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Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands.

A pupal cuticle protein gene has been found within an intron of a Drosophila gene that encodes three purine pathway enzymatic activities. The intronic gene is encoded on the DNA strand opposite the purine pathway gene and is itself interrupted by an intron. Whereas the purine pathway gene is active throughout development, the intronic cuticle protein gene is expressed primarily over a 3 hr period in the abdominal epidermal cells of prepupae that secrete the pupal cuticle. Therefore, a housekeeping gene and a developmentally regulated gene function in a nested arrangement.

Acyltransferases↗

Nested genes in the human genome.

Here we studied one special type of gene, i.e., the nested gene, in the human genome. We collected 373 reliably annotated nested genes. Two-thirds of them were on the strand opposite that of their host gene. About 58% coding nested gene pairs were conserved in mouse and some were even maintained in chicken and fish, while nested pseudogenes were poorly conserved. Ka/Ks analysis revealed that nested genes were under strong selection, although they did not demonstrate greater conservation than other genes. With microarray data we observed that two partners of one nested pair seemed to be expressed reciprocally. A significant proportion of nested genes were tissue-specifically expressed. Gene ontology analysis demonstrated that quite a number of nested genes participated in cellular signal transduction. Based on these observations, we think that nested genes are a group of genes with important physiological functions.

Animals↗

Identification of a novel Drosophila melanogaster gene, angel, a member of a nested gene cluster at locus 59F4,5.

The identification of a novel Drosophila melanogaster gene, angel, is presented in this study. angel is located on the right arm of the second chromosome at locus 59F5, close to the nested genes l(2)tid, l(2)not, l(2)rot and l(2)dtl. We describe the genetic and molecular localization of angel and present its temporal expression in the wild-type. The deduced amino acid sequence of the ANG39 protein is characterized by a nuclear localization signal. Furthermore, the central part of the predicted ANG39 protein shows significant homology to the C-terminal portion of the yeast transcriptional effector CCR4.

Amino Acid Sequence↗

Evolution of nested genes with special reference to cuticle proteins in Drosophila melanogaster.

One of the pupal cuticle protein (PCP) genes has been found within an intron of a Drosophila housekeeping gene (the Gart locus) that encodes three enzymes involved in the purine pathway. This intronic gene has been described as a gene within a gene, and the gene is now called a "nested" gene. Because the intronic PCP gene has sequence similarity with the larval cuticle protein (LCP) gene, it may have been derived from one of the LCP genes or their ancestral gene. We have studied possible phylogenetic relationships among these five genes by comparing nucleotide sequences of four LCP genes with that of the PCP gene. The results obtained suggest that the PCP gene may have originated from an ancestral gene before duplication of the LCP genes occurred. Using the number of synonymous (silent) substitutions, we then estimated the divergence time between the PCP gene and the LCP genes to be about 70 million years (Myr). The divergence time estimated is much larger than that for the sibling species of D. melanogaster (about 2.5 Myr), indicating that the "nested" gene structure can be seen not only in Drosophila melanogaster, but also in other distantly related Drosophila species.

Amino Acid Sequence↗

Potential regulatory relationship between the nested gene DDC8 and its host gene tissue inhibitor of metalloproteinase-2.

Nested genes are fairly common within the mammalian nervous system, yet few studies have examined whether the guest and host genes might be coordinately regulated. Tissue inhibitors of metalloproteinase (TIMPs) inhibit extracellular matrix proteolysis mediated by metzincin proteases. TIMP-2 is the only TIMP not nested within a synapsin gene. It does, however, serve as a host for differential display clone 8 (DDC8), a testis-specific gene whose expression is upregulated during spermatogenesis. Here, we demonstrate that DDC8 is not testis specific. Furthermore, DDC8 expression in nonneural and neural tissues mimics that of TIMP-2, including its upregulation in response to traumatic brain injury, suggesting a potential regulatory relationship. The most striking observation is that the TIMP-2 knockout mouse brain contains TIMP-2 mRNA encoding exons 2-5, which are downstream of DDC8, but not exon 1, which contains the signal sequence and cysteine residue required for MMP inhibition, indicating a functional knockout. That TIMP-2 transcripts in wild-type brain contain DDC8 sequence suggests alternative splicing between the two genes.

Amino Acid Sequence↗

Expression of human F8B, a gene nested within the coagulation factor VIII gene, produces multiple eye defects and developmental alterations in chimeric and transgenic mice.

Factor VIII-associated gene B ( F8B ) is a small human gene of unknown function which is nested within the gene encoding coagulation factor VIII ( FVIII ) in chromosome band Xq28. The sequence of F8B includes the C2 cell adhesion motif of factor VIII, which has also been identified in numerous proteins known to play important roles during development. Here we have constructed both chimeric and transgenic mice expressing normal human F8B to investigate its possible developmental effects. The chimeras produced from embryonic stem cells transfected with normal F8B under control of a cytomegalovirus promoter and selected for neomycin resistance expressed readily detectable levels of F8B mRNA in multiple tissues. They showed growth retardation, microcephaly, reduced longevity and severe ocular defects, and although they were fertile, gave birth to no F8B heterozygous pups. Seven transgenic mouse lines, produced by injection of the transgene into fertilized oocytes, were viable and of normal size but expressed lower levels of F8B mRNA. Strikingly, they showed the same severe eye abnormalities as the chimeras. These defects included anterior segment dysgenesis, absent or abnormal lens, persistence of the primary vitreous, Harderian gland tumors and ectopic pigmented cells, suggesting that migration of neural crest cells might have been perturbed during eye development. In addition, dysplastic retinas and the absence of photoreceptors were observed, providing a mouse model for retinal degeneration.

Animals↗

Nested genes: biological implications and use of AFM for analysis.

A "nested" gene is located within the boundaries of a larger gene, often within an intron and in the opposite orientation. Such structures are common in bacteria and viruses, but have also been described in higher species as diverse as Drosophila and humans. Expression of nested and host genes may be simultaneously up-regulated due to use of common enhancers, or down-regulated through steric hindrance or interference caused by annealing of the complementary RNAs, leading to degradation. Methods for RNA analysis such as RT-PCR and in situ hybridization reveal the presence of specific mRNAs, but do not address regulation of expression within a single cell at a single genetic locus. Atomic force microscopy is a relatively new technology, which allows visualization of the movement of an RNA polymerase along a DNA template. The potential of this technology includes a greater molecular understanding of cellular decision making processes, leading to enhanced opportunities to intervene in disease progression through use of novel treatment modalities.

Animals↗

Tomato bushy stunt virus spread is regulated by two nested genes that function in cell-to-cell movement and host-dependent systemic invasion.

We have investigated the importance of two small nested genes (p19 and p22) located near the 3' end of the genome of tomato bushy stunt virus (TBSV) for infectivity in several hosts. Our results show that both genes are dispensable for replication and transcription and that the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. Assays using TBSV derivatives that have the beta-glucuronidase gene substituted for the capsid protein gene demonstrate that p22 is required for cell-to-cell movement in all plants tested. Mutations inactivating p19 ameliorate the severe necrotic systemic symptoms elicited by wild-type TBSV in Nicotiana benthamiana and Nicotiana clevelandii, but p19 does not obviously affect movement in these hosts. However, in some local lesion hosts p19 influences the lesion diameter, which suggests that it has an auxiliary host-dependent role in movement. This notion is supported by the observation that p19 is required for long-distance spread of TBSV in spinach and for systemic infection of pepper plants. Thus, movement of TBSV is regulated by two nested genes; p22 governs cell-to-cell movement and p19 has a host-specific role in systemic invasion.

Base Sequence↗

A polymorphic gene nested within an intron of the tau gene: implications for Alzheimer's disease.

A previously undescribed gene, Saitohin (STH), has been discovered in the intron between exons 9 and 10 of the human tau gene. STH is an intronless gene that encodes a 128-aa protein with no clear homologs. The tissue expression of STH is similar to tau, a gene that is implicated in many neurodegenerative disorders. In humans, a single nucleotide polymorphism that results in an amino acid change (Q7R) has been identified in STH and was used in a case control study. The Q7R polymorphism appears to be over-represented in the homozygous state in late onset Alzheimer's disease subjects.

Alzheimer Disease↗

Invertebrate tissue inhibitor of metalloproteinase: structure and nested gene organization within the synapsin locus is conserved from Drosophila to human.

Vertebrate tissue inhibitors of metalloproteinases (TIMPs) regulate extracellular matrix metalloproteinases and are thus involved in a wide variety of developmental and physiological processes. By identifying cDNAs of a transcript detected within an intron of the Drosophila synapsin gene we have cloned the Drosophila TIMP gene (Timp), which represents the first invertebrate member of the TIMP gene family. Sequence analysis revealed an open reading frame of 210 amino acids with 35% identity to human TIMPs and a conserved exon-intron structure. Analysis of sequence data from the Sanger Centre demonstrated that the human TIMP3 gene is encoded within intron V of the human synapsin-III gene, indicating that the nested organization of TIMP and synapsin genes may be a general feature conserved in evolution. We therefore speculate that the human TIMP4 gene will be located in intron V of the human synapsin-II gene on chromosome 3p25, and we present preliminary evidence that a human synapsin-IV gene is located near the TIMP2 gene on chromosome 17q23-q25.

Amino Acid Sequence↗

Sequence, molecular organization and products of the Drosophila virilis homologs of the D. melanogaster nested genes lethal(2) tumorous imaginal discs [1(2)tid] and lethal(2) neighbour of tid [1(2)not].

In this study, we describe the isolation of the Drosophila virilis (Dvir) 6201-bp genomic fragment homologous to a 7047-bp genomic region of D. melanogaster (Dmel) that harbors the nested genes lethal(2) tumorous imaginal discs (l(2)tid), lethal(2) neighbour of tid (l(2)not) and lethal(2) relative of tid (l(2)rot). The isolated fragment, which maps at the cytogenetic position 50A5 on chromosome 5, carries the Dvir homologs of the Dmel genes l(2)tid and l(2)not. In both cases, the interspecific comparison of the determined sequences reveals a high homology regarding the protein coding regions and a high degree of evolutionary divergence concerning the intronic parts of the genes. In the two distantly related species, the particular gene within gene arrangement of the two genes is conserved, namely, Dvir tid is located in the intron of Dvir not, on the non-coding DNA strand. Interestingly, the Dvir homolog of the Dmel l(2)rot gene residing in the l(2)not intron on its coding strand, opposite l(2)tid, is not present in the 6201-bp genomic fragment. The protein predicted from the Dvir tid sequence, Dvir Tid58, exhibits 76.5% identity with the putative Tid56 protein of Dmel. The putative Dvir Not58 protein shows 71% identity with its Dmel homolog Not56. The developmental transcript and protein patterns, as well as the characteristics of the protein products encoded by the genes Dvir tid and Dvir not are similar to those identified for their Dmel homologs.

Amino Acid Sequence↗

A new gene nested within the dunce genetic unit of Drosophila melanogaster.

The molecular organization of the dunce gene of Drosophila melanogaster has proved to be particularly complex, with two divergently transcribed genes, Sgs-4 and Pig-1, nested within its 79 kb intron (1). Here we report the identification and the molecular characterization of a third gene nested within the transcription unit of dunce. This newly identified gene is located nearly 6 kb downstream Pig-1, within a more upstream dunce intron. The gene is developmentally regulated and transcribed with the same polarity of dunce; several lines of evidence indicate that it might encode for a salivary gland secreted (Sgs) protein.

Amino Acid Sequence↗

Translation of two nested genes in bacteriophage P4 controls immunity-specific transcription termination.

In phage P4, transcription of the left operon may occur from both the constitutive PLE promoter and the regulated PLL promoter, about 400 nucleotides upstream of PLE. A strong Rho-dependent termination site, timm, is located downstream of both promoters. When P4 immunity is expressed, transcription starting at PLE is efficiently terminated at timm, whereas transcription from PLL is immunity insensitive and reads through timm. We report the identification of two nested genes, kil and eta, located in the P4 left operon. The P4 kil gene, which encodes a 65-amino-acid polypeptide, is the first translated gene downstream of the PLE promoter, and its expression is controlled by P4 immunity. Overexpression of kil causes cell killing. This gene is the terminal part of a longer open reading frame, eta, which begins upstream of PLE. The eta gene is expressed when transcription starts from the PLL promoter. Three likely start codons predict a size between 197 and 199 amino acids for the Eta gene product. Both kil and eta overlap the timm site. By cloning kil upstream of a tRNA reporter gene, we demonstrated that translation of the kil region prevents premature transcription termination at timm. This suggests that P4 immunity might negatively control kil translation, thus enabling transcription termination at timm. Transcription starting from PL proceeds through timm. Mutations that create nonsense codons in eta caused premature termination of transcription starting from PLL. Suppression of the nonsense mutation restored transcription readthrough at timm. Thus, termination of transcription from PLL is prevented by translation of eta.

Amino Acid Sequence↗

P elements inserted in the vicinity of or within the Drosophila snRNP SmD3 gene nested in the first intron of the Ornithine Decarboxylase Antizyme gene affect only the expression of SmD3.

The Drosophila gene for snRNP SmD3 (SmD3) is contained in reverse orientation within the first intron of the Ornithine Decarboxylase Antizyme (AZ) gene. Previous studies show that two closely linked P elements cause the gutfeeling phenotype characterized by embryonic lethality and aberrant neuronal and muscle cell differentiation. However, the exact nature of the gene(s) affected in the gutfeeling phenotype remained unknown. This study shows that a series of P inserts located within the 5'-untranslated region (5'-UTR) of SmD3 or its promoter affects only the expression of SmD3. Our analysis reveals that the gutfeeling phenotype associated with P elements inserted in the 5'-UTR of SmD3 results from amorphic or strongly hypomorphic mutations. In contrast, P inserts in the SmD3 promoter region reduce the expression of SmD3 without abolishing it and produce larval lethality with overgrown imaginal discs, brain hemispheres, and hematopoietic organs. The lethality of these mutations could be rescued by an SmD3+ transgene. Finally, inactivation of AZ was obtained by complementing with SmD3+ the deficiency Df(2R)guf(lex47) that uncovers both SmD3 and AZ. Interestingly, AZ inactivation causes a new phenotype characterized by late larval lethality and atrophy of the brain, imaginal discs, hematopoietic organs, and salivary glands.

Animals↗

Species-directed 16S rRNA gene nested PCR detection of Olsenella species in association with endodontic diseases.

AIMS: To investigate the occurrence of Olsenella uli and Olsenella profusa in samples taken from infections of endodontic origin using a devised 16S RNA gene-based nested PCR protocol. METHODS AND RESULTS: DNA extracted from clinical samples was initially amplified using universal 16S rRNA gene primers followed by a second round of amplification using the first PCR products to detect a specific fragment of either O. uli or O. profusa 16S rRNA gene. Olsenella uli was detected in 27% of samples from teeth with asymptomatic periradicular lesions and in 20% of pus samples taken from symptomatic (abscess) lesions. Olsenella profusa was detected in 7% of asymptomatic teeth and in 13% of symptomatic teeth. A new Olsenella phylotype was also detected. CONCLUSIONS: Olsenella species can take part in the microbiota associated with infections of the root canal of human teeth and a role in the pathogenesis of periradicular diseases is suspected. SIGNIFICANCE AND IMPACT OF THE STUDY: The present study demonstrates that molecular genetic methods keep expanding the list of candidate endodontic pathogens to include Olsenella species.

Actinobacteria↗

Conserved arrangement of nested genes at the Drosophila Gart locus.

The Drosophila melanogaster Gart gene encodes three enzymatic activities in the pathway for purine de novo synthesis. Alternative processing of the primary transcript leads to the synthesis of two overlapping polypeptides. The coding sequence for both polypeptides is interrupted by an intron that contains a functional cuticle protein gene encoded on the opposite DNA strand. Here we show that this nested organization also exists at the homologous locus of a distantly related species, Drosophila pseudoobscura. In both species, the intronic cuticle gene is expressed in wandering larvae and in prepupae. Remarkably, there are 24 different highly conserved noncoding segments within the intron containing the cuticle gene. These are found upstream of the transcriptional start, at the 3' end, and even within the single intronic gene intron. Other introns in the purine gene, including the intron at which alternative processing occurs, show no such homologies. It seems likely that at least some of the conserved noncoding regions are involved in specifying the high level developmental expression of the cuticle gene. We discuss the possibility that shared cis-acting regulatory sites might enhance transcription of both genes and help explain their nested arrangement.

Amino Acid Sequence↗

Cytomegalovirus assembly protein nested gene family: four 3'-coterminal transcripts encode four in-frame, overlapping proteins.

The genomic region encoding the assembly protein of simian cytomegalovirus (CMV) strain Colburn has been cloned, sequenced, and found to be organized as a nested set of four in-frame, 3'-coterminal genes, each with its own TATA promoter element and translational start codon, and all using a single 3' polyadenylation signal. The 3' end of the longest open reading frame (1.770 bp) was identical to the 930-bp sequence coding for the assembly protein precursor, as determined from a cDNA clone. The assembly protein coding region of human CMV strain AD169 was similarly organized, suggesting that both viral genomes could give rise to four independently transcribed 3'-coterminal RNAs coding for four overlapping, in-frame, carboxy-coterminal proteins. These predictions were tested and confirmed. Four mRNAs corresponding in size and sequence to those predicted were identified in both human and simian CMV-infected cells by using transcript-specific antisense oligonucleotide probes in Northern (RNA blot) assays. The 5' ends of the three largest of these Colburn transcripts were determined by S1 nuclease protection assays and found to map between the anticipated TATA sequences and corresponding translational start codons. The four predicted overlapping proteins were identified by immunoassays in lysates of simian and human CMV-infected cells by using an antiserum specific for the carboxyl end of the assembly protein precursor. The structural relationship of both sets of proteins was verified by comparing their peptide patterns following protein cleavage at tryptophan residues by N-chlorosuccinimide. The similar organization of the homologous coding regions in other herpesviruses into at least two nested, in-frame, 3'-coterminal genes is discussed.

Amino Acid Sequence↗