sedimented expectations, prokaryotic organisms also may contain organelles with special arrangements; for instance organelles such as magnetosomes, chlorosomes, pirellulosomes, anammoxosomes, carboxysomes, and so on [110–112].
1.12.3 Membrane-bound Organelles with DNA
Mitochondria arose approximately 2.3–1.8 billion years ago from a unicellular organism related to modern α-proteobacteria. Bacterial species Rickettsia prowazekii of the genus Rickettsia is probably the closest phylogenetic relative to the mitochondria [113, 114]. Also, ATP production in Rickettsia is the same as that in mitochondria. On the other hand, plastids (i.e. chloroplasts and chloroplast-like organelles) arose 1.6–1.5 billion years ago from the ancestors of cyanobacteria [115]. That is, a mitochondriate eukaryote became host to a cyanobacterium-like prokaryote. Organelles with their own genomes, such as plastids and mitochondria, are found in most eukaryotic cells [116]. A multicellular eukaryote contains hundreds to thousands of these organelles in each cell. The number of organelles is specific to each cell type and may vary depending on the state/metabolic needs of the cell.
1.12.4 Membrane-bound Organelles Without DNA
How much of the genome can be transferred to the nucleus or can be permanently lost in evolution? The complete loss of DNA in an organelle is a possibility. Among the organelles that have lost their genome in evolution is the hydrogenosome. Hydrogenosomes are cell organelles that have a double membrane and synthesize ATP via hydrogen-producing fermentations [117]. Hydrogenosomes were once mitochondria and are a classic example of complete mitochondrial genome loss [118]. Considering the hydrogenosome example, it is reasonable to assume that all eukaryotes may contain an organelle of mitochondrial ancestry [119]. However, DNA in the hydrogenosomes of some anaerobic ciliates has been detected [120]. Ciliates are protists with hair-like organelles (i.e. cilia) used for propulsion and adherence inside liquid media. Cases of genome-containing hydrogenosomes show that these organelles are somewhere toward the end of their reductive evolution period. It can also mean that the loss of the genome is not just a one-way street, which would have important implications for elucidating the occurrence of life on Earth. A basic question arises when considering the above: Are the genome-less hydrogenosomes organisms in their own way? This is an interesting question because it shows the versatility of life and the ideas discussed in the “Philosophical transactions” chapter or in the “Viruses vs. the spark of metabolism” subchapter.
1.12.5 Control and Division of Organelles
Both genome and genome-less organelles divide. But how ? Regular bacterial fission (division) uses a dynamin-related protein (DRP) to constrict the membrane at its inner face [121]. However, DRPs are also essential for mitochondrial and peroxisomal fission [122]. Fission is required to provide a population of organelles for daughter cells during mitosis. In contrast to bacterial fission, mitochondria use dynamin and DPRs to constrict the outer membrane (a ring) from the cytosolic face [121]. For instance, the unicellular eukaryote Trichomonas vaginalis is a parasite that uses hydrogenosomes instead of regular mitochondria. The role of DRPs in the division of the hydrogenosome is similar to that described for peroxisomes and mitochondria [123]. Moreover, plastids use similar mechanisms and a plant-specific DPR [124, 125]. In eukaryotes, dynamin and DPRs have their genes stored in the nuclear genome. Thus, control over the division of membrane-bound organelles is held by the nuclear genome. Genes encoding DPRs were once present in the symbiotic α-proteobacterium ancestors of mitochondria or in the symbiotic cyanobacterium ancestors of the plastids. In other words, the alternative self-assembly of a complementary dynamin constriction mechanism on the outer membrane, allowed a transition of the organellar fission genes to the nuclear genome for synchronization of cell division. Moreover, this complementary mechanism allowed a reductive evolution up to the point of complete genome elimination in some organelles, such as in the case of hydrogenosomes. But how do organelle genes physically get into the nucleus to recombine with chromosomal DNA? Insertion of DNA from organelle genomes into the nucleus is DNA-mediated (RNA-mediated insertions may also occur) through a process called HGT [126]. As a side note, peroxisomes are single-membrane organelles that catalyze the breakdown of very-long-chain fatty acids through beta-oxidation [127]. Peroxisomes are a hybrid of mitochondrial and ER-derived (ER – endoplasmic reticulum) pre-peroxisomes [128].
1.12.6 The Horizontal Gene Transfer
The symbiosis between organisms is not possible without the HGT. The HGT is the weak “glue” that unites all species and it has important evolutionary implications [129]. In the future, these implications may very well undo the classification discussed above for the tree of life and how we understand the origin of life on Earth. The HGT refers to the transmission of DNA between different genomes, whereas the vertical gene transfer (VGT) is made between generations by sexual or asexual reproduction. The way in which the classification for the tree of life works is largely based on the VGT concept; thus, one can imagine the issue. HGT was first observed as a phenomenon in Streptococcus pneumoniae species by Frederick Griffith in 1928 [130]. The main observation made by Frederick Griffith was that virulence (pathogenicity) in this species of bacterium is transmitted by contact or proximity. This was an important revelation for the later field of genetics. Since then, increasing evidence shows that DNA fragments of different sizes may be exchanged between the kingdoms of life, to a greater or lesser extent [129]. Not long ago, the transfer of genetic information from the members of the Agrobacterium genus to eukaryote cells was seen as an extraordinary and rare process [131, 132]. Today, evidence indicates clearly that transfer of genetic information between species and inside different cell compartments is a common process, which takes place over the evolutionary time. For instance, bacteria have acquired genetic material from eukaryotic hosts and vice versa [133]. Viruses contain genes derived from their eukaryotic hosts and vice versa [134]. In plants, for instance, the HGT between genomes takes place through intracellular transfer of DNA among the nuclear, mitochondrial, and plastid genomes. The transfer of mitochondrial genes to the nucleus is known to be an ongoing evolutionary process. However, evidence also shows a HGT of mitochondrial DNA to the plastid genome [135]. Moreover, expression of a transferred nuclear gene in a mitochondrial genome was also observed [136]. For example, the orf164 gene in the mitochondrial genome of Arabidopsis is derived from the nuclear ARF17 gene that codes for an auxin-responsive protein [136]. Thus, the transfer of DNA segments from any location to any other location seems to be a rule across all life. However, HGT is most frequent between closely related species with similar genome features and less frequent otherwise [137]. In other words, HGT is a process that occurs at different frequencies between prokaryotes, between eukaryotes, between prokaryotes and eukaryotes and vice versa [138]. Perhaps, the importance of HGT goes as far as the emergence of new species (speciation) [139, 140].
1.12.7 On the Mechanisms of Horizontal Gene Transfer
Understanding of the mechanisms and vectors underpinning HGT across the kingdoms of life is still limited. Mobile genetic elements (MGEs) represent the main known vectors for HGT [137]. Well-known HGT events often include, but are not limited to, transposable elements (TE), plasmids or bacteriophage elements [141]. The behavior of a MGE has a certain degree of stochasticity and may incorporate a complete gene(s) or may include only sections of a gene, or with a high probability none of the two. Sections of genes transferred by MGEs decay in time and are recognized in bioinformatic analyzes as pseudogenes (nonfunctional genes) [126]. Among the MGEs, TE can best show the level of complexity that a DNA fragment can exhibit. The TE were first observed in Zea mays (corn) by Barbara McClintock in 1950 [142]. The main observation made by Barbara McClintock was that the genetic material can jump from one place to another within a genome. The insertion of TEs into the coding pigment-genes was responsible for unstable phenotypes on the kernels of a maize ear (kernels of different colors). Note that each kernel is an embryo produced from an individual fertilization and one ear of corn contains around 800 kernels positioned in 16 rows.
1.13
