A nuclear gene is a gene that has its DNA nucleotide sequence physically situated within the cell nucleus of a eukaryotic organism. This term is employed to differentiate nuclear genes, which are located in the cell nucleus, from genes that are found in mitochondria or chloroplasts. The vast majority of genes in eukaryotes are nuclear.
Mitochondria and plastids evolved from free-living prokaryotes into current cytoplasmic organelles through endosymbiotic evolution. [1] Mitochondria are thought to be necessary for eukaryotic life to exist. They are known as the cell's powerhouses because they provide the majority of the energy or ATP required by the cell. The mitochondrial genome (mtDNA) is replicated separately from the host genome. Human mtDNA codes for 13 proteins, most of which are involved in oxidative phosphorylation (OXPHOS). The nuclear genome encodes the remaining mitochondrial proteins, which are then transported into the mitochondria. [2] The genomes of these organelles have become far smaller than those of their free-living predecessors. This is mostly due to the widespread transfer of genes from prokaryote progenitors to the nuclear genome, followed by their elimination from organelle genomes. In evolutionary timescales, the continuous entry of organelle DNA into the nucleus has provided novel nuclear genes. [1] Furthermore, Mitochondria depend on nuclear genes for essential protein production as they cannot generate all necessary proteins independently. [3]
Though separated from one another within the cell, nuclear genes and those of mitochondria and chloroplasts can affect each other in a number of ways. Nuclear genes play major roles in the expression of chloroplast genes and mitochondrial genes. [4] Additionally, gene products of mitochondria can themselves affect the expression of genes within the cell nucleus. [5] This can be done through metabolites as well as through certain peptides trans-locating from the mitochondria to the nucleus, where they can then affect gene expression. [6] [7] [8]
Eukaryotic genomes have distinct higher-order chromatin structures that are closely packaged functional relates to gene expression. Chromatin compresses the genome to fit into the cell nucleus, while still ensuring that the gene can be accessed when needed, such as during gene transcription, replication, and DNA repair. [9] The entirety of genome function is based on the underlying relationship between nuclear organization and the mechanisms involved in genome organization, in which there are a number of complex mechanisms and biochemical pathways which can affect the expression of individual genes within the genome. [9] The remaining mitochondrial proteins, metabolic enzymes, DNA and RNA polymerases, ribosomal proteins, and mtDNA regulatory factors are all encoded by nuclear genes. Because nuclear genes constitute the genetic foundation of all eukaryotic organisms, anything that might change their genetic expression has a direct impact on the organism's cellular genotypes and phenotypes. [2] The nucleus also contains a number of distinct subnuclear foci known as nuclear bodies, which are dynamically controlled structures that help numerous nuclear processes run more efficiently. [9] Active genes, for instance, might migrate from chromosomal regions and concentrate into subnuclear foci known as transcription factories. [9]
The majority of proteins in a cell are the product of messenger RNA transcribed from nuclear genes, including most of the proteins of the organelles, which are produced in the cytoplasm like all nuclear gene products and then transported to the organelle. Genes in the nucleus are arranged in a linear fashion upon chromosomes, which serve as the scaffold for replication and the regulation of gene expression. As such, they are usually under strict copy-number control, and replicate a single time per cell cycle. [10] Nuclear cells such as platelets do not possess nuclear DNA and therefore must have alternative sources for the RNA that they need to generate proteins. With the nuclear genome's 3.3 billion DNA base pairs in humans, one good example of a nuclear gene is MDH1 or the malate dehydrogenase 1 gene. In various metabolic pathways, including the citric acid cycle, MDH1 is a protein-coding gene that encodes an enzyme that catalyzes the NAD/NADH-dependent, reversible oxidation of malate to oxaloacetate. This gene codes for the cytosolic isozyme, which is involved in the malate-aspartate shuttle, which allows malate to cross past the mitochondrial membrane and be converted to oxaloacetate to perform further cellular functions. [11] This gene among many exhibits its huge purposeful role in the entirety of an organism’s physiologic function. Although non-nuclear genes may exist in its functional nature, the role of nuclear genes in response and in coordination with non-nuclear genes is fundamental.
Many nuclear-derived transcription factors have played a role in respiratory chain expression. These factors may have also contributed to the regulation of mitochondrial functions. Nuclear respiratory factor (NRF-1) fuses to respiratory encoding genes proteins, to the rate-limiting enzyme in biosynthesis, and to elements of replication and transcription of mitochondrial DNA, or mtDNA. The second nuclear respiratory factor (NRF-2) is necessary for the production of cytochrome c oxidase subunit IV (COXIV) and Vb (COXVb) to be maximized. [4]
The studying of gene sequences for the purpose of speciation and determining genetic similarity is just one of the many uses of modern day genetics, and the role that both types of genes have in that process is important. Though both nuclear genes and those within endosymbiotic organelles provide the genetic makeup of an organism, there are distinct features that can be better observed when looking at one compared to the other. Mitochondrial DNA is useful in the study of speciation as it tends to be the first to evolve in the development of a new species, which is different from nuclear genes' chromosomes that can be examined and analyzed individually, each giving its own potential answer as to the speciation of a relatively recently evolved organism. [12]
Low-copy nuclear genes in plants are valuable for improving phylogenetic reconstructions, especially when universal markers like Chloroplast DNA, or cpDNA and Nuclear ribosomal DNA, or nrDNA fall short. Challenges in using these genes include limited universal markers and the complexity of gene families. Nonetheless, they are essential for resolving close species relationships and understanding plant phylogenetic studies. While using low-copy nuclear genes requires additional lab work, advances in sequencing and cloning techniques have made it more accessible. Fast-evolving introns in these genes can offer crucial phylogenetic insights near species boundaries. This approach, along with the analysis of developmentally important genes, enhances the study of plant diversity and evolution. [13]
As nuclear genes are the genetic basis of all eukaryotic organisms, anything that can affect their expression therefore directly affects characteristics about that organism on a cellular level. The interactions between the genes of endosymbiotic organelles like mitochondria and chloroplasts are just a few of the many factors that can act on the nuclear genome.
The cell is the basic structural and functional unit of all forms of life. Every cell consists of cytoplasm enclosed within a membrane; many cells contain organelles, each with a specific function. The term comes from the Latin word cellula meaning 'small room'. Most cells are only visible under a microscope. Cells emerged on Earth about 4 billion years ago. All cells are capable of replication, protein synthesis, and motility.
Cell biology is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and functioning of organisms. Cell biology is the study of the structural and functional units of cells. Cell biology encompasses both prokaryotic and eukaryotic cells and has many subtopics which may include the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells is performed using several microscopy techniques, cell culture, and cell fractionation. These have allowed for and are currently being used for discoveries and research pertaining to how cells function, ultimately giving insight into understanding larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences while also being essential for research in biomedical fields such as cancer, and other diseases. Research in cell biology is interconnected to other fields such as genetics, molecular genetics, molecular biology, medical microbiology, immunology, and cytochemistry.
A mitochondrion is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is 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 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. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
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.
A plastid, pl. plastids, 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.
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.
Human mitochondrial genetics is the study of the genetics of human mitochondrial DNA. The human mitochondrial genome is the entirety of hereditary information contained in human mitochondria. Mitochondria are small structures in cells that generate energy for the cell to use, and are hence referred to as the "powerhouses" of the cell.
Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms or less frequently in daltons, or as the total number of nucleotide base pairs, usually in megabases. One picogram is equal to 978 megabases. In diploid organisms, genome size is often used interchangeably with the term C-value.
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 cancer.
Cellular compartments in cell biology comprise all of the closed parts within the cytosol of a eukaryotic cell, usually surrounded by a single or double lipid layer membrane. These compartments are often, but not always, defined as membrane-bound organelles. The formation of cellular compartments is called compartmentalization.
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.
Nuclear mitochondrial DNA (NUMT) segments or genetic loci describe a transposition of any type of cytoplasmic mitochondrial DNA into the nuclear genome of eukaryotic organisms.
Organellar DNA (oDNA) is DNA contained in organelles (such as mitochondria and chloroplasts), outside the nucleus of eukaryotic cells.
A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό 'before' and κάρυον 'nut, kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain, Eukaryota.
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.
Uniparental inheritance is a non-Mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father. This phenomenon is most commonly observed in eukaryotic organelles such as mitochondria and chloroplasts. This is because such organelles contain their own DNA and are capable of independent mitotic replication that does not endure crossing over with the DNA from another parental type. Although uniparental inheritance is the most common form of inheritance in organelles, there is increased evidence of diversity. Some studies found doubly uniparental inheritance (DUI) and biparental transmission to exist in cells. Evidence suggests that even when there is biparental inheritance, crossing-over doesn't always occur. Furthermore, there is evidence that the form of organelle inheritance varied frequently over time. Uniparental inheritance can be divided into multiple subtypes based on the pathway of inheritance.
Guillardia is a genus of marine biflagellate cryptomonad algae with a plastid obtained through secondary endosymbiosis of a red alga.
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, a great number of chloroplast DNAs from various species have been sequenced.
A plastid is a membrane-bound organelle found in plants, algae and other eukaryotic organisms that contribute to the production of pigment molecules. Most plastids are photosynthetic, thus leading to color production and energy storage or production. There are many types of plastids in plants alone, but all plastids can be separated based on the number of times they have undergone endosymbiotic events. Currently there are three types of plastids; primary, secondary and tertiary. Endosymbiosis is reputed to have led to the evolution of eukaryotic organisms today, although the timeline is highly debated.