Endosymbiosis Cell Evolution And Speciation Pdf
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- Endosymbiosis, cell evolution, and speciation
- What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts
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In , the Russian biologist C. Mereschkowsky postulated that plastids e. In , I. Wallin explicitly postulated that mitochondria likewise evolved from once free-living bacteria. Additionally, we review recent hypotheses about the origin of the nucleus.
Endosymbiosis, cell evolution, and speciation
Intracellular symbiosis is known to be widespread in insects, but there are few described examples in other types of host. These symbionts carry out useful activities such as synthesizing nutrients and conferring resistance against adverse events such as parasitism. Such symbionts persist through host speciation events, being passed down through vertical transmission. Due to various evolutionary forces, symbionts go through a process of genome reduction, eventually resulting in tiny genomes where only those genes essential to immediate survival and those beneficial to the host remain.
In the marine environment, invertebrates such as tunicates are known to harbor complex microbiomes implicated in the production of natural products that are toxic and probably serve a defensive function.
Here, we show that the intracellular symbiont Candidatus Endolissoclinum faulkneri is a long-standing symbiont of the tunicate Lissoclinum patella , that has persisted through cryptic speciation of the host. In contrast to the known examples of insect symbionts, which tend to be either relatively recent or ancient relationships, the genome of Ca.
The almost complete degradation of intergenic regions and stable gene inventory of extant strains of Ca. This is a novel stage of genome reduction and provides insight into how tiny genomes are formed. The ptz pathway, which produces the defensive patellazoles, is shown to date to before the divergence of Ca.
Lastly, as in insects we show that stable symbionts can be lost, as we describe an L. Our results suggest that intracellular symbionts may be an important source of ecologically significant natural products in animals.
This is an open-access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist.
In these systems, the bacteria are typically inherited vertically, with the host and symbiont potentially co-evolving for significant time.
In recent years, genomic sequencing has revealed that intracellular symbionts in insects undergo a process of progressive genome degradation . Through these studies, a model of symbiont evolution has emerged, whereby the low effective populations of host-restricted symbionts gives rise to a situation where deleterious mutations easily become fixed.
Concurrently, the intracellular lifestyle of symbionts reduces the need for many functions that would be essential for independent life. Eventually, the loss of DNA repair pathways accelerates the process and increases the rate of genomic drift. While intracellular symbionts are common in insects, they have never been found in chordates, such as mammals, where the only intracellular bacteria found are pathogenic .
We have been studying a different model of symbiosis, the tunicate Lissoclinum patella. Tunicates are sessile marine filter feeders, and as chordates they are the closest extant relatives of the vertebrates . Extruded water from filter feeding, and waste products, are excreted into the shared cloacal cavities . Much of the previous investigations in this system have focused on an extracellular symbiont that resides in the cloacal cavities of L.
Through sequencing, it has been found that this symbiont produces highly modified cyclic peptides termed cyanobactins  , . More recently it has come to light that L. The genome of this symbiont accession no. Here, we show that Ca. In the one case of an L. This is similar to the phenomenon of symbiont displacement known to occur in insect systems . Collectively, our work captures a novel intermediate stage of genome degradation and reveals similarities to a type of symbiosis previously only well described in insects.
We previously reported that patellazoles-containing L. The intracellular symbiont Ca. We reexamined this clade of L. Although an ascidian molecular clock has not been established, it is known that mitochondrial genomes in this group are highly plastic  and divergence rates of 0. Although the reproductive compatibility of these animals is unknown, such divergence could be the result of physical separation of these sessile animals along with limited ranges for their gametes and larvae.
With evidence that the three L. To this end we carried out shotgun metagenomic sequencing of animal L5, and assembled the chromosome of Ca.
The Ca. These strains share Outer line graphs show protein and nucleotide identities for corresponding coding and noncoding regions as indicated. Note: These graphs are reciprocal and interchangeable, and are plotted against either L2 or L5 for clarity. Immediately inside line graphs are shown the positions of pseudogenes grey , RNA genes green , genes that do not have homologs in BAL, but are shared by both Ca. The remaining genes i. Note: positioning of the gene categories on different tracks are to allow effective visualization of some positions that overlap due to the pxiel width in the figure.
The inner circle shows links between homologous protein coding genes in the two strains of Ca. Analysis of the homologs in Ca. Homologs in the two strains of Ca. This is consistent with intracellular symbionts in insects, such as Buchnera aphidicola  and Sulcia muelleri  , in which genetic isolation and loss of recombination pathways allows complete synteny conservation over hundreds of millions of years, despite significant sequence drift.
These symbionts have genomes in a more advanced stage of reduction than Ca. Similarly, the S. As with B. Brucella melitensis 16M and Brucella ovis are intracellular pathogens of livestock, whose divergence has been dated to 86,—, years ago, which presumably occurred in wild animal populations prior to domestication .
Taken together, the divergence and synteny of L2 and L5 suggest that the two strains have been genetically isolated since the divergence of their hosts, roughly concurrently with the loss of recombination pathways, as evidenced by the two observed inversion events, which presumably occurred shortly before the capability was lost. Intergenic sequences are highly degraded, but still show a strong syntenic signal, indicating that they were once functional genes.
A Venn diagram of homologous proteins in Ca. B Synteny plot of proteins in Ca. C Synteny plot of homologous intergenic sequences in Ca. D Synteny plot of homologous intergenic sequences in Ca.
Note: some genes are repeated in multiple categories. The BAL and Ca. By comparison, a pair of intracellular pathogens that are thought to have diverged before the domestication of their respective hosts exhibits far less sequence drift.
The genomes of Ca. This is similar to the early stages of genome reduction following host-restriction, which are characterized by a proliferation of pseudogenes and therefore low coding density , and pervasive genome rearrangements, with only modest genome reduction . In previously described low-density genomes, large numbers of pseudogenes have been found.
For instance, pseudogenes were described in the 4. In these cases, symbiosis was established fairly recently. For example, a rice weevil symbiont related to S. Recently a closely related free-living pathogen HC was discovered and appears to have diverged from SOPE approvimately 28, years ago .
We searched for pseudogenes in both strains of Ca. These efforts yielded strikingly few identifiable pseudogenes see Table 2. All of these pseudogenes are characterized by numerous frame shifts and in-frame stop codons see Fig.
Their putative functions are in line with the types of losses observed in other intracellular symbionts: replication, gene regulation, stress response and peptidoglycan degradation.
The higher AT content of intergenic sequences likely reflects AT mutation biases acting disproportionately on nonfunctional sections of the genome, as part of a general trend of increased AT content in progressively reduced genomes .
The intergenic sequences of Ca. This strongly suggests that these intergenic sequences were once genes that underwent an extended period of time where synonymous mutations were favored.
This finding is unique amongst symbiont genomes and could suggest that the process of pseudogene formation proceeds in distinct stages, with sequence degradation preceding deletion. Other examples of long-term obligate symbionts in insects all have much smaller genomes where the majority of pseudogenes have already been deleted, and their symbiotic lifestyles date back to much earlier times genome sizes — kbp, 40— million years ago .
Further work would be required to determine if the highly-degraded sparse genome reduction stage is restricted to certain types of organism or systems, or whether it represents an intermediate stage held through which the more reduced insect symbionts have passed. Syntenic regions in Ca. The locations of these regions are shown in relation to the L2 chromosome center.
The GC content of discrete regions for example, all coding sequences from the genomes of both Ca. The individual p values for the pairwise comparisons are shown in B. Analysis of the gene inventories of L2 and L5 showed loss of key genes involved in chromosomal replication, DNA mismatch repair and cell division Fig.
For instance, the replication initiator dnaA  is missing in L2, whereas ftsK , which is involved in the termination of replication, is missing in L5. These genes are detectable as pseudogenes see Table 2 and intact ORFs in the corresponding strain see Table 3 , suggesting that their loss was recent. This is supported by the GC content of the pseudogenes, which are at an intermediate GC content, significantly different from both coding and intergenic regions see Table 1 , Fig.
Other central genes are missing in both L2 and L5, for instance the almost universally conserved protein FtsZ  , which has a central role in bacterial cell division, forming the Z-ring that divides an elongated rod cell in the center. To the best of our knowledge, Ca.
It should be noted that in our analysis we did not include members of the Chlamydieae and Planctomycetes lineages, which do not possess ftsZ but may use other methods to produce a peptidoglycan septum . This cyanobacterium still has a large genome with low-coding density and many pseudogenes, including dnaA , but it still possesses ftsZ .
An ftsZ pseudogene could not be found in either strain of Ca. The nucleotide excision repair pathway appears to be complete, and the base excision repair pathway contains a similar gene complement to BAL, suggesting that while DNA damage caused by UV radiation may be repairable in Ca. The loss of DNA repair pathways is thought to be one of the driving forces for increased rate of evolution observed in some intracellular symbionts .
Shaded blue squares indicate the presence of ftsZ or dnaA. Note: All genomes included above are completed except for Ca. The vast majority of extant genes are shared between Ca. Of the small number of orphan genes in each strain, the majority are found as pseudogenes in the corresponding strain or else are short hypothetical genes see Table 3.
What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts
Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. The criteria that are commonly considered are genetic integration via gene transfer from the endosymbiont to the nucleus , cellular integration synchronization of the cell cycles , and metabolic integration the mutual dependency of the metabolisms. Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. If the partners lose their independence in speciation, I think that they should be considered one species. Not that bacteria smell particularly sweet, but that, as a scientist, I care much more about what mitochondria, plastids or bacteria are , than about how they are called. Semantics are important for science, and not just for science, as the tragic example of Juliet shows.
The electricity consumption for cooling and heating of the house is calculated with and without the EAHE system. Eukaryotic gene expression is tightly regulated at both the transcriptional and translational levels. PDF The origin of eukaryotes remains unclear1—4. The mitochon-.
Symbiogenesis , endosymbiotic theory , or serial endosymbiotic theory  is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.