of the cell. An outer membrane, similar in composition to the plasma membrane surrounds the organelle. The inner membrane is contiguous, at membrane junctions, with the inner membrane that forms the walls of cristae. The inner mitochondrial membrane contains more than 100 different polypeptides. The protein to phospolipid ratio is very high – more than 3:1 by weight, having about 1 protein for 15 phospholipids. The inner membrane is also rich in an unusual phospholipid, cardiolipin, which is usually characteristic of bacterial plasma membranes. This composition, along with other evidence, has led to the assumption that the inner membrane is derived from endosymbiotic prokaryotes.

Mitochondria are believed to have developed from an endosymbiotic union with alpha-proteobacteria, specifically the Rickettsiales. Phylogenetic analyses indicate that genome of R. prowazekii is more closely related to that of mitochondria than is any other microbe yet analyzed. Neither genome contains genes required for anaerobic glycolysis. R. prowazekii does contain a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex, so ATP production in Rickettsia is the same as that in mitochondria. The genes from Rickettsia prowazekii encoding cytochrome b (cob) and cytochrome c oxidase subunit I (cox1) provide further phylogenetic evidence for a link with mitochondrial origins.

History of ideas concerning endosymbiosis

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1883 ~ AFW Schimper noted that the plastids of plant cells resembled free-living Cyanobacteria.
1905 ~ Mereschkowsky proposed a reticulated tree of endosymbiosis for the origin of algal plastids.
1920s ~ Ivan Wallin suggested a bacterial origin for mitochondria.
1959 ~ Stocking and Gifford discovered DNA in the plastids of Spirogyra, a green algae.
1960s ~ Lynn Margulis argued the case for endosymbiotic origins of mitochondria and plastids.
1970 ~ Margulis published her argument for the endosymbiotic origin of eukaryotes in The Origin of Eukaryotic Cells.
1977~ Carl Woese declared the case for prokaryotic endosymbiosis “clear cut” and “proven”. Other biologists subsequently declared the endosymbiotic theory demonstrated beyond a reasonable doubt.
1981 ~ In Symbiosis in Cell Evolution, Margulis argued that eukaryotic cells originated as communities of interacting entities. She extended the argument to including endosymbiotic incorporation of spirochaetes that developed into eukaryotic undulopodia -- flagella and cilia. (This proposal has not gained wide acceptance because flagella lack DNA and do not show ultrastructural similarities to prokaryotes.)

References

Endosymbiotic transfers

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Right - click to enlarge image: Proposed endosymbiotic transfer events between the three Domains and the six Kingdoms of Life. Both the Eubacteria and Archaea are prokaryotes, while animals, fungi, plants, and protists are eukaryotes.

The yellow asterisk * indicates the last universal common ancestor (LUCA), or universal cenancestor, which is hypothesized as being at the ancestral root of all living organisms. Not the earliest or simplest living organism, and not necessarily the sole example of its type, this organism possessed the genetic material that diverged (about 3.5 Ga) into all current living organisms. This diagram is not a cladogram, so branches do not indicate evolutionary timelines.

A number of terms are employed to refer to the universal cenancestor – last universal ancestor (LUA), last common ancestor (LCA), or last universal common ancestor (LUCA).

Woese and Fox proposed the Three Domain system: Eubacteria, Archaea, and Eukaryotes.

The Five Kingdom system was proposed in 1969: Monera (prokaryotes), Protista, Plantae, Fungi, Animalia. Discovery of the Archaea added the sixth kingdom.

History of taxonomic concepts:
Linnaeus, 1735 – 2 Kingdoms – Animalia, Vegetabilia
Haeckel, 1866 – 3 Kingdoms – Protista, Plantae, Animalia. Image Haeckel's tree of life.
Chatton, 1937 – 2 Empires – Prokaryota, Eukaryota
Copeland, 1956 – 4 Kingdoms – Monera, Protoctista, Plantae, Animalia
Whittaker, 1969 – Monera, Fungi, Protista, Plantae, Animalia
Woese et al, 1977 – 6 Kingdom – Eubacteria, Archaea, Protista, Fungi, Plantae, Animalia
Woese and Fox, 1999 – 3 Domain system: Eubacteria, Archaea, and Eukaryotes

References

Endosymbiotic Gene Transfer

2007-12-31T23:39:00.000-08:00

Proteins encoded by mitochondrial DNA do not account for all of the proteins found in mitochondria. Endosymbiotic prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells in a process known as endosymbiotic gene transfer. For this reason, mitochondria and chloroplasts now depend on their host's DNA to direct synthesis of most of their components.

Microbiologist Kwang Jeon has demonstrated endosymbiotic gene transfer within endosymbiotic strains of Amoeba proteus (xD) with which he has worked since the 1970s. (J Eukaryot Microbiol 1997 Sep-Oct;44(5):412-9 Evidence for symbiont-induced alteration of a host's gene expression: irreversible loss of SAM synthetase from Amoeba proteus. Choi JY, Lee TW, Jeon KW, Ahn TI)
Free Full Text Article 2004 : Detailed description xD amoeba experiments

References

Horizontal Gene Transfer

2007-12-31T23:38:00.000-08:00

Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (phylogeny) of prokaryotes (image), and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria.

(see The net of life: Reconstructing the microbial phylogenetic networkV. Kunin, L. Goldovsky, N. Darzentas, and C. A. OuzounisGenome Res. 1 July 2005. pdf)

Three mechanisms of horizontal (lateral) gene transfer are recognized: direct bacterial conjugation, bacteriophage mediated transduction between bacteria, and bacterial transformation by uptake of DNA fragments.

A major form of vertical gene transfer followed serial endosymbiotic events, in which ingested purple bacteria and Cyanobacteria became eukaryotic mitochondria and chloroplasts respectively. The ingested prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells, a process known as endosymbiotic gene transfer.

Horizontal genomics is a new field in prokaryotic biology that examines DNA sequences in prokaryotic chromosomes that appear to have originated from other prokaryotes or eukaryotes. The prokaryotic mobile gene pool is referred to as the 'mobilome'. Various agents agents occur in all prokaryotes and effect DNA movement: plasmids, bacteriophages and transposons.

Diagrams of proposed mechanism of SET

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Simplified diagrams of serial phagocytosis of purple and photosynthetic bacteria, leading to primary* endosymbiotic accommodations. (adapted from)

1. ancestral prokaryote, undergoes

2. infoldings of plasma membrane, which permits

3. development of nuclear membrane and endomembranous system

4. engulfment of aerobic heterotrophic prokaryotes, generates

5. ancestral heterotrophic eukaryote with mitochondria.

~~~

Next, acccording to SET,

an ancestral heterotropic eukaryote (5)

undergoes
6. serial engulfment of photosynthetic prokaryotes, which generates

7. ancestral photosynthetic eukaryote with plastids.

Schematic in FFT Article Protist Images: Endosymbiosis and Parasitism Hatena

*Secondary endosymbiosis is engulfment by a eukaryotic cell of another eukaryote that already possesses endosymbiotic organelles derived from primary endosymbiosis. Similarly, acquisitions may be tertiary. The eukaryotic crown group Alveolata has a particularly complex history of plastid acquisition.

More images: Site with good diagrams tems & drop-down menu of endosymbiosis and chloroplasts : diagram of plastid diversity : diagram ~ endosymbiotic formation of algal groups :

References

Photosynthesis in Eukaryotes

2007-12-31T00:00:00.000-08:00

The photosynthesizing ability of eukaryotes was made possible by one or more endosymbiotic associations between heterotrophic eukaryotes and photosynthetic prokaryotes (or their descendents). Several primary symbioses occurred between eukaryotes and blue green algae. In one of the lineages, the photosynthetic organism lost much of its genetic independence and became functionally and genetically integrated as plastids – chloroplasts within the host cell. At least two types of protists – chloroarachniophytes and cryptomonads –acquired 'plastids' by forming symbioses with eukaryotic algae. Such acquisitions are referred to as secondary symbioses.

Autotrophic prokaryotes derive all their carbon from inorganic sources, and photoautotrophs utilize light energy (anaerobic Chromatium movie and aerobic Cyanobacteria). Some prokaryotes are heterotrophic, utilizing organic substance as a source of carbon, and the purple and green photosynthetic bacteria obtain energy from light (Rhodospirillum rubrum movie).

Photosynthetic bacteria include: Cyanobacteria, green filamentous, green sulfur, prochlorophytes, purple sulfur, and purple nonsulfur bacteria.

Oxygenic photosynthesis, utilizing H2O as electron donor : Cyanobacteria, prochlorophytes. The Cyanobacteria, of course, are considered both the stimulus for and the endosymbionts in chloroplasts.

Nonoxygenic photosynthesis utilizing S– or So or H2 as electron donor:green filamentous, green sulfur, purple sulfur, and purple nonsulfur

symbiozing

2007-12-01T01:00:00.000-08:00

Associated science sites • Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Glossary • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Molecule • Molecular Biology • Molecular Paths • Neurosciences • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Taxonomy Phylogeny • Tissue • Virus • And some philosophy/general interest sites • A-Deistic • Adeistic • Black Out • cosmic • Eine Kleine Nattermusing • eMusings • eVolition • Galaria • Godborygmi • Godspell Follies • Gray Matters • MetaThoughts • Mimble Wimble • Naturalism • BLogodaedaly • palimpsest • Salient • Science of Evolution • Sechuam • Sintheist • Tabula Flexuosa • The Scarlet A • Weltschauung •

Reviews SET

2006-07-31T23:58:00.000-07:00

Mitochondrial genome evolution and the origin of eukaryotes.:
Recent results from ancestral (minimally derived) protists testify to the tremendous diversity of the mitochondrial genome in various eukaryotic lineages, but also reinforce the view that mitochondria, descendants of an endosymbiotic alpha-Proteobacterium, arose only once in evolution. The serial endosymbiosis theory, currently the most popular hypothesis to explain the origin of mitochondria, postulates the capture of an alpha-proteobacterial endosymbiont by a nucleus-containing eukaryotic host resembling extant amitochondriate protists. New sequence data have challenged this scenario, instead raising the possibility that the origin of the mitochondrion was coincident with, and contributed substantially to, the origin of the nuclear genome of the eukaryotic cell. Defining more precisely the alpha-proteobacterial ancestry of the mitochondrial genome, and the contribution of the endosymbiotic event to the nuclear genome, will be essential for a full understanding of the origin and evolution of the eukaryotic cell as a whole.
Lang BF, Gray MW, Burger G. Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet. 1999;33:351-97.

Mitochondrial evolution. [Science. 1999] PMID: 10066161
[Evolution of mitochondria] [Tsitol Genet. 2002] PMID: 12442548
On the origin of mitochondria: a genomics perspective. [Philos Trans R Soc Lond B Biol Sci. 2003] PMID: 12594925
Fungal evolution: the case of the vanishing mitochondrion. [Curr Opin Microbiol. 2005] PMID: 15993645
A comparative genomics approach to the evolution of eukaryotes and their mitochondria. [J Eukaryot Microbiol. 1999] PMID: 10461380
.

Mitochondrial evolution. :
The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha-Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis-based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.
Gray MW, Burger G, Lang BF. Mitochondrial evolution. Science. 1999 Mar 5;283(5407):1476-81.

[Evolution of mitochondria] [Tsitol Genet. 2002] PMID: 12442548
Mitochondrial genome evolution and the origin of eukaryotes. [Annu Rev Genet. 1999] PMID: 10690412
Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times. [Mol Biol Evol. 2003] PMID: 12832624
On the origin of mitochondria: a genomics perspective. [Philos Trans R Soc Lond B Biol Sci. 2003] PMID: 12594925
Mitochondria of protists. [Annu Rev Genet. 2004] PMID: 15568984
.

Free Full Text . Search . evidence

2006-07-31T14:18:00.000-07:00

This message contains search results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).:

Free Full Text Articles Entrez pubmed ResultsItems 1 - 6 of 6
1:
Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS, Kissinger JC.

Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum.Genome Biol. 2004;5(11):R88. Epub 2004 Oct 19.PMID: 15535864 [PubMed - indexed for MEDLINE]
2:
Patron NJ, Rogers MB, Keeling PJ.
Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates.Eukaryot Cell. 2004 Oct;3(5):1169-75.PMID: 15470245 [PubMed - indexed for MEDLINE]
3:
Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D.

A molecular timeline for the origin of photosynthetic eukaryotes.Mol Biol Evol. 2004 May;21(5):809-18. Epub 2004 Feb 12.PMID: 14963099 [PubMed - indexed for MEDLINE]
4:
Harper JT, Keeling PJ.

Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids.Mol Biol Evol. 2003 Oct;20(10):1730-5. Epub 2003 Jul 28.PMID: 12885964 [PubMed - indexed for MEDLINE]
5:
Hannaert V, Saavedra E, Duffieux F, Szikora JP, Rigden DJ, Michels PA, Opperdoes FR.
Plant-like traits associated with metabolism of Trypanosoma parasites.Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1067-71. Epub 2003 Jan 27.PMID: 12552132 [PubMed - indexed for MEDLINE]
6:
Dale C, Plague GR, Wang B, Ochman H, Moran NA.
Type III secretion systems and the evolution of mutualistic endosymbiosis.Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12397-402. Epub 2002 Sep 4.PMID: 12213957 [PubMed - indexed for MEDLINE]
Items 1 - 3 of 31:
1: Gerbod D, Edgcomb VP, Noel C, Vanacova S, Wintjens R, Tachezy J, Sogin ML, Viscogliosi E. Phylogenetic relationships of class II fumarase genes from trichomonad species.Mol Biol Evol. 2001 Aug;18(8):1574-84.PMID: 11470849 [PubMed - indexed for MEDLINE]
2: Fast NM, Kissinger JC, Roos DS, Keeling PJ.Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids.Mol Biol Evol. 2001 Mar;18(3):418-26.PMID: 11230543 [PubMed - indexed for MEDLINE]
3: Henze K, Badr A, Wettern M, Cerff R, Martin W.A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution.Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9122-6.PMID: 7568085 [PubMed - indexed for MEDLINE]

Symbiosis as a mechanism of evolution: status of cell symbiosis theory

2006-07-31T13:49:00.000-07:00

Symbiosis as a mechanism of evolution: status of cell symbiosis theory. :
Entrez PubMed: "Several theories for the origin of eukaryotic (nucleated) cells from prokaryotic (bacterial) ancestors have been published: the progenote, the direct filiation and the serial endosymbiotic theory (SET). Compelling evidence for two aspects of the SET is now available suggesting that both mitochondria and plastids originated by symbioses with a third type of microbe, probably a Thermoplasma-like archaebacterium ancestral to the nucleocytoplasm. We conclude that not enough information is available to negate or substantiate another SET hypothesis: that the undulipodia (cilia, eukaryotic flagella) evolved from spirochetes. Recognizing the power of symbiosis to recombine in single individual semes from widely differing partners, we develop the idea that symbiosis has been important in the origin of species and higher taxa. The abrupt origin of novel life forms through the formation of stable symbioses is consistent with certain patterns of evolution (e.g punctuated equilibria) described by some paleontologists."
Margulis L, Bermudes D. Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis. 1985;1:101-24.

More:
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. [Int J Syst Evol Microbiol. 2002] PMID: 11931142
On the origin of mitosing cells. 1967 [J NIH Res. 1993] PMID: 11541390
Symbiont acquisition as neoseme: origin of species and higher taxa. [Symbiosis. 1987] PMID: 11542098
Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record. [Adv Space Res. 1984] PMID: 11537775
On the origin of mitosing cells [J Theor Biol. 1967] PMID: 11541392

Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain -- Erill et al. 34 (1): 66 -- Nucleic Acids Research

2006-07-29T19:09:00.000-07:00

Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain -- Erill et al. 34 (1): 66 -- Nucleic Acids Research: "Recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under LexA regulation in several proteobacteria species. In this work, we have traced down instances of this multiple gene cassette across the bacteria domain. Phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, lateral gene transfer and duplication. In addition, our analyses show that LexA regulation of this multiple gene cassette is persistent in all the phyla in which it has been detected, and suggest that this regulation is prompted by the combined activity of two of its constituent genes: a polymerase V homolog and an alpha subunit of the DNA polymerase III. "

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

2006-07-29T19:01:00.000-07:00

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.: "Numerous studies have considered the emergence of metabolic pathways, but the modes of recent evolution of metabolic networks are poorly understood. Here, we integrate comparative genomics with flux balance analysis to examine (i) the contribution of different genetic mechanisms to network growth in bacteria, (ii) the selective forces driving network evolution and (iii) the integration of new nodes into the network. Most changes to the metabolic network of Escherichia coli in the past 100 million years are due to horizontal gene transfer, with little contribution from gene duplicates. Networks grow by acquiring genes involved in the transport and catalysis of external nutrients, driven by adaptations to changing environments. Accordingly, horizontally transferred genes are integrated at the periphery of the network, whereas central parts remain evolutionarily stable. Genes encoding physiologically coupled reactions are often transferred together, frequently in operons. Thus, bacterial metabolic networks evolve by direct uptake of peripheral reactions in response to changed environments."

Pal C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 2005 Dec;37(12):1372-5. Epub 2005 Nov 20.

MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA

2006-07-29T13:02:00.000-07:00

MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA : Nature Reviews Microbiology - Reviews: "Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition."Christopher M. Thomas & Kaare M. Nielsen MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA Nature Reviews Microbiology 3, 711-721 (2005); doi:10.1038/nrmicro1234

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

2006-07-28T13:58:00.000-07:00

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. : Entrez PubMed: We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.
Margulis L, Dolan MF, Guerrero R. The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):6954-9. Free Full Text Article.

A molecular timeline for the origin of photosynthetic eukaryotes

2006-07-28T13:03:00.000-07:00

A molecular timeline for the origin of photosynthetic eukaryotes. : Entrez PubMed: "The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution."
Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D. A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol. 2004 May;21(5):809-18. Epub 2004 Feb 12. Free Full Text Article

Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families

2006-07-28T11:06:00.000-07:00

Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. : Entrez PubMed : "Aphids (superfamily Aphidoidea) contain eubacterial endosymbionts localized within specialized cells (mycetocytes). The endosymbionts are essential for the survival of the aphid hosts. Sequence analyses of the 16S rRNAs from endosymbionts of 11 aphid species from seven tribes and four families have indicated that the endosymbionts are monophyletic. Furthermore, phylogenetic relationships within the symbiont clade parallel the relationships of the corresponding aphid hosts. Our findings suggest that this endocytobiotic association was established in a common ancestor of the four aphid families with subsequent diversification into the present species of aphids and their endosymbionts."
Munson MA, Baumann P, Clark MA, Baumann L, Moran NA, Voegtlin DJ, Campbell BC. Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. J Bacteriol. 1991 Oct;173(20):6321-4. Free Full Text Article 1991

New Cellular Evolution Theory Rejects Darwinian Assumptions

2006-07-27T13:00:00.000-07:00

New Cellular Evolution Theory Rejects Darwinian Assumptions: "Cellular evolution, he argues, began in a communal environment in which the loosely organized cells took shape through extensive horizontal gene transfer. Such a transfer previously had been recognized as having a minor role in evolution, but the arrival of microbial genomics, Woese says, is shedding a more accurate light. Horizontal gene transfer, he argues, has the capacity to rework entire genomes. With simple primitive entities this process can 'completely erase an organismal genealogical trace.' "

A secondary symbiosis in progress?

2006-07-25T13:10:00.000-07:00

A secondary symbiosis in progress? : Entrez PubMed : "Algae have acquired plastids by developing an endosymbiotic relationship with either a cyanobacterium (primary endosymbiosis) or other eukaryotic algae (secondary endosymbiosis). We report a protist, which we tentatively refer to as Hatena, that hosts an endosymbiotic green algal partner but inherits it unevenly. The endosymbiosis causes drastic morphological changes to both the symbiont and the host cell architecture. This type of life cycle, in which endosymbiont integration has only partially converted the host from predator to autotroph, may represent an early stage of plastid acquisition through secondary symbiosis."
Okamoto N, Inouye I. A secondary symbiosis in progress? Science. 2005 Oct 14;310(5746):287.You can find a good image here, and a concise commentary on the Science article here.

Continued evolutionary surprises among dinoflagellates -- Morden and Sherwood 99 (18): 11558 -- Proceedings of the National Academy of Sciences

2006-07-24T12:44:00.000-07:00

Continued evolutionary surprises among dinoflagellates -- Morden and Sherwood 99 (18): 11558 -- Proceedings of the National Academy of Sciences:
"It is well established that chloroplasts in green and red algae are derived from a primary endosymbiotic event between a cyanobacterium and a eukaryotic organism 1 billion years ago (Fig. 1; refs. 1 and 2). Although these two groups account for many of the world's photosynthetic species, most other major taxonomic groups of photosynthetic organisms (stramenopilesincluding diatoms, phaeophytes, chrysophytesand haptophytes) have plastids derived from a photosynthetic eukaryote implying a secondary endosymbiosis (1, 2). Still other groups, such as the dinoflagellates, have more complicated associations believed to be derived from tertiary endosymbioses involving the engulfment of a secondary endosymbiont. Each endosymbiotic event has characteristic structural changes associated with it, the most notable of which is the addition of two membranes surrounding the plastid (the inner representing the cell membrane of the engulfed organism and the outer representing the phagocytosis vacuole membrane) (2). Dinoflagellates, although believed to be tertiary endosymbionts, have only 3 membranes surrounding their plastids (1, 2), suggesting that the acquisition of too many membranes may be functionally unstable and can cause some to be lost. "

Clifford W. Morden, and Alison R. Sherwood Continued evolutionary surprises among dinoflagellates PNAS September 3, 2002 vol. 99 no. 18 11558-11560

Gene switching in Amoeba proteus caused by endosymbiotic bacteria

2006-07-23T13:13:00.000-07:00

Gene switching in Amoeba proteus caused by endosymbiotic bacteria -- Jeon and Jeon 117 (4): 535 -- Journal of Cell Science: Entrez PubMed: "The xD strain of Amoeba proteus arose from the D strain by spontaneous infection of X-bacteria (Jeon and Lorch, 1967), and xD amoebae are now dependent on their symbionts for survival. Each xD amoeba contains about 42,000 symbionts within symbiosomes, and established xD amoebae die if their symbionts are removed. Newly infected xD amoebae become dependent on X-bacteria within 18 months (about 200 cell generations) (Jeon and Ahn, 1978)...."
Jeon TJ, Jeon KW. Gene switching in Amoeba proteus caused by endosymbiotic bacteria. J Cell Sci. 2004 Feb 1;117(Pt 4):535-43. Epub 2004 Jan 6.

Also: Free Full Text articles bold:
J Eukaryot Microbiol. 2004 Sep-Oct;51(5):502-8.
J Eukaryot Microbiol. 2003 Jan-Feb;50(1):61-9.
J Eukaryot Microbiol. 1998 Nov-Dec;45(6):600-5.
J Eukaryot Microbiol. 1997 Nov-Dec;44(6):614-9.
J Eukaryot Microbiol. 1997 Sep-Oct;44(5):412-9.
Gene. 1996 May 24;171(1):89-93.
Trends Cell Biol. 1995 Mar;5(3):137-40.
Gene. 1994 Oct 11;148(1):43-9.
Infect Immun. 1994 Jan;62(1):65-71.
J Bacteriol. 1980 Mar;141(3):1466-9.
J Cell Physiol. 1979 Jan;98(1):49-57.
J Protozool. 1977 May;24(2):289-93.
J Cell Physiol. 1976 Oct;89(2):337-44.
J Protozool. 1975 Aug;22(3):402-5.
Science. 1972 Jun 9;176(39):1122-3.

On the origin of mitosing cells. 1967

2006-07-22T14:10:00.001-07:00

On the origin of mitosing cells. 1967 : Entrez PubMed: "A theory of the origin of eukaryotic cells ('higher' cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) [9(2)+2] basal bodies [kinetosomes] of flagella [undulipodia] were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic [anoxic] conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokayotes to form aerobic bacteria (protoflagella [undulipodia] and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates [amoebomastigotes] is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbolically acquired by some of these protozoans to form the ['eukaryotic' deleted] algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower [smaller] organisms is discussed."
Sagan L. On the origin of mitosing cells. 1967 J NIH Res. 1993 Mar;5(3):65-72.

More:

Symbiotic theory of the origin of eukaryotic organelles; criteria for proof. [Symp Soc Exp Biol. 1975] PMID: 822529
Symbiosis as a mechanism of evolution: status of cell symbiosis theory. [Symbiosis. 1985] PMID: 11543608
Origins of the nucleate organisms. [Q Rev Biol. 1977] PMID: 905503
[Evolution of cells] [Naturwissenschaften. 1996] PMID: 8622771
On the origin of mitosing cells [J Theor Biol. 1967] PMID: 11541392
Symbiotic theory of the origin of eukaryotic organelles; criteria for proof. [Symp Soc Exp Biol. 1975] PMID: 822529
Symbiosis as a mechanism of evolution: status of cell symbiosis theory. [Symbiosis. 1985] PMID: 11543608
Origins of the nucleate organisms. [Q Rev Biol. 1977] PMID: 905503
Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record. [Adv Space Res. 1984] PMID: 11537775

On the origin of mitosing cells. 1967

2006-07-22T14:10:00.000-07:00

Search for eukaryotic motility proteins in spirochetes: immunological detection of a tektin-like protein in Spirochaeta halophila.

2006-07-22T14:08:00.000-07:00

Search for eukaryotic motility proteins in spirochetes: immunological detection of a tektin-like protein in Spirochaeta halophila. : Entrez PubMed: "The serial endosymbiotic theory (SET) for the spirochete origin of undulipodia (cilia and eukaryotic flagella) predicts that a greater number of axonemal proteins will show homology to spirochete than to other bacterial proteins. To continue testing, the SET proteins associated with eukaryotic motility (tektin, centrin and calmodulin) were sought in Spirochaeta halophila. Western blot immunological detection techniques (for tektin and centrin) and two-dimensional gel analysis (for calmodulin) were used. Tektins are filamentous proteins extending the length of the axoneme in sperm tails and other undulipodia. Whole cell extracts of S. halophila were probed with antibodies made against three sea urchin (Lytechinus pictus) sperm axonemal tektins (tektins A, B, and C). In the spirochetes, one tektin-like protein was detected as a band on Western blots (a C tektin.) An antibody made against Lytechinus pictus sperm tail axonemes, affinity-purified against the C tektin of another sea urchin, Stronglyocentrotus purpuratus, bound to a 30 kDa protein from Spirochaeta halophila. The C tektin epitope was not detected in Escherichia coli. Both the poly- and monoclonal anti-centrin antibodies cross-reacted with multiple proteins in the control alga (Tetraselmis striata) and in the putatively negative control bacterium E. coli. No cross reaction was seen between any anti-centrin antibody and S. halophila. Neither did a two-dimensional gel analysis reveal the presence of calmodulin in these spirochetes or in the two other prokaryotes tested (Spiroplasma citri, Acholeplasma laidlawii). Although neither centrin nor calmodulin were detected, a 30 kDa tektin-like protein apparently is present in these spirochetes."
Barth AL, Stricker JA, Margulis L. Search for eukaryotic motility proteins in spirochetes: immunological detection of a tektin-like protein in Spirochaeta halophila. Biosystems. 1991;24(4):313-9.

Possible evolutionary significance of spirochaetes

2006-07-22T13:34:00.000-07:00

Margulis' theory of the evolution of undulipodia is not widely accepted.

Possible evolutionary significance of spirochaetes. : Entrez PubMed: "Large symbiotic spirochaetes of the family Pillotaceae (e.g. pillotinas) are found in dry wood and subterranean termites (Hollande & Garagozlou 1967). These morphologically distinctive spirochaetes comprise several genera. Some of them contain microtubules within their protoplasmic cylinders. They demonstrate a variety of relations with their termite and protist hosts. Some are free-living within the lumen of the intestine, some tend to be associated with filamentous and other bacteria, some are found regularly coursing between the numerous undulipodia ( = eukaryotic flagella, cilia, and other (9 + 2) organelles of motility) of hypermastigotes and polymastigotes. Still other smaller termite spirochaetes are regularly attached to protists via specialized attachment sites. Some even form motility symbiosis with their host protists. The analogy between the behaviour of host-associated spirochaetes and the possible steps in the origin of the undulipodia and mitotic system of eukaryotes is discussed briefly."
Margulis L, Chase D, To LP. Possible evolutionary significance of spirochaetes. Proc R Soc Lond B Biol Sci. 1979 Apr 11;204(1155):189-98.

Diatom genomics: genetic acquisitions and mergers

2006-07-22T13:26:00.000-07:00

Diatom genomics: genetic acquisitions and merger : Entrez PubMed: "Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution."
Nisbet RE, Kilian O, McFadden GI. Diatom genomics: genetic acquisitions and mergers. Curr Biol. 2004 Dec 29;14(24):R1048-50.

Division of Endosymbiotic Organelles

2006-07-21T12:58:00.000-07:00

Division of Endosymbiotic Organelles : ScienceWeek: "Like their free-living ancestors, both chloroplasts and mitochondria divide. Organelle division, segregation, and growth are often uncoupled from the cell division cycle, indicating that organelle and cell division are independent processes. Division of mitochondria and chloroplasts is orchestrated by multicomponent protein machines that assemble and drive the constriction and fission of the organellar membranes. Because both organelles are surrounded by inner and outer membranes that differ in composition, their division machines must accomplish the synchronized constriction of both membranes, the subsequent fusion of the four lipid bilayers, the final separation of the two daughter organelles, and possibly the resolution of the fused membranes back into two discrete bilayers."

On the origin of mitochondria: a genomics perspective

2006-07-19T23:59:00.001-07:00

On the origin of mitochondria: a genomics perspective. : Entrez PubMed:
The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.
Andersson SG, Karlberg O, Canback B, Kurland CG. On the origin of mitochondria: a genomics perspective. Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):165-77; discussion 177-9.

More:

Origin and evolution of the mitochondrial proteome. [Microbiol Mol Biol Rev. 2000] PMID: 11104819
Mitochondrial genome evolution and the origin of eukaryotes. [Annu Rev Genet. 1999] PMID: 10690412
Mitochondrial evolution. [Science. 1999] PMID: 10066161
The dual origin of the yeast mitochondrial proteome. [Yeast. 2000] PMID: 11025528
Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times. [Mol Biol Evol. 2003] PMID: 12832624

Shaping the mitochondrial proteome

2006-07-19T23:59:00.000-07:00

Shaping the mitochondrial proteome. : Entrez PubMed: "Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14-16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome."
Gabaldon T, Huynen MA. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004 Dec 6;1659(2-3):212-20.

Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record

2006-07-18T13:46:00.000-07:00

Margulis' theory of the evolution of flagella is not widely accepted.

Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record.
Entrez PubMed: "Recent geological treatises have presented three alternative models of the origins of eukaryotes as if they merited equal treatment. However, modern biological techniques, especially nucleic acid and protein sequencing, have clearly established the validity of the symbiotic theory of the origin of eukaryotic organelles. The serial endosymbiotic theory in its most extreme form states that three classes of eukaryotic cell organelles (mitochondria, plastids and undulipodia) originated as free-living bacteria (aerobic respirers, phototrophic bacteria and spirochetes respectively) in association with hosts that become the nucleocytoplasm (Thermoplasma-like archaebacterial hosts). Molecular biological information, primarily derived from ribosomal RNA nucleotide sequencing studies leads to the conclusion that the symbiotic origin theory for both mitochondria and plastids has been proven. The probability of an ancestral archaebacterial-Thermoplasma-like host for the nucleocytoplasm has been rendered more likely by discoveries by Dennis Searcy and his colleagues and Carl Woese and his colleagues. The most equivocal postulate of the symbiotic theory, the origin of undulipodia (cilia and other organelles of motility that develop from kinetosomes is under investigation now. The status of these postulates, as well as their implications for the fossil record, is briefly summarized here."
Margulis L, Stolz JF. Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record. Adv Space Res. 1984;4(12):195-201.

Undulipodia, flagella and cilia.

2006-07-18T13:40:00.000-07:00

Margulis' theory of the evolution of flagella is not widely accepted.

Undulipodia, flagella and cilia. : Entrez PubMed: "The term flagella is ambiguous. It refers to bacterial structures composed of flagellin protein and to eukaryotic structures composed of microtubule proteins and ATPase (tubulin and dynein). The fact that cilia are nearly identical to eukaryotic flagella and have nothing in common with prokaryotic flagella is not apparent from the terminology. It is proposed that the 30-year old suggestion of Smagina and reiterated by Kuznicki and others, be adopted: that cilia and eukaryotic flagella be called 'undulipodia.' The term flagella ought to be restricted to prokaryotic organelles, bacterial flagella and spirochaete axial filaments: solid structures composed of flagellin which protrude through the plasma membrane and lack intrinsic motility throughout their length. Undulipodia are defined as intrinsically motile intracellular structures showing a 9-fold symmetry in the pattern of arrangement of 24 nm diameter microtubules. They are limited to eukaryotes, members of the protoctist, animal and plant kingdoms."
Margulis L. Undulipodia, flagella and cilia. Biosystems. 1980;12(1-2):105-8.

Evolution of flagella

2006-07-18T01:19:00.000-07:00

Evolution of flagella - Wikipedia, the free encyclopedia: "There are two competing groups of models for the evolutionary origin of the eukaryotic flagellum (referred to as a cilium below to distinguish it from its bacterial counterpart)."

The apicoplast: a review of the derived plastid of apicomplexan parasites

2006-07-16T13:23:00.000-07:00

The apicoplast: a review of the derived plastid of apicomplexan parasites : Entrez PubMed: "The apicoplast is a plastid organelle, homologous to chloroplasts of plants, that is found in apicomplexan parasites such as the causative agents of Malaria Plasmodium spp. It occurs throughout the Apicomplexa and is an ancient feature of this group acquired by the process of endosymbiosis. Like plant chloroplasts, apicoplasts are semi-autonomous with their own genome and expression machinery. In addition, apicoplasts import numerous proteins encoded by nuclear genes. These nuclear genes largely derive from the endosymbiont through a process of intracellular gene relocation. The exact role of a plastid in parasites is uncertain but early clues indicate synthesis of lipids, heme and isoprenoids as possibilities. The various metabolic processes of the apicoplast are potentially excellent targets for drug therapy."
Waller RF, McFadden GI. The apicoplast: a review of the derived plastid of apicomplexan parasites. Curr Issues Mol Biol. 2005 Jan;7(1):57-79.

Mathematical Modeling of Evolution of Horizontally Transferred Genes -- Novozhilov et al. 22 (8): 1721 -- Molecular Biology and Evolution

2006-07-14T19:51:00.000-07:00

Mathematical Modeling of Evolution of Horizontally Transferred Genes -- Novozhilov et al. 22 (8): 1721 -- Molecular Biology and Evolution: "We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate of arrival of a novel sequence from outside of the recipient population), within-population horizontal transmission ('infection') rate, and population size. The model of Berg and Kurland included four parameters, namely, mutational inactivation, selection coefficient, population size, and 'infection.' However, the effect of 'infection' was disregarded in the interpretation of the results, and the overall conclusion was that horizontally acquired sequences can be fixed in a population only when they confer a substantial selective advantage onto the recipient and therefore are subject to strong positive selection. Analysis of the present model in different domains of parameter values shows that, as long as the rate of within-population horizontal transmission is comparable to the mutational inactivation rate and there is even a low rate of invasion, horizontally acquired sequences can be fixed in the population or at least persist for a long time in a substantial fraction of individuals in the population even when they are neutral or slightly deleterious. The available biological data strongly suggest that intense within-population and even between-populations gene flows are realistic for at least some prokaryotic species and environments. Therefore, our modeling results are compatible with the notion of a pivotal role of horizontal gene transfer in the evolution of prokaryotes. "

Artem S. Novozhilov, Georgy P. Karev and Eugene V. Koonin
Mathematical Modeling of Evolution of Horizontally Transferred Genes
Molecular Biology and Evolution 2005 22(8):1721-1732; doi:10.1093/molbev/msi167 link

A Set To!

1990-01-01T13:20:00.000-08:00

Gray Matters
Adeistic
Avidity
Eine Kleine Nattermusing
eMusings
eVolition
Galaria
Godspell Follies
MetaThoughts
Mimble Wimble
Naturalism
Neologisms
palimpsest
Sechuam
Sintheist
Tabula Flexuosa
Weltschauung

o

1990-01-01T01:00:00.002-08:00

• Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Galaria • Glossary • Godspell Follies • Harper's Folly • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Mimble Wimble • Molecule • Molecular Biology • Molecular Paths • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Tabula Flexuosa • Taxonomy Phylogeny • Tissue • Virus •

Item links

1990-01-01T00:00:00.000-08:00

Items
·סּ Serial Endosymbiosis Theory (SET)
·סּ Experimental evidence for Endosymbiosis
·סּ Secondary endosymbiosis
·סּ Mitochondrial origins
·סּ History of ideas concerning endosymbiosis
·סּ Endosymbiotic transfers
·סּ Endosymbiotic Gene Transfer
·סּ Horizontal Gene Transfer
·סּ Diagrams of proposed mechanism of SET
·סּ Photosynthesis in Eukaryotes

Abstracts of Articles •• Reviews SET •
• Free Full Text . Search . evidence • Symbiosis as a mechanism of evolution: status of cell symbiosis theory • Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain -- Erill et al. 34 (1): 66 -- Nucleic Acids Research • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. • MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA • The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists • A molecular timeline for the origin of photosynthetic eukaryotes • Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families • New Cellular Evolution Theory Rejects Darwinian Assumptions • A secondary symbiosis in progress? • A molecular timeline for the origin of photosynthetic eukaryotes • Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families • New Cellular Evolution Theory Rejects Darwinian Assumptions • A secondary symbiosis in progress? • Continued evolutionary surprises among dinoflagellates -- Morden and Sherwood 99 (18): 11558 -- Proceedings of the National Academy of Sciences • Gene switching in Amoeba proteus caused by endosymbiotic bacteria • Possible evolutionary significance of spirochaetes • Diatom genomics: genetic acquisitions and mergers • Division of Endosymbiotic Organelles • Shaping the mitochondrial proteome • On the origin of mitochondria: a genomics perspective • Evolution of flagella • The apicoplast: a review of the derived plastid of apicomplexan parasites • Mathematical Modeling of Evolution of Horizontally Transferred Genes -- Novozhilov et al. 22 (8): 1721 -- Molecular Biology and Evolution
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