88-580: KaiA is a gene in the " kaiABC " gene cluster that plays a crucial role in the regulation of bacterial circadian rhythms , such as in the cyanobacterium Synechococcus elongatus . For these bacteria, regulation of kaiA expression is critical for circadian rhythm, which determines the twenty-four-hour biological rhythm. In addition, KaiA functions with a negative feedback loop in relation with kaiB and KaiC . The kaiA gene makes KaiA protein that enhances phosphorylation of KaiC while KaiB inhibits activity of KaiA. Circadian rhythms have been discovered in
176-584: A promoter sequence. The promoter is recognized and bound by transcription factors that recruit and help RNA polymerase bind to the region to initiate transcription. The recognition typically occurs as a consensus sequence like the TATA box . A gene can have more than one promoter, resulting in messenger RNAs ( mRNA ) that differ in how far they extend in the 5' end. Highly transcribed genes have "strong" promoter sequences that form strong associations with transcription factors, thereby initiating transcription at
264-445: A continuous messenger RNA , referred to as a polycistronic mRNA . The term cistron in this context is equivalent to gene. The transcription of an operon's mRNA is often controlled by a repressor that can occur in an active or inactive state depending on the presence of specific metabolites. When active, the repressor binds to a DNA sequence at the beginning of the operon, called the operator region , and represses transcription of
352-490: A determined sequence on Threonine 432 and Serine 431: KaiA stimulates autophosphorylation by KaiC on Threonine 432, and Serine 431 then follows this mechanism of phosphorylation. When both Threonine 432 and Serine 431 are phosphorylated, KaiB binds to KaiC and this complex, KaiBC, then proceeds to block the effect of KaiA. KaiB can only perform this sequestering action when KaiA is present, and when this action occurs, KaiA cannot then activate KaiC to autophosphorylate. Threonine 432
440-502: A diversity of organisms. These rhythms control a variety of physiological activities and help organisms to adapt to environmental conditions. Cyanobacteria are the most primitive organisms that demonstrate a circadian oscillation. Cyanobacteria clocks were first founded in Blue Green Algae with the oldest known fossils about 3.5 billion years old. Masahiro Ishiura, Susan Golden , Carl H. Johnson , Takao Kondo and their colleagues were
528-495: A double-helix run in opposite directions. Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile . The expression of genes encoded in DNA begins by transcribing the gene into RNA , a second type of nucleic acid that is very similar to DNA, but whose monomers contain
616-488: A few genes and are transferable between individuals. For example, the genes for antibiotic resistance are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via horizontal gene transfer . Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas
704-434: A gene - surprisingly, there is no definition that is entirely satisfactory. A gene is a DNA sequence that codes for a diffusible product. This product may be protein (as is the case in the majority of genes) or may be RNA (as is the case of genes that code for tRNA and rRNA). The crucial feature is that the product diffuses away from its site of synthesis to act elsewhere. The important parts of such definitions are: (1) that
792-443: A gene can be found in the articles Genetics and Gene-centered view of evolution . The molecular gene definition is more commonly used across biochemistry, molecular biology, and most of genetics — the gene that is described in terms of DNA sequence. There are many different definitions of this gene — some of which are misleading or incorrect. Very early work in the field that became molecular genetics suggested
880-565: A gene corresponds to a transcription unit; (2) that genes produce both mRNA and noncoding RNAs; and (3) regulatory sequences control gene expression but are not part of the gene itself. However, there's one other important part of the definition and it is emphasized in Kostas Kampourakis' book Making Sense of Genes . Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. With 'encoding information', I mean that
968-410: A gene may be split across chromosomes but those transcripts are concatenated back together into a functional sequence by trans-splicing . It is also possible for overlapping genes to share some of their DNA sequence, either on opposite strands or the same strand (in a different reading frame, or even the same reading frame). In all organisms, two steps are required to read the information encoded in
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#17330861613261056-404: A gene's DNA and produce the protein it specifies. First, the gene's DNA is transcribed to messenger RNA ( mRNA ). Second, that mRNA is translated to protein. RNA-coding genes must still go through the first step, but are not translated into protein. The process of producing a biologically functional molecule of either RNA or protein is called gene expression , and the resulting molecule
1144-411: A gene), DNA is first copied into RNA . RNA can be directly functional or be the intermediate template for the synthesis of a protein. The transmission of genes to an organism's offspring , is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype , that is specific to every given individual, within
1232-565: A gene: that of bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool. An automated version of the Sanger method was used in early phases of the Human Genome Project . The theories developed in the early 20th century to integrate Mendelian genetics with Darwinian evolution are called
1320-439: A gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence. The majority of eukaryotic genes are stored on a set of large, linear chromosomes. The chromosomes are packed within the nucleus in complex with storage proteins called histones to form a unit called a nucleosome . DNA packaged and condensed in this way is called chromatin . The manner in which DNA
1408-448: A high rate. Others genes have "weak" promoters that form weak associations with transcription factors and initiate transcription less frequently. Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters. Additionally, genes can have regulatory regions many kilobases upstream or downstream of the gene that alter expression. These act by binding to transcription factors which then cause
1496-572: A new expanded definition that includes noncoding genes. However, some modern writers still do not acknowledge noncoding genes although this so-called "new" definition has been recognised for more than half a century. Although some definitions can be more broadly applicable than others, the fundamental complexity of biology means that no definition of a gene can capture all aspects perfectly. Not all genomes are DNA (e.g. RNA viruses ), bacterial operons are multiple protein-coding regions transcribed into single large mRNAs, alternative splicing enables
1584-400: A process known as RNA splicing . Finally, the ends of gene transcripts are defined by cleavage and polyadenylation (CPA) sites , where newly produced pre-mRNA gets cleaved and a string of ~200 adenosine monophosphates is added at the 3' end. The poly(A) tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from
1672-419: A protein-coding gene consists of many elements of which the actual protein coding sequence is often only a small part. These include introns and untranslated regions of the mature mRNA. Noncoding genes can also contain introns that are removed during processing to produce the mature functional RNA. All genes are associated with regulatory sequences that are required for their expression. First, genes require
1760-493: A similar sequence to any eukaryotic clock protein, even though fundamental processes do resemble those of eukaryotic organisms (such as light resetting phase, temperature compensation, ad free running period). Kai genes are found in almost all cyanobacteria. Williams found that 6 of the annotated cyanobacterial genomes had 2 contiguous ORFs maintaining homology to S. elongates kaiB and kaiC genes. Of these sequence associations, only four kaiA genes are distinguishable, thus making it
1848-412: A single genomic region to encode multiple district products and trans-splicing concatenates mRNAs from shorter coding sequence across the genome. Since molecular definitions exclude elements such as introns, promotors, and other regulatory regions , these are instead thought of as "associated" with the gene and affect its function. An even broader operational definition is sometimes used to encompass
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#17330861613261936-472: A strict definition of the word "gene" with which nearly every expert can agree. First, in order for a nucleotide sequence to be considered a true gene, an open reading frame (ORF) must be present. The ORF can be thought of as the "gene itself"; it begins with a starting mark common for every gene and ends with one of three possible finish line signals. One of the key enzymes in this process, the RNA polymerase, zips along
2024-409: A true gene, by this definition, one has to prove that the transcript has a biological function. Early speculations on the size of a typical gene were based on high-resolution genetic mapping and on the size of proteins and RNA molecules. A length of 1500 base pairs seemed reasonable at the time (1965). This was based on the idea that the gene was the DNA that was directly responsible for production of
2112-498: Is a part of the phase resetting mechanism of the cyanobacterial clock. Mutations that mapped to cluster regions of kaiA led to long period phenotypes, thus suggesting that kaiA cluster regions play a role in regulating the period length of circadian oscillation. Regions of KaiA that increase kaiBC expression (allowing for rhythm) are most likely not in cluster regions because arrhythmic mutants (C53S, V76A, F178S, F224S, F274K) were mapped to different part of kaiA. Williams postulated that
2200-456: Is called a gene product . The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code . Sets of three nucleotides, known as codons , each correspond to a specific amino acid. The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4 (see Crick, Brenner et al. experiment ). Additionally,
2288-541: Is dephosphorylated first, followed by the dephosphorylation of Serine 431, at which point KaiA stimulates phosphorylation of the KaiC sites, and the oscillating system starts anew. This circadian oscillation involving the kinase and phosphatase activity occurs in direct relation to ATPase activity. In the initial phases of the oscillation when KaiC does not complex with either KaiA or KaiB, the intrinsic, constant rate of ATP hydrolysis controls ATP levels. KaiA and KaiC bind, forming
2376-400: Is nearly the same for all known organisms. The total complement of genes in an organism or cell is known as its genome , which may be stored on one or more chromosomes . A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. The region of the chromosome at which a particular gene is located is called its locus . Each locus contains one allele of
2464-512: Is observed in the carboxyl terminal 100 residues. Independent carboxyl-terminal domains are the short versions, from the filamentous species Anabaena sp. Strain PCC 7120 and Nostoc punctiforme . There are two independently folded domains of the kaiA protein: KaiA180C (amino terminal with a mainly alpha helical structure) and KaiA189N domain (carboxyl terminal domain, corresponding to residues 1-189). The S. elongates kaiA protein appears to have two domains,
2552-431: Is shown through the demonstration that one KaiA dimer is able to push KaiC to a hyperphosphorylated state. KaiA dimers exhibit a 95% association with KaiC hexamers, in which more kaiA dimers participate in interaction with kaiC. The interaction between KaiA and KaiC is thus not a 1:1 interaction. KaiA dimers likely flexibly associate and disassociate with KaiC dimers rather than forming a stable complex, thus allowing for all
2640-403: Is still part of the definition of a gene in most textbooks. For example, The primary function of the genome is to produce RNA molecules. Selected portions of the DNA nucleotide sequence are copied into a corresponding RNA nucleotide sequence, which either encodes a protein (if it is an mRNA) or forms a 'structural' RNA, such as a transfer RNA (tRNA) or ribosomal RNA (rRNA) molecule. Each region of
2728-399: Is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for gene expression . In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division: replication origins , telomeres , and
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2816-511: The aging process. The centromere is required for binding spindle fibres to separate sister chromatids into daughter cells during cell division . Prokaryotes ( bacteria and archaea ) typically store their genomes on a single, large, circular chromosome . Similarly, some eukaryotic organelles contain a remnant circular chromosome with a small number of genes. Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids , which usually encode only
2904-401: The central dogma of molecular biology , which states that proteins are translated from RNA , which is transcribed from DNA . This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses . The modern study of genetics at the level of DNA is known as molecular genetics . In 1972, Walter Fiers and his team were the first to determine the sequence of
2992-419: The centromere . Replication origins are the sequence regions where DNA replication is initiated to make two copies of the chromosome. Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication . The length of the telomeres decreases each time the genome is replicated and has been implicated in
3080-444: The gene pool of the population of a given species . The genotype, along with environmental and developmental factors, ultimately determines the phenotype of the individual. Most biological traits occur under the combined influence of polygenes (a set of different genes) and gene–environment interactions . Some genetic traits are instantly visible, such as eye color or the number of limbs, others are not, such as blood type ,
3168-549: The modern synthesis , a term introduced by Julian Huxley . This view of evolution was emphasized by George C. Williams ' gene-centric view of evolution . He proposed that the Mendelian gene is a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency." Related ideas emphasizing the centrality of Mendelian genes and the importance of natural selection in evolution were popularized by Richard Dawkins . The development of
3256-475: The neutral theory of evolution in the late 1960s led to the recognition that random genetic drift is a major player in evolution and that neutral theory should be the null hypothesis of molecular evolution. This led to the construction of phylogenetic trees and the development of the molecular clock , which is the basis of all dating techniques using DNA sequences. These techniques are not confined to molecular gene sequences but can be used on all DNA segments in
3344-750: The operon ; when the repressor is inactive transcription of the operon can occur (see e.g. Lac operon ). The products of operon genes typically have related functions and are involved in the same regulatory network . Though many genes have simple structures, as with much of biology, others can be quite complex or represent unusual edge-cases. Eukaryotic genes often have introns that are much larger than their exons, and those introns can even have other genes nested inside them . Associated enhancers may be many kilobase away, or even on entirely different chromosomes operating via physical contact between two chromosomes. A single gene can encode multiple different functional products by alternative splicing , and conversely
3432-753: The A-tail and the C-terminal domain, the C-terminal can remain phosphorylated in the absence of KaiA, thus signaling that a possible function of the A-loop is to assist in the autophosphorylation and autodephosphorylation of KaiC. KaiC has 2 C-terminal binding domains: CI region has the KaiA binding domain of CKABD1; CII region has the KaiA binding domain of CKABD2. The CII C-terminal domain of KaiC maintains kinase and phosphatase function that are regulated by kaiA. KaiA interacts with this domain which fashions an inhibitory loop, stimulating
3520-523: The CII kinase activity and initiating the phosphorylation of Ser431 and Thr432, two adjacent CII residues. KaiC and KaiA binding leads to the unraveling of KaiA into an A-loop, thus increasing the movement of the P-loop region, the loop region holding Thr-432 and Ser-431, and ATP. The displacement of the A-loop allows for the freeing of adjacent loops, further promoting the phosphorylation of KaiC by KaiA. Evidence of this
3608-404: The DNA helix that produces a functional RNA molecule constitutes a gene. We define a gene as a DNA sequence that is transcribed. This definition includes genes that do not encode proteins (not all transcripts are messenger RNA). The definition normally excludes regions of the genome that control transcription but are not themselves transcribed. We will encounter some exceptions to our definition of
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3696-450: The DNA sequence is used as a template for the production of an RNA molecule or a protein that performs some function. The emphasis on function is essential because there are stretches of DNA that produce non-functional transcripts and they do not qualify as genes. These include obvious examples such as transcribed pseudogenes as well as less obvious examples such as junk RNA produced as noise due to transcription errors. In order to qualify as
3784-766: The DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase. The mature messenger RNA produced from protein-coding genes contains untranslated regions at both ends which contain binding sites for ribosomes , RNA-binding proteins , miRNA , as well as terminator , and start and stop codons . In addition, most eukaryotic open reading frames contain untranslated introns , which are removed and exons , which are connected together in
3872-509: The KaiA135N is a pseudo-receiver domain is a timing input device that controls KaiA stimulation of KaiC autophosphorylation, thus crucial for circadian oscillation. There appear to be long and short types of kaiA proteins. The long type, gathered from S.elongatus , Synechocystis sp. Strain PCC 5803, and Synechococcus sp. Strain WH8108, has about 300 aminoacyl residues. A high degree of conservation
3960-508: The KaiAC complex, which stimulates KaiC autophosphorylation. This resulting phosphorylation stimulates ATP hydrolysis. The KaiC protein then reaches a state of hyperphosphorylation, after this binding of KaiA. At this point of hyperphosphorylation, KaiB binds to KaiC, and an inhibition of ATP hydrolysis occurs. KaiC then returns to initial uncomplexed state, and the ATP hydrolysis rates once again stabilize to
4048-469: The KaiC subunits to be phosphorylated in the Kai phosphorylation cycle. Biochemical imaging revealed the assembly and disassembly of various Kai complexes that form during circadian clock oscillations. During the process, KaiA and KaiB bind to sites on KaiC; the model determines that KaiC then becomes KaiAC when KaiA stimulates autophosphorylation, which then transforms into KaiBC, KaiABC, and then returns to KaiC as
4136-462: The PTO constitutes the core of the circadian clock of cyanobacteria. This Kai core confers circadian rhythmicity to ATP hydrolysis activity and kinase / phosphatase activity, both of which are temperature compensated. Additionally, KaiB and KaiC, but not KaiA, have a circadian rhythm of 24 hours in experimental conditions, such as free-running in conditions of constant light. The Kai proteins that comprise
4224-427: The PTO generate a circadian clock of oscillating phosphorylation/dephosphorylation with a period of around 24 hours. The KaiC protein is an enzyme with two specific phosphorylation sites, Threonine 432 and Serine 431, which express rhythmicity in phosphorylation/dephosphorylation, depending on KaiA and KaiB activity. KaiA stimulates the phosphorylation of KaiC until KaiB sequesters KaiA, initiating dephosphorylation in
4312-433: The adenines of one strand are paired with the thymines of the other strand, and so on. Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose ; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end . The two strands of
4400-521: The alleles. There are many different ways to use the term "gene" based on different aspects of their inheritance, selection, biological function, or molecular structure but most of these definitions fall into two categories, the Mendelian gene or the molecular gene. The Mendelian gene is the classical gene of genetics and it refers to any heritable trait. This is the gene described in The Selfish Gene . More thorough discussions of this version of
4488-438: The amino and carboxyl regions, connected by a helical linker of about 50 residues. Cyanobacteria displays a circadian clock system in which three protein oscillators, KaiA, KaiB, and KaiC, constitute a system known as a post-translational oscillator (PTO) that facilitates the oscillation of the larger transcription translation negative feedback loop (TTFL). The TTFL drives gene expression and replenishes KaiA, KaiB, and KaiC, while
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#17330861613264576-436: The center of the concave portion of KaiA is residue His270, which is essential to KaiA function. There are 3 mutations of 19 mutants (single amino substitutions) found in kaiA found from direct sequencing of the cluster. Thus, the cluster as well as the Kai proteins have necessary functions for the circadian clock of Synechococcus . IPTG induced overexpression of kaiA led to arrhythmicity, demonstrating that rhythmicity requires
4664-402: The complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions. The existence of discrete inheritable units
4752-399: The concept that one gene makes one protein (originally 'one gene - one enzyme'). However, genes that produce repressor RNAs were proposed in the 1950s and by the 1960s, textbooks were using molecular gene definitions that included those that specified functional RNA molecules such as ribosomal RNA and tRNA (noncoding genes) as well as protein-coding genes. This idea of two kinds of genes
4840-428: The cyanobacterial TTO model. An example of this is the kaiBC operon. It is still unclear how the transcription-translation feedback loop maintains periodicity and how it is flexible to environmental changes. Since these proteins are essential for the organism to adapt to the environment, understanding the genes are imperative in circadian biology. In cyanobacterium Synechococcus elongates (PCC 7942) kaiA, kaiB, and kaiC are
4928-406: The cycle continues. “Cyanobacteria are the simplest organisms known to exhibit circadian rhythms .” The transcription-translation based oscillator, in other words TTO, is a proposed model that postulates KaiC negatively regulates KaiBC transcription and KaiA positively regulates kaiBC transcription. Kai proteins don’t regulate circadian regulated genes, but do regulate genome wide gene expression in
5016-524: The distinction between a heterozygote and homozygote , and the phenomenon of discontinuous inheritance. Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance , which suggested that each parent contributed fluids to the fertilization process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis , from Greek pan ("all, whole") and genesis ("birth") / genos ("origin"). Darwin used
5104-410: The early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities arranged like beads on a string. The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 (1955–1959) showed that individual genes have a simple linear structure and are likely to be equivalent to a linear section of DNA. Collectively, this body of research established
5192-512: The entrainment mechanism of cellular circadian clock with circadian rhythm in response to intracellular levels of KaiA and the other Kai proteins. KaiA ratios to KaiB and KaiC express a circadian rhythm and guides phosphorylation of KaiC based on KaiA ratios that can entrain in different light dark conditions. Cyanobacteria were one of the oldest organisms on earth and most successful in regards to ecological plasticity and adaptability. Dvornyk performed phylogenetic analysis of kai genes and found that
5280-540: The evolutionary youth of the kaiA gene. KaiA genes are also found in the genomes of the species of the kaiC subtree, in younger clades than Prochlorococcus . Thus kaiA genes most likely arrived after the speciation of Synechococcus and Prochlorococcus , about 1,051 ± 1,16.9 and 944 ± 92.9 Mya. KaiA genes are located only in cyanobacteria with a length ranging from a filamentous cyanobacteria ( Anabaena and Nostoc ) to unicellular cyanobacteria ( Synechoccus and Synechocyti s), which are 852-900 bp longer. The KaiA genes are
5368-463: The experiment "Reconstitution of Circadian Oscillation of Cyanobacterial KaiC Phosphorylation in Vitro" took KaiA, KaiB, and KaiC and put them in tube with ATP, MgCl 2 and buffers only. They used radioactive ATP and the phosphorylated form of KaiC which runs a bit faster than unphosphorylated KaiC. They saw a twenty-four-hour rhythm in autohydrolyzation of KaiC. The system is also temperature compensated and
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#17330861613265456-415: The expression of kaiA as well as the other genes. Mutagenesis of kaiA reveals that there are rarely short-period mutations, but an abundance of long period mutations. Specifically, Nishimura found that there are 301 long period mutations, 92 arrhythmic mutants, and only a single short period mutation. Thus Nishimura concluded that kaiA mutations usually lead to an extension of the period. An exception would be
5544-514: The fact that both protein-coding genes and noncoding genes have been known for more than 50 years, there are still a number of textbooks, websites, and scientific publications that define a gene as a DNA sequence that specifies a protein. In other words, the definition is restricted to protein-coding genes. Here is an example from a recent article in American Scientist. ... to truly assess the potential significance of de novo genes, we relied on
5632-515: The first prokaryotes reported to have a circadian clock. For the adaptation of cyanobacteria, circadian clock genes exhibit forms of significant importance since they regulate fundamental physical processes such as regulation of nitrogen fixation, cell division , and photosynthesis . Early KaiA research was conducted in the 1998 research article, “Expression of a Gene Cluster kaiABC as a Circadian Feedback Process in Cyanobacteria,” where it details
5720-413: The functional product. The discovery of introns in the 1970s meant that many eukaryotic genes were much larger than the size of the functional product would imply. Typical mammalian protein-coding genes, for example, are about 62,000 base pairs in length (transcribed region) and since there are about 20,000 of them they occupy about 35–40% of the mammalian genome (including the human genome). In spite of
5808-596: The functions of the gene cluster and KaiA in that it sustains the oscillations by enhancing Kai C expression. KaiA was discovered while studying the clock mutations in Synechococcus by using bacteria luciferase as a reporter on clock controlled gene expression. This was the first instance where scientists first proposed a mechanism and a naming system for KaiA and the kaiABC gene cluster. Researchers Masato Nakajima, Keiko Imai, Hiroshi Ito, Taeko Nishiwaki, Yoriko Murayama, Hideo Iwasaki, Tokitaka Oyama, and Takao Kondo conducted
5896-421: The genome. The vast majority of organisms encode their genes in long strands of DNA (deoxyribonucleic acid). DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar ( 2-deoxyribose ), a phosphate group, and one of the four bases adenine , cytosine , guanine , and thymine . Two chains of DNA twist around each other to form a DNA double helix with
5984-421: The genomes of complex multicellular organisms , including humans, contain an absolute majority of DNA without an identified function. This DNA has often been referred to as " junk DNA ". However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome , about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer. The structure of
6072-469: The individuals who found that the minimal cyanobacteria clock consists of 3 proteins: KaiA, KaiB, and KaiC. (Note: kai means cycle in Japanese.) The experiment performed by Kondo consisted of attaching the luciferase gene and performing mutagenesis. This was the first identification of possible genes that could reconstitute a biological clock within cyanobacteria, of which KaiA was included. Cyanobacteria were
6160-459: The intrinsic rate. The proteins differ in their C terminal domains, yet both termini facilitate interaction among the proteins. The C terminal domain of KaiA enables dimerization, forming a concave surface that then interacts with the KaiC C-terminal domain. These C-terminal domains neighbor a hairpin loop , or the A-loop, that together confer interest: when a mutation results in loss of both
6248-471: The kai genes have different evolutionary histories the feedback loop that kaiA is in evolved about 1,000 Mya. Minimal amount of kaiA genes prohibits a full dating of their evolution. Since they are found only in some higher cyanobacteria, kaiA genes are the youngest in comparison to kaiB and kaiC, evolutionarily speaking. Synechococcus sp. PCC7942 has kaiA whereas P.marinus does not, even though they are closely related unicellular organisms, further demonstrating
6336-423: The least conserved amongst the kai genes. Shorter homologs of kaiA and kaiB genes match only 1 segment of their longer versions closer to the 3’ terminus, unlike kaiC genes. This implies kaiA and kaiB most likely didn’t evolve through duplication. Specifically, the kaiA gene only had a single copy. KaiA statistics: 284 amino acids; Molecular mass of 32.6 kD; Isoelectric point of 4.69. The Kai proteins do not share
6424-425: The lowering of kaiBC expression. KaiA has been found to enhance kaiBC expression. It is postulated that certain mutant kaiA proteins failed to sustain rhythmicity due to a lack of activation of kaiBC expression. Nishimura found that most KaiA mutations decreased PkaiBC activity to different levels. This is consistent with the finding that kaiA proteins enhance kaiBC activity. His experiment further suggested that kaiA
6512-732: The most sequence diversified of the kai genes. The Synechocystis sp. Strain PCC 6803 genome has only one kaiA gene, whereas multiple are found in kaiB and kaiC. KaiB and kaiC homologues can be found in other eubacteria and archaea, but kaiA appears to only be found in cyanobacteria (currently the only prokaryotes with 24-hour biological oscillation). KaiA Three functional domains: 1) N-terminal domain (amplitude-amplifier) 2) Central period-adjuster domain 3) C-terminal clock-oscillator domain The C-terminal domain assists in dimer formation, thus allowing KaiA to bind to KaiC. This further enhances KaiC phosphorylation. (see functions below) Located at
6600-453: The mutant F224S in which a short period of 22h was found in KaiA. KaiA mutant periods ranged up to 50h in which some mutants demonstrated arrythmicity. KaiA mutations seem to selectively alter period length demonstrating that kaiA can regulate period. Further, kaiA proteins can regulate the length of a period of the circadian oscillation regardless of whether kaiBC was activated or not . Long periods were caused by mutation within kaiA as well as
6688-418: The necessary components that compose the circadian clock. The TTO model of cyanobacteria is questionable due to the finding that phosphorylation of KaiC oscillates regardless of transcription/translation of the kaiBC operon. Thus, it was postulated that the pacemaker is based upon kaiC phosphorylation rather than transcription/translation feedback loop. KaiA augments kaiC autophosphorylation. KaiA and ATP promote
6776-413: The nucleus. Splicing, followed by CPA, generate the final mature mRNA , which encodes the protein or RNA product. Many noncoding genes in eukaryotes have different transcription termination mechanisms and they do not have poly(A) tails. Many prokaryotic genes are organized into operons , with multiple protein-coding sequences that are transcribed as a unit. The genes in an operon are transcribed as
6864-431: The phosphate–sugar backbone spiralling around the outside, and the bases pointing inward with adenine base pairing to thymine and guanine to cytosine. The specificity of base pairing occurs because adenine and thymine align to form two hydrogen bonds , whereas cytosine and guanine form three hydrogen bonds. The two strands in a double helix must, therefore, be complementary , with their sequence of bases matching such that
6952-597: The phosphorylation of T432. KaiB mitigates the effect of kaiA. Thus, “autonomous oscillation of KaiC phosphorylation could be generated by cooperation between kaiA and kaiB." Gene In biology , the word gene has two meanings. The Mendelian gene is a basic unit of heredity . The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA . There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of RNA or protein from
7040-431: The risk for specific diseases, or the thousands of basic biochemical processes that constitute life . A gene can acquire mutations in its sequence , leading to different variants, known as alleles , in the population . These alleles encode slightly different versions of a gene, which may cause different phenotypical traits. Genes evolve due to natural selection or survival of the fittest and genetic drift of
7128-467: The strand of DNA like a train on a monorail, transcribing it into its messenger RNA form. This point brings us to our second important criterion: A true gene is one that is both transcribed and translated. That is, a true gene is first used as a template to make transient messenger RNA, which is then translated into a protein. This restricted definition is so common that it has spawned many recent articles that criticize this "standard definition" and call for
7216-461: The sugar ribose rather than deoxyribose . RNA also contains the base uracil in place of thymine . RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three- nucleotide sequences called codons , which serve as the "words" in the genetic "language". The genetic code specifies the correspondence during protein translation between codons and amino acids . The genetic code
7304-805: The term gemmule to describe hypothetical particles that would mix during reproduction. Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries , Carl Correns , and Erich von Tschermak , who (claimed to have) reached similar conclusions in their own research. Specifically, in 1889, Hugo de Vries published his book Intracellular Pangenesis , in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes" ( Pangens in German), after Darwin's 1868 pangenesis theory. Twenty years later, in 1909, Wilhelm Johannsen introduced
7392-436: The term gene , he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured Wilhelm Johannsen 's distinction between genotype (the genetic material of an organism) and phenotype (the observable traits of that organism). Mendel was also the first to demonstrate independent assortment , the distinction between dominant and recessive traits,
7480-412: The term "gene" (inspired by the ancient Greek : γόνος, gonos , meaning offspring and procreation) and, in 1906, William Bateson , that of " genetics " while Eduard Strasburger , among others, still used the term "pangene" for the fundamental physical and functional unit of heredity. Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid (DNA)
7568-446: Was first suggested by Gregor Mendel (1822–1884). From 1857 to 1864, in Brno , Austrian Empire (today's Czech Republic), he studied inheritance patterns in 8000 common edible pea plants , tracking distinct traits from parent to offspring. He described these mathematically as 2 combinations where n is the number of differing characteristics in the original peas. Although he did not use
7656-618: Was noteworthy because they only needed three proteins, including KaiA, for twenty-four-hour rhythm. Research published in the paper, “Robust and Tunable Circadian Rhythms From Differentially Sensitive Catalytic Domains,” done by Connie Phong, Joseph S. Markson, Crystal M. Wilhoite, and Michael J. Rust, shows the mathematical relationship of KaiA and KaiC where KaiA stimulates the phosphorylation of KaiC. Additionally, KaiB sequesters KaiA, which promotes KaiC dephosphorylation. In addition, “In Vitro Regulation of Circadian phosphorylation rhythm of cyanobacterial clock protein KaiC, KaiA, and KaiB,” shows
7744-430: Was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s. The structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography , which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication. In
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