An organism is defined in a medical dictionary as any living thing that functions as an individual . Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have been proposed to define what an organism is. Among the most common is that an organism has autonomous reproduction , growth , and metabolism . This would exclude viruses , despite the fact that they evolve like organisms. Other problematic cases include colonial organisms ; a colony of eusocial insects is organised adaptively, and has germ-soma specialisation , with some insects reproducing, others not, like cells in an animal's body. The body of a siphonophore , a jelly-like marine animal, is composed of organism-like zooids , but the whole structure looks and functions much like an animal such as a jellyfish , the parts collaborating to provide the functions of the colonial organism.
120-452: Horizontal gene transfer ( HGT ) or lateral gene transfer ( LGT ) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring ( reproduction ). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher-order evolution while more significantly shifting perspectives on bacterial evolution. Horizontal gene transfer
240-408: A mouse , the plant Arabidopsis thaliana , the puffer fish , and the bacteria E. coli . In December 2013, scientists first sequenced the entire genome of a Neanderthal , an extinct species of humans . The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave . New sequencing technologies, such as massive parallel sequencing have also opened up
360-832: A transposase protein, and may or may not have a promoter sequence. Those that do not have promoter sequences encoded within the mobile region rely on adjacent host promoters for expression. Horizontal transfer is thought to play an important role in the TE life cycle. In plants, it appears that LTR retrotransposons of the Copia superfamilies, especially those with low copy numbers from the Ale and Ivana lineages, are more likely to undergo horizontal transfer between different plant species. HTT has been shown to occur between species and across continents in both plants and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize
480-460: A bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent , that is, enter a special physiological state. Competence development in Bacillus subtilis requires expression of about 40 genes. The DNA integrated into the host chromosome is usually (but with infrequent exceptions) derived from another bacterium of the same species , and is thus homologous to
600-430: A big potential to modify the genetic control in a host organism. The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations. Retrotransposons are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form
720-527: A chromosomal-encoded barrier to MGE than an MGE-encoded tool for cell infection. Lateral gene transfer via a mobile genetic element, namely the integrated conjugative element (ICE) Bs1 has been reported for its role in the global DNA damage SOS response of the gram positive Bacillus subtilis . Furthermore, it has been linked with the radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores, isolated from spacecraft cleanroom facilities. Transposon insertion elements have been reported to increase
840-506: A defined structure that are able to change their location in the genome. TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have
960-418: A donor and mixing that with a receptor in the presence of compound in order to test horizontal gene transfer of antibiotic resistance genes but this time in the presence of phenolic compounds . Phenolic compounds are commonly found in wastewater and have been found to change functions and structures of the microbial communities during the wastewater treatment process. Additionally, HGT increases in frequency in
1080-569: A few enzymes and molecules like those in living organisms, they have no metabolism of their own; they cannot synthesize the organic compounds from which they are formed. In this sense, they are similar to inanimate matter. Viruses have their own genes , and they evolve . Thus, an argument that viruses should be classed as living organisms is their ability to undergo evolution and replicate through self-assembly. However, some scientists argue that viruses neither evolve nor self-reproduce. Instead, viruses are evolved by their host cells, meaning that there
1200-618: A genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome . A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity. The decreasing cost of genomic mapping has permitted genealogical sites to offer it as
1320-465: A key player. Plasmids, with their mobile nature and crucial role in horizontal gene transfer, are seen as a significant element in DNA that exchanges genetic information. This mobility makes ptDNA a potential donor for promiscuous DNA to traverse organellar barriers. NUMTs (nuclear sequences of mitochondrial) are a type of promiscuous DNA that arises from the natural transfer of mitochondria DNA (mtDNA) to
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#17327652863231440-534: A large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an RNA intermediate. Retrotransposons are composed of DNA , but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack
1560-405: A main driving role to generate genetic novelty and natural genome editing. Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel Jurassic Park and the subsequent film tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from
1680-413: A major role in shaping the genome. Duplication may range from extension of short tandem repeats , to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes . Such duplications are probably fundamental to the creation of genetic novelty. Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of
1800-467: A major theme of the book. The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of
1920-446: A new TE in a host genome can have detrimental consequences because TE mobility may induce mutation. However, HTT can also be beneficial by introducing new genetic material into a genome and promoting the shuffling of genes and TE domains among hosts, which can be co-opted by the host genome to perform new functions. Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots. HTT detection
2040-428: A new site. This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans . Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome size varies widely across species. Invertebrates have small genomes, this
2160-546: A plethora of antimicrobial genes which if transferred to pathogenic microbes could be detrimental. Conjugation in Mycobacterium smegmatis , like conjugation in E. coli , requires stable and extended contact between a donor and a recipient strain, is DNase resistant , and the transferred DNA is incorporated into the recipient chromosome by homologous recombination . However, unlike E. coli high frequency of recombination conjugation (Hfr), mycobacterial conjugation
2280-503: A process of recombination (a primitive form of sexual interaction ). Genome In the fields of molecular biology and genetics , a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses ). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA ), and often
2400-415: A reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications. DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and
2520-449: A resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance. Horizontal transposon transfer (HTT) refers to the passage of pieces of DNA that are characterized by their ability to move from one locus to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there
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#17327652863232640-487: A reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs). Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of
2760-518: A role in the spread of virulence factors, such as exotoxins and exoenzymes , amongst bacteria. A prime example concerning the spread of exotoxins is the adaptive evolution of Shiga toxins in E. coli through horizontal gene transfer via transduction with Shigella species of bacteria. Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed. For example, horizontally transferred genetic elements play important roles in
2880-651: A service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center , an example both of the economies of scale and of citizen science . Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA , and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of
3000-404: A single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular chromosome , however, some bacterial species have linear or multiple chromosomes. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if
3120-560: A species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174 , of 5386 base pairs. The first bacterial genome to be sequenced
3240-453: A stable, double-stranded DNA intermediate that is thought to be sturdier than the single-stranded RNA intermediate of non-LTR retroelements , which can be highly degradable. Non-autonomous elements may be less likely to transfer horizontally compared to autonomous elements because they do not encode the proteins required for their own mobilization. The structure of these non-autonomous elements generally consists of an intronless gene encoding
3360-487: A substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome . Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics . The genomes of many organisms have been sequenced and various regions have been annotated. The Human Genome Project was started in October 1990, and then reported
3480-588: A transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi-cellular organisms), followed by integration into the recipient host genome. Though the actual mechanism for the transportation of TEs from donor cells to host cells is unknown, it is established that naked DNA and RNA can circulate in bodily fluid. Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs. The arrival of
3600-445: Is a microorganism such as a protist , bacterium , or archaean , composed of a single cell , which may contain functional structures called organelles . A multicellular organism such as an animal , plant , fungus , or alga is composed of many cells, often specialised. A colonial organism such as a siphonophore is a being which functions as an individual but is composed of communicating individuals. A superorganism
3720-401: Is a teleonomic or goal-seeking behaviour that enables them to correct errors of many kinds so as to achieve whatever result they are designed for. Such behaviour is reminiscent of intelligent action by organisms; intelligence is seen as an embodied form of cognition . All organisms that exist today possess a self-replicating informational molecule (genome), and such an informational molecule
Horizontal gene transfer - Misplaced Pages Continue
3840-741: Is a colony, such as of ants , consisting of many individuals working together as a single functional or social unit . A mutualism is a partnership of two or more species which each provide some of the needs of the other. A lichen consists of fungi and algae or cyanobacteria , with a bacterial microbiome ; together, they are able to flourish as a kind of organism, the components having different functions, in habitats such as dry rocks where neither could grow alone. The evolutionary biologists David Queller and Joan Strassmann state that "organismality" has evolved socially, as groups of simpler units (from cells upwards) came to cooperate without conflicts. They propose that cooperation should be used as
3960-434: Is a difficult task because it is an ongoing phenomenon that is constantly changing in frequency of occurrence and composition of TEs inside host genomes. Furthermore, few species have been analyzed for HTT, making it difficult to establish patterns of HTT events between species. These issues can lead to the underestimation or overestimation of HTT events between ancestral and current eukaryotic species. Horizontal gene transfer
4080-485: Is a global concern that ARGs have been found in wastewater treatment plants Textile wastewater has been found to contain 3- to 13-fold higher abundance of mobile genetic elements than other samples of wastewater. The cause of this is the organic compounds used for textile dying ( o -xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green) raising the frequency of conjugative transfer when bacteria and plasmid (with donor) are introduced in
4200-480: Is a growing amount of data showing that HTT is a common and widespread phenomenon in eukaryote evolution as well. On the transposable element side, spreading between genomes via horizontal transfer may be viewed as a strategy to escape purging due to purifying selection, mutational decay and/or host defense mechanisms. HTT can occur with any type of transposable elements, but DNA transposons and LTR retroelements are more likely to be capable of HTT because both have
4320-435: Is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene. For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar. For this reason, it is often ideal to use other information to infer robust phylogenies such as
4440-767: Is a type of HGT that is chromosome rather than plasmid based. Furthermore, in contrast to E. coli (Hfr) conjugation, in M. smegmatis all regions of the chromosome are transferred with comparable efficiencies. Substantial blending of the parental genomes was found as a result of conjugation, and this blending was regarded as reminiscent of that seen in the meiotic products of sexual reproduction. Haloarchaea are aerobic halophiles thought to have evolved from anaerobic methanogens . A large amount of their genome, 126 composite gene families, are derived from genetic material from bacterial genomes. This has allowed them to adapt to extremely salty environments. The archaeon Sulfolobus solfataricus , when UV irradiated, strongly induces
4560-485: Is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight. Before this loss, DNA methylation allows the adequate expansion of the genome. In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules,
4680-535: Is an argument for viewing viruses as cellular organisms. Some researchers perceive viruses not as virions alone, which they believe are just spores of an organism, but as a virocell - an ontologically mature viral organism that has cellular structure. Such virus is a result of infection of a cell and shows all major physiological properties of other organisms: metabolism , growth, and reproduction , therefore, life in its effective presence. The philosopher Jack A. Wilson examines some boundary cases to demonstrate that
4800-432: Is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes. Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome. Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on
4920-444: Is carried in plasmids . For this, the word genome should not be used as a synonym of chromosome . Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode , which each have only one pair, to a fern species that has 720 pairs. It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount
Horizontal gene transfer - Misplaced Pages Continue
5040-408: Is commonly used in the scientific literature is usually restricted to the large chromosomal DNA molecules in bacteria. Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in the mitochondria . In addition, algae and plants have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and
5160-671: Is difficult to trace organismal phylogeny in the presence of horizontal gene transfer. Combining the simple coalescence model of cladogenesis with rare HGT horizontal gene transfer events suggest there was no single most recent common ancestor that contained all of the genes ancestral to those shared among the three domains of life . Each contemporary molecule has its own history and traces back to an individual molecule cenancestor . However, these molecular ancestors were likely to be present in different organisms at different times." Organism The evolutionary biologists David Queller and Joan Strassmann state that "organismality",
5280-418: Is essentially horizontal gene transfer, albeit with synthetic expression cassettes. The Sleeping Beauty transposon system (SB) was developed as a synthetic gene transfer agent that was based on the known abilities of Tc1/mariner transposons to invade genomes of extremely diverse species. The SB system has been used to introduce genetic sequences into a wide variety of animal genomes. Horizontal gene transfer
5400-564: Is even more than what is necessary for DNA protein-coding and noncoding genes due to the fact that eukaryotic genomes show as much as 64,000-fold variation in their sizes. However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical human cell has two copies of each of 22 autosomes , one inherited from each parent, plus two sex chromosomes , making it diploid. Gametes , such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to
5520-492: Is facilitated by active DNA demethylation , a process that entails the DNA base excision repair pathway. This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to 5-hydroxymethylcytosine (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2 . Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to
5640-439: Is likely an important mechanism for providing increased repair of damaged DNA via homologous recombination. This process can be regarded as a simple form of sexual interaction. Another thermophilic species , Sulfolobus acidocaldarius , is able to undergo HGT. S. acidocaldarius can exchange and recombine chromosomal markers at temperatures up to 84 °C. UV exposure induces pili formation and cellular aggregation. Cells with
5760-472: Is likely intrinsic to life. Thus, the earliest organisms also presumably possessed a self-replicating informational molecule ( genome ), perhaps RNA or an informational molecule more primitive than RNA. The specific nucleotide sequences in all currently extant organisms contain information that functions to promote survival, reproduction , and the ability to acquire resources necessary for reproduction, and sequences with such functions probably emerged early in
5880-415: Is passed on to succeeding generations. Although transduction is the form of HGT most commonly associated with bacteriophages , certain phages may also be able to promote transformation. As mentioned before, conjugation is a method of horizontal gene transfer through cell to cell contact. Through the process of conjugation, type IV Secretion Systems (T4SS) are used to passage on DNA from the donor cell to
6000-401: Is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA. High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to
6120-417: Is relatively common among many eukaryotic species and can have an impact on adaptation to novel environments. Its study, however, is hindered by the complexity of eukaryotic genomes and the abundance of repeat-rich regions, which complicate the accurate identification and characterization of transferred genes. It is postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently,
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#17327652863236240-502: Is significantly accelerated when donor cells with plasmids and recipient cells are introduced to each other in the presence of one of the pharmaceuticals. Non-antibiotic pharmaceuticals were also found to cause some responses in bacteria similar to those responses to antibiotics, such as increasing expression of the genes lexA, umuC, umuD and soxR involved in the bacteria's SOS response as well as other genes also expressed during exposure to antibiotics. These findings are from 2021 and due to
6360-402: Is still significant. The study that came to this conclusion is similar to the study on horizontal gene transfer and non-antibiotic pharmaceuticals in that it was done in 2021 and leaves room for more research, specifically in the focus of the study which is activated sludge . Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes. The paper that led to
6480-572: Is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence . It often involves temperate bacteriophages and plasmids . Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation , transduction and conjugation , subsequently arming
6600-421: Is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see developmental biology ). The work is both in vivo and in silico . There are many enormous differences in size in genomes, specially mentioned before in
6720-577: Is typically inferred using bioinformatics methods, either by identifying atypical sequence signatures ("parametric" methods) or by identifying strong discrepancies between the evolutionary history of particular sequences compared to that of their hosts. The transferred gene ( xenolog ) found in the receiving species is more closely related to the genes of the donor species than would be expected. The virus called Mimivirus infects amoebae . Another virus, called Sputnik , also infects amoebae, but it cannot reproduce unless mimivirus has already infected
6840-535: Is very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is difficult to decide which molecules to include in the definition; for example, bacteria usually have one or two large DNA molecules ( chromosomes ) that contain all of the essential genetic material but they also contain smaller extrachromosomal plasmid molecules that carry important genetic information. The definition of 'genome' that
6960-548: The Ancient Greek ὀργανισμός , derived from órganon , meaning instrument, implement, tool, organ of sense or apprehension) first appeared in the English language in the 1660s with the now-obsolete meaning of an organic structure or organization. It is related to the verb "organize". In his 1790 Critique of Judgment , Immanuel Kant defined an organism as "both an organized and a self-organizing being". Among
7080-1060: The lysogenic cycle . Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of bacteria . In the mid-1980s, Syvanen postulated that biologically significant lateral gene transfer has existed since the beginning of life on Earth and has been involved in shaping all of evolutionary history. As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes " (see also Lake and Rivera, 2007). The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution." Grafting of one plant to another can transfer chloroplasts ( organelles in plant cells that conduct photosynthesis ), mitochondrial DNA , and
7200-486: The nuclear genome (nDNA). These NUMTs, with their varying frequencies, sizes, and features, contribute to the genetic diversity across all eukaryotes and, in some cases, to diseases among humans. NUPTs (nuclear plastid DNA sequences) are a type of promiscuous DNA that arises from the natural transfer of ptDNA ( plastid DNA ) into nDNA . These fragments of ptDNA, similar to NUMTs in frequency, size, and features, also exhibit variability across species. Genetic engineering
7320-642: The "defining trait" of an organism. Samuel Díaz‐Muñoz and colleagues (2016) accept Queller and Strassmann's view that organismality can be measured wholly by degrees of cooperation and of conflict. They state that this situates organisms in evolutionary time, so that organismality is context dependent. They suggest that highly integrated life forms, which are not context dependent, may evolve through context-dependent stages towards complete unification. Viruses are not typically considered to be organisms, because they are incapable of autonomous reproduction , growth , metabolism , or homeostasis . Although viruses have
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#17327652863237440-426: The X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome. A genome sequence is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or
7560-563: The ability to aggregate have greater survival than mutants lacking pili that are unable to aggregate. The frequency of recombination is increased by DNA damage induced by UV-irradiation and by DNA damaging chemicals. The ups operon , containing five genes, is highly induced by UV irradiation. The proteins encoded by the ups operon are employed in UV-induced pili assembly and cellular aggregation leading to intercellular DNA exchange and homologous recombination . Since this system increases
7680-500: The acquisition of antibiotic resistance genes. Mycobacterium tuberculosis is a species that has evolved through methods like conjugation while gaining antibiotic resistance. This evolution or increase in genetic diversity is also seen in many other species. Due to this, there is a huge concern on how impactful conjugation or horizontal gene transfer can be on human health and your microbiome as pathogenic microbes can become more pathogenic. Studies have shown that even our own microbiome has
7800-616: The antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming a challenge to manage in the field of medicine. Ecological factors may also play a role in the HGT of antibiotic resistant genes. Horizontal gene transfer is recognized as a pervasive evolutionary process that distributes genes between divergent prokaryotic lineages and can also involve eukaryotes. HGT events are thought to occur less frequently in eukaryotes than in prokaryotes. However, growing evidence indicates that HGT
7920-412: The blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are
8040-549: The cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes. However, some symbiotic bacteria (e.g. Serratia symbiotica ) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. Some bacteria have auxiliary genetic material, also part of their genome, which
8160-424: The cells more permeable. These are the mechanisms that make even low levels of heavy metal pollution in the environment impact HGT and therefore the spread of ARGs. Promiscuous DNA is a form of horizontal gene transfer that transmits genetic information across organellar barriers. Promiscuous DNA transfer has substantial evidence in its movement across the genome of numerous organisms, from movements in chloroplast to
8280-478: The chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the " mitochondrial genome ". The DNA found within the chloroplast may be referred to as the " plastome ". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome. Unlike prokaryotes where exon-intron organization of protein coding genes exists but
8400-678: The concept of organism is not sharply defined. In his view, sponges , lichens , siphonophores , slime moulds , and eusocial colonies such as those of ants or naked molerats , all lie in the boundary zone between being definite colonies and definite organisms (or superorganisms). Scientists and bio-engineers are experimenting with different types of synthetic organism , from chimaeras composed of cells from two or more species, cyborgs including electromechanical limbs, hybrots containing both electronic and biological elements, and other combinations of systems that have variously evolved and been designed. An evolved organism takes its form by
8520-476: The criteria that have been proposed for being an organism are: Other scientists think that the concept of the organism is inadequate in biology; that the concept of individuality is problematic; and from a philosophical point of view, question whether such a definition is necessary. Problematic cases include colonial organisms : for instance, a colony of eusocial insects fulfills criteria such as adaptive organisation and germ-soma specialisation. If so,
8640-445: The details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size , gene order, codon usage bias , and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005). Duplications play
8760-468: The discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research. Metals assist in the spread of antibiotic resistance through both co-resistance as well as cross-resistance mechanisms. In quantities relevant to the environment, Cu(II) , Ag(I) , Cr(VI) , and Zn(II) promote HGT from donor and receptor strains of E. coli . The presence of these metals triggered SOS response from bacterial cells and made
8880-404: The entire cell nucleus containing the genome to potentially make a new species. Some Lepidoptera (e.g. monarch butterflies and silkworms ) have been genetically modified by horizontal gene transfer from the wasp bracovirus . Bites from insects in the family Reduviidae (assassin bugs) can, via a parasite, infect humans with the trypanosomal Chagas disease , which can insert its DNA into
9000-422: The evolution of life. It is also likely that survival sequences present early in the evolution of organisms included sequences that facilitate the avoidance of damage to the self-replicating molecule and promote the capability to repair such damages that do occur. Repair of some of the genome damages in these early organisms may have involved the capacity to use undamaged information from another similar genome by
9120-514: The fitness of S. acidocaldarius cells after UV exposure, Wolferen et al. considered that transfer of DNA likely takes place in order to repair UV-induced DNA damages by homologous recombination. "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes." Through research into
9240-503: The fitness of gram-negative E. coli strains through either major transpositions or genome rearrangements, and increasing mutation rates. In a study on the effects of long-term exposure of simulated microgravity on non-pathogenic E. coli , the results showed transposon insertions occur at loci, linked to SOS stress response. When the same E. coli strain was exposed to a combination of simulated microgravity and trace (background) levels of (the broad spectrum) antibiotic ( chloramphenicol ),
9360-722: The formation of type IV pili which then facilitates cellular aggregation. Exposure to chemical agents that cause DNA damage also induces cellular aggregation. Other physical stressors, such as temperature shift or pH, do not induce aggregation, suggesting that DNA damage is a specific inducer of cellular aggregation. UV-induced cellular aggregation mediates intercellular chromosomal HGT marker exchange with high frequency, and UV-induced cultures display recombination rates that exceed those of uninduced cultures by as much as three orders of magnitude. S. solfataricus cells aggregate preferentially with other cells of their own species. Frols et al. and Ajon et al. suggested that UV-inducible DNA transfer
9480-519: The genomes of certain species over others. Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals. It is unknown how the density of a population may affect the rate of HTT events within a population, but close proximity due to parasitism and cross contamination due to crowding have been proposed to favor HTT in both plants and animals. In plants, the interaction between lianas and trees has been shown to facilitate HTT in natural ecosystems. Successful transfer of
9600-406: The genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes . Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent
9720-617: The growing issue of antibiotic resistance certain compounds have been observed to promote horizontal gene transfer. Antibiotics given to bacteria at non-lethal levels have been known to be a cause of antibiotic resistance but emerging research is now showing that certain non-antibiotic pharmaceuticals ( ibuprofen , naproxen , gemfibrozil , diclofenac , propranolol , etc.) also have a role in promoting antibiotic resistance through their ability to promote horizontal gene transfer (HGT) of genes responsible for antibiotic resistance. The transfer of antibiotic resistance genes (ARGs) through conjugation
9840-455: The human genome All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. In certain lymphocytes in
9960-425: The human genome and 9% of the fruit fly genome. Tandem repeats can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome. In other cases, expansions in the number of tandem repeats in exons or introns can cause disease . For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of
10080-421: The human genome. It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer. Aaron Richardson and Jeffrey D. Palmer state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear." Due to
10200-517: The human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors. During meiosis , diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome. Genome-wide reprogramming in mouse primordial germ cells involves epigenetic imprint erasure leading to totipotency . Reprogramming
10320-413: The increasing amount of evidence suggesting the importance of these phenomena for evolution (see below ) molecular biologists such as Peter Gogarten have described horizontal gene transfer as "A New Paradigm for Biology". There are several mechanisms for horizontal gene transfer: A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up
10440-438: The likelihood of horizontally transferred secondary metabolite-producing genes. The promiscuity of enzymes is a reoccurring theme in this particular theatre. Natural transformation is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process. In general, transformation is a complex, energy-requiring developmental process. In order for
10560-476: The multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes. Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective. Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes. Initial sequencing and analysis of
10680-795: The nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in Huntington's disease , a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression. Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion. Transposable elements (TEs) are sequences of DNA with
10800-543: The nucleus, chloroplast to the mitochondria, and mitochondria to the nucleus. Barbara McClintock ’s work on maize demonstrated the first studied movement of DNA within nuclear genomes. Concluded as a type of contextual mutation known as conservative transposition , McClintock defined the genetic discovery as chromosomal units, Ds and Ac, having the ability to move locations within the chromosome. In 1982, R. John Ellis defined this type of transpositional transfer mutation as “ intracellular promiscuity .” Ellis further explored
10920-447: The organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus. This is the most common use of 'genome' in the scientific literature. Most eukaryotes are diploid , meaning that there are two of each chromosome in the nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as
11040-501: The partially understood mechanisms of evolutionary developmental biology , in which the genome directs an elaborated series of interactions to produce successively more elaborate structures. The existence of chimaeras and hybrids demonstrates that these mechanisms are "intelligently" robust in the face of radically altered circumstances at all levels from molecular to organismal. Synthetic organisms already take diverse forms, and their diversity will increase. What they all have in common
11160-408: The phenomenon of “intracellular promiscuity” through the experiments of David Stern and David Lonsdale, in which genetic transfer between chloroplasts to mitochondria was discovered, aiding in the definition and discovery of promiscuous DNA. While much remains to be understood about how promiscuous DNA undergoes movement and transfer, numerous experiments have pointed to plastid sequences, ptDNA, as
11280-449: The plasmid pCF10 from Enterococcus faecalis , a gram-positive bacterium, has a SSB like-protein called PrgE and was classified for not being required for conjugation. More work needs to be done on why proteins that bind to ssDNA are encoded into conjugative plasmids. Conjugation in the case of microbiomes and symbioses is very important. From this process new genes are acquired that lead to increasing genetic diversity and evolution such as
11400-495: The presence of the compounds p-nitrophenol (PNP), p-aminophenol (PAP), and phenol. These compounds result in a 2- to 9-fold increase in HGT (p-nitrophenol being on the lower side of 2-fold increases and p-aminophenol and phenol having a maximum increase of 9-fold). This increase in HGT is on average less than the compounds ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green but their increases
11520-464: The presence of these molecules. When textile wastewater combines with wastewater from domestic sewage , the ARGs present in wastewater are transferred at a higher rate due to the addition of textile dyeing compounds increasing the occurrence of HGT. Other organic pollutants commonly found in wastewater have been the subject of similar experiments. A 2021 study used similar methods of using plasmid in
11640-550: The presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible. For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred. Although this may be infrequent,
11760-466: The production of secondary or specialized metabolites. This is clearly exhibited within certain groups of bacteria including P. aeruginosa and actinomycetales , an order of Actinomycetota. Polyketide synthases (PKSs) and biosynthetic gene clusters provide modular organizations of associated genes making these bacteria well-adapted to acquire and discard helpful modular modifications via HGT. Certain areas of genes known as hotspots further increase
11880-590: The proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes. Noncoding sequences include introns , sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats. Short, non-coding sequences that are repeated head-to-tail are called tandem repeats . Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of
12000-412: The prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine . A major step toward that goal was the completion in 2007 of the full genome of James D. Watson , one of the co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than
12120-439: The proteins encoded by LINEs for transposition. The Alu element is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies. DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in
12240-480: The qualities or attributes that define an entity as an organism, has evolved socially as groups of simpler units (from cells upwards) came to cooperate without conflicts. They propose that cooperation should be used as the "defining trait" of an organism. This would treat many types of collaboration, including the fungus / alga partnership of different species in a lichen , or the permanent sexual partnership of an anglerfish , as an organism. The term "organism" (from
12360-718: The recipient cell. These T4SS encoded within the plasmid carry other proteins and genes that help supplement the cell in conjugation. Research has shown that there are Single Binding DNA Binding proteins (SSBs) also encoded within the conjugative plasmid may help with conjugation and cell viability. This is thought to be the case because SSBs naturally are expressed to help with stabilizing single-stranded DNA (ssDNA). SSBs will also recruit other proteins like RadD or RecA expressed in events of DNA recombination, repair, and replication. Further showcasing their possible role in conjugation. Although it may help, studies have also shown for proteins like SSB to not be essential in conjugation. For example,
12480-508: The resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species. Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence appears to be an adaptation for DNA repair. Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that
12600-407: The results showed transposon-mediated rearrangements (TMRs), disrupting genes involved in bacterial adhesion, and deleting an entire segment of several genes involved with motility and chemotaxis . Both these studies have implications for microbial growth, adaptation to and antibiotic resistance in real time space conditions. Horizontal gene transfer is particularly active in bacterial genomes around
12720-612: The same argument, or a criterion of high co-operation and low conflict, would include some mutualistic (e.g. lichens) and sexual partnerships (e.g. anglerfish ) as organisms. If group selection occurs, then a group could be viewed as a superorganism , optimized by group adaptation . Another view is that attributes like autonomy, genetic homogeneity and genetic uniqueness should be examined separately rather than demanding that an organism should have all of them; if so, there are multiple dimensions to biological individuality, resulting in several types of organism. A unicellular organism
12840-414: The same cell. Sputnik's genome reveals further insight into its biology. Although 13 of its genes show little similarity to any other known genes, three are closely related to mimivirus and mamavirus genes, perhaps cannibalized by the tiny virus as it packaged up particles sometime in its history. This suggests that the satellite virus could perform horizontal gene transfer between viruses, paralleling
12960-555: The sequence of the human genome in April 2003, although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequencing of the many repetitive sequences found in human DNA that were not fully uncovered by the original Human Genome Project study, scientists reported the first end-to-end human genome sequence in March 2022. The term genome
13080-423: The shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome. There is no clear and consistent correlation between morphological complexity and genome size in either prokaryotes or lower eukaryotes . Genome size is largely a function of the expansion and contraction of repetitive DNA elements. Since genomes are very complex, one research strategy
13200-442: The universality of the genetic code. Griffith's experiment , reported in 1928 by Frederick Griffith , was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation . Griffith's findings were followed by research in the late 1930s and early 1940s that isolated DNA as the material that communicated this genetic information. Horizontal genetic transfer
13320-559: The validity of 16s rRNA-constructed phylogenetic trees must be reevaluated. Biologist Johann Peter Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists should use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes". There exist several methods to infer such phylogenetic networks . Using single genes as phylogenetic markers , it
13440-551: The virulence of E. coli , Salmonella , Streptococcus and Clostridium perfringens . In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within mobile genetic elements (MGE) such as plasmids , prophages , insertion sequences/transposons, integrative conjugative elements (ICE), and integrons . Still, they are more frequently
13560-541: The virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size. Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs). In Dictyostelium discoideum , there
13680-633: The way that bacteriophages ferry genes between bacteria. Horizontal transfer is also seen between geminiviruses and tobacco plants. Horizontal gene transfer is common among bacteria, even among very distantly related ones. This process is thought to be a significant cause of increased drug resistance when one bacterial cell acquires resistance, and the resistance genes are transferred to the other species. Transposition and horizontal gene transfer, along with strong natural selective forces have led to multi-drug resistant strains of S. aureus and many other pathogenic bacteria. Horizontal gene transfer also plays
13800-431: The widespread use of non-antibiotic pharmaceuticals, more research needs to be done in order to further understanding on the issue. Alongside non-antibiotic pharmaceuticals, other compounds relevant to antibiotic resistance have been tested such as malachite green , ethylbenzene , styrene , 2,4-dichloroaniline , trioxymethylene , o-xylene solutions, p-nitrophenol (PNP), p-aminophenol (PAP), and phenol (PhOH). It
13920-459: Was co-evolution of viruses and host cells. If host cells did not exist, viral evolution would be impossible. As for reproduction, viruses rely on hosts' machinery to replicate. The discovery of viruses with genes coding for energy metabolism and protein synthesis fuelled the debate about whether viruses are living organisms, but the genes have a cellular origin. Most likely, they were acquired through horizontal gene transfer from viral hosts. There
14040-429: Was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice ,
14160-529: Was created in 1920 by Hans Winkler , professor of botany at the University of Hamburg , Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest the name is a blend of the words gene and chromosome . However, see omics for a more thorough discussion. A few related -ome words already existed, such as biome and rhizome , forming a vocabulary into which genome fits systematically. It
14280-400: Was that of Haemophilus influenzae , completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon , Methanococcus jannaschii ,
14400-469: Was then described in Seattle in 1951, in a paper demonstrating that the transfer of a viral gene into Corynebacterium diphtheriae created a virulent strain from a non-virulent strain, simultaneously revealing the mechanism of diphtheria (that patients could be infected with the bacteria but not have any symptoms, and then suddenly convert later or never), and giving the first example for the relevance of
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