CoRR hypothesis

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The CoRR hypothesis states that the location of genetic information in cytoplasmic organelles permits regulation of its expression by the reduction-oxidation ("redox") state of its gene products.

Contents

CoRR is short for "co-location for redox regulation", itself a shortened form of "co-location (of gene and gene product) for (evolutionary) continuity of redox regulation of gene expression". [1] [2]

CoRR was put forward explicitly in 1993 in a paper in the Journal of Theoretical Biology with the title "Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes". [3] The central concept had been outlined in a review of 1992. [4] The term CoRR was introduced in 2003 in a paper in Philosophical Transactions of the Royal Society entitled "The function of genomes in bioenergetic organelles". [5]

The problem

Chloroplasts and mitochondria

Chloroplasts and mitochondria are energy-converting organelles in the cytoplasm of eukaryotic cells. Chloroplasts in plant cells perform photosynthesis; the capture and conversion of the energy of sunlight. Mitochondria in both plant and animal cells perform respiration; the release of this stored energy when work is done. In addition to these key reactions of bioenergetics, chloroplasts and mitochondria each contain specialized and discrete genetic systems. These genetic systems enable chloroplasts and mitochondria to make some of their own proteins.

Both the genetic and energy-converting systems of chloroplasts and mitochondria are descended, with little modification, from those of the free-living bacteria that these organelles once were. The existence of these cytoplasmic genomes is consistent with, and counts as evidence for, the endosymbiont hypothesis. Most genes for proteins of chloroplasts and mitochondria are, however, now located on chromosomes in the nuclei of eukaryotic cells. There they code for protein precursors that are made in the cytosol for subsequent import into the organelles.

Why do mitochondria and chloroplasts have their own genetic systems?

Why do mitochondria and chloroplasts require their own separate genetic systems, when other organelles that share the same cytoplasm, such as peroxisomes and lysosomes, do not? The question is not trivial, because maintaining a separate genetic system is costly: more than 90 proteins ... must be encoded by nuclear genes specifically for this purpose. ... The reason for such a costly arrangement is not clear, and the hope that the nucleotide sequences of mitochondrial and chloroplast genomes would provide the answer has proved to be unfounded. We cannot think of compelling reasons why the proteins made in mitochondria and chloroplasts should be made there rather than in the cytosol.

— Alberts et al., The Molecular Biology of the Cell. Garland Science. All editions (pgs 868-869 in 5th edition) [6]

Cytoplasmic inheritance

CoRR seeks to explain why chloroplasts and mitochondria retain DNA, and thus why some characters are inherited through the cytoplasm in the phenomenon of cytoplasmic, non-Mendelian, uniparental, or maternal inheritance. CoRR does so by offering an answer to this question: why, in evolution, did some bacterial, endosymbiont genes move to the cell nucleus, while others did not?

Proposed solution

CoRR states that chloroplasts and mitochondria contain those genes whose expression is required to be under the direct, regulatory control of the redox state of their gene products, or of electron carriers with which those gene products interact. Such genes comprise a core, or primary subset, of organellar genes. The requirement for redox control of each gene in the primary subset then confers an advantage upon location of that gene within the organelle. Natural selection therefore anchors some genes in organelles, while favouring location of others in the cell nucleus.

Chloroplast and mitochondrial genomes also contain genes for components of the chloroplast and mitochondrial genetic systems themselves. These genes comprise a secondary subset of organellar genes: genetic system genes. There is generally no requirement for redox control of expression of genetic system genes, though their being subject to redox control may, in some cases, allow amplification of redox signals acting upon genes in the primary subset (bioenergetic genes).

Retention of genes of the secondary subset (genetic system genes) is necessary for the operation of redox control of expression of genes in the primary subset. If all genes disappear from the primary subset, CoRR predicts that there is no function for genes in the secondary subset, and such organelles will then, eventually, lose their genomes completely. However, if even only one gene remains under redox control, then an organelle genetic system is required for the synthesis of its single gene product.

Evidence

See also

Related Research Articles

Chloroplast Plant organelle that conducts photosynthesis

A chloroplast is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.

Mitochondrion Organelle in eukaryotic cells responsible for respiration

A mitochondrion is a double-membrane-bound organelle found in most eukaryotic organisms. Mitochondria use aerobic respiration to generate most of the cell's supply of adenosine triphosphate (ATP), which is subsequently used throughout the cell as a source of chemical energy. They were discovered by Albert von Kölliker in 1857 in the voluntary muscles of insects. The term mitochondrion was coined by Carl Benda in 1898. The mitochondrion is popularly nicknamed the "powerhouse of the cell", a phrase coined by Philip Siekevitz in a 1957 article of the same name.

Symbiogenesis Evolutionary theory holding that eukaryotic organelles evolved through symbiosis with prokaryotes

Symbiogenesis, endosymbiotic theory, or serial endosymbiotic theory, is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. The idea that chloroplasts were originally independent organisms that merged into a symbiotic relationship with other one-celled organisms dates back to the 19th century, when it was espoused by researchers such as Andreas Schimper.

Mitochondrial DNA DNA located in cellular organelles called mitochondria

Mitochondrial DNA is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also in plastids such as chloroplasts.

Plastid Plant cell organelles that perform photosynthesis and store starch

The plastid is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cyanobacteria. Examples include chloroplasts, chromoplasts, and leucoplasts.

Reactive oxygen species Class of compounds

Reactive oxygen species (ROS) are highly reactive chemicals formed from O2. Examples of ROS include peroxides, superoxide, hydroxyl radical, singlet oxygen, and alpha-oxygen.

Heteroplasmy is the presence of more than one type of organellar genome within a cell or individual. It is an important factor in considering the severity of mitochondrial diseases. Because most eukaryotic cells contain many hundreds of mitochondria with hundreds of copies of mitochondrial DNA, it is common for mutations to affect only some mitochondria, leaving most unaffected.

Non-Mendelian inheritance Type of pattern of inheritance

Non-Mendelian inheritance is any pattern of inheritance in which traits do not segregate in accordance with Mendel's laws. These laws describe the inheritance of traits linked to single genes on chromosomes in the nucleus. In Mendelian inheritance, each parent contributes one of two possible alleles for a trait. If the genotypes of both parents in a genetic cross are known, Mendel's laws can be used to determine the distribution of phenotypes expected for the population of offspring. There are several situations in which the proportions of phenotypes observed in the progeny do not match the predicted values.

Nuclear gene Gene located in the cell nucleus of a eukaryote

A gene is a genetic unit of inheritance that consists of a segment of DNA that encodes for a functional RNA or a messenger RNA that is used to make proteins. All of the genes together make us the organism's genome and direct organismal phenotypes. Genes can be located in three distinct places in eukaryotic cells. The vast majority of genes are found in the chromosomes within the nucleus.

Extrachromosomal DNA is any DNA that is found off the chromosomes, either inside or outside the nucleus of a cell. Most DNA in an individual genome is found in chromosomes contained in the nucleus. Multiple forms of extrachromosomal DNA exist, and, while some of these serve important biological functions, they can also play a role in diseases, such as ecDNA in cancer.

Extranuclear inheritance or cytoplasmic inheritance is the transmission of genes that occur outside the nucleus. It is found in most eukaryotes and is commonly known to occur in cytoplasmic organelles such as mitochondria and chloroplasts or from cellular parasites like viruses or bacteria.

NUMT, pronounced "new might," is an acronym for "nuclear mitochondrial DNA" segment coined by evolutionary geneticist, Jose V. Lopez, which describes a transposition of any type of cytoplasmic mitochondrial DNA into the nuclear genome of eukaryotic organisms.

Organellar DNA (oDNA) is DNA contained in organelles, outside the nucleus of Eukaryotic cells.

Two-component regulatory system

In the field of molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.

Plant evolution Subset of evolutionary phenomena that concern plants

Plant evolution is the subset of evolutionary phenomena that concern plants. Evolutionary phenomena are characteristics of populations that are described by averages, medians, distributions, and other statistical methods. This distinguishes plant evolution from plant development, a branch of developmental biology which concerns the changes that individuals go through in their lives. The study of plant evolution attempts to explain how the present diversity of plants arose over geologic time. It includes the study of genetic change and the consequent variation that often results in speciation, one of the most important types of radiation into taxonomic groups called clades. A description of radiation is called a phylogeny and is often represented by type of diagram called a phylogenetic tree.

Mitochondrial biogenesis is the process by which cells increase mitochondrial numbers. It was first described by John Holloszy in the 1960s, when it was discovered that physical endurance training induced higher mitochondrial content levels, leading to greater glucose uptake by muscles. Mitochondrial biogenesis is activated by numerous different signals during times of cellular stress or in response to environmental stimuli, such as aerobic exercise.

Chloroplast DNA DNA located in cellular organelles called chloroplasts

Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, hundreds of chloroplast DNAs from various species have been sequenced.

<i>Cyanidioschyzon</i> Species of alga

Cyanidioschyzon merolae is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments. The cellular architecture of C. merolae is extremely simple, containing only a single chloroplast and a single mitochondrion and lacking a vacuole and cell wall. In addition, the cellular and organelle divisions can be synchronized. For these reasons, C. merolae is considered an excellent model system for study of cellular and organelle division processes, as well as biochemistry and structural biology. The organism's genome was the first full algal genome to be sequenced in 2004; its plastid was sequenced in 2000 and 2003, and its mitochondrion in 1998. The organism has been considered the simplest of eukaryotic cells for its minimalist cellular organization.

Chloroplast Sensor Kinase (CSK) is a protein in chloroplasts and cyanobacteria, bacteria from which chloroplasts evolved by endosymbiosis. It is part of a two-component system. In the plant Arabidopsis thaliana CSK is the product of the gene At1g67840. CSK is known in cyanobacteria as the histidine kinase 2.

John F. Allen (biochemist) British biochemist

John Allen is a British biochemist. He is an honorary professor at the Department of Genetics, Evolution and Environment at the University College London in the United Kingdom.

References

  1. ↑ Allen JF (August 2015). "Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression". Proc. Natl. Acad. Sci. U.S.A. 112 (33): 10231–10238. Bibcode:2015PNAS..11210231A. doi: 10.1073/pnas.1500012112 . PMC   4547249 . PMID   26286985.
  2. ↑ Allen JF (December 2017). "The CoRR hypothesis for genes in organelles". J. Theor. Biol. 434: 50–57. Bibcode:2017JThBi.434...50A. doi: 10.1016/j.jtbi.2017.04.008 . PMID   28408315.
  3. ↑ Allen JF (December 1993). "Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes". J. Theor. Biol. 165 (4): 609–31. Bibcode:1993JThBi.165..609A. doi:10.1006/jtbi.1993.1210. PMID   8114509.
  4. ↑ Allen JF (January 1992). "Protein phosphorylation in regulation of photosynthesis". Biochim. Biophys. Acta. 1098 (3): 275–335. doi:10.1016/s0005-2728(09)91014-3. PMID   1310622.
  5. ↑ Allen JF (January 2003). "The function of genomes in bioenergetic organelles". Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (1429): 19–37, discussion 37–8. doi:10.1098/rstb.2002.1191. PMC   1693096 . PMID   12594916.
  6. ↑ Bruce Alberts; Alexander Johnson; Julian Lewis; Martin Raff; Keith Roberts; Peter Walter (16 November 2007). Molecular Biology of the Cell. Garland Science. pp. 868–869. ISBN   9781136844423.
  7. ↑ Allen CA, Hakansson G, Allen JF (1995). "Redox Conditions Specify the Proteins Synthesized by Isolated-Chloroplasts and Mitochondria" (PDF). Redox Report. 1 (2): 119–123. doi:10.1080/13510002.1995.11746969. PMID   27405554.
  8. ↑ Pfannschmidt T, Nilsson A, Allen JF (February 1997). "Photosynthetic control of chloroplast gene expression". Nature. 397 (6720): 625–628. doi:10.1038/17624. S2CID   4423836.
  9. ↑ Puthiyaveetil S, Kavanagh TA, Cain P, Sullivan JA, Newell CA, Gray JC, Robinson C, van der Giezen M, Rogers MB, Allen JF (July 2008). "The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts". Proc. Natl. Acad. Sci. U.S.A. 105 (29): 10061–6. Bibcode:2008PNAS..10510061P. doi: 10.1073/pnas.0803928105 . PMC   2474565 . PMID   18632566.
  10. ↑ Puthiyaveetil S, Allen JF (June 2009). "Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression". Proc. Biol. Sci. 276 (1665): 2133–45. doi:10.1098/rspb.2008.1426. PMC   2677595 . PMID   19324807.
  11. ↑ Johnston, I. G.; Williams, B. P. (2016). "Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention" (PDF). Cell Systems. 2 (2): 101–111. doi: 10.1016/j.cels.2016.01.013 . PMID   27135164.

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