Why are there no operons in eukaryotic cells

Wheat and rye have undergone a shared genomic event that has led to the splitting of the Bx gene cluster into two parts that are located on different chromosomes. This can be explained by a reciprocal translocation in the ancestor of wheat and rye [ ].

Bx-deficient variants of a diploid accession of wild wheat Triticum boeoticum have recently been identified. Molecular characterization suggests that Bx deficiency in these accessions arose by disintegration of the Bx1 coding sequence, followed by degeneration and loss of all five Bx biosynthetic genes examined [ ].

Barley species that do not produce benzoxazinoids have also lost all Bx genes [ , ]. The precise physical distances between all of the genes within the Bx cluster are not known. However, in maize, Bx1 and Bx2 genes are 2. In hexaploid wheat, the Bx3 and Bx4 genes are 7—11 kb apart within the three genomes [ ]. Although several of the Bx genes are in close physical proximity this gene cluster appears to be less tightly linked than the other examples that have been considered so far in this review.

Interestingly, barley lines that produce benzoxazinoids do not synthesize gramine, a defense compound that is also derived from the tryptophan pathway. Conversely, gramine-accumulating barley species are deficient in benzoxazinoids. This has led to the suggestion that the biosynthetic pathways for these two different classes of defense compound are mutually exclusive, possibly due to competition for common substrates [ ].

Outside the Poaceae, benzoxazinoids in particular DIBOA and its glucoside are found in certain isolated eudicot species belonging to the orders Ranunculales e. Comparison of the BX1 enzymes of grasses and benzoxazinone-producing eudicots indicates that these enzymes do not share a common monophyletic origin. Furthermore, the CYP71C family of CYPs to which BX belong is not represented in the model eudicot, thale cress Arabidopsis thaliana , and all members of this family described to date originate from the Poaceae.

It therefore seems likely that the ability to synthesize benzoxazinones has evolved independently in grasses and eudicots. Investigation of triterpene biosynthesis in plants has led to the discovery of two other examples of operon-like metabolic gene clusters, namely the avenacin gene cluster in oat Avena species and the thalianol gene cluster in A.

Avenacins are antimicrobial triterpene glycosides that confer broad spectrum disease resistance to soil-borne pathogens [ , ]. Analysis of the genes and enzymes for avenacin synthesis has revealed that the pathway has evolved recently, since the divergence of oats from other cereals and grasses [ 99 , , , , ].

Transferal of genes for the synthesis of antimicrobial triterpenes into cereals such as wheat holds potential for crop improvement but first requires the necessary genes and enzymes to be characterized.

Synthesis of avenacins is developmentally regulated and occurs in the epidermal cells of the root meristem. The major avenacin, A-1, has strong fluorescence under ultra-violet light and can be readily visualized in these cells.

This fluorescence, which is an extremely unusual property amongst triterpenes, has enabled isolation of over 90 avenacin-deficient mutants using a simple screen for reduced root fluorescence [ , ]. This mutant collection has facilitated gene cloning and pathway elucidation.

Sad1 encodes an oxidosqualene cyclase enzyme that catalyses the first committed step in the avenacin pathway [ 99 , ], while Sad2 encodes a second early pathway enzyme—a novel cytochrome P enzyme belonging to the newly described monocot-specific CYP51H subfamily [ ].

Sterols and avenacins are both synthesized from the mevalonate pathway [ ]. While the genes for sterol synthesis are generally regarded as being constitutively expressed throughout the plant, the expression of Sad1 , Sad2 , and other cloned genes for avenacin biosynthesis is tightly regulated and is restricted to the epidermal cells of the root meristem [ 99 , , ].

Recruitment of Sad1 and Sad2 from the sterol pathway by gene duplication has therefore involved a change in expression pattern as well as neofunctionalisation. A third gene has recently been cloned and shown to encode a serine carboxypeptidase-like acyltransferase that is required for avenacin acylation.

Four other loci that are required for avenacin synthesis also co-segregate with these cloned genes, indicating that most of the genes for the pathway are likely to be clustered [ 99 ].

Since avenacins confer broad spectrum disease resistance, the gene cluster is likely to have arisen through strong epistatic selection for maintenance and co-inheritance of this gene collective. In addition, interference with the integrity of the gene cluster can in some cases lead to the accumulation of toxic intermediates, with detrimental consequences for plant growth, so providing further selection for cluster maintenance [ ].

Gene clustering may also facilitate co-ordinate regulation of gene expression at the level of chromatin [ 2 ]. The thalianol gene cluster in A. The BAHD acyltransferase gene is predicted to be part of the cluster based on its location and expression pattern, but an acylated downstream product has not as yet been identified. In the related crucifer, A. This may be indicative of paralogy rather than orthology [ ]. Alternatively it may indicate that the BAHD acyltransferase genes are not under strong selection and so are divergent.

The thalianol gene cluster in Arabidopsis. The A. The organization of the equivalent region from the related crucifer, A. Adapted from Ref. The genes within the A. As is the case for the avenacin pathway, tight regulation of the pathway appears to be critical since accumulation of thalianol pathway intermediates can impact on plant growth and development. There are superficial similarities between the avenacin and thalianol gene clusters in that they are both required for triterpene synthesis and contain genes for oxidosqualene cyclases, CYPs, and acyltransferases.

However, phylogenetic analysis indicates that the genes within these clusters are monocot and eudicot specific, respectively, and that the assembly of these clusters has occurred recently and independently in the two plant lineages [ ].

This suggests that selection pressure may act during the formation of certain plant metabolic pathways to drive gene clustering, and that triterpene pathways are predisposed to such clustering.

A third example of a gene cluster for synthesis of terpenes in plants has been reported from rice, in this case for synthesis of diterpene defense compounds known as momilactones [ , ].

Momilactones were originally identified as dormancy factors from rice seed husks and are also constitutively secreted from the roots of rice seedlings.

In rice cell suspension cultures and in leaves, expression of the rice momilactone genes can be co-ordinately induced in response to challenge with pathogens, elicitor treatment, or exposure to UV irradiation [ , ]. Synthesis of momilactones is initiated by terpene synthases that are distinct from the oxidosqualene cyclases that catalyze the first committed step in triterpene synthesis.

These genes are all co-ordinately induced in response to treatment with a chitin oligosaccharide elicitor. Analysis of the promoters of the genes within this cluster has revealed the presence of potential recognition sites for WRKY and basic leucine zipper bZIP transcription factors, proteins that are associated with activation of defense responses.

Gene clustering has been suggested to facilitate efficient coordinated expression of the momilactone gene cluster in response to elicitation [ ]. Global gene expression analysis has revealed extensive clustering of non-homologous genes that are co-ordinately expressed in eukaryotes, including in animals for reviews, see [ 2 , , ].

These groups of genes may be expressed during development, or in certain tissues and diseased states, and have been reported in studies of Drosophila , nematode, mouse, and humans. Such co-expression domains may therefore be an important source for the discovery of new functional gene clusters in animals and other eukaryotes. However, more research is needed before we can fully understand the functional significance of co-expression domains [ ]. Of the known functional gene clusters in animals, the best characterized is the major histocompatability complex MHC , which encodes proteins involved in innate and adaptive immunity.

The latter two examples consist of genes that share sequence similarity and so are distinct from classical operons and from the functional gene clusters discussed above. However, investigation of these loci has revealed important insights into the mechanisms of regulation of arrayed gene clusters in eukaryotes and so these gene clusters will also be considered here.

The MHC was discovered in mouse in and was investigated for its genetic role in tissue graft and organ transplant compatibility histocompatibility.

It later transpired that the primary function of the classical MHC gene-products was to provide protection against pathogens in innate and adaptive immunity. However, three of the largest gene families in the extended MHC are not obviously immune-related. These are the tRNA, histone, and olfactory receptor gene families.

Histones and tRNAs are required for DNA replication and protein synthesis, and enormous quantities of transcript must be produced to meet the needs of a single cell. Therefore, in the majority of eukaryotes, histone and tRNA genes tend to be found in tandem duplicated arrays that are also regions of high transcription [ ].

In the human genome, the largest tRNA and histone gene arrays reside within the extended MHC comprising and 66 loci, respectively. For this reason, it has been suggested that the immune-related genes of the MHC may be hitchhiking with the histone and tRNA gene arrays, and in doing so benefiting from the inherent high transcriptional activity of the region [ ].

The human major histocompatibility complex MHC. Each coloured block represents multiple genes and the number of blocks indicates their approximate abundance. Single genes, which are interspersed throughout, are not shown. The drawing is not to scale. The majority of genes from the MHC class I and III regions are constitutively expressed in all somatic cell types, although expression levels can vary over two orders of magnitude depending on the cell-type or extracellular stimuli [ ].

By contrast, genes in the MHC class II region are expressed only in antigen-presenting cells or in other cell-types after induction by cytokines such as interferon-gamma. CIITA acts by stabilizing a multi-subunit complex on the promoters of target genes to activate their transcription [ ].

Formation of the CIITA-complex results in a large wave of histone acetylation and intergenic transcription that spreads out bi-directionally from the target promoter [ ]. Despite the presence of such specific transcription factors, the physical clustering of genes in the MHC does appear to be important for their regulation. Treatment with interferon-gamma results in remodeling of the loopscape and differential regulation of genes within the affected regions [ ].

Remodeling also leads to alterations in the composition of MAR binding proteins associated with the chromatin fibre and the subsequent recruitment of promyelocytic leukemia nuclear bodies, which may act as transcriptional factories for specific chromosomal loci [ , ]. The MHC region varies greatly in structure and size between species. This diversity is likely to have been driven by adaptive changes in response to selection pressure from pathogens and parasites [ ].

The linkage between MHC Class I and Class II genes has been preserved from the cartilaginous fish to humans, except in the bony fish where linkage has disintegrated [ ]. The MHC is also highly variable within species; in humans, as many as alleles can be found at a single locus. Some alleles are so divergent that their common ancestor is likely to predate the formation of the species.

The MHC is also a site of strong linkage disequilibrium, and large conserved blocks of specific alleles, or haplotypes, of up to 3. Therefore, particular patterns of MHC alleles may be fine-tuned to work together, and this may be one of the mechanisms by which clustering of the MHC is maintained [ ]. A number of regions in the human genome are paralogous to the MHC, and these are thought to have arisen by the duplication and fragmentation of a single proto-MHC after two rounds of whole genome duplication [ ].

Remarkably, the MHC of chicken contains two C-type lectin receptor genes that are highly homologous to the receptor genes in the human NKC. The presence of these NK receptors in the chicken MHC suggests that the proto-MHC may have contained at least one ancestral C-type lectin receptor gene that was differentially retained at different loci after whole genome duplication in the lineages that gave rise to chicken and man.

The leukocyte receptor complex LRC , which contains a large array of immunoglobulin family NK receptors, is similarly thought to be derived from the proto-MHC [ ]. Together, these results suggest that the clustering of immune-related genes at the MHC, NKC, and LRC was not independent, but instead was derived from the more ancient clustering of immune-related genes at the proto-MHC. How the ancestral genes became clustered remains a matter of debate. Homeotic mutations in animals result in the transformation of one body segment into another and have played a crucial role in shaping our understanding of animal development.

In the late s, it was discovered that many homeotic mutations in Drosophila mapped to the Bithorax and Antennapedia complexes [ , ], complexes that we now know to consist of tandem duplicated arrays of genes encoding homeodomain Hox transcription factors [ , ].

The first ancestral Hox cluster is thought to have appeared before the separation of the Cnidarians and Bilaterians, some million years ago [ ].

Diversification of the ancestral cluster facilitated the development of diverse and complex body plans across the metazoa. For example, in mammals, there are four Hox clusters that have arisen through whole genome duplications with up to 14 Hox genes within each cluster. Expression of Hox genes is regulated in a remarkable fashion. The order of the genes along the chromosome corresponds to the region of expression along the length of the developing animal spatial collinearity of expression Fig.

In some species, the Hox cluster has become disrupted. This is at its most extreme in the tunicate Oikopleura dioica where the Hox cluster has completely disintegrated and the remaining Hox genes are dispersed throughout the genome [ ]. Cluster disintegration in O.

However, the spatial expression pattern of the Hox genes appears to be largely maintained. Through comparisons with other species lacking complete Hox clusters, it appears likely that cluster disintegration marks a switch to a more rapid life-cycle and a determinative mode of development where cell fate is fixed and flexible Hox regulation is no longer required [ ].

Physical linkage of the Hox genes therefore appears to be important for choreographing Hox expression. Confocal image of septuple in situ hybridization exhibiting the spatial expression of Hox gene transcripts in a developing Drosophila embryo, with the chromosomal organization of the Hox gene cluster shown below: lab labial, pb proboscipedia not shown in the in situ hybridization , Dfd deformed, Scr sex combs reduced, Antp antennapedia, Ubx ultrabithorax, Abd-A abdominal-A, Abd-B abdominal-B.

The in situ hybridization image has been reproduced with permission from [ ]. Retinoic acid RA , a vitamin A-derived morphogen, can stimulate the sequential induction of Hox genes [ ]. Components of the RA signaling pathway either predate the Hox cluster or appeared shortly after its emergence, suggesting that temporal collinearity of expression may be an ancestral feature of the Hox cluster [ ].

The sequential activation of Hox genes in different metazoans is accompanied by directional changes in histone modifications, the opening up of the chromatin, and in some cases looping out of the chromatin fibre [ ]. The orchestration of this complex series of events is still not fully understood.

Transcriptional repression of Hox genes through histone modifications and chromatin condensation is equally important for the establishment of appropriate Hox expression domains. Hox expression can in addition be controlled post-transcriptionally and perhaps also epigenetically by non-coding RNAs and micro RNAs miRNAs , the genes for which are embedded in the Hox cluster [ ]. Cis -regulated clusters of structurally related genes such as the Hox cluster are a recurring feature of animal genomes.

An LCR is defined as a sequence that is able to confer copy number-dependent and position-independent expression of a transgene. Adapted from [ ]. In the early s, structures with remarkable similarities to classical prokaryotic operons were discovered in the genome of the nematode Caenorhabditis elegans [ , ].

These operons consist of linked genes that are under the control of a single promoter and are transcribed as a single polycistronic mRNA [ , ] Fig.

However, unlike the situation in prokaryotes, this polycistronic mRNA is then trans -spliced into monocistronic mRNAs that are translated individually.

Genes within C. This suggests that C. The adoption of trans -splicing is likely to be the key event that led to the flourishing of operons in nematodes. The benefits offered by trans -splicing are not well understood, but once established, this mRNA processing mechanism appears to favor operon formation and maintenance [ — ]. Operon breakup may be disfavored because downstream genes within an operon usually lack promoters and so are unlikely to be expressed following segmental duplication or disruption of the operon.

Beyond the nematodes, trans -spliced operons have been detected in the genomes of several other animals including the tunicates Oikopleura dioica and Ciona intestinalis [ — ] and the chaetognath arrow worm, Spadella cephaloptera [ ]. It has been predicted that operons may be present in all species able to carry out trans- splicing [ ]. The origins of trans -splicing are unclear, and the scattered distribution of this mechanism across the animal kingdom could be due to convergent evolution or to extensive loss of an ancient feature [ ].

A number of operon-like structures have also been identified in Drosophila , which lacks the trans -splicing machinery. Subsequent bioinformatic analysis identified Drosophila gene pairs that may also produce bicistronic mRNA [ ]. Unlike C. Further research is required to determine whether Drosophila has particular mechanisms in place that promote operon formation.

Operon-like loci have also been identified in mammals [ — ], plants [ — ], and the filamentous fungi [ ]. The small number of examples identified so far would suggest that such structures are very rare in the genomes of these intensively studied organisms. Different strategies for the processing of eukaryotic operons. When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized.

However, when tryptophan accumulates in the cell, two tryptophan molecules bind to the trp repressor molecule, which changes its shape, allowing it to bind to the trp operator. This binding of the active form of the trp repressor to the operator blocks RNA polymerase from transcribing the structural genes, stopping expression of the operon.

Thus, the actual product of the biosynthetic pathway controlled by the operon regulates the expression of the operon. Figure 2. The five structural genes needed to synthesize tryptophan in E. When tryptophan is absent, the repressor protein does not bind to the operator, and the genes are transcribed. When tryptophan is plentiful, tryptophan binds the repressor protein at the operator sequence.

This physically blocks the RNA polymerase from transcribing the tryptophan biosynthesis genes. The lac operon is an example of an inducible operon that is also subject to activation in the absence of glucose Figure 3. The lac operon encodes three structural genes necessary to acquire and process the disaccharide lactose from the environment, breaking it down into the simple sugars glucose and galactose. For the lac operon to be expressed, lactose must be present.

This makes sense for the cell because it would be energetically wasteful to create the enzymes to process lactose if lactose was not available. In the absence of lactose, the lac repressor is bound to the operator region of the lac operon, physically preventing RNA polymerase from transcribing the structural genes.

However, when lactose is present, the lactose inside the cell is converted to allolactose. Allolactose serves as an inducer molecule, binding to the repressor and changing its shape so that it is no longer able to bind to the operator DNA. Removal of the repressor in the presence of lactose allows RNA polymerase to move through the operator region and begin transcription of the lac structural genes.

Figure 3. The three structural genes that are needed to degrade lactose in E. When lactose is absent, the repressor protein binds to the operator, physically blocking the RNA polymerase from transcribing the lac structural genes. When lactose is available, a lactose molecule binds the repressor protein, preventing the repressor from binding to the operator sequence, and the genes are transcribed.

Figure 4. When grown in the presence of two substrates, E. Then, enzymes needed for the metabolism of the second substrate are expressed and growth resumes, although at a slower rate. Bacteria typically have the ability to use a variety of substrates as carbon sources.

However, because glucose is usually preferable to other substrates, bacteria have mechanisms to ensure that alternative substrates are only used when glucose has been depleted.

Additionally, bacteria have mechanisms to ensure that the genes encoding enzymes for using alternative substrates are expressed only when the alternative substrate is available. In the s, Jacques Monod was the first to demonstrate the preference for certain substrates over others through his studies of E. Such studies generated diauxic growth curves, like the one shown in Figure 4. Although the preferred substrate glucose is used first, E.

However, once glucose levels are depleted, growth rates slow, inducing the expression of the enzymes needed for the metabolism of the second substrate, lactose. Notice how the growth rate in lactose is slower, as indicated by the lower steepness of the growth curve. As a result, cAMP levels begin to rise in the cell Figure 5. Figure 5. Thus, increased cAMP levels signal glucose depletion. The lac operon also plays a role in this switch from using glucose to using lactose.

The complex binds to the promoter region of the lac operon Figure 6. In the regulatory regions of these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. Binding of the CAP-cAMP complex to this site increases the binding ability of RNA polymerase to the promoter region to initiate the transcription of the structural genes.

Thus, in the case of the lac operon, for transcription to occur, lactose must be present removing the lac repressor protein and glucose levels must be depleted allowing binding of an activating protein.

When glucose levels are high, there is catabolite repression of operons encoding enzymes for the metabolism of alternative substrates. See Table 1 for a summary of the regulation of the lac operon. Figure 6. In prokaryotes, there are also several higher levels of gene regulation that have the ability to control the transcription of many related operons simultaneously in response to an environmental signal.

A group of operons all controlled simultaneously is called a regulon. When sensing impending stress, prokaryotes alter the expression of a wide variety of operons to respond in coordination. How do eukaryotes regulate gene expression? Control at the DNA level. Figure 1: Eukaryotic cells must tightly fold their DNA so that it fits within the cellular nucleus. Control at the transcription level. Control via RNA splicing. More on gene expression. Can the central dogma be reversed?

How can the environment affect gene expression? How does eukaryotic DNA unfold and open? How, exactly, does RNA splicing occur? Control via RNA stability. Control at the translation level. Key Questions What else is there to know about operons?

How do environmental influences affect gene expression? What role does noncoding RNA play in gene expression? How do genes express and regulate themselves? Key Concepts intron exon splicing transcription factor. Topic rooms within Genetics Close. No topic rooms are there. Browse Visually. Other Topic Rooms Genetics. Student Voices. Creature Cast. Simply Science. By contrast, the genes of eukaryotes are generally considered to be monocistronic, each with its own promoter at the 5' end and a transcription terminator at the 3' end; however, it has recently become clear that not all eukaryotic genes are transcribed monocistronically.

Numerous instances of polycistronic transcription in eukaryotes, from protists to chordates, have been reported.